From 63ae952608ae023ef4915f62d029e7b81b788ce1 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matthew.e.ware@gmail.com>
Date: Tue, 25 Sep 2018 12:00:29 -0400
Subject: [PATCH 001/235] Adding Guilhem's GST qubit map.  -MW

---
 QGL/GSTTools.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/QGL/GSTTools.py b/QGL/GSTTools.py
index fda0a579..4b8f71c2 100644
--- a/QGL/GSTTools.py
+++ b/QGL/GSTTools.py
@@ -57,6 +57,31 @@ def gst_map_1Q(gst_list, qubit, qgl_map=gst_gate_map, append_meas=True):
         elif isinstance(item, list):
             yield list(gst_map_1Q(item, qubit, qgl_map=qgl_map, append_meas=append_meas))
 
+def gst_map_2Q(gst_list, qubits, qgl_map=None, append_meas=False):
+    """
+    Helper function that takes an arbitrarily nested list of pygsti gatestrings
+    and converts them into QGL sequences, keeping the same nesting of lists.
+
+    Inputs:
+        gst_list: GateString to convert, or possibly nested list of pyGSTi GateStrings.
+        qubit: QGL qubit to apply the sequence to
+        qgl_map: Dictionary that maps between pyGSTi "Gx" string to QGL pulse
+        append_meas: Append a measurement to each sequence.
+    Returns:
+        QGL sequences, preserving the input list nesting (as a generator)
+    """
+    if isinstance(gst_list, GateString):
+        gst_list = [gst_list]
+    for item in gst_list:
+        if isinstance(item, GateString):
+            mapped = map(lambda x: qgl_map[x], item.tup)
+            if append_meas:
+                yield list(chain(mapped, [reduce(lambda x,y: x*y, map(MEAS, qubits))]))
+            else:
+                yield list(mapped)
+        elif isinstance(item, list):
+            yield list(gst_map_2Q(item, qubit, qgl_map=qgl_map, append_meas=append_meas))
+
 def create_gst_sequence_from_pygsti(gst_list, qubit, gate_map=gst_gate_map):
     """ Returns list of QGL sequences from a pyGSTi GateString list. See gst_map_1Q.
         The return value is a list of sequences that can be complied by QGL.

From 02b9e3ce4f4499fa4213ce7c826ee54ed425063a Mon Sep 17 00:00:00 2001
From: Matthew Ware <matt.ware@raytheon.com>
Date: Tue, 25 Sep 2018 16:15:15 -0400
Subject: [PATCH 002/235] Fix embarrassing typo

---
 QGL/GSTTools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/GSTTools.py b/QGL/GSTTools.py
index 4b8f71c2..b0bf2b75 100644
--- a/QGL/GSTTools.py
+++ b/QGL/GSTTools.py
@@ -28,8 +28,8 @@
 from random import choices
 
 #Default mapping from pyGSTi naming convention to QGL gates.
-gst_gate_map = {"Gx": X,
-                "Gy": Y,
+gst_gate_map = {"Gx": X90,
+                "Gy": Y90,
                 "Gi": Id}
 
 def gst_map_1Q(gst_list, qubit, qgl_map=gst_gate_map, append_meas=True):

From f7e9806e801e6bf6e3e213171b853c0a70f26081 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matt.ware@raytheon.com>
Date: Thu, 27 Sep 2018 12:08:24 -0400
Subject: [PATCH 003/235] Adding a test skeleton for the gate maps.  Things are
 currently failing.

---
 tests/test_Sequences.py                       |  25 ++++++++++++++++++
 .../awg/TestAPS2/GST/listOfExperiments.npy    | Bin 0 -> 33634 bytes
 .../awg/TestAPS2/GST2Q/listOfExperiments.npy  | Bin 0 -> 138231 bytes
 3 files changed, 25 insertions(+)
 create mode 100644 tests/test_data/awg/TestAPS2/GST/listOfExperiments.npy
 create mode 100644 tests/test_data/awg/TestAPS2/GST2Q/listOfExperiments.npy

diff --git a/tests/test_Sequences.py b/tests/test_Sequences.py
index e4f63ddb..fe0abe7b 100644
--- a/tests/test_Sequences.py
+++ b/tests/test_Sequences.py
@@ -372,6 +372,31 @@ def test_RB_SimultaneousRB_AC(self):
         SimultaneousRB_AC((self.q1, self.q2), (seqs1, seqs2))
         self.compare_sequences('RB')
 
+    def test_1Q_GST(self):
+        self.set_awg_dir()
+        # list of GST gate strings
+        listOfExperiments = list(np.load('GST/listOfExperiments.npy'))
+        exps = list(GSTTools.gst_map_1Q(listOfExperiments, self.q1))
+        filenames = compile_to_hardware(seqs, 'GST/GST')
+        #self.compare_sequences('GST')
+
+    def test_2Q_GST(self):
+        self.set_awg_dir()
+        def gst_2Qgate_map(q1, q2):
+            return {"Gxi": X90(q1)*Id(q2),
+                     "Gyi": Y90(q1)*Id(q2),
+                     "Gii": Id(q1)*Id(q2),
+                     "Gix": Id(q1)*X90(q2),
+                     "Giy": Id(q1)*Y90(q2),
+                     "Gcnot": CNOT_CR(q2,q1)}
+
+        # list of GST gate strings
+        listOfExperiments = list(np.load('GST2Q/listOfExperiments.npy'))
+        seqs = list(gst_map_2Q(listOfExperiments, (self.q1, self.q2), qgl_map = gst_2Qgate_map(q1, q2), append_meas=True))
+
+        filenames = compile_to_hardware(seqs, 'GST2Q/GST2Q')
+        #self.compare_sequences('GST2Q')
+
 
 class APS2Helper(AWGTestHelper):
     def setUp(self):
diff --git a/tests/test_data/awg/TestAPS2/GST/listOfExperiments.npy b/tests/test_data/awg/TestAPS2/GST/listOfExperiments.npy
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HcmV?d00001


From aec44f6199aec9a2035d0a880a9cdc565cf910f4 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matt.ware@raytheon.com>
Date: Thu, 27 Sep 2018 15:32:47 -0400
Subject: [PATCH 004/235] Fixed unit test with Brian Donovan's help

---
 .travis.yml                                   |   1 +
 QGL/GSTTools.py                               |   8 ++-
 tests/test_Sequences.py                       |  61 +++++++++++++++---
 tests/test_data/awg/TestAPS1/.DS_Store        | Bin 0 -> 8196 bytes
 tests/test_data/awg/TestAPS1/GST/.DS_Store    | Bin 0 -> 10244 bytes
 .../test_data/awg/TestAPS1/GST/GST/.DS_Store  | Bin 0 -> 6148 bytes
 tests/test_data/awg/TestAPS2/.DS_Store        | Bin 0 -> 8196 bytes
 tests/test_data/awg/TestAPS2/GST/.DS_Store    | Bin 0 -> 8196 bytes
 .../GST/{ => GST}/listOfExperiments.npy       | Bin
 .../{ => GST}/GST2Q/listOfExperiments.npy     | Bin
 10 files changed, 59 insertions(+), 11 deletions(-)
 create mode 100644 tests/test_data/awg/TestAPS1/.DS_Store
 create mode 100644 tests/test_data/awg/TestAPS1/GST/.DS_Store
 create mode 100644 tests/test_data/awg/TestAPS1/GST/GST/.DS_Store
 create mode 100644 tests/test_data/awg/TestAPS2/.DS_Store
 create mode 100644 tests/test_data/awg/TestAPS2/GST/.DS_Store
 rename tests/test_data/awg/TestAPS2/GST/{ => GST}/listOfExperiments.npy (100%)
 rename tests/test_data/awg/TestAPS2/{ => GST}/GST2Q/listOfExperiments.npy (100%)

diff --git a/.travis.yml b/.travis.yml
index 6e781a45..c8206609 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -38,6 +38,7 @@ install:
   - source activate test-environment
   - conda install -c ecpy atom;
   - pip install watchdog coveralls
+  - pip install pygsti
 
 script:
   - coverage run -m unittest discover
diff --git a/QGL/GSTTools.py b/QGL/GSTTools.py
index b0bf2b75..0052b1c6 100644
--- a/QGL/GSTTools.py
+++ b/QGL/GSTTools.py
@@ -23,10 +23,16 @@
 from .Cliffords import *
 from .BasicSequences.helpers import create_cal_seqs
 from .Compiler import compile_to_hardware
-from pygsti.objects import GateString
 from itertools import chain
 from random import choices
 
+PYGSTI_PRESENT = False
+try:
+   from pygsti.objects import GateString
+   PYGSTI_PRESENT = True
+except:
+   pass
+
 #Default mapping from pyGSTi naming convention to QGL gates.
 gst_gate_map = {"Gx": X90,
                 "Gy": Y90,
diff --git a/tests/test_Sequences.py b/tests/test_Sequences.py
index fe0abe7b..59c4fff8 100644
--- a/tests/test_Sequences.py
+++ b/tests/test_Sequences.py
@@ -3,6 +3,7 @@
 import unittest, time, os, random, sys
 
 from QGL import *
+from QGL import GSTTools
 import QGL
 
 from QGL.Channels import Edge, Measurement, LogicalChannel, LogicalMarkerChannel, PhysicalMarkerChannel, PhysicalQuadratureChannel
@@ -373,15 +374,29 @@ def test_RB_SimultaneousRB_AC(self):
         self.compare_sequences('RB')
 
     def test_1Q_GST(self):
-        self.set_awg_dir()
+        self.set_awg_dir('GST')
         # list of GST gate strings
-        listOfExperiments = list(np.load('GST/listOfExperiments.npy'))
-        exps = list(GSTTools.gst_map_1Q(listOfExperiments, self.q1))
+        if GSTTools.PYGSTI_PRESENT:
+            # generate the gate gatestrings
+            import pygsti
+            from pygsti.construction import std1Q_XYI
+
+            #Create a data set
+            gs_target = std1Q_XYI.gs_target
+            fiducials = std1Q_XYI.fiducials
+            germs = std1Q_XYI.germs
+            maxLengths = [1,2,4]
+
+            listOfExperiments = pygsti.construction.make_lsgst_experiment_list(gs_target.gates.keys(), fiducials, fiducials, germs, maxLengths)
+        else:
+            listOfExperiments = list(np.load('tests/test_data/awg/TestAPS2/GST/GST/listOfExperiments.npy'))
+
+        seqs = list(GSTTools.gst_map_1Q(listOfExperiments, self.q1))
         filenames = compile_to_hardware(seqs, 'GST/GST')
-        #self.compare_sequences('GST')
+        self.compare_sequences('GST')
 
     def test_2Q_GST(self):
-        self.set_awg_dir()
+        self.set_awg_dir('GST')
         def gst_2Qgate_map(q1, q2):
             return {"Gxi": X90(q1)*Id(q2),
                      "Gyi": Y90(q1)*Id(q2),
@@ -390,12 +405,31 @@ def gst_2Qgate_map(q1, q2):
                      "Giy": Id(q1)*Y90(q2),
                      "Gcnot": CNOT_CR(q2,q1)}
 
-        # list of GST gate strings
-        listOfExperiments = list(np.load('GST2Q/listOfExperiments.npy'))
-        seqs = list(gst_map_2Q(listOfExperiments, (self.q1, self.q2), qgl_map = gst_2Qgate_map(q1, q2), append_meas=True))
+        if GSTTools.PYGSTI_PRESENT:
+            import pygsti
+            from pygsti.construction import std1Q_XYI, std2Q_XYICNOT
+            from itertools import product
+            from QGL.GSTTools import SingleQubitCliffordGST, gst_map_2Q
+            # note the use of the germs_lite!
+            gs = std2Q_XYICNOT
+            gs_target = std2Q_XYICNOT.gs_target.copy()
+
+            prep_fiducials = std2Q_XYICNOT.prepStrs
+            effect_fiducials = std2Q_XYICNOT.effectStrs
+            gs_germs = std2Q_XYICNOT.germs_lite
+            #maxLengths = [1,2,4,8,16]
+            maxLengths = [1,2]
+
+            print('Creating GST sequences...')
+            listOfExperiments = pygsti.construction.make_lsgst_experiment_list(gs_target.gates.keys(), prep_fiducials, effect_fiducials, gs_germs, maxLengths)
+        else:
+            # list of GST gate strings
+            listOfExperiments = list(np.load('tests/test_data/awg/TestAPS2/GST/GST2Q/listOfExperiments.npy'))
 
-        filenames = compile_to_hardware(seqs, 'GST2Q/GST2Q')
-        #self.compare_sequences('GST2Q')
+        seqs = list(GSTTools.gst_map_2Q(listOfExperiments, (self.q1, self.q2), qgl_map = gst_2Qgate_map(self.q1, self.q2), append_meas=True))
+
+        filenames = compile_to_hardware(seqs, 'GST/GST2Q')
+        self.compare_sequences('GST2Q')
 
 
 class APS2Helper(AWGTestHelper):
@@ -713,6 +747,13 @@ def test_RB_SingleQubitRB(self):
     def test_RB_SimultaneousRB_AC(self):
         TestSequences.test_RB_SimultaneousRB_AC(self)
 
+    @unittest.skip("Tek5014 unused in years")
+    def test_1Q_GST(self):
+        TestSequences.test_1Q_GST(self)
+
+    @unittest.skip("Tek5014 unused in years")
+    def test_2Q_GST(self):
+        TestSequences.test_2Q_GST(self)
 # class TestTek7000(unittest.TestCase, AWGTestHelper, TestSequences):
 
 # 	def setUp(self):
diff --git a/tests/test_data/awg/TestAPS1/.DS_Store b/tests/test_data/awg/TestAPS1/.DS_Store
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diff --git a/tests/test_data/awg/TestAPS2/GST/listOfExperiments.npy b/tests/test_data/awg/TestAPS2/GST/GST/listOfExperiments.npy
similarity index 100%
rename from tests/test_data/awg/TestAPS2/GST/listOfExperiments.npy
rename to tests/test_data/awg/TestAPS2/GST/GST/listOfExperiments.npy
diff --git a/tests/test_data/awg/TestAPS2/GST2Q/listOfExperiments.npy b/tests/test_data/awg/TestAPS2/GST/GST2Q/listOfExperiments.npy
similarity index 100%
rename from tests/test_data/awg/TestAPS2/GST2Q/listOfExperiments.npy
rename to tests/test_data/awg/TestAPS2/GST/GST2Q/listOfExperiments.npy

From a9bf3ba30c472fdf286ca0c86e1f5133955eec12 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matt.ware@raytheon.com>
Date: Thu, 27 Sep 2018 17:07:48 -0400
Subject: [PATCH 005/235] Fix python version error in travis

---
 .travis.yml                                |   3 ++-
 tests/test_data/awg/TestAPS1/.DS_Store     | Bin 8196 -> 0 bytes
 tests/test_data/awg/TestAPS2/.DS_Store     | Bin 8196 -> 0 bytes
 tests/test_data/awg/TestAPS2/GST/.DS_Store | Bin 8196 -> 0 bytes
 4 files changed, 2 insertions(+), 1 deletion(-)
 delete mode 100644 tests/test_data/awg/TestAPS1/.DS_Store
 delete mode 100644 tests/test_data/awg/TestAPS2/.DS_Store
 delete mode 100644 tests/test_data/awg/TestAPS2/GST/.DS_Store

diff --git a/.travis.yml b/.travis.yml
index c8206609..a76dc173 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,6 +4,7 @@
 language: python
 python:
   - 3.5
+  - 3.6
 
 before_install:
   # install git lfs and fetch test data
@@ -38,7 +39,7 @@ install:
   - source activate test-environment
   - conda install -c ecpy atom;
   - pip install watchdog coveralls
-  - pip install pygsti
+  - if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then  pip install pygsti; fi
 
 script:
   - coverage run -m unittest discover
diff --git a/tests/test_data/awg/TestAPS1/.DS_Store b/tests/test_data/awg/TestAPS1/.DS_Store
deleted file mode 100644
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GIT binary patch
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From a5ec75d2aeae2b531eef2dd5d70243eaa1623225 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matt.ware@raytheon.com>
Date: Thu, 27 Sep 2018 20:04:54 -0400
Subject: [PATCH 006/235] added some missing files

---
 tests/test_data/awg/TestAPS1/GST/.DS_Store     | Bin 10244 -> 0 bytes
 .../awg/TestAPS1/GST/GST/listOfExperiments.npy | Bin 0 -> 33634 bytes
 .../TestAPS1/GST/GST2Q/listOfExperiments.npy   | Bin 0 -> 138231 bytes
 3 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 tests/test_data/awg/TestAPS1/GST/.DS_Store
 create mode 100644 tests/test_data/awg/TestAPS1/GST/GST/listOfExperiments.npy
 create mode 100644 tests/test_data/awg/TestAPS1/GST/GST2Q/listOfExperiments.npy

diff --git a/tests/test_data/awg/TestAPS1/GST/.DS_Store b/tests/test_data/awg/TestAPS1/GST/.DS_Store
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diff --git a/tests/test_data/awg/TestAPS1/GST/GST/listOfExperiments.npy b/tests/test_data/awg/TestAPS1/GST/GST/listOfExperiments.npy
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diff --git a/tests/test_data/awg/TestAPS1/GST/GST2Q/listOfExperiments.npy b/tests/test_data/awg/TestAPS1/GST/GST2Q/listOfExperiments.npy
new file mode 100644
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literal 0
HcmV?d00001


From b42c1aef746747462634f28519ca9f48ef95b345 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matt.ware@raytheon.com>
Date: Sat, 5 Jan 2019 19:37:44 -0500
Subject: [PATCH 007/235] Remove unncessary .DS_Store file

---
 tests/test_data/awg/TestAPS1/GST/GST/.DS_Store | Bin 6148 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 tests/test_data/awg/TestAPS1/GST/GST/.DS_Store

diff --git a/tests/test_data/awg/TestAPS1/GST/GST/.DS_Store b/tests/test_data/awg/TestAPS1/GST/GST/.DS_Store
deleted file mode 100644
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 6148
zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3
zem<@ulZcFPQ@L2!n>{z**<q8>++&mCkOWA81W14cNZ<zv;LbK1Poaz?KmsK2CSc!(
z0ynLxE!0092;Krf2c+FF_Fe*7ECH>lEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ
zLs35+`xjp>T0<F0fCPF1$Cyrb|F7^5{eNG?83~ZUUlGt@xh*qZDeu<Z%US-OSsOPv
j)R!Z4KLME7ReXlK;d!wEw5GODWMKRea10D2@KpjYNUI8I


From a6d0bdcec5340cd33544d13f24eb1144c59a4f2c Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Thu, 10 Jan 2019 10:18:18 -0500
Subject: [PATCH 008/235] Change np.isclose -> np.all(np.less()) in APS2
 pattern generator

---
 QGL/drivers/APS2Pattern.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 64dd96c1..1f174564 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -619,11 +619,11 @@ def inject_modulation_cmds(seqs):
         freqs = np.unique([entry.frequency for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)])
         if len(freqs) > 2:
             raise Exception("Max 2 frequencies on the same channel allowed.")
-        no_freq_cmds = np.allclose(freqs, 0)
+        no_freq_cmds = np.all(np.less(np.abs(freqs), 1e-8))
         phases = [entry.phase for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
-        no_phase_cmds = np.allclose(phases, 0)
+        no_phase_cmds = np.all(np.less(np.abs(phases), 1e-8))
         frame_changes = [entry.frameChange for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
-        no_frame_cmds = np.allclose(frame_changes, 0)
+        no_frame_cmds = np.all(np.less(np.abs(frame_changes), 1e-8))
         no_modulation_cmds = no_freq_cmds and no_phase_cmds and no_frame_cmds
 
         if no_modulation_cmds:

From 476520134cef38cbf3e6a089c59f59dbd8ed6509 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Thu, 10 Jan 2019 10:41:19 -0500
Subject: [PATCH 009/235] Simple script to look at cProfile info.

---
 tests/test_perf.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 tests/test_perf.py

diff --git a/tests/test_perf.py b/tests/test_perf.py
new file mode 100644
index 00000000..aea99755
--- /dev/null
+++ b/tests/test_perf.py
@@ -0,0 +1,18 @@
+#simple file added for performace testing...
+
+from QGL import *
+import random
+
+N = 1000
+
+cl = ChannelLibrary()
+q1 = QubitFactory("q1")
+
+gates = (X90(q1), Y90(q1), X(q1), Y(q1), Id(q1, length=1e-7))
+
+seqs = []
+ks = random.choices(range(1,100), k = N)
+for k in ks:
+    seqs.append(random.choices(gates, k=k) + [MEAS(q1)])
+
+compile_to_hardware(seqs, 'test/test')

From fd7b5f8cd048ca9d93fe5422b0d1c7c4153da528 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matthewware@users.noreply.github.com>
Date: Fri, 4 Jan 2019 17:02:57 -0500
Subject: [PATCH 010/235] Update README.md

QGL compiler needs networkx 2.0
---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 77a91176..34c0da2a 100644
--- a/README.md
+++ b/README.md
@@ -60,6 +60,6 @@ The QGL config file will be created the first time you run `import QGL` or `from
 * h5py
 * watchdog
 * Bokeh 0.11
-* networkx
+* networkx 2.0
 * iPython/Jupyter 4.0 (only for Jupyter notebooks)
 * ruamel_yaml

From dfc91e608eb8fd9b7d6f2f8bdd3eec5b895f6ece Mon Sep 17 00:00:00 2001
From: Matthew Ware <matthewware@users.noreply.github.com>
Date: Fri, 4 Jan 2019 17:03:58 -0500
Subject: [PATCH 011/235] Update setup.py

The compiler needs networkx 2.0 or higher now for edge identification.
---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 3a7ee80b..dee9e96b 100644
--- a/setup.py
+++ b/setup.py
@@ -10,7 +10,7 @@
             "jupyter >= 1.0.0",
             "atom >= 0.4.1",
             "h5py >= 2.6.0",
-            "networkx >= 1.11",
+            "networkx >= 2.0",
             "future >= 0.16",
             "watchdog >= 0.8.3",
             "bokeh >= 0.11",

From 52251f637bb0162504f134f7a823460b105e97b5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Mon, 30 Jul 2018 10:47:51 -0400
Subject: [PATCH 012/235] Consistent order (qc,qt) for CR

Consistent order for all standard sequences, including two-qubit RB and cal_seqs
---
 QGL/BasicSequences/CR.py | 8 ++++++--
 QGL/BasicSequences/RB.py | 2 +-
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/QGL/BasicSequences/CR.py b/QGL/BasicSequences/CR.py
index e94cdda5..f5185b20 100644
--- a/QGL/BasicSequences/CR.py
+++ b/QGL/BasicSequences/CR.py
@@ -80,7 +80,11 @@ def EchoCRLen(controlQ,
              echoCR(controlQ, targetQ, length=l, phase= phase, amp=amp, riseFall=riseFall, canc_amp=canc_amp, canc_phase=canc_phase),
              X(controlQ),
              MEAS(targetQ)*MEAS(controlQ)] for l in lengths] + \
+<<<<<<< HEAD
            create_cal_seqs((targetQ,controlQ), calRepeats, measChans=(targetQ, controlQ))
+=======
+           create_cal_seqs((controlQ,targetQ), calRepeats, measChans=(targetQ,controlQ))
+>>>>>>> 3e7c872... Consistent order (qc,qt) for CR
 
     metafile = compile_to_hardware(seqs, 'EchoCR/EchoCR',
         axis_descriptor=[
@@ -126,7 +130,7 @@ def EchoCRPhase(controlQ,
              echoCR(controlQ, targetQ, length=length, phase= ph, amp=amp, riseFall = riseFall, canc_amp=canc_amp, canc_phase=canc_phase),
              X90(targetQ)*X(controlQ),
              MEAS(targetQ)*MEAS(controlQ)] for ph in phases] + \
-             create_cal_seqs((targetQ,controlQ), calRepeats, measChans=(targetQ,controlQ))
+             create_cal_seqs((controlQ, targetQ), calRepeats, measChans=(targetQ,controlQ))
 
     axis_descriptor = [
         {
@@ -177,7 +181,7 @@ def EchoCRAmp(controlQ,
              echoCR(controlQ, targetQ, length=length, phase= phase, riseFall=riseFall,amp=a),
              X(controlQ),
              MEAS(targetQ)*MEAS(controlQ)] for a in amps] + \
-           create_cal_seqs((targetQ,controlQ), calRepeats, measChans=(targetQ,controlQ))
+           create_cal_seqs((controlQ ,targetQ), calRepeats, measChans=(targetQ,controlQ))
 
     axis_descriptor = [
         {
diff --git a/QGL/BasicSequences/RB.py b/QGL/BasicSequences/RB.py
index 6075445d..11285889 100644
--- a/QGL/BasicSequences/RB.py
+++ b/QGL/BasicSequences/RB.py
@@ -99,7 +99,7 @@ def TwoQubitRB(q1, q2, seqs, showPlot=False, suffix="", add_cals=True):
     """
     seqsBis = []
     for seq in seqs:
-        seqsBis.append(reduce(operator.add, [clifford_seq(c, q1, q2)
+        seqsBis.append(reduce(operator.add, [clifford_seq(c, q2, q1)
                                              for c in seq]))
 
     #Add the measurement to all sequences

From 20391fbb8fd9eb62976144a4e2e4f135c98c2ff8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Fri, 4 Jan 2019 16:36:39 -0500
Subject: [PATCH 013/235] Fix test sequences

---
 tests/test_Sequences.py                                       | 4 ++--
 tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.h5  | 4 ++--
 tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.h5  | 4 ++--
 tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS3.h5  | 4 ++--
 .../test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS1.h5  | 4 ++--
 .../test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS2.h5  | 4 ++--
 .../test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS3.h5  | 4 ++--
 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS1.h5  | 4 ++--
 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS2.h5  | 4 ++--
 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS3.h5  | 4 ++--
 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS4.h5  | 4 ++--
 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS5.h5  | 4 ++--
 .../test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS1.h5  | 4 ++--
 .../test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS2.h5  | 4 ++--
 .../test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS3.h5  | 4 ++--
 .../test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS4.h5  | 4 ++--
 .../test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS5.h5  | 4 ++--
 17 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/tests/test_Sequences.py b/tests/test_Sequences.py
index 59c4fff8..1531ed85 100644
--- a/tests/test_Sequences.py
+++ b/tests/test_Sequences.py
@@ -343,8 +343,8 @@ def test_RB_TwoQubitRB(self):
 		"""
         self.set_awg_dir('TwoQubitRB')
         np.random.seed(20152606)  # set seed for create_RB_seqs()
-        TwoQubitRB(self.q1,
-                   self.q2,
+        TwoQubitRB(self.q2,
+                   self.q1,
                    create_RB_seqs(2, [2, 4, 8, 16, 32],
                                   repeats=16))
         self.compare_sequences('RB')
diff --git a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.h5 b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.h5
index 27ff6fb2..0f589d2c 100644
--- a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.h5
+++ b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.h5
@@ -1,3 +1,3 @@
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-size 20568
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+size 20552
diff --git a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.h5 b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.h5
index 17d18bd4..b5872b5f 100644
--- a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.h5
+++ b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.h5
@@ -1,3 +1,3 @@
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diff --git a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS3.h5 b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS3.h5
index 94abd59e..953bfa04 100644
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+++ b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS3.h5
@@ -1,3 +1,3 @@
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diff --git a/tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS1.h5 b/tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS1.h5
index 8c321d08..9c6f0102 100644
--- a/tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS1.h5
+++ b/tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS1.h5
@@ -1,3 +1,3 @@
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index 6e676ef3..041cb89c 100644
--- a/tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS2.h5
+++ b/tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS2.h5
@@ -1,3 +1,3 @@
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index de0e0e3b..9898ef3b 100644
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+++ b/tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS3.h5
@@ -1,3 +1,3 @@
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index 9f64875d..ab15aa85 100644
--- a/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS1.h5
+++ b/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS1.h5
@@ -1,3 +1,3 @@
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index 7b3fb1f2..9d8b12af 100644
--- a/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS2.h5
+++ b/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS2.h5
@@ -1,3 +1,3 @@
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diff --git a/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS3.h5 b/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS3.h5
index 392ee3e1..0ab91628 100644
--- a/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS3.h5
+++ b/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS3.h5
@@ -1,3 +1,3 @@
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-size 10896
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+size 10800
diff --git a/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS4.h5 b/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS4.h5
index 7b3fb1f2..9d8b12af 100644
--- a/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS4.h5
+++ b/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS4.h5
@@ -1,3 +1,3 @@
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-size 11440
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+size 11344
diff --git a/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS5.h5 b/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS5.h5
index e4233b17..fae1d541 100644
--- a/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS5.h5
+++ b/tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS5.h5
@@ -1,3 +1,3 @@
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-size 14288
+oid sha256:e7da7ea9ae19ea57b6e1cc5783c4ebb53ad2522ef51979d1fb656738ecc0aaf6
+size 14192
diff --git a/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS1.h5 b/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS1.h5
index c919b2a9..8696d76b 100644
--- a/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS1.h5
+++ b/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS1.h5
@@ -1,3 +1,3 @@
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diff --git a/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS2.h5 b/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS2.h5
index 39f1f02d..0779fc89 100644
--- a/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS2.h5
+++ b/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS2.h5
@@ -1,3 +1,3 @@
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index 67fc1946..3944eb32 100644
--- a/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS3.h5
+++ b/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS3.h5
@@ -1,3 +1,3 @@
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index 39f1f02d..9220854d 100644
--- a/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS4.h5
+++ b/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS4.h5
@@ -1,3 +1,3 @@
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diff --git a/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS5.h5 b/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS5.h5
index 23d10721..043f2ada 100644
--- a/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS5.h5
+++ b/tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS5.h5
@@ -1,3 +1,3 @@
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From 8fc971e6595efd39972f80641cbf1367e096b958 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Wed, 7 Nov 2018 10:19:53 -0500
Subject: [PATCH 014/235] Allow for slave trigger for APS1

Even with the TDM triggering, we need a slave trigger for the APS1s
---
 QGL/ChannelLibraries.py | 45 ++++++++++++++++++++++-------------------
 1 file changed, 24 insertions(+), 21 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index c84de4e7..6afb03b2 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -265,32 +265,35 @@ def load_from_library(self, return_only=False):
                     else:
                         master_awgs.append(name)
                 # Eventually we should support multiple masters...
-                # if "slave_trig" in instr.keys():
-                #     params = {}
-                #     params["label"]        = name + "_slave_trig"
-                #     params["phys_chan"]    = name + "-" + instr["slave_trig"]
-                #     params["pulse_params"] = {"length": 1e-7, "shape_fun": "constant"}
-                #     params["__module__"]   = "QGL.Channels"
-                #     params["__class__"]    = "LogicalMarkerChannel"
-                #     print(params["label"], "***")
-                #     channel_dict[params["label"]] = params
+                if "slave_trig" in instr.keys():
+                    params = {}
+                    params["label"]        = "slave_trig"
+                    params["phys_chan"]    = name + "-" + instr["slave_trig"]
+                    if params["phys_chan"] in marker_lens.keys():
+                        length = marker_lens[params["phys_chan"]]
+                    else:
+                        length = 1e-7
+                    params["pulse_params"] = {"length": length, "shape_fun": "constant"}
+                    params["__module__"]   = "QGL.Channels"
+                    params["__class__"]    = "LogicalMarkerChannel"
+                    channel_dict[params["label"]] = params
 
             # Establish the slave trigger, assuming for now that we have a single
             # APS master. This might change later.
             if len(master_awgs) > 1:
                 raise ValueError("More than one AWG is marked as master.")
-            elif len(master_awgs) == 1  and instr_dict[master_awgs[0].split('-')[0]]['type'] != 'TDM':
-                params = {}
-                params["label"]       = "slave_trig"
-                params["phys_chan"]    = master_awgs[0]
-                if params["phys_chan"] in marker_lens.keys():
-                    length = marker_lens[params["phys_chan"]]
-                else:
-                    length = 1e-7
-                params["pulse_params"] = {"length": length, "shape_fun": "constant"}
-                params["__module__"]  = "QGL.Channels"
-                params["__class__"]   = "LogicalMarkerChannel"
-                channel_dict[params["label"]] = params
+            # elif len(master_awgs) == 1  and instr_dict[master_awgs[0].split('-')[0]]['type'] != 'TDM':
+            #     params = {}
+            #     params["label"]       = "slave_trig"
+            #     params["phys_chan"]    = master_awgs[0]
+            #     if params["phys_chan"] in marker_lens.keys():
+            #         length = marker_lens[params["phys_chan"]]
+            #     else:
+            #         length = 1e-7
+            #     params["pulse_params"] = {"length": length, "shape_fun": "constant"}
+            #     params["__module__"]  = "QGL.Channels"
+            #     params["__class__"]   = "LogicalMarkerChannel"
+            #     channel_dict[params["label"]] = params
 
             for name, filt in filter_dict.items():
                 if "StreamSelector" in filt["type"]:

From 09ff7eefe3c30680da3ed8c9e941b8f61a8abc5d Mon Sep 17 00:00:00 2001
From: "T.J.Rogers" <trogers@bbn.com>
Date: Wed, 7 Nov 2018 18:03:19 -0500
Subject: [PATCH 015/235] Added a __main__ reference to get simple python
 invocation unittest working Re:  python test_Scheduler.py -v

---
 tests/test_Scheduler.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/test_Scheduler.py b/tests/test_Scheduler.py
index e29a1e25..003b5f4e 100644
--- a/tests/test_Scheduler.py
+++ b/tests/test_Scheduler.py
@@ -121,3 +121,6 @@ def test_measurements(self):
 
         # should be unchanged
         assert seq == result
+
+if __name__ == "__main__":
+    unittest.main()

From 8505202ae233b69fb11ab92a75dc452b4113f9ac Mon Sep 17 00:00:00 2001
From: "T.J.Rogers" <trogers@bbn.com>
Date: Fri, 9 Nov 2018 12:07:34 -0500
Subject: [PATCH 016/235] Added test_QGL comments regarding Git LFS data file
 usage (and error encountered when git-lfs library is NOT installed).

---
 tests/test_QGL.py         | 14 ++++++++++++++
 tests/test_pulse_types.py |  9 ++++++++-
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/tests/test_QGL.py b/tests/test_QGL.py
index 89615e54..b91156b0 100644
--- a/tests/test_QGL.py
+++ b/tests/test_QGL.py
@@ -88,7 +88,21 @@ def load(self):
                     'Warning: valid waveform file for {0} not found at: {1}'.format(
                         caseName, fileName))
                 continue
+            # -----
+            # print( "\n\rDBG::Calling \"with h5py.File( {0}, 'r')\"...".format( fileName) )
+            # -----
+            # The following pulls in Git Large File Storage (LFS) data files
+            # from cached signature references;  if the h5py.File call fails
+            # with an OSError, double-check git-lfs library installation (in
+            # addition to git) -- <https://git-lfs.github.com/>
+            #
+            # Where git-lfs was NOT installed the h5py.File() call was observed
+            # returning:
+            #
+            # OSError: Unable to open file (file signature not found))
+            #
             with h5py.File(fileName, 'r') as FID:
+                # print( "DBG::FID: {0}".format( FID))
                 for name, waveform in FID['/channels'].items():
                     validWaveform[name] = waveform[:]
             self.validWaveforms[caseName] = validWaveform
diff --git a/tests/test_pulse_types.py b/tests/test_pulse_types.py
index 69d8221f..7f574b4a 100644
--- a/tests/test_pulse_types.py
+++ b/tests/test_pulse_types.py
@@ -16,7 +16,9 @@ def setUp(self):
         self.q3 = QubitFactory('q3')
         self.q4 = QubitFactory('q4')
 
-    @unittest.skip("Type promition for CNOT(q1, q2) * X(q3) gives PulseBlock not CompoundGate. Looking into this issue.")
+    # This appears to run successfully with the skip commented out;
+    # TJR, 07 Nov 2018
+    #@unittest.skip("Type promition for CNOT(q1, q2) * X(q3) gives PulseBlock not CompoundGate. Looking into this issue.")
     def test_promotion_rules(self):
         q1, q2, q3, q4 = self.q1, self.q2, self.q3, self.q4
 
@@ -28,3 +30,8 @@ def test_promotion_rules(self):
         assert( type(CNOT_CR(q1, q2) * X(q3)) == CompoundGate )
         assert( type(X(q3) * CNOT_CR(q1, q2)) == CompoundGate )
         assert( type(CNOT_CR(q1, q2) * CNOT_CR(q3, q4)) == CompoundGate )
+
+# Added to support simple python invocation
+#
+if __name__ == "__main__":
+    unittest.main()

From a3654d2333bfe6bdc23bbc31d697e6f79cab91e6 Mon Sep 17 00:00:00 2001
From: "T.J.Rogers" <trogers@bbn.com>
Date: Fri, 9 Nov 2018 12:27:18 -0500
Subject: [PATCH 017/235] Added README.md tail comment regarding Git LFS usage
 for some unittest data files.

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 34c0da2a..57b51930 100644
--- a/README.md
+++ b/README.md
@@ -63,3 +63,7 @@ The QGL config file will be created the first time you run `import QGL` or `from
 * networkx 2.0
 * iPython/Jupyter 4.0 (only for Jupyter notebooks)
 * ruamel_yaml
+
+## UnitTest data support
+This repository uses the Git Large File Storage (LFS) extension to manage a few
+UnitTest data files (see https://git-lfs.github.com/).

From 86f36b9993b0af515a322004af8bb13ff2b567fd Mon Sep 17 00:00:00 2001
From: "T.J.Rogers" <trogers@bbn.com>
Date: Wed, 14 Nov 2018 17:25:53 -0500
Subject: [PATCH 018/235] Defined ReadMeDocs.txt to briefly describe the MkDocs
 document library use case.

---
 ReadMe_Docs.txt | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 ReadMe_Docs.txt

diff --git a/ReadMe_Docs.txt b/ReadMe_Docs.txt
new file mode 100644
index 00000000..0e42164e
--- /dev/null
+++ b/ReadMe_Docs.txt
@@ -0,0 +1,6 @@
+#---------- 14 Nov 2018
+This repository uses the MkDocs (v0.17.2) utilities for documentation rendering.
+From the repo root directory, "mkdocs --help" shows the options.
+"mkdocs build" for example, writes a set of html documents under the ./site subdirectory
+
+(Aside: ./site is NOT currently in the .gitignore file; insertion pending for consistency). 

From 75b4ef9e4eef6d06d7b14da11d004c54720d4934 Mon Sep 17 00:00:00 2001
From: "T.J.Rogers" <trogers@bbn.com>
Date: Fri, 30 Nov 2018 13:12:02 -0500
Subject: [PATCH 019/235] Defined renderDocs.sh and runUnitTests.sh shell
 scripts to automate documentation rendering and unit test invocation logic.

---
 renderDocs.sh   | 26 ++++++++++++++++++
 runUnitTests.sh | 72 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 98 insertions(+)
 create mode 100755 renderDocs.sh
 create mode 100755 runUnitTests.sh

diff --git a/renderDocs.sh b/renderDocs.sh
new file mode 100755
index 00000000..04b03d12
--- /dev/null
+++ b/renderDocs.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+echo ""
+echo "#---------- $0 (QGL) start..."
+echo ""
+#----- Simple script to capture basic documentation rendering logic.
+
+echo "#-----Building QGL docs via ~:"
+
+export CMD="mkdocs build"
+echo $CMD
+echo ""
+$CMD
+
+pushd .
+
+cd site
+echo ""
+echo "Target QGL documents list as follows:"
+pwd
+ls -l
+
+
+echo ""
+echo "#---------- $0 (QGL) stop."
+echo ""
+
diff --git a/runUnitTests.sh b/runUnitTests.sh
new file mode 100755
index 00000000..d063b6bf
--- /dev/null
+++ b/runUnitTests.sh
@@ -0,0 +1,72 @@
+#!/bin/bash
+echo ""
+echo "#---------- $0 (QGL) start..."
+echo ""
+#----- Simple script to capture basic documentation rendering logic.
+
+pwd
+
+export szGit_LFS_Path=`which git-lfs`
+echo "szGit_LFS_Path: [${szGit_LFS_Path}]"
+
+
+# Instantiate the git lfs cached data files...
+export CMD="git lfs pull"
+echo ""
+if [ -z ${szGit_LFS_Path} ]; then
+    echo ""
+    echo "#--------------------"
+    echo "#   W A R N I N G   -- git-lfs extension library unavailable;"
+    echo "#                      -- QGL h5 data file processing may fail."
+    echo "#                         << [${szGit_LFS_Path}] << 'which git-lfs'"
+    echo "#--------------------"
+else
+    echo "git-lfs available;  retrieving/instantiating cached QGL h5 data files via ~:"
+    echo $CMD
+    echo ""
+    $CMD
+fi
+echo ""
+
+
+# Don't forget to set the BBN_MEAS_FILE reference.
+export BBN_MEAS_FILE=tests/test_measure.yml
+
+echo ""
+echo "#-----Unit-Testing general QGL (BBN_MEAS_FILE=${BBN_MEAS_FILE}) via ~:"
+# -f option fails fast
+#export CMD="python -m unittest discover . -v -f"
+#export CMD="python -m unittest discover . -v"
+# Trimm'ed down (non LFS unitest calls) syntax as follows:
+export CMD="python -m unittest  tests/test_A*.py tests/test_C*.py tests/test_Scheduler.py tests/test_config.py tests/test_pulse_types.py -v"
+echo $CMD
+echo ""
+$CMD
+
+if [ -z ${szGit_LFS_Path} ]; then
+    echo ""
+    echo "#-----   W A R N I N G:"
+    echo "    Fast-failing unittest modules test_QGL.py, and test_Sequences.py,"
+    echo "    currently, due to git lfs data file dependencies;  in-short, the"
+    echo "    docker continuumio/miniconda load appears to omit the necessary"
+    echo "    git-lfs library installation."
+    echo ""
+    echo "    Without the git-lfs library extension, h5 data calls from these"
+    echo "    modules typically error out with ~:"
+    echo "    OSError: Unable to open file (file signature not found)"
+    echo ""
+    echo "    If/when the git-lfs library becomes available in the docker load, "
+    echo "    remove the \"-f\"from the invocation, below:"
+fi
+
+echo ""
+echo "#----- Testing LFS data file dependent QGL modules via ~:"
+export CMD="python -m unittest tests.test_QGL tests.test_Sequences.py -v -f"
+echo $CMD
+echo ""
+$CMD
+
+echo ""
+echo "#---------- $0 (QGL) stop."
+echo ""
+

From 00ecab37dc20252b034f58fa6f0ec28ee7eb4796 Mon Sep 17 00:00:00 2001
From: "T.J.Rogers" <trogers@bbn.com>
Date: Fri, 30 Nov 2018 13:22:22 -0500
Subject: [PATCH 020/235] Corrected runUnitTests.sh description header.

---
 runUnitTests.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/runUnitTests.sh b/runUnitTests.sh
index d063b6bf..5ff573ab 100755
--- a/runUnitTests.sh
+++ b/runUnitTests.sh
@@ -2,7 +2,7 @@
 echo ""
 echo "#---------- $0 (QGL) start..."
 echo ""
-#----- Simple script to capture basic documentation rendering logic.
+#----- Simple script to capture unittest preparation and invocation logic.
 
 pwd
 

From a2153f640480d7d282b865d3c5819bba3d4d4ec5 Mon Sep 17 00:00:00 2001
From: "T.J.Rogers" <trogers@bbn.com>
Date: Tue, 4 Dec 2018 14:28:54 -0500
Subject: [PATCH 021/235] Fixed a typo in runUnitTests.sh (removed the .py
 reference in second test set). Added test_Sequences.py logic (set_awg_dir) to
 invoke config.load_conifg() when config.AWGDir is undefined. (when running as
 a stand-alone test, this case was causing failures).

---
 runUnitTests.sh         |  4 +++-
 tests/test_Sequences.py | 12 ++++++++++++
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/runUnitTests.sh b/runUnitTests.sh
index 5ff573ab..ffab4f0f 100755
--- a/runUnitTests.sh
+++ b/runUnitTests.sh
@@ -61,7 +61,9 @@ fi
 
 echo ""
 echo "#----- Testing LFS data file dependent QGL modules via ~:"
-export CMD="python -m unittest tests.test_QGL tests.test_Sequences.py -v -f"
+# Careful -- in this format (tests.moduleName) DON'T cite the .py suffix
+# (it will render an odd error regarding missing 'py' attribute)
+export CMD="python -m unittest tests.test_QGL tests.test_Sequences -v -f"
 echo $CMD
 echo ""
 $CMD
diff --git a/tests/test_Sequences.py b/tests/test_Sequences.py
index 1531ed85..ada1e278 100644
--- a/tests/test_Sequences.py
+++ b/tests/test_Sequences.py
@@ -9,6 +9,11 @@
 from QGL.Channels import Edge, Measurement, LogicalChannel, LogicalMarkerChannel, PhysicalMarkerChannel, PhysicalQuadratureChannel
 from QGL.drivers import APSPattern, APS2Pattern, TekPattern
 
+# Pulled in logger to help debug stand-alone run issue with the config.AWGDir
+# (the configuration was NOT gettng loaded when run independently)
+#
+import logging
+logger = logging.getLogger( 'sequences')
 
 class AWGTestHelper(object):
     testFileDirectory = './tests/test_data/awg/'
@@ -94,6 +99,13 @@ def get_qubits(self):
     def set_awg_dir(self, footer=""):
         cn = self.__class__.__name__
 
+        if None == QGL.config.AWGDir:
+            logger.warning( "\n\r#----- EEE NULL QGL.config.AWGDir {%s} cited; calling load_config()...", QGL.config.AWGDir)
+            QGL.config.load_config()
+            logger.warning( "#----- Post load-config QGL.config.AWGDir: {%s}.\n\r", QGL.config.AWGDir)
+        #else:
+        #    logger.warning( "\n\r#----- Using QGL.config.AWGDir {%s} 8-p", QGL.config.AWGDir)
+
         self.awg_dir = os.path.abspath(QGL.config.AWGDir + os.path.sep + cn)
         self.truth_dir = os.path.abspath(self.testFileDirectory + os.path.sep +
                                          cn)

From c9da2dc2e377bbc310c078e934514bca39a43b66 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matt.ware@raytheon.com>
Date: Sat, 5 Jan 2019 19:14:29 -0500
Subject: [PATCH 022/235] fixed a mkdocs dep warning

---
 mkdocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mkdocs.yml b/mkdocs.yml
index 5d43ff40..6ff817c8 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,5 +1,5 @@
 site_name: QGL
-pages:
+nav:
     - Intro: index.md
     - Configuration: config.md
     - Examples: examples.md

From 8d9853ae45bd2e96bf88de49536afad1b01b8e26 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Thu, 10 Jan 2019 10:18:18 -0500
Subject: [PATCH 023/235] Change np.isclose -> np.all(np.less()) in APS2
 pattern generator

---
 QGL/drivers/APS2Pattern.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 64dd96c1..1f174564 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -619,11 +619,11 @@ def inject_modulation_cmds(seqs):
         freqs = np.unique([entry.frequency for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)])
         if len(freqs) > 2:
             raise Exception("Max 2 frequencies on the same channel allowed.")
-        no_freq_cmds = np.allclose(freqs, 0)
+        no_freq_cmds = np.all(np.less(np.abs(freqs), 1e-8))
         phases = [entry.phase for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
-        no_phase_cmds = np.allclose(phases, 0)
+        no_phase_cmds = np.all(np.less(np.abs(phases), 1e-8))
         frame_changes = [entry.frameChange for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
-        no_frame_cmds = np.allclose(frame_changes, 0)
+        no_frame_cmds = np.all(np.less(np.abs(frame_changes), 1e-8))
         no_modulation_cmds = no_freq_cmds and no_phase_cmds and no_frame_cmds
 
         if no_modulation_cmds:

From 5821b5e2b75ba04897fa96608fd17014faa4c443 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Thu, 10 Jan 2019 10:41:19 -0500
Subject: [PATCH 024/235] Simple script to look at cProfile info.

---
 tests/test_perf.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 tests/test_perf.py

diff --git a/tests/test_perf.py b/tests/test_perf.py
new file mode 100644
index 00000000..aea99755
--- /dev/null
+++ b/tests/test_perf.py
@@ -0,0 +1,18 @@
+#simple file added for performace testing...
+
+from QGL import *
+import random
+
+N = 1000
+
+cl = ChannelLibrary()
+q1 = QubitFactory("q1")
+
+gates = (X90(q1), Y90(q1), X(q1), Y(q1), Id(q1, length=1e-7))
+
+seqs = []
+ks = random.choices(range(1,100), k = N)
+for k in ks:
+    seqs.append(random.choices(gates, k=k) + [MEAS(q1)])
+
+compile_to_hardware(seqs, 'test/test')

From 3c76064e70d1ed11fc6f54a7645e8bab73fe77de Mon Sep 17 00:00:00 2001
From: Matthew Ware <matthew.e.ware@gmail.com>
Date: Thu, 10 Jan 2019 14:33:17 -0500
Subject: [PATCH 025/235] Add IR compile function

---
 QGL/Compiler.py | 118 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 118 insertions(+)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 599e8d18..4c53d381 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -299,6 +299,124 @@ def collect_specializations(seqs):
             done.append(target)
     return funcs
 
+def compile_to_qgl_IR(seqs,
+                        suffix='',
+                        axis_descriptor=None,
+                        add_slave_trigger=True,
+                        extra_meta=None,
+                        tdm_seq = False):
+    '''
+    Compiles 'seqs' to a hardware description and saves it to 'fileName'.
+    Other inputs:
+        suffix (optional): string to append to end of fileName, e.g. with
+            fileNames = 'test' and suffix = 'foo' might save to test-APSfoo.h5
+        axis_descriptor (optional): a list of dictionaries describing the effective
+            axes of the measurements that the sequence will yield. For instance,
+            if `seqs` generates a Ramsey experiment, axis_descriptor would describe
+            the time delays between pulses.
+        add_slave_trigger (optional): add the slave trigger(s)
+        tdm_seq (optional): compile for TDM
+    '''
+    logger.debug("Compiling %d sequence(s)", len(seqs))
+
+    # save input code to file
+    save_code(seqs, fileName + suffix)
+
+    # all sequences should start with a WAIT for synchronization
+    for seq in seqs:
+        if not isinstance(seq[0], ControlFlow.Wait):
+            logger.debug("Adding a WAIT - first sequence element was %s", seq[0])
+            seq.insert(0, ControlFlow.Wait())
+
+    # Add the digitizer trigger to measurements
+    logger.debug("Adding digitizer trigger")
+    PatternUtils.add_digitizer_trigger(seqs)
+
+    # Add gating/blanking pulses
+    logger.debug("Adding blanking pulses")
+    for seq in seqs:
+        PatternUtils.add_gate_pulses(seq)
+
+    if add_slave_trigger and 'slave_trig' in ChannelLibraries.channelLib:
+        # Add the slave trigger
+        logger.debug("Adding slave trigger")
+        PatternUtils.add_slave_trigger(seqs,
+                                       ChannelLibraries.channelLib['slave_trig'])
+    else:
+        logger.debug("Not adding slave trigger")
+
+    # find channel set at top level to account for individual sequence channel variability
+    channels = set()
+    for seq in seqs:
+        channels |= find_unique_channels(seq)
+
+    # Compile all the pulses/pulseblocks to sequences of pulses and control flow
+    wireSeqs = compile_sequences(seqs, channels)
+
+    if not validate_linklist_channels(wireSeqs.keys()):
+        print("Compile to hardware failed")
+        return
+
+    logger.debug('')
+    logger.debug("Now after gating constraints:")
+    # apply gating constraints
+    for chan, seq in wireSeqs.items():
+        if isinstance(chan, Channels.LogicalMarkerChannel):
+            wireSeqs[chan] = PatternUtils.apply_gating_constraints(
+                chan.phys_chan, seq)
+    debug_print(wireSeqs, 'Gated sequence')
+
+    # save number of measurements for meta info
+    num_measurements = count_measurements(wireSeqs)
+    wire_measurements = count_measurements_per_wire(wireSeqs)
+
+    # map logical to physical channels, physWires is a list of
+    # PhysicalQuadratureChannels and PhysicalMarkerChannels
+    # for the APS, the naming convention is:
+    # ASPName-12, or APSName-12m1
+    physWires = map_logical_to_physical(wireSeqs)
+
+    # Pave the way for composite instruments, not useful yet...
+    files = {}
+    label_to_inst   = {}
+    label_to_chan   = {}
+    old_wire_names  = {}
+    old_wire_instrs = {}
+    for wire, pulses in physWires.items():
+        pattern_module = import_module('QGL.drivers.' + wire.translator)
+        if pattern_module.SEQFILE_PER_CHANNEL:
+            inst_name = pattern_module.get_true_inst_name(wire.label)
+            chan_name = pattern_module.get_true_chan_name(wire.label)
+            has_non_id_pulses = any([len([p for p in ps if isinstance(p,Pulse) and p.label!="Id"]) > 0 for ps in pulses])
+            label_to_inst[wire.label] = inst_name
+            if has_non_id_pulses:
+                label_to_chan[wire.label] = chan_name
+            # Change the name/inst for uniqueness, but we must restore this later!
+            old_wire_names[wire] = wire.label
+            old_wire_instrs[wire] = wire.instrument
+            wire.instrument = wire.label
+            wire.label = chan_name
+            files[inst_name] = {}
+
+    # construct channel delay map
+    delays = channel_delay_map(physWires)
+
+    # apply delays
+    for chan, wire in physWires.items():
+        PatternUtils.delay(wire, delays[chan])
+    debug_print(physWires, 'Delayed wire')
+
+    # generate wf library (base shapes)
+    wfs = generate_waveforms(physWires)
+
+    # replace Pulse objects with Waveforms
+    physWires = pulses_to_waveforms(physWires)
+
+    # bundle wires on instruments, or channels depending
+    # on whether we have one sequence per channel
+    awgData = bundle_wires(physWires, wfs)
+
+    return awgData
 
 def compile_to_hardware(seqs,
                         fileName,

From 7f7e434905b1836e337160213ae5cac77317afd0 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matthew.e.ware@gmail.com>
Date: Thu, 10 Jan 2019 16:56:09 -0500
Subject: [PATCH 026/235] Add memory info

---
 QGL/BasicSequences/CR.py |  4 ----
 QGL/Compiler.py          | 39 ++++++++++++++++++++++++++++++---------
 2 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/QGL/BasicSequences/CR.py b/QGL/BasicSequences/CR.py
index f5185b20..39f26e45 100644
--- a/QGL/BasicSequences/CR.py
+++ b/QGL/BasicSequences/CR.py
@@ -80,11 +80,7 @@ def EchoCRLen(controlQ,
              echoCR(controlQ, targetQ, length=l, phase= phase, amp=amp, riseFall=riseFall, canc_amp=canc_amp, canc_phase=canc_phase),
              X(controlQ),
              MEAS(targetQ)*MEAS(controlQ)] for l in lengths] + \
-<<<<<<< HEAD
-           create_cal_seqs((targetQ,controlQ), calRepeats, measChans=(targetQ, controlQ))
-=======
            create_cal_seqs((controlQ,targetQ), calRepeats, measChans=(targetQ,controlQ))
->>>>>>> 3e7c872... Consistent order (qc,qt) for CR
 
     metafile = compile_to_hardware(seqs, 'EchoCR/EchoCR',
         axis_descriptor=[
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 4c53d381..901d20d1 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -19,6 +19,7 @@
 import numpy as np
 import os
 import operator
+import psutil
 from warnings import warn
 from copy import copy
 from functools import reduce
@@ -317,10 +318,10 @@ def compile_to_qgl_IR(seqs,
         add_slave_trigger (optional): add the slave trigger(s)
         tdm_seq (optional): compile for TDM
     '''
-    logger.debug("Compiling %d sequence(s)", len(seqs))
+    process = psutil.Process(os.getpid())
 
-    # save input code to file
-    save_code(seqs, fileName + suffix)
+    logger.info("Compiling %d sequence(s)", len(seqs))
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
 
     # all sequences should start with a WAIT for synchronization
     for seq in seqs:
@@ -329,21 +330,25 @@ def compile_to_qgl_IR(seqs,
             seq.insert(0, ControlFlow.Wait())
 
     # Add the digitizer trigger to measurements
-    logger.debug("Adding digitizer trigger")
+    logger.info("Adding digitizer trigger")
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     PatternUtils.add_digitizer_trigger(seqs)
 
     # Add gating/blanking pulses
-    logger.debug("Adding blanking pulses")
+    logger.info("Adding blanking pulses")
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     for seq in seqs:
         PatternUtils.add_gate_pulses(seq)
 
     if add_slave_trigger and 'slave_trig' in ChannelLibraries.channelLib:
         # Add the slave trigger
-        logger.debug("Adding slave trigger")
+        logger.info("Adding slave trigger")
+        logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
         PatternUtils.add_slave_trigger(seqs,
                                        ChannelLibraries.channelLib['slave_trig'])
     else:
-        logger.debug("Not adding slave trigger")
+        logger.info("Not adding slave trigger")
+        logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
 
     # find channel set at top level to account for individual sequence channel variability
     channels = set()
@@ -351,14 +356,17 @@ def compile_to_qgl_IR(seqs,
         channels |= find_unique_channels(seq)
 
     # Compile all the pulses/pulseblocks to sequences of pulses and control flow
+    logger.info("Compiling sequences")
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     wireSeqs = compile_sequences(seqs, channels)
 
     if not validate_linklist_channels(wireSeqs.keys()):
         print("Compile to hardware failed")
         return
 
-    logger.debug('')
-    logger.debug("Now after gating constraints:")
+    logger.info('')
+    logger.info("Now after gating constraints:")
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     # apply gating constraints
     for chan, seq in wireSeqs.items():
         if isinstance(chan, Channels.LogicalMarkerChannel):
@@ -367,6 +375,8 @@ def compile_to_qgl_IR(seqs,
     debug_print(wireSeqs, 'Gated sequence')
 
     # save number of measurements for meta info
+    logger.info("Counting measurements")
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     num_measurements = count_measurements(wireSeqs)
     wire_measurements = count_measurements_per_wire(wireSeqs)
 
@@ -374,6 +384,8 @@ def compile_to_qgl_IR(seqs,
     # PhysicalQuadratureChannels and PhysicalMarkerChannels
     # for the APS, the naming convention is:
     # ASPName-12, or APSName-12m1
+    logger.info("Mapping logical to physical")
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     physWires = map_logical_to_physical(wireSeqs)
 
     # Pave the way for composite instruments, not useful yet...
@@ -399,6 +411,8 @@ def compile_to_qgl_IR(seqs,
             files[inst_name] = {}
 
     # construct channel delay map
+    logger.info("Building delay map")
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     delays = channel_delay_map(physWires)
 
     # apply delays
@@ -407,15 +421,22 @@ def compile_to_qgl_IR(seqs,
     debug_print(physWires, 'Delayed wire')
 
     # generate wf library (base shapes)
+    logger.info("Generating waveforms")
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     wfs = generate_waveforms(physWires)
 
     # replace Pulse objects with Waveforms
+    logger.info("Mapping pulses to waveforms")
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     physWires = pulses_to_waveforms(physWires)
 
     # bundle wires on instruments, or channels depending
     # on whether we have one sequence per channel
+    logger.info("Bundling wires!")
+    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     awgData = bundle_wires(physWires, wfs)
 
+    logger.info("DONE!")
     return awgData
 
 def compile_to_hardware(seqs,

From 087bf2f1a177ade5cf5c7a8beeaf45c44de31d39 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Fri, 11 Jan 2019 13:20:01 -0500
Subject: [PATCH 027/235] Memoize waveform objects to save on memory.

---
 QGL/Compiler.py | 24 +++++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 901d20d1..cd3030b3 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -22,10 +22,9 @@
 import psutil
 from warnings import warn
 from copy import copy
-from functools import reduce
+from functools import reduce, lru_cache
 from importlib import import_module
 import json
-
 from . import config
 from . import PatternUtils
 from .PatternUtils import flatten, has_gate
@@ -388,6 +387,8 @@ def compile_to_qgl_IR(seqs,
     logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
     physWires = map_logical_to_physical(wireSeqs)
 
+    del wireSeqs
+
     # Pave the way for composite instruments, not useful yet...
     files = {}
     label_to_inst   = {}
@@ -437,6 +438,7 @@ def compile_to_qgl_IR(seqs,
     awgData = bundle_wires(physWires, wfs)
 
     logger.info("DONE!")
+    logger.info("Used {} GB of memory".format(process.memory_info().rss/1e9))
     return awgData
 
 def compile_to_hardware(seqs,
@@ -795,12 +797,24 @@ def normalize(seq, channels=None):
             block.pulses[ch] = Id(ch, blocklen)
     return seq
 
-class Waveform(object):
+class MemoizedObject(type):
+    """Metaclass for memoizing objects. Designed to save memory when processing
+    very long sequences. Overrides __call__ to prevent creating a new instance.
+    Idea from https://stackoverflow.com/questions/47785795/memoized-objects-still-have-their-init-invoked
+    """
+    def __init__(self, name, bases, namespace):
+        super().__init__(name, bases, namespace)
+        self.cache = {}
+    def __call__(self, pulse=None):
+        hash = pulse.hashshape()
+        if pulse is not None and hash not in self.cache:
+            self.cache[hash] = super().__call__(pulse=pulse)
+        return self.cache[hash]
+
+class Waveform(metaclass=MemoizedObject):
     """
     Simplified channel independent version of a Pulse with a key into waveform library.
     """
-
-
     def __init__(self, pulse=None):
         if pulse is None:
             self.label = ""

From 3f346dff67c036d13e7869a702609a25055e03f2 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Fri, 11 Jan 2019 14:52:53 -0500
Subject: [PATCH 028/235] Remove debug stuff.

---
 QGL/Compiler.py | 147 +-----------------------------------------------
 1 file changed, 2 insertions(+), 145 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index cd3030b3..61bc01d1 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -19,10 +19,9 @@
 import numpy as np
 import os
 import operator
-import psutil
 from warnings import warn
 from copy import copy
-from functools import reduce, lru_cache
+from functools import reduce
 from importlib import import_module
 import json
 from . import config
@@ -299,148 +298,6 @@ def collect_specializations(seqs):
             done.append(target)
     return funcs
 
-def compile_to_qgl_IR(seqs,
-                        suffix='',
-                        axis_descriptor=None,
-                        add_slave_trigger=True,
-                        extra_meta=None,
-                        tdm_seq = False):
-    '''
-    Compiles 'seqs' to a hardware description and saves it to 'fileName'.
-    Other inputs:
-        suffix (optional): string to append to end of fileName, e.g. with
-            fileNames = 'test' and suffix = 'foo' might save to test-APSfoo.h5
-        axis_descriptor (optional): a list of dictionaries describing the effective
-            axes of the measurements that the sequence will yield. For instance,
-            if `seqs` generates a Ramsey experiment, axis_descriptor would describe
-            the time delays between pulses.
-        add_slave_trigger (optional): add the slave trigger(s)
-        tdm_seq (optional): compile for TDM
-    '''
-    process = psutil.Process(os.getpid())
-
-    logger.info("Compiling %d sequence(s)", len(seqs))
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-
-    # all sequences should start with a WAIT for synchronization
-    for seq in seqs:
-        if not isinstance(seq[0], ControlFlow.Wait):
-            logger.debug("Adding a WAIT - first sequence element was %s", seq[0])
-            seq.insert(0, ControlFlow.Wait())
-
-    # Add the digitizer trigger to measurements
-    logger.info("Adding digitizer trigger")
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-    PatternUtils.add_digitizer_trigger(seqs)
-
-    # Add gating/blanking pulses
-    logger.info("Adding blanking pulses")
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-    for seq in seqs:
-        PatternUtils.add_gate_pulses(seq)
-
-    if add_slave_trigger and 'slave_trig' in ChannelLibraries.channelLib:
-        # Add the slave trigger
-        logger.info("Adding slave trigger")
-        logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-        PatternUtils.add_slave_trigger(seqs,
-                                       ChannelLibraries.channelLib['slave_trig'])
-    else:
-        logger.info("Not adding slave trigger")
-        logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-
-    # find channel set at top level to account for individual sequence channel variability
-    channels = set()
-    for seq in seqs:
-        channels |= find_unique_channels(seq)
-
-    # Compile all the pulses/pulseblocks to sequences of pulses and control flow
-    logger.info("Compiling sequences")
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-    wireSeqs = compile_sequences(seqs, channels)
-
-    if not validate_linklist_channels(wireSeqs.keys()):
-        print("Compile to hardware failed")
-        return
-
-    logger.info('')
-    logger.info("Now after gating constraints:")
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-    # apply gating constraints
-    for chan, seq in wireSeqs.items():
-        if isinstance(chan, Channels.LogicalMarkerChannel):
-            wireSeqs[chan] = PatternUtils.apply_gating_constraints(
-                chan.phys_chan, seq)
-    debug_print(wireSeqs, 'Gated sequence')
-
-    # save number of measurements for meta info
-    logger.info("Counting measurements")
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-    num_measurements = count_measurements(wireSeqs)
-    wire_measurements = count_measurements_per_wire(wireSeqs)
-
-    # map logical to physical channels, physWires is a list of
-    # PhysicalQuadratureChannels and PhysicalMarkerChannels
-    # for the APS, the naming convention is:
-    # ASPName-12, or APSName-12m1
-    logger.info("Mapping logical to physical")
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-    physWires = map_logical_to_physical(wireSeqs)
-
-    del wireSeqs
-
-    # Pave the way for composite instruments, not useful yet...
-    files = {}
-    label_to_inst   = {}
-    label_to_chan   = {}
-    old_wire_names  = {}
-    old_wire_instrs = {}
-    for wire, pulses in physWires.items():
-        pattern_module = import_module('QGL.drivers.' + wire.translator)
-        if pattern_module.SEQFILE_PER_CHANNEL:
-            inst_name = pattern_module.get_true_inst_name(wire.label)
-            chan_name = pattern_module.get_true_chan_name(wire.label)
-            has_non_id_pulses = any([len([p for p in ps if isinstance(p,Pulse) and p.label!="Id"]) > 0 for ps in pulses])
-            label_to_inst[wire.label] = inst_name
-            if has_non_id_pulses:
-                label_to_chan[wire.label] = chan_name
-            # Change the name/inst for uniqueness, but we must restore this later!
-            old_wire_names[wire] = wire.label
-            old_wire_instrs[wire] = wire.instrument
-            wire.instrument = wire.label
-            wire.label = chan_name
-            files[inst_name] = {}
-
-    # construct channel delay map
-    logger.info("Building delay map")
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-    delays = channel_delay_map(physWires)
-
-    # apply delays
-    for chan, wire in physWires.items():
-        PatternUtils.delay(wire, delays[chan])
-    debug_print(physWires, 'Delayed wire')
-
-    # generate wf library (base shapes)
-    logger.info("Generating waveforms")
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-    wfs = generate_waveforms(physWires)
-
-    # replace Pulse objects with Waveforms
-    logger.info("Mapping pulses to waveforms")
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-    physWires = pulses_to_waveforms(physWires)
-
-    # bundle wires on instruments, or channels depending
-    # on whether we have one sequence per channel
-    logger.info("Bundling wires!")
-    logger.info("Using {} GB of memory".format(process.memory_info().rss/1e9))
-    awgData = bundle_wires(physWires, wfs)
-
-    logger.info("DONE!")
-    logger.info("Used {} GB of memory".format(process.memory_info().rss/1e9))
-    return awgData
-
 def compile_to_hardware(seqs,
                         fileName,
                         suffix='',
@@ -963,7 +820,7 @@ def count_measurements_per_wire(wireSeqs):
     seq_len = len(wireSeqs[list(wireSeqs)[0]])
     meas_wires = list(filter(lambda x: isinstance(x, Channels.Measurement), wireSeqs))
     measurements = {wire: 0 for wire in meas_wires}
-    for ct in range(seq_len):
+    for ct in range(seq_lendef
         seq_measurements = count_measurements_per_wire_idx(wireSeqs, ct)
         for wire in meas_wires:
             measurements[wire] += seq_measurements[wire]

From 9fc12f213f49822e2e05fce42b4ff1e6a61fd53f Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Fri, 11 Jan 2019 16:28:33 -0500
Subject: [PATCH 029/235] More typos.

---
 QGL/Compiler.py    |  2 +-
 tests/test_perf.py | 19 ++++++++++---------
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 61bc01d1..40ac4fb0 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -820,7 +820,7 @@ def count_measurements_per_wire(wireSeqs):
     seq_len = len(wireSeqs[list(wireSeqs)[0]])
     meas_wires = list(filter(lambda x: isinstance(x, Channels.Measurement), wireSeqs))
     measurements = {wire: 0 for wire in meas_wires}
-    for ct in range(seq_lendef
+    for ct in range(seq_len):
         seq_measurements = count_measurements_per_wire_idx(wireSeqs, ct)
         for wire in meas_wires:
             measurements[wire] += seq_measurements[wire]
diff --git a/tests/test_perf.py b/tests/test_perf.py
index aea99755..1830e1e2 100644
--- a/tests/test_perf.py
+++ b/tests/test_perf.py
@@ -3,16 +3,17 @@
 from QGL import *
 import random
 
-N = 1000
+def random_sequence_test():
+    N = 1000
 
-cl = ChannelLibrary()
-q1 = QubitFactory("q1")
+    cl = ChannelLibrary()
+    q1 = QubitFactory("q1")
 
-gates = (X90(q1), Y90(q1), X(q1), Y(q1), Id(q1, length=1e-7))
+    gates = (X90(q1), Y90(q1), X(q1), Y(q1), Id(q1, length=1e-7))
 
-seqs = []
-ks = random.choices(range(1,100), k = N)
-for k in ks:
-    seqs.append(random.choices(gates, k=k) + [MEAS(q1)])
+    seqs = []
+    ks = random.choices(range(1,100), k = N)
+    for k in ks:
+        seqs.append(random.choices(gates, k=k) + [MEAS(q1)])
 
-compile_to_hardware(seqs, 'test/test')
+    compile_to_hardware(seqs, 'test/test')

From 2d26637a2846ce92b28c29c6550c8868ebb56af2 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 14 Jan 2019 15:27:53 -0500
Subject: [PATCH 030/235] Use __slots__ for Waveform class to save on memory...

---
 QGL/Compiler.py       | 76 +++++++++++++++++++++++++++++++++++++++----
 QGL/PulseSequencer.py |  6 ++++
 2 files changed, 76 insertions(+), 6 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 40ac4fb0..312176bf 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -36,6 +36,8 @@
 from . import BlockLabel
 from . import TdmInstructions # only for APS2-TDM
 
+import psutil
+
 logger = logging.getLogger(__name__)
 
 def map_logical_to_physical(wires):
@@ -298,6 +300,9 @@ def collect_specializations(seqs):
             done.append(target)
     return funcs
 
+def _get_mem():
+    return psutil.Process(os.getpid()).memory_info().rss
+
 def compile_to_hardware(seqs,
                         fileName,
                         suffix='',
@@ -322,6 +327,8 @@ def compile_to_hardware(seqs,
     # save input code to file
     save_code(seqs, fileName + suffix)
 
+    mem = _get_mem()
+
     # all sequences should start with a WAIT for synchronization
     for seq in seqs:
         if not isinstance(seq[0], ControlFlow.Wait):
@@ -329,13 +336,19 @@ def compile_to_hardware(seqs,
             seq.insert(0, ControlFlow.Wait())
 
     # Add the digitizer trigger to measurements
-    logger.debug("Adding digitizer trigger")
+    logger.info("Adding digitizer trigger")
     PatternUtils.add_digitizer_trigger(seqs)
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     # Add gating/blanking pulses
-    logger.debug("Adding blanking pulses")
+    logger.info("Adding blanking pulses")
     for seq in seqs:
         PatternUtils.add_gate_pulses(seq)
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     if add_slave_trigger and 'slave_trig' in ChannelLibraries.channelLib:
         # Add the slave trigger
@@ -343,15 +356,23 @@ def compile_to_hardware(seqs,
         PatternUtils.add_slave_trigger(seqs,
                                        ChannelLibraries.channelLib['slave_trig'])
     else:
-        logger.debug("Not adding slave trigger")
+        logger.info("Not adding slave trigger")
 
     # find channel set at top level to account for individual sequence channel variability
+    logger.info("Finding unique channels.")
     channels = set()
     for seq in seqs:
         channels |= find_unique_channels(seq)
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     # Compile all the pulses/pulseblocks to sequences of pulses and control flow
+    logger.info("Compiling sequences.")
     wireSeqs = compile_sequences(seqs, channels)
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     if not validate_linklist_channels(wireSeqs.keys()):
         print("Compile to hardware failed")
@@ -360,21 +381,33 @@ def compile_to_hardware(seqs,
     logger.debug('')
     logger.debug("Now after gating constraints:")
     # apply gating constraints
+    logger.info("Applying gating constraints")
     for chan, seq in wireSeqs.items():
         if isinstance(chan, Channels.LogicalMarkerChannel):
             wireSeqs[chan] = PatternUtils.apply_gating_constraints(
                 chan.phys_chan, seq)
     debug_print(wireSeqs, 'Gated sequence')
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     # save number of measurements for meta info
+    logger.info("Counting measurements.")
     num_measurements = count_measurements(wireSeqs)
     wire_measurements = count_measurements_per_wire(wireSeqs)
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     # map logical to physical channels, physWires is a list of
     # PhysicalQuadratureChannels and PhysicalMarkerChannels
     # for the APS, the naming convention is:
     # ASPName-12, or APSName-12m1
+    logger.info("Mapping logical to physical channels.")
     physWires = map_logical_to_physical(wireSeqs)
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     # Pave the way for composite instruments, not useful yet...
     files = {}
@@ -399,22 +432,43 @@ def compile_to_hardware(seqs,
             files[inst_name] = {}
 
     # construct channel delay map
+    logger.info("Constructing delay map.")
     delays = channel_delay_map(physWires)
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     # apply delays
+    logger.info("Applying delays.")
     for chan, wire in physWires.items():
         PatternUtils.delay(wire, delays[chan])
     debug_print(physWires, 'Delayed wire')
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     # generate wf library (base shapes)
+    logger.info("Generating waveform library.")
     wfs = generate_waveforms(physWires)
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     # replace Pulse objects with Waveforms
+    logger.info("Replacing pulses with waveforms")
     physWires = pulses_to_waveforms(physWires)
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
 
     # bundle wires on instruments, or channels depending
     # on whether we have one sequence per channel
+    logger.info("Bundling wires.")
     awgData = bundle_wires(physWires, wfs)
+    new_mem = _get_mem()
+    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+    mem = new_mem
+
 
     # convert to hardware formats
     # files = {}
@@ -428,7 +482,11 @@ def compile_to_hardware(seqs,
         fullFileName = os.path.normpath(os.path.join(
             config.AWGDir, fileName + '-' + awgName + suffix + data[
                 'seqFileExt']))
+        logger.info("Writing sequence file for: {}".format(awgName))
         new_meta = data['translator'].write_sequence_file(data, fullFileName)
+        new_mem = _get_mem()
+        logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
+        mem = new_mem
         if new_meta:
             awg_metas[awgName] = new_meta
 
@@ -668,10 +726,15 @@ def __call__(self, pulse=None):
             self.cache[hash] = super().__call__(pulse=pulse)
         return self.cache[hash]
 
-class Waveform(metaclass=MemoizedObject):
+class Waveform(object):
     """
     Simplified channel independent version of a Pulse with a key into waveform library.
     """
+
+    #Use slots to create attributes to save on memory.
+    __slots__ = ["label", "key", "amp", "length", "phase", "frameChange",
+                    "isTimeAmp", "frequency", "logicalChan", "maddr", "startTime"]
+
     def __init__(self, pulse=None):
         if pulse is None:
             self.label = ""
@@ -709,14 +772,15 @@ def __str__(self):
 
     def __eq__(self, other):
         if isinstance(other, self.__class__):
-            return self.__dict__ == other.__dict__
+            #No __dict__ property so we check all properties.
+            return all((getattr(self, attr, None) == getattr(other, attr, None) for attr in self.__slots__))
         return False
 
     def __ne__(self, other):
         return not self == other
 
     def __hash__(self):
-        return hash(frozenset(self.__dict__.items()))
+        return hash(frozenset((attr, getattr(self, attr, None)) for attr in self.__slots__))
 
     @property
     def isZero(self):
diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 0d9e78d0..9f4d6913 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -77,6 +77,12 @@ def _repr_pretty_(self, p, cycle):
     def hashshape(self):
         return hash(frozenset(self.shapeParams.items()))
 
+    def __hash__(self):
+        d = self._asdict()
+        d['shapeParams'] = self.hashshape()
+        del d['ignoredStrParams']
+        return hash(frozenset(d.items()))
+
     def __add__(self, other):
         if self.channel != other.channel:
             raise NameError(

From b39125c59bc81440214b810ee05df5431b3972c5 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matthew.e.ware@gmail.com>
Date: Thu, 24 Jan 2019 15:19:49 -0500
Subject: [PATCH 031/235] Attempt at manual garbage collection.

---
 QGL/Compiler.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 312176bf..5c3c1a9e 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -35,6 +35,7 @@
 from . import ControlFlow
 from . import BlockLabel
 from . import TdmInstructions # only for APS2-TDM
+import gc
 
 import psutil
 
@@ -469,11 +470,14 @@ def compile_to_hardware(seqs,
     logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
     mem = new_mem
 
+    del wireSeqs
+    gc.collect()
 
     # convert to hardware formats
     # files = {}
     awg_metas = {}
-    for awgName, data in awgData.items():
+    for awgName in list(awgData.keys()):
+        data = awgData[awgName]
         # create the target folder if it does not exist
         targetFolder = os.path.split(os.path.normpath(os.path.join(
             config.AWGDir, fileName)))[0]
@@ -496,6 +500,11 @@ def compile_to_hardware(seqs,
                 files[label_to_inst[awgName]][label_to_chan[awgName]] = fullFileName
         else:
             files[awgName] = fullFileName
+
+        del data
+        del awgData[awgName]
+        gc.collect()
+
     # generate TDM sequences FIXME: what's the best way to identify the need for a TDM seq.? Support for single TDM
     if tdm_seq and 'APS2Pattern' in [wire.translator for wire in physWires]:
             aps2tdm_module = import_module('QGL.drivers.APS2Pattern') # this is redundant with above

From 1cac1609514776a1f234eac66f674ef501bc6234 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Mon, 28 Jan 2019 15:30:36 -0500
Subject: [PATCH 032/235] Remove memory debug info

---
 QGL/Compiler.py | 47 -----------------------------------------------
 1 file changed, 47 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 5c3c1a9e..97bf28ae 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -37,8 +37,6 @@
 from . import TdmInstructions # only for APS2-TDM
 import gc
 
-import psutil
-
 logger = logging.getLogger(__name__)
 
 def map_logical_to_physical(wires):
@@ -301,9 +299,6 @@ def collect_specializations(seqs):
             done.append(target)
     return funcs
 
-def _get_mem():
-    return psutil.Process(os.getpid()).memory_info().rss
-
 def compile_to_hardware(seqs,
                         fileName,
                         suffix='',
@@ -328,8 +323,6 @@ def compile_to_hardware(seqs,
     # save input code to file
     save_code(seqs, fileName + suffix)
 
-    mem = _get_mem()
-
     # all sequences should start with a WAIT for synchronization
     for seq in seqs:
         if not isinstance(seq[0], ControlFlow.Wait):
@@ -339,17 +332,11 @@ def compile_to_hardware(seqs,
     # Add the digitizer trigger to measurements
     logger.info("Adding digitizer trigger")
     PatternUtils.add_digitizer_trigger(seqs)
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     # Add gating/blanking pulses
     logger.info("Adding blanking pulses")
     for seq in seqs:
         PatternUtils.add_gate_pulses(seq)
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     if add_slave_trigger and 'slave_trig' in ChannelLibraries.channelLib:
         # Add the slave trigger
@@ -364,16 +351,10 @@ def compile_to_hardware(seqs,
     channels = set()
     for seq in seqs:
         channels |= find_unique_channels(seq)
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     # Compile all the pulses/pulseblocks to sequences of pulses and control flow
     logger.info("Compiling sequences.")
     wireSeqs = compile_sequences(seqs, channels)
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     if not validate_linklist_channels(wireSeqs.keys()):
         print("Compile to hardware failed")
@@ -388,17 +369,11 @@ def compile_to_hardware(seqs,
             wireSeqs[chan] = PatternUtils.apply_gating_constraints(
                 chan.phys_chan, seq)
     debug_print(wireSeqs, 'Gated sequence')
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     # save number of measurements for meta info
     logger.info("Counting measurements.")
     num_measurements = count_measurements(wireSeqs)
     wire_measurements = count_measurements_per_wire(wireSeqs)
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     # map logical to physical channels, physWires is a list of
     # PhysicalQuadratureChannels and PhysicalMarkerChannels
@@ -406,9 +381,6 @@ def compile_to_hardware(seqs,
     # ASPName-12, or APSName-12m1
     logger.info("Mapping logical to physical channels.")
     physWires = map_logical_to_physical(wireSeqs)
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     # Pave the way for composite instruments, not useful yet...
     files = {}
@@ -435,41 +407,25 @@ def compile_to_hardware(seqs,
     # construct channel delay map
     logger.info("Constructing delay map.")
     delays = channel_delay_map(physWires)
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     # apply delays
     logger.info("Applying delays.")
     for chan, wire in physWires.items():
         PatternUtils.delay(wire, delays[chan])
     debug_print(physWires, 'Delayed wire')
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     # generate wf library (base shapes)
     logger.info("Generating waveform library.")
     wfs = generate_waveforms(physWires)
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     # replace Pulse objects with Waveforms
     logger.info("Replacing pulses with waveforms")
     physWires = pulses_to_waveforms(physWires)
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
 
     # bundle wires on instruments, or channels depending
     # on whether we have one sequence per channel
     logger.info("Bundling wires.")
     awgData = bundle_wires(physWires, wfs)
-    new_mem = _get_mem()
-    logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-    mem = new_mem
-
     del wireSeqs
     gc.collect()
 
@@ -488,9 +444,6 @@ def compile_to_hardware(seqs,
                 'seqFileExt']))
         logger.info("Writing sequence file for: {}".format(awgName))
         new_meta = data['translator'].write_sequence_file(data, fullFileName)
-        new_mem = _get_mem()
-        logger.info("Used {} MB of memory.".format((new_mem - mem)/1e6))
-        mem = new_mem
         if new_meta:
             awg_metas[awgName] = new_meta
 

From f32df2ca7f564848ba6b1b2b6689aae8e32493a3 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Mon, 28 Jan 2019 15:44:23 -0500
Subject: [PATCH 033/235] Skip GSTTools unit tests if running in Travis.

---
 tests/test_Sequences.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tests/test_Sequences.py b/tests/test_Sequences.py
index ada1e278..1e145046 100644
--- a/tests/test_Sequences.py
+++ b/tests/test_Sequences.py
@@ -15,6 +15,11 @@
 import logging
 logger = logging.getLogger( 'sequences')
 
+import os
+istravis = os.environ.get('TRAVIS') == 'true'
+
+#Determine if tests are running in Travis
+
 class AWGTestHelper(object):
     testFileDirectory = './tests/test_data/awg/'
 
@@ -386,6 +391,10 @@ def test_RB_SimultaneousRB_AC(self):
         self.compare_sequences('RB')
 
     def test_1Q_GST(self):
+
+        if istravis:
+            raise unittest.SkipTest("FIX ME -- Figure out pygsti integration for Travis.")
+
         self.set_awg_dir('GST')
         # list of GST gate strings
         if GSTTools.PYGSTI_PRESENT:
@@ -408,6 +417,10 @@ def test_1Q_GST(self):
         self.compare_sequences('GST')
 
     def test_2Q_GST(self):
+
+        if istravis:
+            raise unittest.SkipTest("FIX ME -- Figure out pygsti integration for Travis.")
+
         self.set_awg_dir('GST')
         def gst_2Qgate_map(q1, q2):
             return {"Gxi": X90(q1)*Id(q2),

From cbeb82a272043e3a047758ac983345c3f0a91a83 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Mon, 28 Jan 2019 15:58:17 -0500
Subject: [PATCH 034/235] Fix deprecation warning for empty array check

---
 QGL/Compiler.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 97bf28ae..42cfd7fe 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -101,7 +101,7 @@ def merge_channels(wires, channels):
                 [e.amp * e.frequency for e in entries])[0]
             assert len(nonZeroSSBChan) <= 1, \
                 "Unable to handle merging more than one non-zero entry with non-zero frequency."
-            if nonZeroSSBChan:
+            if nonZeroSSBChan.size > 0:
                 frequency = entries[nonZeroSSBChan[0]].frequency
             else:
                 frequency = 0.0

From 575239e588e138411a9ab3739e203abc1f0876e2 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Mon, 28 Jan 2019 15:58:29 -0500
Subject: [PATCH 035/235] Get rid of 3.5 CI testing.

---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index a76dc173..d936dc77 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,7 +3,6 @@
 
 language: python
 python:
-  - 3.5
   - 3.6
 
 before_install:

From 6af2cf2e88f20aa15093398535bf819e6845cf24 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 23 May 2018 11:56:49 -0400
Subject: [PATCH 036/235] Autogen stream selectors

---
 QGL/ChannelLibraries.py | 52 ++++++++++++++++++++++++-----------------
 1 file changed, 31 insertions(+), 21 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 6afb03b2..caac68e5 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -204,13 +204,13 @@ def load_from_library(self, return_only=False):
                     loader.dispose()
 
             # Check to see if we have the mandatory sections
-            for section in ['instruments', 'qubits', 'filters']:
+            for section in ['instruments', 'qubits']: #, 'filters']:
                 if section not in tmpLib.keys():
                     raise ValueError("{} section not present in config file {}.".format(section, self.library_file))
 
             instr_dict   = tmpLib['instruments']
             qubit_dict   = tmpLib['qubits']
-            filter_dict  = tmpLib['filters']
+            # filter_dict  = tmpLib['filters']
             trigger_dict = tmpLib.get('markers', {}) # This section is optional
             edge_dict    = tmpLib.get('edges', {}) # This section is optional
             master_awgs  = []
@@ -295,23 +295,33 @@ def load_from_library(self, return_only=False):
             #     params["__class__"]   = "LogicalMarkerChannel"
             #     channel_dict[params["label"]] = params
 
-            for name, filt in filter_dict.items():
-                if "StreamSelector" in filt["type"]:
-                    params = {k: v for k,v in filt.items() if k in Channels.ReceiverChannel.__atom_members__.keys()}
-                    params["label"]      = "RecvChan-" + name # instr_dict[filt["instrument"]]["name"] + "-" + name
-                    params["channel"]    = str(params["channel"]) # Convert to a string
-                    params["instrument"] = filt["source"]
-                    params["__module__"] = "QGL.Channels"
-                    params["__class__"]  = "ReceiverChannel"
-                    if "source" not in filt.keys():
-                        raise ValueError("No instrument (source) specified for Stream Selector")
-                    if filt["source"] not in instr_dict.keys() and filt["source"] not in channel_dict.keys():
-                        raise ValueError("Stream Selector source {} not found among list of instruments.".format(filt["source"]))
-                    params["instrument"] = filt["source"]
-
-                    channel_dict[params["label"]] = params
+            # for name, filt in filter_dict.items():
+            #     if "StreamSelector" in filt["type"]:
+            #         params = {k: v for k,v in filt.items() if k in Channels.ReceiverChannel.__atom_members__.keys()}
+            #         params["label"]      = "RecvChan-" + name # instr_dict[filt["instrument"]]["name"] + "-" + name
+            #         params["channel"]    = str(params["channel"]) # Convert to a string
+            #         params["instrument"] = filt["source"]
+            #         params["__module__"] = "QGL.Channels"
+            #         params["__class__"]  = "ReceiverChannel"
+            #         if "source" not in filt.keys():
+            #             raise ValueError("No instrument (source) specified for Stream Selector")
+            #         if filt["source"] not in instr_dict.keys() and filt["source"] not in channel_dict.keys():
+            #             raise ValueError("Stream Selector source {} not found among list of instruments.".format(filt["source"]))
+            #         params["instrument"] = filt["source"]
+
+            #         channel_dict[params["label"]] = params
 
             for name, qubit in qubit_dict.items():
+                # Create a stream selector
+                rcv_inst, rcv_chan, rcv_stream = qubit["measure"]["receiver"].split()
+                rcv_params = {}
+                rcv_params["label"]      = "RecvChan-" + name + "-SS"
+                rcv_params["channel"]    = str(rcv_chan)
+                rcv_params["instrument"] = rcv_inst
+                rcv_params["__module__"] = "QGL.Channels"
+                rcv_params["__class__"]  = "ReceiverChannel"
+                channel_dict[rcv_params["label"]] = rcv_params
+
                 # Create the Qubits
                 if len(qubit["control"]["AWG"].split()) != 2:
                     print("Control AWG specification for {} ({}) must have a device, channel".format(name, qubit["control"]["AWG"]))
@@ -319,7 +329,7 @@ def load_from_library(self, return_only=False):
                 ctrl_instr, ctrl_chan = qubit["control"]["AWG"].split()
                 params = {k: v for k,v in qubit["control"].items() if k in Channels.Qubit.__atom_members__.keys()}
                 params["label"]      = name
-                params["phys_chan"]   = ctrl_instr + "-" + ctrl_chan
+                params["phys_chan"]   = ctrl_instr + "-" + ctrl_chan 
                 params["__module__"] = "QGL.Channels"
                 params["__class__"]  = "Qubit"
                 channel_dict[params["label"]] = params
@@ -338,7 +348,7 @@ def load_from_library(self, return_only=False):
                 params["trig_chan"]     = "digTrig-" + dig_trig
                 params["phys_chan"]     = meas_instr + "-" + meas_chan
                 params["meas_type"]     = "autodyne"
-                params["receiver_chan"] = "RecvChan-" + qubit["measure"]["receiver"]
+                params["receiver_chan"] = rcv_params["label"]
                 params["__module__"]   = "QGL.Channels"
                 params["__class__"]    = "Measurement"
                 channel_dict[params["label"]] = params
@@ -347,8 +357,8 @@ def load_from_library(self, return_only=False):
 
                 # Create the receiver channels
                 if "receiver" in qubit["measure"].keys():
-                    if len(qubit["measure"]["receiver"].split()) != 1:
-                        print("Receiver specification for {} ({}) must have a stream selector".format(name, qubit["measure"]["receiver"]))
+                    if len(qubit["measure"]["receiver"].split()) != 3:
+                        print("Receiver specification for {} ({}) must have an instrument name, physical channel, and stream".format(name, qubit["measure"]["receiver"]))
                         raise ValueError("Receiver specification for {} ({}) must have a stream selector".format(name, qubit["measure"]["receiver"]))
                     phys_instr, phys_marker = dig_trig.split()
                     params = {}

From c3055e4cb7d9b627f362a42f0db0b2ef475ff8c1 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 31 May 2018 16:41:16 -0400
Subject: [PATCH 037/235] Ditch atom, move to Pony.orm for all channel library
 objects.

---
 QGL/ChannelLibraries.py | 327 +++++-----------------------------------
 QGL/Channels.py         | 214 +++++++++++---------------
 QGL/Compiler.py         |   2 +
 QGL/PulseSequencer.py   |   5 +-
 QGL/PulseShapes.py      |   5 +-
 QGL/config.py           |  12 +-
 6 files changed, 142 insertions(+), 423 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index caac68e5..1078716d 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -33,7 +33,7 @@
 import traceback
 import datetime
 import importlib
-from atom.api import Atom, Str, Int, Typed
+from pony.orm import *
 import networkx as nx
 import yaml
 
@@ -46,118 +46,37 @@
 from watchdog.events import FileSystemEventHandler
 import time
 
+from . import config
 from . import Channels
 from . import PulseShapes
-from . import config
 
 channelLib = None
 
-class MyEventHandler(FileSystemEventHandler):
-
-    def __init__(self, file_paths, callback):
-        super(MyEventHandler, self).__init__()
-        self.file_paths = [os.path.normpath(fn) for fn in file_paths]
-        self.callback = callback
-        self.paused = True
-
-        # The spotlight indexer in MacOSX retriggers events... maybe we should hash the files?
-        self.grace_period = 3.0 if sys.platform == 'darwin' else 1.0 
-        self.last_library_update = datetime.datetime.now()
-
-    def on_modified(self, event):
-        try:
-            if any([os.path.samefile(event.src_path, fp) for fp in self.file_paths]):
-                if not self.paused:
-                    # Build in some sanity checking since we seem to get multiple
-                    # events firing in a number of situations.
-                    now = datetime.datetime.now()
-                    
-                    if (now-self.last_library_update).total_seconds() > (self.grace_period):
-                        self.last_library_update = now
-                        """
-                        Hold off for half a second
-                        If the event is from the file being opened to be written this gives
-                        time for it to be written.
-                        """
-                        time.sleep(0.5)
-                        self.callback()
-        except FileNotFoundError:
-            #Temporary settings files generated using yaml_dump get deleted
-            #faster than the above code can catch it.
-            pass
-
-class LibraryFileWatcher(object):
-    def __init__(self, main_path, callback):
-        super(LibraryFileWatcher, self).__init__()
-        
-        self.main_path = os.path.normpath(main_path)
-        self.callback = callback
-
-        # Perform a preliminary loading to find all of the connected files...
-        # TODO: modularity
-        with open(os.path.abspath(self.main_path), 'r') as FID:
-            loader = config.Loader(FID)
+def set_from_dict(obj, settings):
+    for prop_name in obj.to_dict().keys():
+        if prop_name in settings.keys():
             try:
-                tmpLib = loader.get_single_data()
-                self.filenames = [os.path.normpath(lf) for lf in loader.filenames]
-            finally:
-                loader.dispose()
-
-        self.eventHandler = MyEventHandler(self.filenames, self.callback)
-        self.observer = Observer()
-        self.observer.schedule(self.eventHandler, path=os.path.dirname(os.path.abspath(main_path)))
-
-        self.observer.start()
-        self.resume()
-
-    def __del__(self):
-        self.observer.stop()
-        self.observer.join()
-
-    def pause(self):
-        self.eventHandler.paused = True
+                setattr(obj, prop_name, settings[prop_name])
+            except Exception as e:
+                print(f"{obj.label}: Error loading {prop_name} from config")
 
-    def resume(self):
-        self.eventHandler.paused = False
-
-class ChannelLibrary(Atom):
-    # channelDict = Dict(Str, Channel)
-    channelDict = Typed(dict)
-    connectivityG = Typed(nx.DiGraph)
-    library_file = Str()
-    fileWatcher = Typed(LibraryFileWatcher)
-    version = Int(5)
-    last_library_update = Str()
-
-    specialParams = ['phys_chan', 'gate_chan', 'trig_chan', 'receiver_chan',
-                     'source', 'target']
+class ChannelLibrary(object):
 
     def __init__(self, library_file=None, blank=False, channelDict={}, **kwargs):
         """Create the channel library. We assume that the user wants the config file in the 
         usual locations specified in the config files."""
-        
+
         # Load the basic config options from the yaml
         self.library_file = config.load_config(library_file)
 
-        if blank: # we want a blank library if library_file is none
-            super(ChannelLibrary, self).__init__(channelDict={})
-            self.connectivityG = nx.DiGraph()
-        else:
-            super(ChannelLibrary, self).__init__(channelDict=channelDict, library_file=self.library_file, **kwargs)
-            self.connectivityG = nx.DiGraph()
-            yaml_filenames = self.load_from_library()
-            if self.library_file and yaml_filenames:
-                self.fileWatcher = LibraryFileWatcher(self.library_file, self.update_from_file)
+        self.connectivityG = nx.DiGraph()
+        
+        self.channelDict = {c.label: c for  c in select(c for c in Channels.Channel)}
 
         # Update the global reference
         global channelLib
-        if channelLib:
-            # Don't let the 
-            channelLib.fileWatcher = None
         channelLib = self
 
-        self.last_library_update = str(datetime.datetime.now())
-
     #Dictionary methods
     def __getitem__(self, key):
         return self.channelDict[key]
@@ -179,6 +98,7 @@ def values(self):
 
     def build_connectivity_graph(self):
         # build connectivity graph
+<<<<<<< HEAD
         self.connectivityG.clear()
         for chan in self.channelDict.values():
             if isinstance(chan,
@@ -374,210 +294,40 @@ def load_from_library(self, return_only=False):
                     # Don't duplicate triggers to the same digitizer
                     if params["label"] not in channel_dict.keys():
                         channel_dict[params["label"]] = params
+=======
+        for chan in select(q for q in Channels.Qubit if q not in self.connectivityG):
+            self.connectivityG.add_node(chan)
+        for chan in select(e for e in Channels.Edge):
+            self.connectivityG.add_edge(chan.source, chan.target)
+            self.connectivityG[chan.source][chan.target]['channel'] = chan
+>>>>>>> Ditch atom, move to Pony.orm for all channel library objects.
 
-                # Create the measurement gate chan:
-                if "gate" in qubit["measure"].keys():
-                    phys_instr, phys_marker = qubit["measure"]["gate"].split()
-                    params = {}
-                    params["label"]      = "M-{}-gate".format(name)
-                    params["phys_chan"]   = phys_instr + "-" + phys_marker
-                    params["__module__"] = "QGL.Channels"
-                    params["__class__"]  = "LogicalMarkerChannel"
-                    channel_dict[params["label"]] = params
-                    channel_dict["M-{}".format(name)]["gate_chan"] = params["label"]
-
-                # Create the control gate chan:
-                if "gate" in qubit["control"].keys():
-                    phys_instr, phys_marker = qubit["control"]["gate"].split()
-                    params = {}
-                    params["label"]      = "{}-gate".format(name)
-                    params["phys_chan"]   = phys_instr + "-" + phys_marker
-                    params["__module__"] = "QGL.Channels"
-                    params["__class__"]  = "LogicalMarkerChannel"
-                    channel_dict[params["label"]] = params
-                    channel_dict[name]["gate_chan"] = params["label"]
-
-
-            for trig_name, trigger in trigger_dict.items():
-                phys_instr, phys_marker = trigger.split()
-                params = {}
-                params["label"]      = trig_name
-                params["phys_chan"]   = phys_instr + "-" + phys_marker
-                if params["phys_chan"] in marker_lens.keys():
-                    length = marker_lens[params["phys_chan"]]
-                else:
-                    length = 1e-7
-                params["__module__"] = "QGL.Channels"
-                params["__class__"]  = "LogicalMarkerChannel"
-                channel_dict[params["label"]] = params
-
-            for name, edge in edge_dict.items():
-                # Create the Edges
-                if len(edge["AWG"].split()) != 2:
-                    print("Control AWG specification for {} ({}) must have a device, channel".format(name, edge["AWG"]))
-                    raise ValueError("Control AWG specification for {} ({}) must have a device, channel".format(name, edge["AWG"]))
-                ctrl_instr, ctrl_chan = edge["AWG"].split()
-                params = {k: v for k,v in edge.items() if k in Channels.Edge.__atom_members__.keys()}
-                params["label"]      = name
-                params["phys_chan"]   = ctrl_instr + "-" + ctrl_chan
-                params["__module__"] = "QGL.Channels"
-                params["__class__"]  = "Edge"
-                channel_dict[params["label"]] = params
-                if 'generator' in edge.keys():
-                    channel_dict[params["phys_chan"]]["generator"] = edge["generator"]
-
-                # Create the edge gate chan:
-                if "gate" in edge.keys():
-                    phys_instr, phys_marker = edge["gate"].split()
-                    params = {}
-                    params["label"]      = "{}-gate".format(name)
-                    params["phys_chan"]   = phys_instr + "-" + phys_marker
-                    params["__module__"] = "QGL.Channels"
-                    params["__class__"]  = "LogicalMarkerChannel"
-                    channel_dict[params["label"]] = params
-                    channel_dict[name]["gate_chan"] = params["label"]
-
-            if return_only:
-                return channel_dict
-            else:
-                channel_dict = {k: self.instantiate(v) for k,v in channel_dict.items()}
-                # connect objects labeled by strings
-                for chan in channel_dict.values():
-                    for param in self.specialParams:
-                        if hasattr(chan, param) and getattr(chan, param) is not None:
-                            chan_to_find = channel_dict.get(getattr(chan, param), None)
-                            if not chan_to_find:
-                                print("Couldn't find {} of {} in the channel_dict!".format(param, chan))
-                            setattr(chan, param, chan_to_find)
-
-                self.channelDict.update(channel_dict)
-                self.build_connectivity_graph()
-                return filenames
-
-        except IOError:
-            print('No channel library found.')
-        except Exception as e:
-            print('Failed to load channel library: received exception', e)
-            exc_type, exc_value, exc_traceback = sys.exc_info()
-            traceback.print_tb(exc_traceback, limit=4, file=sys.stdout)
-
-    def instantiate(self, paramDict):
-        if 'pulse_params' in paramDict:
-            if 'shape_fun' in paramDict['pulse_params']:
-                shape_fun = paramDict['pulse_params']['shape_fun']
-                paramDict['pulse_params']['shape_fun'] = getattr(PulseShapes, shape_fun)
-        if '__class__' in paramDict:
-            className  = paramDict.pop('__class__')
-            moduleName = paramDict.pop('__module__')
-            __import__(moduleName)
-            return getattr(sys.modules[moduleName], className)(**paramDict)
-
-
-    def update_from_file(self):
-        """
-        Only update relevant parameters
-        Helps avoid both stale references from replacing whole channel objects (as in load_from_library)
-        and the overhead of recreating everything.
-        """
-
-        if not self.library_file:
-            return
-        try:
-            all_params = self.load_from_library(return_only=True)
-
-            # update & insert
-            for chName, chParams in all_params.items():
-                if chName in self.channelDict:
-                    self.update_from_json(chName, chParams)
-                else:
-                    self.channelDict[chName] = self.instantiate(chParams)
-                    self.update_from_json(chName, chParams)
-
-            # remove
-            for chName in list(self.channelDict.keys()):
-                if chName not in all_params:
-                    del self.channelDict[chName]
-
-            self.build_connectivity_graph()
-
-            print("Updated library")
-            self.last_library_update = str(datetime.datetime.now())
-        except:
-            print('Failed to update channel library from file. Is there a typo?.')
-            return
-
-        # reset pulse cache
-        from . import PulsePrimitives
-        PulsePrimitives._memoize.cache.clear()
-
-
-    def update_from_json(self, chName, chParams):
-        # connect objects labeled by strings
-        if 'pulse_params' in chParams.keys():
-            paramDict = {str(k): v for k, v in chParams['pulse_params'].items()}
-            shapeFunName = paramDict.pop('shape_fun', None)
-            if shapeFunName:
-                paramDict['shape_fun'] = getattr(PulseShapes, shapeFunName)
-            self.channelDict[chName].pulse_params = paramDict
-
-        for param in self.specialParams:
-            if param in chParams.keys():
-                setattr(self.channelDict[chName],
-                        param,
-                        self.channelDict.get(chParams[param], None)
-                        )
-        # TODO: how do we follow changes to selected AWG or generator?
-
-        # ignored or specially handled parameters
-        ignoreList = self.specialParams + ['pulse_params', 'AWG', 'generator', '__class__', '__module__']
-        for paramName in chParams:
-            if paramName not in ignoreList:
-                setattr(self.channelDict[chName], paramName, chParams[paramName])
-
-    def on_awg_change(self, oldName, newName):
-        print("Change AWG", oldName, newName)
-        for chName in self.channelDict:
-            if isinstance(self.channelDict[chName],
-                          (Channels.PhysicalMarkerChannel,
-                           Channels.PhysicalQuadratureChannel)):
-                awgName, awgChannel = chName.rsplit('-', 1)
-                if awgName == oldName:
-                    newLabel = "{0}-{1}".format(newName, awgChannel)
-                    print("Changing {0} to {1}".format(chName, newLabel))
-                    self.physicalChannelManager.name_changed(chName, newLabel)
-
-def MarkerFactory(label, **kwargs):
-    '''Return a marker channel by name. Must be defined under top-level `markers`
-    keyword in measurement configuration YAML.
-    '''
-    if not channelLib:
-        raise ValueError('ChannelLibrary not found, has an instance of ChannelLibrary been created?')
-    if label in channelLib and isinstance(channelLib[label], Channels.LogicalMarkerChannel):
-        return channelLib[label]
-    else:
-        raise ValueError("Marker channel {} not found in channel library.".format(label))
 
 def QubitFactory(label, **kwargs):
     ''' Return a saved qubit channel or create a new one. '''
-    if not channelLib:
-        raise ValueError('ChannelLibrary not found, has an instance of ChannelLibrary been created?')
-    if label in channelLib and isinstance(channelLib[label], Channels.Qubit):
-        return channelLib[label]
+    thing = select(el for el in Channels.Qubit if el.label==label).first()
+    if thing:
+        return thing
     else:
         return Channels.Qubit(label=label, **kwargs)
-
-def MeasFactory(label, meas_type='autodyne', **kwargs):
+    
+def MeasFactory(label, **kwargs):
     ''' Return a saved measurement channel or create a new one. '''
-    if not channelLib:
-        raise ValueError('ChannelLibrary not found, has an instance of ChannelLibrary been created?')
-    if label in channelLib and isinstance(channelLib[label], Channels.Measurement):
-        return channelLib[label]
+    thing = select(el for el in Channels.Measurement if el.label==label).first()
+    if thing:
+        return thing
     else:
-        return Channels.Measurement(label=label, meas_type=meas_type, **kwargs)
+        return Channels.Measurement(label=label, **kwargs)
+
+def MarkerFactory(label, **kwargs):
+    ''' Return a saved Marker channel or create a new one. '''
+    thing = select(el for el in Channels.LogicalMarkerChannel if el.label==label).first()
+    if thing:
+        return thing
+    else:
+        return Channels.LogicalMarkerChannel(label=label, **kwargs)
 
 def EdgeFactory(source, target):
-    if not channelLib:
-        raise ValueError('Connectivity graph not found. Has a ChannelLibrary has been created?')
     if channelLib.connectivityG.has_edge(source, target):
         return channelLib.connectivityG[source][target]['channel']
     elif channelLib.connectivityG.has_edge(target, source):
@@ -585,3 +335,4 @@ def EdgeFactory(source, target):
     else:
         raise ValueError('Edge {0} not found in connectivity graph'.format((
             source, target)))
+
diff --git a/QGL/Channels.py b/QGL/Channels.py
index c0c85163..3a9b7b8b 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -4,6 +4,7 @@
 Created on Jan 19, 2012
 
 Original Author: Colm Ryan
+Modified By: Graham Rowlands
 
 Copyright 2013 Raytheon BBN Technologies
 
@@ -20,162 +21,137 @@
 limitations under the License.
 '''
 
+from . import config
 from . import PulseShapes
 import numpy as np
-
 from math import tan, cos, pi
-# Python 2/3 compatibility: use the py3 meaning of 'str'
-from builtins import str
-
-from atom.api import Atom, Str, Float, Instance, \
-    Dict, Enum, Bool, Typed, Int
-
+from pony.orm import *
 from copy import deepcopy
 
 
-class Channel(Atom):
+class Channel(config.db.Entity):
     '''
     Every channel has a label and some printers.
     '''
-    label = Str()
-    enabled = Bool(True)
+    label   = Required(str)
 
     def __repr__(self):
         return str(self)
-
     def __str__(self):
         return "{0}('{1}')".format(self.__class__.__name__, self.label)
 
-    def json_encode(self):
-        jsonDict = self.__getstate__()
-
-        #Turn objects into labels
-        for member in ["phys_chan", "gate_chan", "trig_chan", "receiver_chan", "source", "target"]:
-            if member in jsonDict and not isinstance(jsonDict[member], str):
-                obj = jsonDict.pop(member)
-                if obj:
-                    jsonDict[member] = obj.label
-
-        #We want the name of shape functions
-        if "pulse_params" in jsonDict:
-            pulse_params = deepcopy(jsonDict.pop("pulse_params"))
-            if "shape_fun" in pulse_params:
-                pulse_params["shape_fun"] = pulse_params["shape_fun"].__name__
-            jsonDict["pulse_params"] = pulse_params
-
-        return jsonDict
-
-
 class PhysicalChannel(Channel):
     '''
     The main class for actual AWG channels.
     '''
-    instrument = Str() # i.e. the AWG or receiver
-    translator = Str()
-    generator = Str()
-    sampling_rate = Float(default=1.2e9)
-    delay = Float()
+    instrument      = Optional(str) # i.e. the AWG or receiver
+    translator      = Optional(str)
+    generator       = Optional(str)
+    sampling_rate   = Optional(float, default=1.2e9)
+    delay           = Required(float, default=0.0)
 
+    # Required reverse connections
+    logical_channel = Optional("LogicalChannel")
+    quad_channel_I  = Optional("PhysicalQuadratureChannel", reverse="I_channel")
+    quad_channel_Q  = Optional("PhysicalQuadratureChannel", reverse="Q_channel")
+    marker_channel  = Optional("PhysicalMarkerChannel")
 
 class LogicalChannel(Channel):
     '''
     The main class from which we will generate sequences.
     At some point it needs to be assigned to a physical channel.
+        frequency: modulation frequency of the channel (can be positive or negative)
     '''
     #During initilization we may just have a string reference to the channel
-    phys_chan = Instance((str, PhysicalChannel))
-
-    def __init__(self, **kwargs):
-        super(LogicalChannel, self).__init__(**kwargs)
-        if self.phys_chan is None:
-            self.phys_chan = PhysicalChannel(label=kwargs['label'] + '-phys')
-
+    phys_chan     = Optional(PhysicalChannel)
+    frequency     = Required(float, default=0.0)
+    pulse_params  = Optional(Json, default={}) 
+    gate_chan     = Optional("LogicalMarkerChannel")
+    receiver_chan = Optional("ReceiverChannel")
 
 class PhysicalMarkerChannel(PhysicalChannel):
     '''
     A digital output channel on an AWG.
+        gate_buffer: How much extra time should be added onto the beginning of a gating pulse
+        gate_min_width: The minimum marker pulse width
     '''
-    gate_buffer = Float(0.0).tag(
-        desc="How much extra time should be added onto the beginning of a gating pulse")
-    gate_min_width = Float(0.0).tag(desc="The minimum marker pulse width")
-
+    gate_buffer    = Required(float, default=0.0)
+    gate_min_width = Required(float, default=0.0)
+    phys_channel   = Optional(PhysicalChannel)
 
 class PhysicalQuadratureChannel(PhysicalChannel):
     '''
     Something used to implement a standard qubit channel with two analog channels and a microwave gating channel.
     '''
-    I_channel = Str()
-    Q_channel = Str()
-    #During initilization we may just have a string reference to the channel
-    amp_factor = Float(1.0)
-    phase_skew = Float(0.0)
-
-    @property
-    def correctionT(self):
-        return np.array(
-            [[self.amp_factor, self.amp_factor * tan(self.phase_skew * pi / 180)],
-             [0, 1 / cos(self.phase_skew * pi / 180)]])
+    I_channel  = Optional(PhysicalChannel)
+    Q_channel  = Optional(PhysicalChannel)
+    amp_factor = Required(float, default=1.0)
+    phase_skew = Required(float, default=0.0)
+#     marker_channel = Optional(PhysicalMarkerChannel)
 
 class ReceiverChannel(PhysicalChannel):
     '''
     A trigger input on a receiver.
     '''
-    channel = Str()
+    triggering_channel = Optional(LogicalChannel)
+    channel            = Optional(int)
 
+def pulse_check(name):
+    return name in ["constant", "gaussian", "drag", "gaussOn", "gaussOff", "dragGaussOn", "dragGaussOff",
+                   "tanh", "exp_decay", "autodyne", "arb_axis_drag"]
+    
 class LogicalMarkerChannel(LogicalChannel):
     '''
     A class for digital channels for gating sources or triggering other things.
     '''
-    pulse_params = Dict(default={'shape_fun': PulseShapes.constant,
-                                'length': 10e-9})
+    meas_channel = Optional(LogicalChannel)
+    trig_channel = Optional("Measurement")
 
+    def __init__(self, label="lm", pulse_params=None):
+        if not pulse_params:
+            pulse_params =  {'shape_fun': "constant",'length': 10e-9}
+        super(LogicalMarkerChannel, self).__init__(label=label, pulse_params=pulse_params)
 
 class Qubit(LogicalChannel):
     '''
     The main class for generating qubit pulses.  Effectively a logical "QuadratureChannel".
-    '''
-    pulse_params = Dict(default={'length': 20e-9,
-                                'piAmp': 1.0,
-                                'pi2Amp': 0.5,
-                                'shape_fun': PulseShapes.gaussian,
-                                'cutoff': 2,
-                                'drag_scaling': 0,
-                                'sigma': 5e-9})
-    gate_chan = Instance((str, LogicalMarkerChannel))
-    frequency = Float(0.0).tag(
-        desc='modulation frequency of the channel (can be positive or negative)')
-
-    def __init__(self, **kwargs):
-        super(Qubit, self).__init__(**kwargs)
-
+        frequency: modulation frequency of the channel (can be positive or negative)
+    '''
+    edge_source = Optional("Edge", reverse="source")
+    edge_target = Optional("Edge", reverse="target")
+
+    def __init__(self, label="q", pulse_params=None):
+        if not pulse_params:
+            pulse_params =  {'length': 20e-9,
+                            'piAmp': 1.0,
+                            'pi2Amp': 0.5,
+                            'shape_fun': "gaussian",
+                            'cutoff': 2,
+                            'drag_scaling': 0,
+                            'sigma': 5e-9}
+        super(Qubit, self).__init__(label=label, pulse_params=pulse_params)
 
 class Measurement(LogicalChannel):
     '''
     A class for measurement channels.
     Measurements are special because they can be different types:
     autodyne which needs an IQ pair or hetero/homodyne which needs just a marker channel.
+        meas_type: Type of measurement (autodyne, homodyne)
+        autodyne_freq: use to bake the modulation into the pulse, so that it has constant phase
+        frequency: use to asssociate modulation with the channel
     '''
-    meas_type = Enum('autodyne', 'homodyne').tag(
-        desc='Type of measurement (autodyne, homodyne)')
+    meas_type     = Required(str, default='autodyne', py_check=lambda x: x in ['autodyne', 'homodyne'])
+    autodyne_freq = Required(float, default=0.0)
+    trig_chan     = Optional(LogicalMarkerChannel)
 
-    autodyne_freq = Float(0.0).tag(
-        desc='use to bake the modulation into the pulse, so that it has constant phase')
-    frequency = Float(0.0).tag(
-        desc='use frequency to asssociate modulation with the channel')
-    pulse_params = Dict(default={'length': 100e-9,
+    def __init__(self, label="m", pulse_params=None):
+        if not pulse_params:
+            pulse_params =  {'length': 100e-9,
                                 'amp': 1.0,
-                                'shape_fun': PulseShapes.tanh,
+                                'shape_fun': "tanh",
                                 'cutoff': 2,
-                                'sigma': 1e-9})
-    gate_chan = Instance((str, LogicalMarkerChannel))
-    trig_chan = Instance((str, LogicalMarkerChannel))
-    receiver_chan = Instance((str, ReceiverChannel))
-
-    def __init__(self, **kwargs):
-        super(Measurement, self).__init__(**kwargs)
-        if self.trig_chan is None:
-            self.trig_chan = LogicalMarkerChannel(label='digitizerTrig')
-
+                                'sigma': 1e-9}
+        super(Measurement, self).__init__(label=label, pulse_params=pulse_params)
 
 class Edge(LogicalChannel):
     '''
@@ -186,38 +162,18 @@ class Edge(LogicalChannel):
     Qubit channel.
     '''
     # allow string in source and target so that we can store a label or an object
-    source = Instance((str, Qubit))
-    target = Instance((str, Qubit))
-    pulse_params = Dict(default={'length': 20e-9,
-                                'amp': 1.0,
-                                'phase': 0.0,
-                                'shape_fun': PulseShapes.gaussian,
-                                'cutoff': 2,
-                                'drag_scaling': 0,
-                                'sigma': 5e-9,
-                                'riseFall': 20e-9})
-    gate_chan = Instance((str, LogicalMarkerChannel))
-    frequency = Float(0.0).tag(
-        desc='modulation frequency of the channel (can be positive or negative)')
-
-    def __init__(self, **kwargs):
-        super(Edge, self).__init__(**kwargs)
-
-    def isforward(self, source, target):
-        ''' Test whether (source, target) matches the directionality of the edge. '''
-        nodes = (self.source, self.target)
-        if (source not in nodes) or (target not in nodes):
-            raise ValueError('One of {0} is not a node in the edge'.format((
-                source, target)))
-        if (self.source, self.target) == (source, target):
-            return True
-        else:
-            return False
-
-
-NewLogicalChannelList = [Qubit, Edge, LogicalMarkerChannel, Measurement]
-NewPhysicalChannelList = [
-    PhysicalMarkerChannel,
-    PhysicalQuadratureChannel,
-    ReceiverChannel
-]
+    source = Required(Qubit)
+    target = Required(Qubit)
+    
+    def __init__(self, label="e", pulse_params=None):
+        if not pulse_params:
+            pulse_params =  {'length': 20e-9,
+                                    'amp': 1.0,
+                                    'phase': 0.0,
+                                    'shape_fun': "gaussian",
+                                    'cutoff': 2,
+                                    'drag_scaling': 0,
+                                    'sigma': 5e-9,
+                                    'riseFall': 20e-9}
+        super(Edge, self).__init__(label=label, pulse_params=pulse_params)
+
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 42cfd7fe..a8769f50 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -338,6 +338,8 @@ def compile_to_hardware(seqs,
     for seq in seqs:
         PatternUtils.add_gate_pulses(seq)
 
+    # ChannelLibraries.channelLib = {c.label: c for  c in select(c for c in Channel)}
+
     if add_slave_trigger and 'slave_trig' in ChannelLibraries.channelLib:
         # Add the slave trigger
         logger.debug("Adding slave trigger")
diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 9f4d6913..7b79d9af 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -113,7 +113,10 @@ def shape(self):
         params = copy(self.shapeParams)
         params['sampling_rate'] = self.channel.phys_chan.sampling_rate
         params.pop('shape_fun')
-        return self.shapeParams['shape_fun'](**params)
+        if isinstance(self.shapeParams['shape_fun'],str):
+            return getattr(PulseShapes, self.shapeParams['shape_fun'])(**params)
+        else:
+            return self.shapeParams['shape_fun'](**params)
 
 
 def TAPulse(label,
diff --git a/QGL/PulseShapes.py b/QGL/PulseShapes.py
index 2ba601bf..17899d33 100644
--- a/QGL/PulseShapes.py
+++ b/QGL/PulseShapes.py
@@ -174,7 +174,10 @@ def autodyne(frequency=10e6, baseShape=constant, **params):
     '''
     A pulse with modulation at a particular frequency baked in.
     '''
-    shape = baseShape(**params)
+    if isinstance(baseShape,str):
+        shape = globals()[baseShape](**params)
+    else:
+        shape = baseShape(**params)
     # Apply the autodyne frequency
     timePts = np.linspace(0, params['length'], len(shape))
     shape *= np.exp(-1j * 2 * np.pi * frequency * timePts)
diff --git a/QGL/config.py b/QGL/config.py
index ef088fd6..91b1a563 100644
--- a/QGL/config.py
+++ b/QGL/config.py
@@ -3,16 +3,20 @@
 import os.path
 import re
 import yaml
+from pony.orm import *
+
+# Here is a placeholder db
+db             = Database()
 
 # Where to store AWG data
-AWGDir               = None
+AWGDir         = None
 
 # The measurement file
-meas_file            = None
+meas_file      = None
 
 # plotting options
-plotBackground       = '#EAEAF2'
-gridColor            = None
+plotBackground = '#EAEAF2'
+gridColor      = None
 
 # select pulse library (standard or all90)
 pulse_primitives_lib = "standard"

From b9f3c0c3ff10830082119f5c9531ba3d6a6ab385 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 1 Jun 2018 10:23:27 -0400
Subject: [PATCH 038/235] Adding python configuration file, supporting
 infrastructure

---
 QGL/ChannelLibraries.py |  76 ++++++++--
 QGL/Channels.py         | 317 ++++++++++++++++++++++------------------
 QGL/Compiler.py         |   4 +-
 QGL/__init__.py         |   2 +-
 QGL/config.py           |  86 +----------
 QGL/config_location.py  |   2 +-
 6 files changed, 243 insertions(+), 244 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 1078716d..379bb375 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -3,8 +3,10 @@
 real channels.
 
 Split from Channels.py on Jan 14, 2016.
+Moved to pony ORM from atom June 1, 2018
 
 Original Author: Colm Ryan
+Modified By: Graham Rowlands
 
 Copyright 2016 Raytheon BBN Technologies
 
@@ -33,18 +35,9 @@
 import traceback
 import datetime
 import importlib
+import inspect
 from pony.orm import *
 import networkx as nx
-import yaml
-
-# FSEvents observer in watchdog cannot have multiple watchers of the same path
-# use kqueue instead
-if sys.platform == 'darwin':
-    from watchdog.observers.kqueue import KqueueObserver as Observer
-else:
-    from watchdog.observers import Observer
-from watchdog.events import FileSystemEventHandler
-import time
 
 from . import config
 from . import Channels
@@ -62,21 +55,34 @@ def set_from_dict(obj, settings):
 
 class ChannelLibrary(object):
 
-    def __init__(self, library_file=None, blank=False, channelDict={}, **kwargs):
-        """Create the channel library. We assume that the user wants the config file in the 
-        usual locations specified in the config files."""
+    def __init__(self, database_file=":memory:", blank=False, channelDict={}, **kwargs):
+        """Create the channel library."""
+
+        db = Database()
+        Channels.define_entities(db)
+        db.bind('sqlite', filename=database_file)
+        db.generate_mapping(create_tables=True)
 
-        # Load the basic config options from the yaml
-        self.library_file = config.load_config(library_file)
+        config.load_config()
+
+        # Dirty trick: push the correct entity defs to the calling context
+        for var in ["Measurement","Qubit","Edge"]:
+            inspect.stack()[1][0].f_globals[var] = getattr(Channels, var)
+        # print(a)
+        # import ipdb; ipdb.set_trace()
 
         self.connectivityG = nx.DiGraph()
         
-        self.channelDict = {c.label: c for  c in select(c for c in Channels.Channel)}
+        # This is still somewhere legacy QGL behavior. Massage db into dict for lookup.
+        self.channelDict = {}
 
         # Update the global reference
         global channelLib
         channelLib = self
 
+    def update_channelDict(self):
+        self.channelDict = {c.label: c for  c in select(c for c in Channels.Channel)}
+
     #Dictionary methods
     def __getitem__(self, key):
         return self.channelDict[key]
@@ -302,6 +308,44 @@ def load_from_library(self, return_only=False):
             self.connectivityG[chan.source][chan.target]['channel'] = chan
 >>>>>>> Ditch atom, move to Pony.orm for all channel library objects.
 
+# Convenience functions for generating and linking channels
+class APS2(object):
+    def __init__(self, label):
+        self.chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern")
+        self.m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern")
+        self.m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern")
+        self.m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern")
+        self.m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern")
+        
+class X6(object):
+    def __init__(self, label):
+        self.chan1 = Channels.ReceiverChannel(label=f"{label}-1")
+        self.chan2 = Channels.ReceiverChannel(label=f"{label}-2")
+        available_streams = ["raw", "demodulated", "integrated", "averaged"]
+
+def new_qubit(label):
+    return Channels.Qubit(label=label)
+
+def set_control(qubit, awg):
+    qubit.phys_chan = awg.chan12
+    
+def set_measure(qubit, awg, dig, dig_channel=1, trig_channel=1, gate=False, gate_channel=2, trigger_length=1e-7):
+    meas = Channels.Measurement(label=f"M-{qubit.label}")
+    meas.phys_chan     = awg.chan12
+    
+    meas.trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}")
+    meas.trig_chan.phys_chan    = getattr(awg, f"m{trig_channel}")
+    meas.trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
+    
+    if gate:
+        meas.gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate")
+        meas.gate_chan.phys_chan = getattr(awg, f"m{gate_channel}")
+        
+def set_master(awg, trig_channel=2, pulse_length=1e-7):
+    st = Channels.LogicalMarkerChannel(label="slave_trig")
+    st.phys_chan = getattr(awg, f"m{trig_channel}")
+    st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
+
 
 def QubitFactory(label, **kwargs):
     ''' Return a saved qubit channel or create a new one. '''
diff --git a/QGL/Channels.py b/QGL/Channels.py
index 3a9b7b8b..4bcbf219 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -28,152 +28,177 @@
 from pony.orm import *
 from copy import deepcopy
 
-
-class Channel(config.db.Entity):
-    '''
-    Every channel has a label and some printers.
-    '''
-    label   = Required(str)
-
-    def __repr__(self):
-        return str(self)
-    def __str__(self):
-        return "{0}('{1}')".format(self.__class__.__name__, self.label)
-
-class PhysicalChannel(Channel):
-    '''
-    The main class for actual AWG channels.
-    '''
-    instrument      = Optional(str) # i.e. the AWG or receiver
-    translator      = Optional(str)
-    generator       = Optional(str)
-    sampling_rate   = Optional(float, default=1.2e9)
-    delay           = Required(float, default=0.0)
-
-    # Required reverse connections
-    logical_channel = Optional("LogicalChannel")
-    quad_channel_I  = Optional("PhysicalQuadratureChannel", reverse="I_channel")
-    quad_channel_Q  = Optional("PhysicalQuadratureChannel", reverse="Q_channel")
-    marker_channel  = Optional("PhysicalMarkerChannel")
-
-class LogicalChannel(Channel):
-    '''
-    The main class from which we will generate sequences.
-    At some point it needs to be assigned to a physical channel.
-        frequency: modulation frequency of the channel (can be positive or negative)
-    '''
-    #During initilization we may just have a string reference to the channel
-    phys_chan     = Optional(PhysicalChannel)
-    frequency     = Required(float, default=0.0)
-    pulse_params  = Optional(Json, default={}) 
-    gate_chan     = Optional("LogicalMarkerChannel")
-    receiver_chan = Optional("ReceiverChannel")
-
-class PhysicalMarkerChannel(PhysicalChannel):
-    '''
-    A digital output channel on an AWG.
-        gate_buffer: How much extra time should be added onto the beginning of a gating pulse
-        gate_min_width: The minimum marker pulse width
-    '''
-    gate_buffer    = Required(float, default=0.0)
-    gate_min_width = Required(float, default=0.0)
-    phys_channel   = Optional(PhysicalChannel)
-
-class PhysicalQuadratureChannel(PhysicalChannel):
-    '''
-    Something used to implement a standard qubit channel with two analog channels and a microwave gating channel.
-    '''
-    I_channel  = Optional(PhysicalChannel)
-    Q_channel  = Optional(PhysicalChannel)
-    amp_factor = Required(float, default=1.0)
-    phase_skew = Required(float, default=0.0)
-#     marker_channel = Optional(PhysicalMarkerChannel)
-
-class ReceiverChannel(PhysicalChannel):
-    '''
-    A trigger input on a receiver.
-    '''
-    triggering_channel = Optional(LogicalChannel)
-    channel            = Optional(int)
-
-def pulse_check(name):
-    return name in ["constant", "gaussian", "drag", "gaussOn", "gaussOff", "dragGaussOn", "dragGaussOff",
-                   "tanh", "exp_decay", "autodyne", "arb_axis_drag"]
-    
-class LogicalMarkerChannel(LogicalChannel):
-    '''
-    A class for digital channels for gating sources or triggering other things.
-    '''
-    meas_channel = Optional(LogicalChannel)
-    trig_channel = Optional("Measurement")
-
-    def __init__(self, label="lm", pulse_params=None):
-        if not pulse_params:
-            pulse_params =  {'shape_fun': "constant",'length': 10e-9}
-        super(LogicalMarkerChannel, self).__init__(label=label, pulse_params=pulse_params)
-
-class Qubit(LogicalChannel):
-    '''
-    The main class for generating qubit pulses.  Effectively a logical "QuadratureChannel".
-        frequency: modulation frequency of the channel (can be positive or negative)
-    '''
-    edge_source = Optional("Edge", reverse="source")
-    edge_target = Optional("Edge", reverse="target")
-
-    def __init__(self, label="q", pulse_params=None):
-        if not pulse_params:
-            pulse_params =  {'length': 20e-9,
-                            'piAmp': 1.0,
-                            'pi2Amp': 0.5,
-                            'shape_fun': "gaussian",
-                            'cutoff': 2,
-                            'drag_scaling': 0,
-                            'sigma': 5e-9}
-        super(Qubit, self).__init__(label=label, pulse_params=pulse_params)
-
-class Measurement(LogicalChannel):
-    '''
-    A class for measurement channels.
-    Measurements are special because they can be different types:
-    autodyne which needs an IQ pair or hetero/homodyne which needs just a marker channel.
-        meas_type: Type of measurement (autodyne, homodyne)
-        autodyne_freq: use to bake the modulation into the pulse, so that it has constant phase
-        frequency: use to asssociate modulation with the channel
-    '''
-    meas_type     = Required(str, default='autodyne', py_check=lambda x: x in ['autodyne', 'homodyne'])
-    autodyne_freq = Required(float, default=0.0)
-    trig_chan     = Optional(LogicalMarkerChannel)
-
-    def __init__(self, label="m", pulse_params=None):
-        if not pulse_params:
-            pulse_params =  {'length': 100e-9,
-                                'amp': 1.0,
-                                'shape_fun': "tanh",
+# Get these in global scope for module imports
+Channel = None
+PhysicalChannel = None
+LogicalChannel = None
+PhysicalQuadratureChannel = None
+PhysicalMarkerChannel = None
+LogicalMarkerChannel = None
+ReceiverChannel = None
+Measurement = None
+Qubit = None
+Edge = None
+
+def define_entities(db):
+
+    class Channel(db.Entity):
+        '''
+        Every channel has a label and some printers.
+        '''
+        label   = Required(str)
+
+        def __repr__(self):
+            return str(self)
+        def __str__(self):
+            return "{0}('{1}')".format(self.__class__.__name__, self.label)
+
+    class PhysicalChannel(Channel):
+        '''
+        The main class for actual AWG channels.
+        '''
+        instrument      = Optional(str) # i.e. the AWG or receiver
+        translator      = Optional(str)
+        generator       = Optional(str)
+        sampling_rate   = Optional(float, default=1.2e9)
+        delay           = Required(float, default=0.0)
+
+        # Required reverse connections
+        logical_channel = Optional("LogicalChannel")
+        quad_channel_I  = Optional("PhysicalQuadratureChannel", reverse="I_channel")
+        quad_channel_Q  = Optional("PhysicalQuadratureChannel", reverse="Q_channel")
+        marker_channel  = Optional("PhysicalMarkerChannel")
+
+    class LogicalChannel(Channel):
+        '''
+        The main class from which we will generate sequences.
+        At some point it needs to be assigned to a physical channel.
+            frequency: modulation frequency of the channel (can be positive or negative)
+        '''
+        #During initilization we may just have a string reference to the channel
+        phys_chan     = Optional(PhysicalChannel)
+        frequency     = Required(float, default=0.0)
+        pulse_params  = Optional(Json, default={}) 
+        gate_chan     = Optional("LogicalMarkerChannel")
+        receiver_chan = Optional("ReceiverChannel")
+
+    class PhysicalMarkerChannel(PhysicalChannel):
+        '''
+        A digital output channel on an AWG.
+            gate_buffer: How much extra time should be added onto the beginning of a gating pulse
+            gate_min_width: The minimum marker pulse width
+        '''
+        gate_buffer    = Required(float, default=0.0)
+        gate_min_width = Required(float, default=0.0)
+        phys_channel   = Optional(PhysicalChannel)
+
+    class PhysicalQuadratureChannel(PhysicalChannel):
+        '''
+        Something used to implement a standard qubit channel with two analog channels and a microwave gating channel.
+        '''
+        I_channel  = Optional(PhysicalChannel)
+        Q_channel  = Optional(PhysicalChannel)
+        amp_factor = Required(float, default=1.0)
+        phase_skew = Required(float, default=0.0)
+    #     marker_channel = Optional(PhysicalMarkerChannel)
+
+    class ReceiverChannel(PhysicalChannel):
+        '''
+        A trigger input on a receiver.
+        '''
+        triggering_channel = Optional(LogicalChannel)
+        channel            = Optional(int)
+
+    def pulse_check(name):
+        return name in ["constant", "gaussian", "drag", "gaussOn", "gaussOff", "dragGaussOn", "dragGaussOff",
+                       "tanh", "exp_decay", "autodyne", "arb_axis_drag"]
+        
+    class LogicalMarkerChannel(LogicalChannel):
+        '''
+        A class for digital channels for gating sources or triggering other things.
+        '''
+        meas_channel = Optional(LogicalChannel)
+        trig_channel = Optional("Measurement")
+
+        def __init__(self, label="lm", pulse_params=None):
+            if not pulse_params:
+                pulse_params =  {'shape_fun': "constant",'length': 10e-9}
+            super(LogicalMarkerChannel, self).__init__(label=label, pulse_params=pulse_params)
+
+    class Qubit(LogicalChannel):
+        '''
+        The main class for generating qubit pulses.  Effectively a logical "QuadratureChannel".
+            frequency: modulation frequency of the channel (can be positive or negative)
+        '''
+        edge_source = Optional("Edge", reverse="source")
+        edge_target = Optional("Edge", reverse="target")
+
+        def __init__(self, label="q", pulse_params=None):
+            if not pulse_params:
+                pulse_params =  {'length': 20e-9,
+                                'piAmp': 1.0,
+                                'pi2Amp': 0.5,
+                                'shape_fun': "gaussian",
                                 'cutoff': 2,
-                                'sigma': 1e-9}
-        super(Measurement, self).__init__(label=label, pulse_params=pulse_params)
-
-class Edge(LogicalChannel):
-    '''
-    Defines an arc/directed edge between qubit vertices. If a device supports bi-directional
-    connectivity, that is represented with two independent Edges.
-
-    An Edge is also effectively an abstract channel, so it carries the same properties as a
-    Qubit channel.
-    '''
-    # allow string in source and target so that we can store a label or an object
-    source = Required(Qubit)
-    target = Required(Qubit)
-    
-    def __init__(self, label="e", pulse_params=None):
-        if not pulse_params:
-            pulse_params =  {'length': 20e-9,
+                                'drag_scaling': 0,
+                                'sigma': 5e-9}
+            super(Qubit, self).__init__(label=label, pulse_params=pulse_params)
+
+    class Measurement(LogicalChannel):
+        '''
+        A class for measurement channels.
+        Measurements are special because they can be different types:
+        autodyne which needs an IQ pair or hetero/homodyne which needs just a marker channel.
+            meas_type: Type of measurement (autodyne, homodyne)
+            autodyne_freq: use to bake the modulation into the pulse, so that it has constant phase
+            frequency: use to asssociate modulation with the channel
+        '''
+        meas_type     = Required(str, default='autodyne', py_check=lambda x: x in ['autodyne', 'homodyne'])
+        autodyne_freq = Required(float, default=0.0)
+        trig_chan     = Optional(LogicalMarkerChannel)
+
+        def __init__(self, label="m", pulse_params=None):
+            if not pulse_params:
+                pulse_params =  {'length': 100e-9,
                                     'amp': 1.0,
-                                    'phase': 0.0,
-                                    'shape_fun': "gaussian",
+                                    'shape_fun': "tanh",
                                     'cutoff': 2,
-                                    'drag_scaling': 0,
-                                    'sigma': 5e-9,
-                                    'riseFall': 20e-9}
-        super(Edge, self).__init__(label=label, pulse_params=pulse_params)
-
+                                    'sigma': 1e-9}
+            super(Measurement, self).__init__(label=label, pulse_params=pulse_params)
+
+    class Edge(LogicalChannel):
+        '''
+        Defines an arc/directed edge between qubit vertices. If a device supports bi-directional
+        connectivity, that is represented with two independent Edges.
+
+        An Edge is also effectively an abstract channel, so it carries the same properties as a
+        Qubit channel.
+        '''
+        # allow string in source and target so that we can store a label or an object
+        source = Required(Qubit)
+        target = Required(Qubit)
+        
+        def __init__(self, label="e", pulse_params=None):
+            if not pulse_params:
+                pulse_params =  {'length': 20e-9,
+                                        'amp': 1.0,
+                                        'phase': 0.0,
+                                        'shape_fun': "gaussian",
+                                        'cutoff': 2,
+                                        'drag_scaling': 0,
+                                        'sigma': 5e-9,
+                                        'riseFall': 20e-9}
+            super(Edge, self).__init__(label=label, pulse_params=pulse_params)
+
+    globals()["Channel"] = Channel
+    globals()["PhysicalChannel"] = PhysicalChannel
+    globals()["LogicalChannel"] = LogicalChannel
+    globals()["PhysicalQuadratureChannel"] = PhysicalQuadratureChannel
+    globals()["PhysicalMarkerChannel"] = PhysicalMarkerChannel
+    globals()["LogicalMarkerChannel"] = LogicalMarkerChannel
+    globals()["ReceiverChannel"] = ReceiverChannel
+    globals()["Measurement"] = Measurement
+    globals()["Qubit"] = Qubit
+    globals()["Edge"] = Edge
+
+    
\ No newline at end of file
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index a8769f50..717e9a4d 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -318,6 +318,8 @@ def compile_to_hardware(seqs,
         add_slave_trigger (optional): add the slave trigger(s)
         tdm_seq (optional): compile for TDM
     '''
+    ChannelLibraries.channelLib.update_channelDict()
+
     logger.debug("Compiling %d sequence(s)", len(seqs))
 
     # save input code to file
@@ -338,8 +340,6 @@ def compile_to_hardware(seqs,
     for seq in seqs:
         PatternUtils.add_gate_pulses(seq)
 
-    # ChannelLibraries.channelLib = {c.label: c for  c in select(c for c in Channel)}
-
     if add_slave_trigger and 'slave_trig' in ChannelLibraries.channelLib:
         # Add the slave trigger
         logger.debug("Adding slave trigger")
diff --git a/QGL/__init__.py b/QGL/__init__.py
index 2433b99a..6f8a6e68 100644
--- a/QGL/__init__.py
+++ b/QGL/__init__.py
@@ -1,5 +1,5 @@
 from .Channels import Qubit, Measurement, Edge
-from .ChannelLibraries import QubitFactory, MeasFactory, EdgeFactory, MarkerFactory, ChannelLibrary, channelLib
+from .ChannelLibraries import QubitFactory, MeasFactory, EdgeFactory, MarkerFactory, ChannelLibrary, channelLib, APS2, X6, new_qubit, set_control, set_measure, set_master
 from .PulsePrimitives import *
 from .Compiler import compile_to_hardware, set_log_level
 from .PulseSequencer import align
diff --git a/QGL/config.py b/QGL/config.py
index 91b1a563..c54e5666 100644
--- a/QGL/config.py
+++ b/QGL/config.py
@@ -1,12 +1,9 @@
 #Package configuration information
 
 import os.path
+import sys
 import re
-import yaml
-from pony.orm import *
-
-# Here is a placeholder db
-db             = Database()
+import importlib
 
 # Where to store AWG data
 AWGDir         = None
@@ -25,77 +22,10 @@
 # CNOT in your gate set, e.g. CNOT_simple or CNOT_CR)
 cnot_implementation  = "CNOT_simple"
 
-class LoaderMeta(type):
-    def __new__(metacls, __name__, __bases__, __dict__):
-        """Add include constructer to class."""
-        # register the include constructor on the class
-        cls = super().__new__(metacls, __name__, __bases__, __dict__)
-        cls.add_constructor('!include', cls.construct_include)
-        return cls
-class Loader(yaml.Loader, metaclass=LoaderMeta):
-    """YAML Loader with `!include` constructor."""
-    def __init__(self, stream):
-        """Initialise Loader."""
-        try:
-            self._root = os.path.split(stream.name)[0]
-        except AttributeError:
-            self._root = os.path.curdir
-        super().__init__(stream)
-        self.add_implicit_resolver(
-            u'tag:yaml.org,2002:float',
-            re.compile(u'''^(?:
-             [-+]?(?:[0-9][0-9_]*)\\.[0-9_]*(?:[eE][-+]?[0-9]+)?
-            |[-+]?(?:[0-9][0-9_]*)(?:[eE][-+]?[0-9]+)
-            |\\.[0-9_]+(?:[eE][-+][0-9]+)?
-            |[-+]?[0-9][0-9_]*(?::[0-5]?[0-9])+\\.[0-9_]*
-            |[-+]?\\.(?:inf|Inf|INF)
-            |\\.(?:nan|NaN|NAN))$''', re.X),
-            list(u'-+0123456789.'))
-        self.filenames = [os.path.abspath(stream.name)]
-    def construct_include(self, node):
-        """Include file referenced at node."""
-        filename = os.path.abspath(os.path.join(
-            self._root, self.construct_scalar(node)
-        ))
-        extension = os.path.splitext(filename)[1].lstrip('.')
-        self.filenames.append(filename)
-        with open(filename, 'r') as f:
-            if extension in ('yaml', 'yml'):
-                return yaml.load(f, Loader)
-            else:
-                return ''.join(f.readlines())
-
-def find_meas_file():
-    if os.getenv('BBN_MEAS_FILE'):
-        return os.getenv('BBN_MEAS_FILE')
-    raise Exception("Could not find the measurement file in the environment variables or the auspex globals.")
-
-def load_config(filename=None):
-    global meas_file, AWGDir, plotBackground, gridColor, pulse_primitives_lib, cnot_implementation
-
-    if filename:
-        meas_file = filename
+def load_config():
+    if os.getenv('BBN_CONFIG_FILE'):
+        cfg = os.getenv("BBN_CONFIG_FILE")
+        sys.path.append(os.path.dirname(cfg))
+        importlib.import_module(os.path.splitext(os.path.basename(cfg))[0])
     else:
-        meas_file = find_meas_file()
-
-    with open(meas_file, 'r') as FID:
-        # cfg = yaml.load(f)
-        loader = Loader(FID)
-        try:
-            cfg = loader.get_single_data()
-        finally:
-            loader.dispose()
-
-    # pull out the variables
-    # abspath allows the use of relative file names in the config file
-    if 'AWGDir' in cfg['config'].keys():
-        AWGDir = os.path.abspath(cfg['config']['AWGDir'])
-    else:
-        raise KeyError("Could not find AWGDir in the YAML config section")
-
-    plotBackground       = cfg['config'].get('PlotBackground', '#EAEAF2')
-    gridColor            = cfg['config'].get('GridColor', None)
-    pulse_primitives_lib = cfg['config'].get('PulsePrimitivesLibrary', 'standard')
-    cnot_implementation  = cfg['config'].get('cnot_implementation', 'CNOT_simple')
-
-    return meas_file
\ No newline at end of file
+        raise Exception("Could not find the measurement file in the environment variables or the auspex globals.")
diff --git a/QGL/config_location.py b/QGL/config_location.py
index 16566195..d9304dec 100644
--- a/QGL/config_location.py
+++ b/QGL/config_location.py
@@ -50,7 +50,7 @@
 
 CONFIG_PATH = None
 
-_CONFIG_FILE_NAME = 'config.json'
+_CONFIG_FILE_NAME = 'BBN_config.py'
 
 def _set_default_config_path():
     """

From 2e63ef90ca47fc4bc101ff9ac2e18dc30f816bf7 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Mon, 4 Jun 2018 21:45:53 -0400
Subject: [PATCH 039/235] Can now load/save to a database with labels and
 datestamps

---
 QGL/ChannelLibraries.py | 109 +++++++++++++++++++++++++++++++++-------
 QGL/Channels.py         |  27 ++++++++--
 QGL/Compiler.py         |   2 +-
 QGL/__init__.py         |   4 +-
 QGL/config.py           |  12 +++--
 5 files changed, 125 insertions(+), 29 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 379bb375..c0eac234 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -32,6 +32,7 @@
 import sys
 import os
 import re
+import datetime
 import traceback
 import datetime
 import importlib
@@ -53,35 +54,86 @@ def set_from_dict(obj, settings):
             except Exception as e:
                 print(f"{obj.label}: Error loading {prop_name} from config")
 
+def copy_entity(obj):
+    """Copy a pony entity instance"""
+    kwargs = {a.name: getattr(obj, a.name) for a in obj._attrs_}
+    kwargs.pop("id")
+    kwargs.pop("classtype")
+    return obj.__class__(**kwargs)
+
 class ChannelLibrary(object):
 
-    def __init__(self, database_file=":memory:", blank=False, channelDict={}, **kwargs):
+    def __init__(self, channel_db_name=None, database_file=":memory:", channelDict={}, **kwargs):
         """Create the channel library."""
 
         db = Database()
         Channels.define_entities(db)
-        db.bind('sqlite', filename=database_file)
+        db.bind('sqlite', filename=database_file, create_db=True)
         db.generate_mapping(create_tables=True)
 
-        config.load_config()
-
         # Dirty trick: push the correct entity defs to the calling context
         for var in ["Measurement","Qubit","Edge"]:
             inspect.stack()[1][0].f_globals[var] = getattr(Channels, var)
-        # print(a)
-        # import ipdb; ipdb.set_trace()
 
         self.connectivityG = nx.DiGraph()
         
         # This is still somewhere legacy QGL behavior. Massage db into dict for lookup.
         self.channelDict = {}
+        self.channels = []
+        self.sources = []
+        self.channelDatabase = None
+        self.channel_db_name = channel_db_name if channel_db_name else "temp"
+
+        self.load_most_recent()
+        # config.load_config()
 
         # Update the global reference
         global channelLib
         channelLib = self
 
-    def update_channelDict(self):
-        self.channelDict = {c.label: c for  c in select(c for c in Channels.Channel)}
+    def list(self):
+        select((c.label, c.time, c.id) for c in Channels.ChannelDatabase).show()
+
+    def load_by_id(self, id_num):
+        obj = select(c for c in Channels.ChannelDatabase if c.id==id_num).first()
+        self.load(obj)
+
+        self.channels = list(obj.channels)
+        self.sources  = list(obj.sources)
+        self.channel_db_name = obj.label
+
+    def load(self, obj):
+        self.channels = list(obj.channels)
+        self.sources  = list(obj.sources)
+        self.channel_db_name = obj.label
+        self.channelDatabase = obj
+
+    def load_most_recent(self, name=None):
+        if name is None:
+            name = self.channel_db_name
+        mrcd = Channels.ChannelDatabase.select(lambda d: d.label==name).order_by(desc(Channels.ChannelDatabase.time)).first()
+        if mrcd:
+            self.load(mrcd)
+
+    def new(self, name):
+        self.channelDatabase = None
+        self.channel_db_name = name
+        self.channels = []
+        self.sources = []
+
+    def save(self):
+        self.save_as(self.channel_db_name)
+
+    def save_as(self, name):
+        # Get channels that are part of the currently active db, or find those that aren't yet part of a db
+        chans = list(select(c for c in Channels.Channel if (c.channel_db == self.channelDatabase) or (c.channel_db is None)))
+        srcs  = list(select(c for c in Channels.MicrowaveSource if (c.channel_db == self.channelDatabase) or (c.channel_db is None)))
+        cd = Channels.ChannelDatabase(label=name, time=datetime.datetime.now(), channels=chans, sources=srcs)
+        self.channels = chans
+        self.sources = srcs
+        self.channelDatabase = cd
+        commit()
+        self.channel_db_name = name
 
     #Dictionary methods
     def __getitem__(self, key):
@@ -309,34 +361,56 @@ def load_from_library(self, return_only=False):
 >>>>>>> Ditch atom, move to Pony.orm for all channel library objects.
 
 # Convenience functions for generating and linking channels
+# TODO: move these to a shim layer shared by Auspex/QGL
+
 class APS2(object):
-    def __init__(self, label):
+    def __init__(self, label, address=None, delay=0.0):
         self.chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern")
         self.m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern")
         self.m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern")
         self.m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern")
         self.m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern")
         
+        self.trigger_interval = None
+        self.trigger_source   = "External"
+        self.address          = address
+        self.delay            = delay
+        self.master           = False
+
 class X6(object):
-    def __init__(self, label):
-        self.chan1 = Channels.ReceiverChannel(label=f"{label}-1")
-        self.chan2 = Channels.ReceiverChannel(label=f"{label}-2")
-        available_streams = ["raw", "demodulated", "integrated", "averaged"]
+    def __init__(self, label, address=None):
+        self.chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1")
+        self.chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2")
+        
+        self.address          = address
+        self.reference        = "external"
+        self.nbr_segments     = 1
+        self.nbr_round_robins = 100
+        self.acquire_mode     = "digitizer"
 
 def new_qubit(label):
     return Channels.Qubit(label=label)
 
-def set_control(qubit, awg):
+def new_source(label, source_type, address, power=-30.0):
+    return Channels.MicrowaveSource(label=label, source_type=source_type, address=address, power=power)
+
+def set_control(qubit, awg, generator=None):
     qubit.phys_chan = awg.chan12
+    if generator:
+        qubit.phys_chan.generator = generator
     
-def set_measure(qubit, awg, dig, dig_channel=1, trig_channel=1, gate=False, gate_channel=2, trigger_length=1e-7):
+def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=1, gate=False, gate_channel=2, trigger_length=1e-7):
     meas = Channels.Measurement(label=f"M-{qubit.label}")
     meas.phys_chan     = awg.chan12
     
     meas.trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}")
     meas.trig_chan.phys_chan    = getattr(awg, f"m{trig_channel}")
     meas.trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
-    
+    meas.receiver_chan          = getattr(dig, f"chan{dig_channel}")
+
+    if generator:
+        meas.phys_chan.generator = generator
+
     if gate:
         meas.gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate")
         meas.gate_chan.phys_chan = getattr(awg, f"m{gate_channel}")
@@ -345,7 +419,8 @@ def set_master(awg, trig_channel=2, pulse_length=1e-7):
     st = Channels.LogicalMarkerChannel(label="slave_trig")
     st.phys_chan = getattr(awg, f"m{trig_channel}")
     st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
-
+    awg.master = True
+    awg.trigger_source = "Internal"
 
 def QubitFactory(label, **kwargs):
     ''' Return a saved qubit channel or create a new one. '''
diff --git a/QGL/Channels.py b/QGL/Channels.py
index 4bcbf219..2b8ea34b 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -27,6 +27,7 @@
 from math import tan, cos, pi
 from pony.orm import *
 from copy import deepcopy
+import datetime
 
 # Get these in global scope for module imports
 Channel = None
@@ -39,14 +40,31 @@
 Measurement = None
 Qubit = None
 Edge = None
+MicrowaveSource = None
+ChannelDatabase = None
 
 def define_entities(db):
 
+    class ChannelDatabase(db.Entity):
+        label    = Required(str)
+        channels = Set("Channel")
+        sources  = Set("MicrowaveSource")
+        time     = Optional(datetime.datetime)
+
+    class MicrowaveSource(db.Entity):
+        label           = Required(str)
+        source_type     = Required(str)
+        address         = Optional(str)
+        power           = Optional(float)
+        logical_channel = Optional("PhysicalChannel")
+        channel_db      = Optional("ChannelDatabase")
+
     class Channel(db.Entity):
         '''
         Every channel has a label and some printers.
         '''
-        label   = Required(str)
+        label      = Required(str)
+        channel_db = Optional("ChannelDatabase")
 
         def __repr__(self):
             return str(self)
@@ -59,8 +77,8 @@ class PhysicalChannel(Channel):
         '''
         instrument      = Optional(str) # i.e. the AWG or receiver
         translator      = Optional(str)
-        generator       = Optional(str)
-        sampling_rate   = Optional(float, default=1.2e9)
+        generator       = Optional(MicrowaveSource, reverse="logical_channel")
+        sampling_rate   = Required(float, default=1.2e9)
         delay           = Required(float, default=0.0)
 
         # Required reverse connections
@@ -200,5 +218,6 @@ def __init__(self, label="e", pulse_params=None):
     globals()["Measurement"] = Measurement
     globals()["Qubit"] = Qubit
     globals()["Edge"] = Edge
-
+    globals()["MicrowaveSource"] = MicrowaveSource
+    globals()["ChannelDatabase"] = ChannelDatabase
     
\ No newline at end of file
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 717e9a4d..8ceaa8c4 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -318,7 +318,7 @@ def compile_to_hardware(seqs,
         add_slave_trigger (optional): add the slave trigger(s)
         tdm_seq (optional): compile for TDM
     '''
-    ChannelLibraries.channelLib.update_channelDict()
+    # ChannelLibraries.channelLib.update_channelDict()
 
     logger.debug("Compiling %d sequence(s)", len(seqs))
 
diff --git a/QGL/__init__.py b/QGL/__init__.py
index 6f8a6e68..e11ea869 100644
--- a/QGL/__init__.py
+++ b/QGL/__init__.py
@@ -1,5 +1,5 @@
-from .Channels import Qubit, Measurement, Edge
-from .ChannelLibraries import QubitFactory, MeasFactory, EdgeFactory, MarkerFactory, ChannelLibrary, channelLib, APS2, X6, new_qubit, set_control, set_measure, set_master
+from .Channels import Qubit, Measurement, Edge, MicrowaveSource, ChannelDatabase
+from .ChannelLibraries import QubitFactory, MeasFactory, EdgeFactory, MarkerFactory, ChannelLibrary, channelLib, APS2, X6, new_qubit, set_control, set_measure, set_master, new_source
 from .PulsePrimitives import *
 from .Compiler import compile_to_hardware, set_log_level
 from .PulseSequencer import align
diff --git a/QGL/config.py b/QGL/config.py
index c54e5666..152cb750 100644
--- a/QGL/config.py
+++ b/QGL/config.py
@@ -24,8 +24,10 @@
 
 def load_config():
     if os.getenv('BBN_CONFIG_FILE'):
-        cfg = os.getenv("BBN_CONFIG_FILE")
-        sys.path.append(os.path.dirname(cfg))
-        importlib.import_module(os.path.splitext(os.path.basename(cfg))[0])
-    else:
-        raise Exception("Could not find the measurement file in the environment variables or the auspex globals.")
+        try:
+            cfg = os.getenv("BBN_CONFIG_FILE")
+            sys.path.append(os.path.dirname(cfg))
+            importlib.import_module(os.path.splitext(os.path.basename(cfg))[0])
+        except:
+            raise Exception("Could not find the measurement file in the environment variables or the auspex globals.")
+            
\ No newline at end of file

From 4c83141cdcbefab1b916030f3ab7a537562e04f5 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 6 Jun 2018 10:51:50 -0400
Subject: [PATCH 040/235] Fix factories to pull most recent qubits, etc.

---
 QGL/ChannelLibraries.py | 69 +++++++++++++++++++++++++++++++++++++----
 QGL/Channels.py         | 46 +++++++++++++--------------
 QGL/Compiler.py         |  2 +-
 QGL/config.py           | 22 ++++++++-----
 4 files changed, 102 insertions(+), 37 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index c0eac234..fc4294fb 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -54,21 +54,65 @@ def set_from_dict(obj, settings):
             except Exception as e:
                 print(f"{obj.label}: Error loading {prop_name} from config")
 
+def copy_objs(chans, srcs):
+    new_chans       = []
+    new_srcs        = []
+    old_to_new_chan = {}
+    old_to_new_src  = {}
+
+    for chan in chans:
+        c = copy_entity(chan)
+        print("Copied", chan, "to", c)
+        new_chans.append(c)
+        old_to_new_chan[chan] = c
+
+    for src in srcs:
+        c = copy_entity(src)
+        print("Copied", src, "to", c)
+        new_srcs.append(c)
+        old_to_new_src[src] = c
+
+    # # Fix links... pony updates the relationships symmetriacally so we get some for free
+    # for thing in new_chans + new_srcs:
+    #     print(f"Fixing {thing}")
+    #     for attr in thing._attrs_:
+    #         print(f"\t{attr}")
+    #         if attr:
+    #             if isinstance(getattr(thing, attr.name), Channels.Channel):
+    #                 if getattr(thing, attr.name) in old_to_new_chan.keys():
+    #                     print(f"setting {thing} {attr.name} to {old_to_new_chan[getattr(thing, attr.name)]}")
+    #                     setattr(thing, attr.name, old_to_new_chan[getattr(thing, attr.name)])
+    #             elif isinstance(getattr(thing, attr.name), Channels.MicrowaveSource):
+    #                 if getattr(thing, attr.name) in old_to_new_src.keys():
+    #                     print(f"setting {thing} {attr.name} to {old_to_new_src[getattr(thing, attr.name)]}")
+    #                     setattr(thing, attr.name, old_to_new_src[getattr(thing, attr.name)])
+
+    return new_chans, new_srcs
+
 def copy_entity(obj):
     """Copy a pony entity instance"""
     kwargs = {a.name: getattr(obj, a.name) for a in obj._attrs_}
     kwargs.pop("id")
-    kwargs.pop("classtype")
+    # kwargs.pop("classtype")
+    kwargs.pop("channel_db")
     return obj.__class__(**kwargs)
 
 class ChannelLibrary(object):
 
-    def __init__(self, channel_db_name=None, database_file=":memory:", channelDict={}, **kwargs):
+    def __init__(self, channel_db_name=None, database_file=None, channelDict={}, **kwargs):
         """Create the channel library."""
 
+        config.load_db()
+        if database_file:
+            self.database_file = database_file
+        elif config.db_file:
+            self.database_file = config.db_file
+        else:
+            self.database_file = ":memory:"
+
         db = Database()
         Channels.define_entities(db)
-        db.bind('sqlite', filename=database_file, create_db=True)
+        db.bind('sqlite', filename=self.database_file, create_db=True)
         db.generate_mapping(create_tables=True)
 
         # Dirty trick: push the correct entity defs to the calling context
@@ -84,6 +128,8 @@ def __init__(self, channel_db_name=None, database_file=":memory:", channelDict={
         self.channelDatabase = None
         self.channel_db_name = channel_db_name if channel_db_name else "temp"
 
+        config.load_config()
+
         self.load_most_recent()
         # config.load_config()
 
@@ -91,6 +137,12 @@ def __init__(self, channel_db_name=None, database_file=":memory:", channelDict={
         global channelLib
         channelLib = self
 
+    def get_current_channels(self):
+        return list(select(c for c in Channels.Channel if (c.channel_db == self.channelDatabase) or (c.channel_db is None)))
+
+    def update_channelDict(self):
+        self.channelDict = {c.label: c for c in self.get_current_channels()}
+
     def list(self):
         select((c.label, c.time, c.id) for c in Channels.ChannelDatabase).show()
 
@@ -128,6 +180,9 @@ def save_as(self, name):
         # Get channels that are part of the currently active db, or find those that aren't yet part of a db
         chans = list(select(c for c in Channels.Channel if (c.channel_db == self.channelDatabase) or (c.channel_db is None)))
         srcs  = list(select(c for c in Channels.MicrowaveSource if (c.channel_db == self.channelDatabase) or (c.channel_db is None)))
+        
+        # chans, src = copy_objs(chans, srcs)
+
         cd = Channels.ChannelDatabase(label=name, time=datetime.datetime.now(), channels=chans, sources=srcs)
         self.channels = chans
         self.sources = srcs
@@ -424,7 +479,9 @@ def set_master(awg, trig_channel=2, pulse_length=1e-7):
 
 def QubitFactory(label, **kwargs):
     ''' Return a saved qubit channel or create a new one. '''
-    thing = select(el for el in Channels.Qubit if el.label==label).first()
+    # TODO: this will just get the first entry in the whole damned DB!
+    # thing = select(el for el in Channels.Qubit if el.label==label).first()
+    thing = {c.label: c for c in channelLib.get_current_channels()}[label]
     if thing:
         return thing
     else:
@@ -432,7 +489,7 @@ def QubitFactory(label, **kwargs):
     
 def MeasFactory(label, **kwargs):
     ''' Return a saved measurement channel or create a new one. '''
-    thing = select(el for el in Channels.Measurement if el.label==label).first()
+    thing = {c.label: c for c in channelLib.get_current_channels()}[label]
     if thing:
         return thing
     else:
@@ -440,7 +497,7 @@ def MeasFactory(label, **kwargs):
 
 def MarkerFactory(label, **kwargs):
     ''' Return a saved Marker channel or create a new one. '''
-    thing = select(el for el in Channels.LogicalMarkerChannel if el.label==label).first()
+    thing = {c.label: c for c in channelLib.get_current_channels()}[label]
     if thing:
         return thing
     else:
diff --git a/QGL/Channels.py b/QGL/Channels.py
index 2b8ea34b..274a0d47 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -138,10 +138,10 @@ class LogicalMarkerChannel(LogicalChannel):
         meas_channel = Optional(LogicalChannel)
         trig_channel = Optional("Measurement")
 
-        def __init__(self, label="lm", pulse_params=None):
-            if not pulse_params:
-                pulse_params =  {'shape_fun': "constant",'length': 10e-9}
-            super(LogicalMarkerChannel, self).__init__(label=label, pulse_params=pulse_params)
+        def __init__(self, **kwargs):
+            if "pulse_params" not in kwargs.keys():
+                kwargs["pulse_params"] =  {'shape_fun': "constant",'length': 10e-9}
+            super(LogicalMarkerChannel, self).__init__(**kwargs)
 
     class Qubit(LogicalChannel):
         '''
@@ -151,16 +151,16 @@ class Qubit(LogicalChannel):
         edge_source = Optional("Edge", reverse="source")
         edge_target = Optional("Edge", reverse="target")
 
-        def __init__(self, label="q", pulse_params=None):
-            if not pulse_params:
-                pulse_params =  {'length': 20e-9,
+        def __init__(self, **kwargs):
+            if "pulse_params" not in kwargs.keys():
+                kwargs["pulse_params"] =  {'length': 20e-9,
                                 'piAmp': 1.0,
                                 'pi2Amp': 0.5,
                                 'shape_fun': "gaussian",
                                 'cutoff': 2,
                                 'drag_scaling': 0,
                                 'sigma': 5e-9}
-            super(Qubit, self).__init__(label=label, pulse_params=pulse_params)
+            super(Qubit, self).__init__(**kwargs)
 
     class Measurement(LogicalChannel):
         '''
@@ -175,14 +175,14 @@ class Measurement(LogicalChannel):
         autodyne_freq = Required(float, default=0.0)
         trig_chan     = Optional(LogicalMarkerChannel)
 
-        def __init__(self, label="m", pulse_params=None):
-            if not pulse_params:
-                pulse_params =  {'length': 100e-9,
+        def __init__(self, **kwargs):
+            if "pulse_params" not in kwargs.keys():
+                kwargs["pulse_params"] =  {'length': 100e-9,
                                     'amp': 1.0,
                                     'shape_fun': "tanh",
                                     'cutoff': 2,
                                     'sigma': 1e-9}
-            super(Measurement, self).__init__(label=label, pulse_params=pulse_params)
+            super(Measurement, self).__init__(**kwargs)
 
     class Edge(LogicalChannel):
         '''
@@ -196,17 +196,17 @@ class Edge(LogicalChannel):
         source = Required(Qubit)
         target = Required(Qubit)
         
-        def __init__(self, label="e", pulse_params=None):
-            if not pulse_params:
-                pulse_params =  {'length': 20e-9,
-                                        'amp': 1.0,
-                                        'phase': 0.0,
-                                        'shape_fun': "gaussian",
-                                        'cutoff': 2,
-                                        'drag_scaling': 0,
-                                        'sigma': 5e-9,
-                                        'riseFall': 20e-9}
-            super(Edge, self).__init__(label=label, pulse_params=pulse_params)
+        def __init__(self, **kwargs):
+            if "pulse_params" not in kwargs.keys():
+                kwargs["pulse_params"] =   {'length': 20e-9,
+                                            'amp': 1.0,
+                                            'phase': 0.0,
+                                            'shape_fun': "gaussian",
+                                            'cutoff': 2,
+                                            'drag_scaling': 0,
+                                            'sigma': 5e-9,
+                                            'riseFall': 20e-9}
+            super(Edge, self).__init__(**kwargs)
 
     globals()["Channel"] = Channel
     globals()["PhysicalChannel"] = PhysicalChannel
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 8ceaa8c4..717e9a4d 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -318,7 +318,7 @@ def compile_to_hardware(seqs,
         add_slave_trigger (optional): add the slave trigger(s)
         tdm_seq (optional): compile for TDM
     '''
-    # ChannelLibraries.channelLib.update_channelDict()
+    ChannelLibraries.channelLib.update_channelDict()
 
     logger.debug("Compiling %d sequence(s)", len(seqs))
 
diff --git a/QGL/config.py b/QGL/config.py
index 152cb750..085c48d8 100644
--- a/QGL/config.py
+++ b/QGL/config.py
@@ -8,8 +8,11 @@
 # Where to store AWG data
 AWGDir         = None
 
-# The measurement file
-meas_file      = None
+# The db file, where the channel libraries are stored
+db_file        = None
+
+# The config file (executed upon channel library loading)
+config_file    = None
 
 # plotting options
 plotBackground = '#EAEAF2'
@@ -23,11 +26,16 @@
 cnot_implementation  = "CNOT_simple"
 
 def load_config():
+    global config_file
     if os.getenv('BBN_CONFIG_FILE'):
         try:
-            cfg = os.getenv("BBN_CONFIG_FILE")
-            sys.path.append(os.path.dirname(cfg))
-            importlib.import_module(os.path.splitext(os.path.basename(cfg))[0])
+            config_file = os.getenv("BBN_CONFIG_FILE")
+            sys.path.append(os.path.dirname(config_file))
+            importlib.import_module(os.path.splitext(os.path.basename(config_file))[0])
         except:
-            raise Exception("Could not find the measurement file in the environment variables or the auspex globals.")
-            
\ No newline at end of file
+            raise Exception(f"Could not import/execute the BBN_CONFIG_FILE {cfg}")
+            
+def load_db():
+    global db_file
+    if os.getenv('BBN_DB'):
+        db_file = os.getenv("BBN_DB")
\ No newline at end of file

From 10c7944499c884fda12a7603f83bf664c0ca4084 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Mon, 11 Jun 2018 21:22:28 -0400
Subject: [PATCH 041/235] Adding save/load functionality

---
 QGL/ChannelLibraries.py | 174 ++++++++++++++++++++++++----------------
 QGL/Channels.py         |  20 ++---
 2 files changed, 114 insertions(+), 80 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index fc4294fb..afd109cc 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -54,49 +54,60 @@ def set_from_dict(obj, settings):
             except Exception as e:
                 print(f"{obj.label}: Error loading {prop_name} from config")
 
-def copy_objs(chans, srcs):
+def copy_objs(chans, srcs, new_channel_db):
     new_chans       = []
     new_srcs        = []
     old_to_new_chan = {}
     old_to_new_src  = {}
 
     for chan in chans:
-        c = copy_entity(chan)
-        print("Copied", chan, "to", c)
+        c = copy_entity(chan, new_channel_db)
         new_chans.append(c)
         old_to_new_chan[chan] = c
 
     for src in srcs:
-        c = copy_entity(src)
-        print("Copied", src, "to", c)
+        c = copy_entity(src, new_channel_db)
         new_srcs.append(c)
         old_to_new_src[src] = c
 
-    # # Fix links... pony updates the relationships symmetriacally so we get some for free
-    # for thing in new_chans + new_srcs:
-    #     print(f"Fixing {thing}")
-    #     for attr in thing._attrs_:
-    #         print(f"\t{attr}")
-    #         if attr:
-    #             if isinstance(getattr(thing, attr.name), Channels.Channel):
-    #                 if getattr(thing, attr.name) in old_to_new_chan.keys():
-    #                     print(f"setting {thing} {attr.name} to {old_to_new_chan[getattr(thing, attr.name)]}")
-    #                     setattr(thing, attr.name, old_to_new_chan[getattr(thing, attr.name)])
-    #             elif isinstance(getattr(thing, attr.name), Channels.MicrowaveSource):
-    #                 if getattr(thing, attr.name) in old_to_new_src.keys():
-    #                     print(f"setting {thing} {attr.name} to {old_to_new_src[getattr(thing, attr.name)]}")
-    #                     setattr(thing, attr.name, old_to_new_src[getattr(thing, attr.name)])
+    # Fix links... pony updates the relationships symmetriacally so we get some for free
+    for thing in new_chans + new_srcs:
+        for attr in thing._attrs_:
+            if attr:
+                if isinstance(getattr(thing, attr.name), Channels.Channel):
+                    if getattr(thing, attr.name) in old_to_new_chan.keys():
+                        setattr(thing, attr.name, old_to_new_chan[getattr(thing, attr.name)])
+                elif isinstance(getattr(thing, attr.name), Channels.MicrowaveSource):
+                    if getattr(thing, attr.name) in old_to_new_src.keys():
+                        setattr(thing, attr.name, old_to_new_src[getattr(thing, attr.name)])
 
     return new_chans, new_srcs
 
-def copy_entity(obj):
+def copy_entity(obj, new_channel_db):
     """Copy a pony entity instance"""
-    kwargs = {a.name: getattr(obj, a.name) for a in obj._attrs_}
-    kwargs.pop("id")
-    # kwargs.pop("classtype")
-    kwargs.pop("channel_db")
+    kwargs = {a.name: getattr(obj, a.name) for a in obj.__class__._attrs_ if a.name not in ["id", "classtype", "pulse_params"]}
+    # if "pulse_params" in kwargs.keys():
+    #     kwargs["pulse_params"] = dict(kwargs["pulse_params"])
+    kwargs["channel_db"] = new_channel_db
     return obj.__class__(**kwargs)
 
+# def copy_entity(obj, new_channel_db):
+#     """Copy a pony entity instance"""
+#     attr_names = [a.name for a in obj.__class__._attrs_]
+#     skip = ["id", "classtype", "channel_db"]
+#     print(obj)
+#     kwargs = {"channel_db": new_channel_db}
+#     for a in attr_names: #["label", "source_type"]:
+#         print("\t", a)
+#         if a in dir(obj):
+#             val = getattr(obj, a)
+#             if a == "pulse_params":
+#                 val = dict(val)
+#             if val is not None and a not in skip:
+#                 print("\t\t", getattr(obj, a))
+#                 kwargs[a] = val
+#     return obj.__class__(**kwargs)
+
 class ChannelLibrary(object):
 
     def __init__(self, channel_db_name=None, database_file=None, channelDict={}, **kwargs):
@@ -125,12 +136,12 @@ def __init__(self, channel_db_name=None, database_file=None, channelDict={}, **k
         self.channelDict = {}
         self.channels = []
         self.sources = []
-        self.channelDatabase = None
+        self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
         self.channel_db_name = channel_db_name if channel_db_name else "temp"
 
         config.load_config()
 
-        self.load_most_recent()
+        # self.load_most_recent()
         # config.load_config()
 
         # Update the global reference
@@ -138,7 +149,7 @@ def __init__(self, channel_db_name=None, database_file=None, channelDict={}, **k
         channelLib = self
 
     def get_current_channels(self):
-        return list(select(c for c in Channels.Channel if (c.channel_db == self.channelDatabase) or (c.channel_db is None)))
+        return list(select(c for c in Channels.Channel if c.channel_db is None)) + list(select(c for c in Channels.MicrowaveSource if c.channel_db is None))
 
     def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
@@ -150,45 +161,68 @@ def load_by_id(self, id_num):
         obj = select(c for c in Channels.ChannelDatabase if c.id==id_num).first()
         self.load(obj)
 
-        self.channels = list(obj.channels)
-        self.sources  = list(obj.sources)
-        self.channel_db_name = obj.label
+    def clear(self):
+        select(c for c in Channels.Channel if c.channel_db == self.channelDatabase).delete(bulk=True)
+        select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase).delete(bulk=True)
+        self.channelDatabase.time  = datetime.datetime.now()
+
+    def load(self, obj): #, delete=True):
+        self.clear()
 
-    def load(self, obj):
-        self.channels = list(obj.channels)
-        self.sources  = list(obj.sources)
+        chans = list(obj.channels)
+        srcs  = list(obj.sources)
+
+        # self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
+        new_chans, new_srcs = copy_objs(chans, srcs, self.channelDatabase)
+
+        self.channels = new_chans
+        self.sources = new_srcs
         self.channel_db_name = obj.label
-        self.channelDatabase = obj
-
-    def load_most_recent(self, name=None):
-        if name is None:
-            name = self.channel_db_name
-        mrcd = Channels.ChannelDatabase.select(lambda d: d.label==name).order_by(desc(Channels.ChannelDatabase.time)).first()
-        if mrcd:
-            self.load(mrcd)
-
-    def new(self, name):
-        self.channelDatabase = None
-        self.channel_db_name = name
-        self.channels = []
-        self.sources = []
+        # self.channelDatabase = None
+
+    # def load_most_recent(self, name=None):
+    #     if name is None:
+    #         name = self.channel_db_name
+    #     mrcd = Channels.ChannelDatabase.select(lambda d: d.label==name).order_by(desc(Channels.ChannelDatabase.time)).first()
+    #     if mrcd:
+    #         self.load(mrcd)
+
+    # def new(self, name):
+    #     # self.channelDatabase.delete()
+    #     self.clear()
+    #     commit()
+
+    #     # self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
+
+    #     # self.channelDatabase = None
+    #     self.channel_db_name = name
+    #     self.channels = []
+    #     self.sources = []
 
     def save(self):
         self.save_as(self.channel_db_name)
 
     def save_as(self, name):
-        # Get channels that are part of the currently active db, or find those that aren't yet part of a db
-        chans = list(select(c for c in Channels.Channel if (c.channel_db == self.channelDatabase) or (c.channel_db is None)))
-        srcs  = list(select(c for c in Channels.MicrowaveSource if (c.channel_db == self.channelDatabase) or (c.channel_db is None)))
+        # self.channelDatabase.label = name
+        # self.channelDatabase.time  = datetime.datetime.now()
+        # cd = self.channelDatabase
+        # self.channelDatabase = None
+        # commit()
+        # self.load(cd, delete=False)
         
-        # chans, src = copy_objs(chans, srcs)
-
-        cd = Channels.ChannelDatabase(label=name, time=datetime.datetime.now(), channels=chans, sources=srcs)
-        self.channels = chans
-        self.sources = srcs
-        self.channelDatabase = cd
+        # Get channels that are part of the currently active db
+        # chans = list(select(c for c in Channels.Channel if c.channel_db is None))
+        # srcs  = list(select(c for c in Channels.MicrowaveSource if c.channel_db is None))
+        chans = list(self.channelDatabase.channels)
+        srcs  = list(self.channelDatabase.sources)
+        cd    = Channels.ChannelDatabase(label=name, time=datetime.datetime.now(), channels=chans, sources=srcs)
+        new_chans, new_srcs = copy_objs(chans, srcs, cd)
+
+        # self.channels = new_chans
+        # self.sources = new_srcs
+        # self.channelDatabase = None
         commit()
-        self.channel_db_name = name
+        # self.channel_db_name = name
 
     #Dictionary methods
     def __getitem__(self, key):
@@ -420,11 +454,11 @@ def load_from_library(self, return_only=False):
 
 class APS2(object):
     def __init__(self, label, address=None, delay=0.0):
-        self.chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern")
-        self.m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern")
-        self.m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern")
-        self.m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern")
-        self.m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern")
+        self.chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+        self.m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+        self.m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+        self.m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+        self.m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
         
         self.trigger_interval = None
         self.trigger_source   = "External"
@@ -434,8 +468,8 @@ def __init__(self, label, address=None, delay=0.0):
 
 class X6(object):
     def __init__(self, label, address=None):
-        self.chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1")
-        self.chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2")
+        self.chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel_db=channelLib.channelDatabase)
+        self.chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel_db=channelLib.channelDatabase)
         
         self.address          = address
         self.reference        = "external"
@@ -444,10 +478,10 @@ def __init__(self, label, address=None):
         self.acquire_mode     = "digitizer"
 
 def new_qubit(label):
-    return Channels.Qubit(label=label)
+    return Channels.Qubit(label=label, channel_db=channelLib.channelDatabase)
 
 def new_source(label, source_type, address, power=-30.0):
-    return Channels.MicrowaveSource(label=label, source_type=source_type, address=address, power=power)
+    return Channels.MicrowaveSource(label=label, source_type=source_type, address=address, power=power, channel_db=channelLib.channelDatabase)
 
 def set_control(qubit, awg, generator=None):
     qubit.phys_chan = awg.chan12
@@ -455,10 +489,10 @@ def set_control(qubit, awg, generator=None):
         qubit.phys_chan.generator = generator
     
 def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=1, gate=False, gate_channel=2, trigger_length=1e-7):
-    meas = Channels.Measurement(label=f"M-{qubit.label}")
+    meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=channelLib.channelDatabase)
     meas.phys_chan     = awg.chan12
     
-    meas.trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}")
+    meas.trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}", channel_db=channelLib.channelDatabase)
     meas.trig_chan.phys_chan    = getattr(awg, f"m{trig_channel}")
     meas.trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
     meas.receiver_chan          = getattr(dig, f"chan{dig_channel}")
@@ -467,11 +501,11 @@ def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=1,
         meas.phys_chan.generator = generator
 
     if gate:
-        meas.gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate")
+        meas.gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=channelLib.channelDatabase)
         meas.gate_chan.phys_chan = getattr(awg, f"m{gate_channel}")
         
 def set_master(awg, trig_channel=2, pulse_length=1e-7):
-    st = Channels.LogicalMarkerChannel(label="slave_trig")
+    st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=channelLib.channelDatabase)
     st.phys_chan = getattr(awg, f"m{trig_channel}")
     st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
     awg.master = True
diff --git a/QGL/Channels.py b/QGL/Channels.py
index 274a0d47..bf50ca71 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -47,8 +47,8 @@ def define_entities(db):
 
     class ChannelDatabase(db.Entity):
         label    = Required(str)
-        channels = Set("Channel")
-        sources  = Set("MicrowaveSource")
+        channels = Set("Channel", cascade_delete=True)
+        sources  = Set("MicrowaveSource", cascade_delete=True)
         time     = Optional(datetime.datetime)
 
     class MicrowaveSource(db.Entity):
@@ -57,14 +57,14 @@ class MicrowaveSource(db.Entity):
         address         = Optional(str)
         power           = Optional(float)
         logical_channel = Optional("PhysicalChannel")
-        channel_db      = Optional("ChannelDatabase")
+        channel_db      = Required("ChannelDatabase")
 
     class Channel(db.Entity):
         '''
         Every channel has a label and some printers.
         '''
         label      = Required(str)
-        channel_db = Optional("ChannelDatabase")
+        channel_db = Required("ChannelDatabase")
 
         def __repr__(self):
             return str(self)
@@ -83,9 +83,9 @@ class PhysicalChannel(Channel):
 
         # Required reverse connections
         logical_channel = Optional("LogicalChannel")
-        quad_channel_I  = Optional("PhysicalQuadratureChannel", reverse="I_channel")
-        quad_channel_Q  = Optional("PhysicalQuadratureChannel", reverse="Q_channel")
-        marker_channel  = Optional("PhysicalMarkerChannel")
+        # quad_channel_I  = Optional("PhysicalQuadratureChannel", reverse="I_channel")
+        # quad_channel_Q  = Optional("PhysicalQuadratureChannel", reverse="Q_channel")
+        # marker_channel  = Optional("PhysicalMarkerChannel")
 
     class LogicalChannel(Channel):
         '''
@@ -108,14 +108,14 @@ class PhysicalMarkerChannel(PhysicalChannel):
         '''
         gate_buffer    = Required(float, default=0.0)
         gate_min_width = Required(float, default=0.0)
-        phys_channel   = Optional(PhysicalChannel)
+        # phys_channel   = Optional(PhysicalChannel)
 
     class PhysicalQuadratureChannel(PhysicalChannel):
         '''
         Something used to implement a standard qubit channel with two analog channels and a microwave gating channel.
         '''
-        I_channel  = Optional(PhysicalChannel)
-        Q_channel  = Optional(PhysicalChannel)
+        # I_channel  = Optional(PhysicalChannel)
+        # Q_channel  = Optional(PhysicalChannel)
         amp_factor = Required(float, default=1.0)
         phase_skew = Required(float, default=0.0)
     #     marker_channel = Optional(PhysicalMarkerChannel)

From 7f02f9f12816b2f8af334eaa3f23994090c71df9 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Mon, 11 Jun 2018 21:27:38 -0400
Subject: [PATCH 042/235] ChannelLibrary can now close and reopen db
 connections on instantiation

---
 QGL/ChannelLibraries.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index afd109cc..c7a4eca2 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -113,6 +113,10 @@ class ChannelLibrary(object):
     def __init__(self, channel_db_name=None, database_file=None, channelDict={}, **kwargs):
         """Create the channel library."""
 
+        global channelLib
+        if channelLib is not None:
+            channelLib.db.disconnect()
+
         config.load_db()
         if database_file:
             self.database_file = database_file
@@ -121,10 +125,10 @@ def __init__(self, channel_db_name=None, database_file=None, channelDict={}, **k
         else:
             self.database_file = ":memory:"
 
-        db = Database()
-        Channels.define_entities(db)
-        db.bind('sqlite', filename=self.database_file, create_db=True)
-        db.generate_mapping(create_tables=True)
+        self.db = Database()
+        Channels.define_entities(self.db)
+        self.db.bind('sqlite', filename=self.database_file, create_db=True)
+        self.db.generate_mapping(create_tables=True)
 
         # Dirty trick: push the correct entity defs to the calling context
         for var in ["Measurement","Qubit","Edge"]:
@@ -145,7 +149,6 @@ def __init__(self, channel_db_name=None, database_file=None, channelDict={}, **k
         # config.load_config()
 
         # Update the global reference
-        global channelLib
         channelLib = self
 
     def get_current_channels(self):

From 72d5c0bf982f811e28c572c849fe279f48ccfe44 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Jun 2018 14:14:48 -0400
Subject: [PATCH 043/235] Fixed copying and relinking

---
 QGL/ChannelLibraries.py | 150 +++++++++++++++++++---------------------
 QGL/Channels.py         |   4 +-
 QGL/config.py           |   6 +-
 3 files changed, 77 insertions(+), 83 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index c7a4eca2..ee0ce764 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -57,60 +57,76 @@ def set_from_dict(obj, settings):
 def copy_objs(chans, srcs, new_channel_db):
     new_chans       = []
     new_srcs        = []
-    old_to_new_chan = {}
-    old_to_new_src  = {}
+    old_to_new      = {}
+    links_to_change = {}
+    # old_to_new_chan = {}
+    # old_to_new_src  = {}
 
     for chan in chans:
-        c = copy_entity(chan, new_channel_db)
+        c, links = copy_entity(chan, new_channel_db)
         new_chans.append(c)
-        old_to_new_chan[chan] = c
+        links_to_change[c] = links
+        #old_to_new[(c.id, c.label)] = c
+        old_to_new[c.label] = c
 
     for src in srcs:
-        c = copy_entity(src, new_channel_db)
+        c, links = copy_entity(src, new_channel_db)
         new_srcs.append(c)
-        old_to_new_src[src] = c
-
-    # Fix links... pony updates the relationships symmetriacally so we get some for free
-    for thing in new_chans + new_srcs:
-        for attr in thing._attrs_:
-            if attr:
-                if isinstance(getattr(thing, attr.name), Channels.Channel):
-                    if getattr(thing, attr.name) in old_to_new_chan.keys():
-                        setattr(thing, attr.name, old_to_new_chan[getattr(thing, attr.name)])
-                elif isinstance(getattr(thing, attr.name), Channels.MicrowaveSource):
-                    if getattr(thing, attr.name) in old_to_new_src.keys():
-                        setattr(thing, attr.name, old_to_new_src[getattr(thing, attr.name)])
+        links_to_change[c] = links
+        #old_to_new[(c.id, c.label)] = c
+        old_to_new[c.label] = c
+
+    for chan, link_info in links_to_change.items():
+        print(f"Updating links for {chan}")
+        for attr_name, link_name in link_info.items():
+            # link is an (id, label) tuple
+            new = old_to_new[link_name]
+            print(f"\tSetting {attr_name} for {link_name} to {new}")
+            setattr(chan, attr_name, new)
+
+    # # Fix links... pony updates the relationships symmetrically so we get some for free
+    # for thing in new_chans + new_srcs:
+    #     # print(f"Relinking {thing}")
+    #     for attr in thing._attrs_:
+    #         obj = getattr(thing, attr.name)
+    #         if hasattr(obj, "id"):
+    #             # print(f"\tChecking {attr.name}: {getattr(thing, attr.name)} {getattr(thing, attr.name).id}")
+
+    #             # if isinstance(obj, Channels.Channel) or isinstance(obj, Channels.MicrowaveSource):
+    #             if (obj.id, obj.label) in old_to_new.keys():
+    #                 # print(f"setting {thing} {attr.name} to {old_to_new[(obj.id, obj.label)]} (was {obj})")
+    #                 setattr(thing, attr.name, old_to_new[(obj.id, obj.label)])
+    #         # if isinstance(obj, Channels.Channel):
+    #         #     if obj in old_to_new.keys():
+    #         #         setattr(thing, attr.name, old_to_new[obj])
+    #         # elif isinstance(obj, Channels.MicrowaveSource):
+    #         #     if obj in old_to_new.keys():
+    #         #         setattr(thing, attr.name, old_to_new[obj])
 
     return new_chans, new_srcs
 
 def copy_entity(obj, new_channel_db):
     """Copy a pony entity instance"""
-    kwargs = {a.name: getattr(obj, a.name) for a in obj.__class__._attrs_ if a.name not in ["id", "classtype", "pulse_params"]}
-    # if "pulse_params" in kwargs.keys():
-    #     kwargs["pulse_params"] = dict(kwargs["pulse_params"])
+    kwargs = {a.name: getattr(obj, a.name) for a in obj._attrs_ if a.name not in ["id", "classtype"]}
+
+    # Extract any links to other entities
+    links = {}
+    print(f"Copying {obj}")
+    for attr in obj._attrs_:
+        if attr.name not in ["channel_db"]:
+            obj_attr = getattr(obj, attr.name)
+            # print(f"\tChecking out {attr.name}")
+            if hasattr(obj_attr, "id"):
+                kwargs.pop(attr.name)
+                print(f"\tWill relink {attr.name} to {(obj_attr.id, obj_attr.label)}")
+                links[attr.name] = obj_attr.label #(obj_attr.id, obj_attr.label)
+
     kwargs["channel_db"] = new_channel_db
-    return obj.__class__(**kwargs)
-
-# def copy_entity(obj, new_channel_db):
-#     """Copy a pony entity instance"""
-#     attr_names = [a.name for a in obj.__class__._attrs_]
-#     skip = ["id", "classtype", "channel_db"]
-#     print(obj)
-#     kwargs = {"channel_db": new_channel_db}
-#     for a in attr_names: #["label", "source_type"]:
-#         print("\t", a)
-#         if a in dir(obj):
-#             val = getattr(obj, a)
-#             if a == "pulse_params":
-#                 val = dict(val)
-#             if val is not None and a not in skip:
-#                 print("\t\t", getattr(obj, a))
-#                 kwargs[a] = val
-#     return obj.__class__(**kwargs)
+    return obj.__class__(**kwargs), links
 
 class ChannelLibrary(object):
 
-    def __init__(self, channel_db_name=None, database_file=None, channelDict={}, **kwargs):
+    def __init__(self, database_file=None, channelDict={}, **kwargs):
         """Create the channel library."""
 
         global channelLib
@@ -140,8 +156,17 @@ def __init__(self, channel_db_name=None, database_file=None, channelDict={}, **k
         self.channelDict = {}
         self.channels = []
         self.sources = []
+
+        # Check to see whether there is already a temp database
+        # if "__temp__" in select(c.label for c in Channels.ChannelDatabase):
+        #     for cdb in select(cdb for cdb in Channels.ChannelDatabase if cdb.label == "__temp__"):
+        #         cdb.channels.clear()
+        #         cdb.sources.clear()
+        #         select(c for c in Channels.Channel if c.channel_db.label is None).delete(bulk=True)
+        #         select(c for c in Channels.MicrowaveSource if c.channel_db.label is None).delete(bulk=True)
+                # select(c for c in Channels.ChannelDatabase if c.label=="__temp__").delete()
+
         self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
-        self.channel_db_name = channel_db_name if channel_db_name else "temp"
 
         config.load_config()
 
@@ -152,7 +177,7 @@ def __init__(self, channel_db_name=None, database_file=None, channelDict={}, **k
         channelLib = self
 
     def get_current_channels(self):
-        return list(select(c for c in Channels.Channel if c.channel_db is None)) + list(select(c for c in Channels.MicrowaveSource if c.channel_db is None))
+        return list(select(c for c in Channels.Channel if c.channel_db == self.channelDatabase)) + list(select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase))
 
     def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
@@ -175,57 +200,26 @@ def load(self, obj): #, delete=True):
         chans = list(obj.channels)
         srcs  = list(obj.sources)
 
-        # self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
         new_chans, new_srcs = copy_objs(chans, srcs, self.channelDatabase)
 
         self.channels = new_chans
         self.sources = new_srcs
         self.channel_db_name = obj.label
-        # self.channelDatabase = None
-
-    # def load_most_recent(self, name=None):
-    #     if name is None:
-    #         name = self.channel_db_name
-    #     mrcd = Channels.ChannelDatabase.select(lambda d: d.label==name).order_by(desc(Channels.ChannelDatabase.time)).first()
-    #     if mrcd:
-    #         self.load(mrcd)
-
-    # def new(self, name):
-    #     # self.channelDatabase.delete()
-    #     self.clear()
-    #     commit()
-
-    #     # self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
-
-    #     # self.channelDatabase = None
-    #     self.channel_db_name = name
-    #     self.channels = []
-    #     self.sources = []
 
     def save(self):
         self.save_as(self.channel_db_name)
 
     def save_as(self, name):
-        # self.channelDatabase.label = name
-        # self.channelDatabase.time  = datetime.datetime.now()
-        # cd = self.channelDatabase
-        # self.channelDatabase = None
-        # commit()
-        # self.load(cd, delete=False)
-        
-        # Get channels that are part of the currently active db
-        # chans = list(select(c for c in Channels.Channel if c.channel_db is None))
-        # srcs  = list(select(c for c in Channels.MicrowaveSource if c.channel_db is None))
         chans = list(self.channelDatabase.channels)
         srcs  = list(self.channelDatabase.sources)
-        cd    = Channels.ChannelDatabase(label=name, time=datetime.datetime.now(), channels=chans, sources=srcs)
-        new_chans, new_srcs = copy_objs(chans, srcs, cd)
+        commit()
 
-        # self.channels = new_chans
-        # self.sources = new_srcs
-        # self.channelDatabase = None
+        cd = Channels.ChannelDatabase(label=name, time=datetime.datetime.now())
+        new_chans, new_srcs = copy_objs(chans, srcs, cd)
+        cd.channels = new_chans
+        cd.sources  = new_srcs
         commit()
-        # self.channel_db_name = name
+        
 
     #Dictionary methods
     def __getitem__(self, key):
diff --git a/QGL/Channels.py b/QGL/Channels.py
index bf50ca71..f503bd69 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -57,14 +57,14 @@ class MicrowaveSource(db.Entity):
         address         = Optional(str)
         power           = Optional(float)
         logical_channel = Optional("PhysicalChannel")
-        channel_db      = Required("ChannelDatabase")
+        channel_db      = Optional("ChannelDatabase")
 
     class Channel(db.Entity):
         '''
         Every channel has a label and some printers.
         '''
         label      = Required(str)
-        channel_db = Required("ChannelDatabase")
+        channel_db = Optional("ChannelDatabase")
 
         def __repr__(self):
             return str(self)
diff --git a/QGL/config.py b/QGL/config.py
index 085c48d8..eaeb6322 100644
--- a/QGL/config.py
+++ b/QGL/config.py
@@ -27,13 +27,13 @@
 
 def load_config():
     global config_file
-    if os.getenv('BBN_CONFIG_FILE'):
+    if os.getenv('BBN_CONFIG'):
         try:
-            config_file = os.getenv("BBN_CONFIG_FILE")
+            config_file = os.getenv("BBN_CONFIG")
             sys.path.append(os.path.dirname(config_file))
             importlib.import_module(os.path.splitext(os.path.basename(config_file))[0])
         except:
-            raise Exception(f"Could not import/execute the BBN_CONFIG_FILE {cfg}")
+            raise Exception(f"Could not import/execute the BBN_CONFIG {os.getenv('BBN_CONFIG')}")
             
 def load_db():
     global db_file

From 02f777ab2705cdbe47715822248cef2e04537aaf Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Jun 2018 15:50:47 -0400
Subject: [PATCH 044/235] Deletion working more reliably

---
 QGL/ChannelLibraries.py | 71 ++++++++++++++++++++---------------------
 1 file changed, 35 insertions(+), 36 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index ee0ce764..f981f7f1 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -77,11 +77,11 @@ def copy_objs(chans, srcs, new_channel_db):
         old_to_new[c.label] = c
 
     for chan, link_info in links_to_change.items():
-        print(f"Updating links for {chan}")
+        # print(f"Updating links for {chan}")
         for attr_name, link_name in link_info.items():
             # link is an (id, label) tuple
             new = old_to_new[link_name]
-            print(f"\tSetting {attr_name} for {link_name} to {new}")
+            # print(f"\tSetting {attr_name} for {link_name} to {new}")
             setattr(chan, attr_name, new)
 
     # # Fix links... pony updates the relationships symmetrically so we get some for free
@@ -111,14 +111,14 @@ def copy_entity(obj, new_channel_db):
 
     # Extract any links to other entities
     links = {}
-    print(f"Copying {obj}")
+    # print(f"Copying {obj}")
     for attr in obj._attrs_:
         if attr.name not in ["channel_db"]:
             obj_attr = getattr(obj, attr.name)
             # print(f"\tChecking out {attr.name}")
             if hasattr(obj_attr, "id"):
                 kwargs.pop(attr.name)
-                print(f"\tWill relink {attr.name} to {(obj_attr.id, obj_attr.label)}")
+                # print(f"\tWill relink {attr.name} to {(obj_attr.id, obj_attr.label)}")
                 links[attr.name] = obj_attr.label #(obj_attr.id, obj_attr.label)
 
     kwargs["channel_db"] = new_channel_db
@@ -154,30 +154,22 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
         
         # This is still somewhere legacy QGL behavior. Massage db into dict for lookup.
         self.channelDict = {}
-        self.channels = []
-        self.sources = []
 
-        # Check to see whether there is already a temp database
-        # if "__temp__" in select(c.label for c in Channels.ChannelDatabase):
-        #     for cdb in select(cdb for cdb in Channels.ChannelDatabase if cdb.label == "__temp__"):
-        #         cdb.channels.clear()
-        #         cdb.sources.clear()
-        #         select(c for c in Channels.Channel if c.channel_db.label is None).delete(bulk=True)
-        #         select(c for c in Channels.MicrowaveSource if c.channel_db.label is None).delete(bulk=True)
-                # select(c for c in Channels.ChannelDatabase if c.label=="__temp__").delete()
-
-        self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
+        Check to see whether there is already a temp database
+        if "__temp__" in select(c.label for c in Channels.ChannelDatabase):
+            self.channelDatabase = select(c.label for c in Channels.ChannelDatabase).first()
+            self.clear()
+        else:
+            self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
 
         config.load_config()
-
-        # self.load_most_recent()
-        # config.load_config()
-
+        
         # Update the global reference
         channelLib = self
 
     def get_current_channels(self):
-        return list(select(c for c in Channels.Channel if c.channel_db == self.channelDatabase)) + list(select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase))
+        return list(self.channelDatabase.channels) + list(self.channelDatabase.sources)
+        # return list(select(c for c in Channels.Channel if c.channel_db == self.channelDatabase)) + list(select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase))
 
     def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
@@ -190,9 +182,14 @@ def load_by_id(self, id_num):
         self.load(obj)
 
     def clear(self):
-        select(c for c in Channels.Channel if c.channel_db == self.channelDatabase).delete(bulk=True)
         select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase).delete(bulk=True)
+        select(c for c in Channels.Channel if c.channel_db == self.channelDatabase).delete(bulk=True)
+        
         self.channelDatabase.time  = datetime.datetime.now()
+        commit()
+        # select(c for c in Channels.Channel if c.channel_db == self.channelDatabase).delete(bulk=True)
+        # select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase).delete(bulk=True)
+        # self.channelDatabase.time  = datetime.datetime.now()
 
     def load(self, obj): #, delete=True):
         self.clear()
@@ -202,12 +199,12 @@ def load(self, obj): #, delete=True):
 
         new_chans, new_srcs = copy_objs(chans, srcs, self.channelDatabase)
 
-        self.channels = new_chans
-        self.sources = new_srcs
-        self.channel_db_name = obj.label
 
-    def save(self):
-        self.save_as(self.channel_db_name)
+        # self.channelDatabase.label = obj.label
+        # self.channel_db_name = obj.label
+
+    # def save(self):
+    #     self.save_as(self.channel_db_name)
 
     def save_as(self, name):
         chans = list(self.channelDatabase.channels)
@@ -487,19 +484,21 @@ def set_control(qubit, awg, generator=None):
     
 def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=1, gate=False, gate_channel=2, trigger_length=1e-7):
     meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=channelLib.channelDatabase)
+    if generator:
+        awg.chan12.generator = generator
     meas.phys_chan     = awg.chan12
     
-    meas.trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}", channel_db=channelLib.channelDatabase)
-    meas.trig_chan.phys_chan    = getattr(awg, f"m{trig_channel}")
-    meas.trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
-    meas.receiver_chan          = getattr(dig, f"chan{dig_channel}")
-
-    if generator:
-        meas.phys_chan.generator = generator
+    trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}", channel_db=channelLib.channelDatabase)
+    trig_chan.phys_chan    = getattr(awg, f"m{trig_channel}")
+    trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
+    meas.trig_chan         = trig_chan
+    
+    meas.receiver_chan     = getattr(dig, f"chan{dig_channel}")
 
     if gate:
-        meas.gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=channelLib.channelDatabase)
-        meas.gate_chan.phys_chan = getattr(awg, f"m{gate_channel}")
+        gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=channelLib.channelDatabase)
+        gate_chan.phys_chan = getattr(awg, f"m{gate_channel}")
+        meas.gate_chan      = gate_chan
         
 def set_master(awg, trig_channel=2, pulse_length=1e-7):
     st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=channelLib.channelDatabase)

From a3506715975b418c26dbfbc4e0b5da38aaa84214 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Jun 2018 16:26:44 -0400
Subject: [PATCH 045/235] Fix initial loading

---
 QGL/ChannelLibraries.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index f981f7f1..fbfe589d 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -155,15 +155,15 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
         # This is still somewhere legacy QGL behavior. Massage db into dict for lookup.
         self.channelDict = {}
 
-        Check to see whether there is already a temp database
+        # Check to see whether there is already a temp database
         if "__temp__" in select(c.label for c in Channels.ChannelDatabase):
-            self.channelDatabase = select(c.label for c in Channels.ChannelDatabase).first()
+            self.channelDatabase = select(c for c in Channels.ChannelDatabase if c.label == "__temp__").first()
             self.clear()
         else:
             self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
 
         config.load_config()
-        
+
         # Update the global reference
         channelLib = self
 

From 5ccb57e3c27668e90f48e4a0f79461264d1c06fc Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Jun 2018 16:54:39 -0400
Subject: [PATCH 046/235] Fixed deletion of additional temporary channel dbs

---
 QGL/ChannelLibraries.py | 58 +++++------------------------------------
 1 file changed, 7 insertions(+), 51 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index fbfe589d..deba7f20 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -59,50 +59,24 @@ def copy_objs(chans, srcs, new_channel_db):
     new_srcs        = []
     old_to_new      = {}
     links_to_change = {}
-    # old_to_new_chan = {}
-    # old_to_new_src  = {}
 
     for chan in chans:
         c, links = copy_entity(chan, new_channel_db)
         new_chans.append(c)
         links_to_change[c] = links
-        #old_to_new[(c.id, c.label)] = c
         old_to_new[c.label] = c
 
     for src in srcs:
         c, links = copy_entity(src, new_channel_db)
         new_srcs.append(c)
         links_to_change[c] = links
-        #old_to_new[(c.id, c.label)] = c
         old_to_new[c.label] = c
 
     for chan, link_info in links_to_change.items():
-        # print(f"Updating links for {chan}")
         for attr_name, link_name in link_info.items():
-            # link is an (id, label) tuple
             new = old_to_new[link_name]
-            # print(f"\tSetting {attr_name} for {link_name} to {new}")
             setattr(chan, attr_name, new)
 
-    # # Fix links... pony updates the relationships symmetrically so we get some for free
-    # for thing in new_chans + new_srcs:
-    #     # print(f"Relinking {thing}")
-    #     for attr in thing._attrs_:
-    #         obj = getattr(thing, attr.name)
-    #         if hasattr(obj, "id"):
-    #             # print(f"\tChecking {attr.name}: {getattr(thing, attr.name)} {getattr(thing, attr.name).id}")
-
-    #             # if isinstance(obj, Channels.Channel) or isinstance(obj, Channels.MicrowaveSource):
-    #             if (obj.id, obj.label) in old_to_new.keys():
-    #                 # print(f"setting {thing} {attr.name} to {old_to_new[(obj.id, obj.label)]} (was {obj})")
-    #                 setattr(thing, attr.name, old_to_new[(obj.id, obj.label)])
-    #         # if isinstance(obj, Channels.Channel):
-    #         #     if obj in old_to_new.keys():
-    #         #         setattr(thing, attr.name, old_to_new[obj])
-    #         # elif isinstance(obj, Channels.MicrowaveSource):
-    #         #     if obj in old_to_new.keys():
-    #         #         setattr(thing, attr.name, old_to_new[obj])
-
     return new_chans, new_srcs
 
 def copy_entity(obj, new_channel_db):
@@ -111,15 +85,12 @@ def copy_entity(obj, new_channel_db):
 
     # Extract any links to other entities
     links = {}
-    # print(f"Copying {obj}")
     for attr in obj._attrs_:
         if attr.name not in ["channel_db"]:
             obj_attr = getattr(obj, attr.name)
-            # print(f"\tChecking out {attr.name}")
             if hasattr(obj_attr, "id"):
                 kwargs.pop(attr.name)
-                # print(f"\tWill relink {attr.name} to {(obj_attr.id, obj_attr.label)}")
-                links[attr.name] = obj_attr.label #(obj_attr.id, obj_attr.label)
+                links[attr.name] = obj_attr.label 
 
     kwargs["channel_db"] = new_channel_db
     return obj.__class__(**kwargs), links
@@ -157,10 +128,8 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
 
         # Check to see whether there is already a temp database
         if "__temp__" in select(c.label for c in Channels.ChannelDatabase):
-            self.channelDatabase = select(c for c in Channels.ChannelDatabase if c.label == "__temp__").first()
-            self.clear()
-        else:
-            self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
+            select(d for d in Channels.ChannelDatabase if d.label == "__temp__").delete(bulk=True)
+        self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
 
         config.load_config()
 
@@ -169,7 +138,6 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
 
     def get_current_channels(self):
         return list(self.channelDatabase.channels) + list(self.channelDatabase.sources)
-        # return list(select(c for c in Channels.Channel if c.channel_db == self.channelDatabase)) + list(select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase))
 
     def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
@@ -184,40 +152,28 @@ def load_by_id(self, id_num):
     def clear(self):
         select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase).delete(bulk=True)
         select(c for c in Channels.Channel if c.channel_db == self.channelDatabase).delete(bulk=True)
-        
         self.channelDatabase.time  = datetime.datetime.now()
         commit()
-        # select(c for c in Channels.Channel if c.channel_db == self.channelDatabase).delete(bulk=True)
-        # select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase).delete(bulk=True)
-        # self.channelDatabase.time  = datetime.datetime.now()
+        select(d for d in Channels.ChannelDatabase if d.label == "__temp__").delete(bulk=True)
+        commit()
+        self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
 
-    def load(self, obj): #, delete=True):
+    def load(self, obj):
         self.clear()
-
         chans = list(obj.channels)
         srcs  = list(obj.sources)
-
         new_chans, new_srcs = copy_objs(chans, srcs, self.channelDatabase)
 
-
-        # self.channelDatabase.label = obj.label
-        # self.channel_db_name = obj.label
-
-    # def save(self):
-    #     self.save_as(self.channel_db_name)
-
     def save_as(self, name):
         chans = list(self.channelDatabase.channels)
         srcs  = list(self.channelDatabase.sources)
         commit()
-
         cd = Channels.ChannelDatabase(label=name, time=datetime.datetime.now())
         new_chans, new_srcs = copy_objs(chans, srcs, cd)
         cd.channels = new_chans
         cd.sources  = new_srcs
         commit()
         
-
     #Dictionary methods
     def __getitem__(self, key):
         return self.channelDict[key]

From 45e37a97305b5f63acc1dc630d46b3cb4d6088e4 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 13 Jun 2018 10:09:29 -0400
Subject: [PATCH 047/235] Clean up loading and purging temp channel dbs

---
 QGL/ChannelLibraries.py | 41 +++++++++++++++++++++++++++++++++++------
 QGL/PulseSequencer.py   |  7 +++++++
 2 files changed, 42 insertions(+), 6 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index deba7f20..b24533f9 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -97,7 +97,7 @@ def copy_entity(obj, new_channel_db):
 
 class ChannelLibrary(object):
 
-    def __init__(self, database_file=None, channelDict={}, **kwargs):
+    def __init__(self, database_file=None, channelDict={}, auto_update=True, **kwargs):
         """Create the channel library."""
 
         global channelLib
@@ -128,11 +128,22 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
 
         # Check to see whether there is already a temp database
         if "__temp__" in select(c.label for c in Channels.ChannelDatabase):
-            select(d for d in Channels.ChannelDatabase if d.label == "__temp__").delete(bulk=True)
+            for cdb in select(d for d in Channels.ChannelDatabase if d.label == "__temp__"):
+                print("Trying to clear", cdb.label)
+                select(c for c in Channels.MicrowaveSource if c.channel_db == cdb).delete(bulk=True)
+                select(c for c in Channels.Channel if c.channel_db == cdb).delete(bulk=True)
+                commit()
+                select(d for d in Channels.ChannelDatabase if d == cdb).delete(bulk=True)
+                commit()
+
         self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
 
         config.load_config()
 
+        # Whether or not we try to keep qubitfactories up to date
+        self.auto_update = auto_update
+        self.blub = {}
+
         # Update the global reference
         channelLib = self
 
@@ -143,11 +154,16 @@ def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
 
     def list(self):
-        select((c.label, c.time, c.id) for c in Channels.ChannelDatabase).show()
+        select((c.label, c.time, c.id) for c in Channels.ChannelDatabase if c.label != "__temp__").sort_by(1, 2).show()
+
+    def load(self, name, index=1):
+        """Load the latest instance for a particular name. Specifying index = 2 will select the second most recent instance """
+        obj = list(select(c for c in Channels.ChannelDatabase if c.label==name).sort_by(desc(Channels.ChannelDatabase.time)))
+        self.load_obj(obj[-index])
 
     def load_by_id(self, id_num):
         obj = select(c for c in Channels.ChannelDatabase if c.id==id_num).first()
-        self.load(obj)
+        self.load_obj(obj)
 
     def clear(self):
         select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase).delete(bulk=True)
@@ -158,12 +174,23 @@ def clear(self):
         commit()
         self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
 
-    def load(self, obj):
+    def load_obj(self, obj):
+        commit()
         self.clear()
         chans = list(obj.channels)
         srcs  = list(obj.sources)
         new_chans, new_srcs = copy_objs(chans, srcs, self.channelDatabase)
 
+        self.update_channelDict()
+
+        # # Try to fix factories
+        if self.auto_update:
+            for k in list(self.blub.keys()):
+                self.blub[k] = self.channelDict[k]
+        #     for k,v in globals().items():
+        #         if isinstance(v, Channels.Qubit):
+        #             globals()[k] = self.channelDict[k]
+
     def save_as(self, name):
         chans = list(self.channelDatabase.channels)
         srcs  = list(self.channelDatabase.sources)
@@ -468,8 +495,10 @@ def QubitFactory(label, **kwargs):
     # TODO: this will just get the first entry in the whole damned DB!
     # thing = select(el for el in Channels.Qubit if el.label==label).first()
     thing = {c.label: c for c in channelLib.get_current_channels()}[label]
+
     if thing:
-        return thing
+        channelLib.blub[label] = thing
+        return channelLib.blub[label]
     else:
         return Channels.Qubit(label=label, **kwargs)
     
diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 7b79d9af..34d1f07f 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -280,7 +280,14 @@ def flatten_to_pulses(obj):
             for pulse in obj.pulses.values():
                 yield from flatten_to_pulses(pulse)
 
+    def rec_length(obj):
+        if hasattr(obj, "length"):
+            return obj.length
+        else:
+            return rec_length(obj[0])
+
     pulse_lengths = np.array([pulse.length for pulse in pulses])
+    # pulse_lengths = np.array([rec_length(pulse) for pulse in pulses])
     pad_lengths = max(pulse_lengths) - pulse_lengths
     pulse_list = []
     for k,pulse in enumerate(pulses):

From b83b0b1af8504af5c7f44078e5a3dd247e2fead1 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 13 Jun 2018 21:02:07 -0400
Subject: [PATCH 048/235] Strip out autoupdate for now

---
 QGL/ChannelLibraries.py | 18 ++----------------
 1 file changed, 2 insertions(+), 16 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index b24533f9..3b37ed05 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -97,7 +97,7 @@ def copy_entity(obj, new_channel_db):
 
 class ChannelLibrary(object):
 
-    def __init__(self, database_file=None, channelDict={}, auto_update=True, **kwargs):
+    def __init__(self, database_file=None, channelDict={}, **kwargs):
         """Create the channel library."""
 
         global channelLib
@@ -140,10 +140,6 @@ def __init__(self, database_file=None, channelDict={}, auto_update=True, **kwarg
 
         config.load_config()
 
-        # Whether or not we try to keep qubitfactories up to date
-        self.auto_update = auto_update
-        self.blub = {}
-
         # Update the global reference
         channelLib = self
 
@@ -183,14 +179,6 @@ def load_obj(self, obj):
 
         self.update_channelDict()
 
-        # # Try to fix factories
-        if self.auto_update:
-            for k in list(self.blub.keys()):
-                self.blub[k] = self.channelDict[k]
-        #     for k,v in globals().items():
-        #         if isinstance(v, Channels.Qubit):
-        #             globals()[k] = self.channelDict[k]
-
     def save_as(self, name):
         chans = list(self.channelDatabase.channels)
         srcs  = list(self.channelDatabase.sources)
@@ -495,10 +483,8 @@ def QubitFactory(label, **kwargs):
     # TODO: this will just get the first entry in the whole damned DB!
     # thing = select(el for el in Channels.Qubit if el.label==label).first()
     thing = {c.label: c for c in channelLib.get_current_channels()}[label]
-
     if thing:
-        channelLib.blub[label] = thing
-        return channelLib.blub[label]
+        return thing
     else:
         return Channels.Qubit(label=label, **kwargs)
     

From 6df5c9ea0d2ec214cb924f5c13a3f03d14cd2b07 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 15 Jun 2018 15:34:19 -0400
Subject: [PATCH 049/235] Starting to add instrument entities to db

---
 QGL/ChannelLibraries.py | 118 +++++++++++++++++++++++++++++-----------
 QGL/Channels.py         |  61 +++++++++++++++++----
 QGL/__init__.py         |   4 +-
 3 files changed, 139 insertions(+), 44 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 3b37ed05..1eeac1d4 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -417,58 +417,112 @@ def load_from_library(self, return_only=False):
 # Convenience functions for generating and linking channels
 # TODO: move these to a shim layer shared by Auspex/QGL
 
-class APS2(object):
-    def __init__(self, label, address=None, delay=0.0):
-        self.chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-        self.m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-        self.m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-        self.m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-        self.m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+# class APS2(object):
+#     def __init__(self, label, address=None, delay=0.0):
+#         self.chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+#         self.m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+#         self.m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+#         self.m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+#         self.m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
         
-        self.trigger_interval = None
-        self.trigger_source   = "External"
-        self.address          = address
-        self.delay            = delay
-        self.master           = False
-
-class X6(object):
-    def __init__(self, label, address=None):
-        self.chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel_db=channelLib.channelDatabase)
-        self.chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel_db=channelLib.channelDatabase)
-        
-        self.address          = address
-        self.reference        = "external"
-        self.nbr_segments     = 1
-        self.nbr_round_robins = 100
-        self.acquire_mode     = "digitizer"
+#         self.trigger_interval = None
+#         self.trigger_source   = "External"
+#         self.address          = address
+#         self.delay            = delay
+#         self.master           = False
+
+def new_APS2(label, address):
+    chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="new_APS2Pattern", channel_db=channelLib.channelDatabase)
+    m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+    m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+    m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+    m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
+    
+    this_awg = Channels.AWG(label=label, address=address, channels=[chan12, m1, m2, m3, m4])
+    this_awg.trigger_source = "External"
+    this_awg.address        = address
+
+    commit()
+    return this_awg
+
+def new_X6(label, address):
+    chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel_db=channelLib.channelDatabase)
+    chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel_db=channelLib.channelDatabase)
+    
+    this_dig = Channels.Digitizer(label=label, address=address, channels=[chan1, chan2])
+    this_dig.trigger_source = "External"
+    this_dig.address        = address
+
+    commit()
+    return this_dig
 
 def new_qubit(label):
-    return Channels.Qubit(label=label, channel_db=channelLib.channelDatabase)
+    thing = Channels.Qubit(label=label, channel_db=channelLib.channelDatabase)
+    return thing
 
 def new_source(label, source_type, address, power=-30.0):
-    return Channels.MicrowaveSource(label=label, source_type=source_type, address=address, power=power, channel_db=channelLib.channelDatabase)
+    thing = Channels.MicrowaveSource(label=label, source_type=source_type, address=address, power=power, channel_db=channelLib.channelDatabase)
+    return thing
 
 def set_control(qubit, awg, generator=None):
-    qubit.phys_chan = awg.chan12
+    quads   = [c for c in awg.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
+    markers = [c for c in awg.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
+
+    if isinstance(awg, Channels.AWG) and len(quads) > 1:
+        raise ValueError("In set_control the AWG must have a single quadrature channel or a specific channel must be passed instead")
+    elif isinstance(awg, Channels.AWG) and len(quads) == 1:
+        phys_chan = quads[0]
+    elif isinstance(awg, Channels.PhysicalQuadratureChannel):
+        phys_chan = awg
+    else:
+        raise ValueError("In set_control the AWG must have a single quadrature channel or a specific channel must be passed instead")
+
+    qubit.phys_chan = phys_chan
     if generator:
         qubit.phys_chan.generator = generator
     
-def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=1, gate=False, gate_channel=2, trigger_length=1e-7):
+def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
+    print(qubit, awg, dig)
+
+    quads   = [c for c in awg.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
+    markers = [c for c in awg.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
+
+    if isinstance(awg, Channels.AWG) and len(quads) > 1:
+        raise ValueError("In set_measure the AWG must have a single quadrature channel or a specific channel must be passed instead")
+    elif isinstance(awg, Channels.AWG) and len(quads) == 1:
+        phys_chan = quads[0]
+    elif isinstance(awg, Channels.PhysicalQuadratureChannel):
+        phys_chan = awg
+    else:
+        raise ValueError("In set_measure the AWG must have a single quadrature channel or a specific channel must be passed instead")
+
     meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=channelLib.channelDatabase)
+    meas.phys_chan = phys_chan
     if generator:
-        awg.chan12.generator = generator
-    meas.phys_chan     = awg.chan12
+        meas.phys_chan.generator = generator
     
+    phys_trig_channel = trig_channel if trig_channel else awg.get_chan("12m1")
+
     trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}", channel_db=channelLib.channelDatabase)
-    trig_chan.phys_chan    = getattr(awg, f"m{trig_channel}")
+    trig_chan.phys_chan    = phys_trig_channel
     trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
     meas.trig_chan         = trig_chan
     
-    meas.receiver_chan     = getattr(dig, f"chan{dig_channel}")
+    if isinstance(dig, Channels.Digitizer) and len(dig.channels) > 1:
+        raise ValueError("In set_measure the Digitizer must have a single receiver channel or a specific channel must be passed instead")
+    elif isinstance(dig, Channels.Digitizer) and len(dig.channels) == 1:
+        rcv_chan = dig.channels[0]
+    elif isinstance(dig, Channels.ReceiverChannel):
+        rcv_chan = dig
+    else:
+        raise ValueError("In set_measure the AWG must have a single quadrature channel or a specific channel must be passed instead")
+
+    meas.receiver_chan = rcv_chan
 
     if gate:
+        phys_gate_channel   = gate_channel if gate_channel else awg.get_chan("12m2")
         gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=channelLib.channelDatabase)
-        gate_chan.phys_chan = getattr(awg, f"m{gate_channel}")
+        gate_chan.phys_chan = phys_gate_channel
         meas.gate_chan      = gate_chan
         
 def set_master(awg, trig_channel=2, pulse_length=1e-7):
diff --git a/QGL/Channels.py b/QGL/Channels.py
index f503bd69..64fe2910 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -42,14 +42,18 @@
 Edge = None
 MicrowaveSource = None
 ChannelDatabase = None
+Digitizer = None
+AWG = None
 
 def define_entities(db):
 
     class ChannelDatabase(db.Entity):
-        label    = Required(str)
-        channels = Set("Channel", cascade_delete=True)
-        sources  = Set("MicrowaveSource", cascade_delete=True)
-        time     = Optional(datetime.datetime)
+        label      = Required(str)
+        channels   = Set("Channel", cascade_delete=True)
+        sources    = Set("MicrowaveSource", cascade_delete=True)
+        awgs       = Set("AWG", cascade_delete=True)
+        digitizers = Set("Digitizer", cascade_delete=True)
+        time       = Optional(datetime.datetime)
 
     class MicrowaveSource(db.Entity):
         label           = Required(str)
@@ -59,6 +63,33 @@ class MicrowaveSource(db.Entity):
         logical_channel = Optional("PhysicalChannel")
         channel_db      = Optional("ChannelDatabase")
 
+    class Digitizer(db.Entity):
+        label           = Required(str)
+        address         = Optional(str)
+        # stream_types    = Set(str)
+        channels        = Set("ReceiverChannel")
+        trigger_source  = Required(str, default="External", py_check=lambda x: x in ['External', 'Internal'])
+        channel_db      = Optional("ChannelDatabase")
+        # nbr_segments     = Required(int, default=1) # This should be automatic
+        # nbr_round_robins = Required(int, default=100) # This should be automatic
+        # acquire_mode     = Required(str,default="digitizer", py_check=lambda x: x in ['digitizer', 'averager'])
+        
+        def get_chan(self, name):
+            return self.channels.select(lambda x: x.label.endswith(name)).first()
+
+    class AWG(db.Entity):
+        label            = Required(str)
+        address          = Optional(str)
+        channels         = Set("PhysicalChannel", reverse="awg")
+        trigger_interval = Required(float, default=100e-6)
+        trigger_source   = Required(str, default="External", py_check=lambda x: x in ['External', 'Internal'])
+        delay            = Required(float, default=0.0)
+        master           = Required(bool, default=False)
+        channel_db       = Optional("ChannelDatabase")
+
+        def get_chan(self, name):
+            return self.channels.select(lambda x: x.label.endswith(name)).first()
+
     class Channel(db.Entity):
         '''
         Every channel has a label and some printers.
@@ -86,6 +117,7 @@ class PhysicalChannel(Channel):
         # quad_channel_I  = Optional("PhysicalQuadratureChannel", reverse="I_channel")
         # quad_channel_Q  = Optional("PhysicalQuadratureChannel", reverse="Q_channel")
         # marker_channel  = Optional("PhysicalMarkerChannel")
+        awg             = Optional(AWG)
 
     class LogicalChannel(Channel):
         '''
@@ -114,11 +146,12 @@ class PhysicalQuadratureChannel(PhysicalChannel):
         '''
         Something used to implement a standard qubit channel with two analog channels and a microwave gating channel.
         '''
-        # I_channel  = Optional(PhysicalChannel)
-        # Q_channel  = Optional(PhysicalChannel)
-        amp_factor = Required(float, default=1.0)
-        phase_skew = Required(float, default=0.0)
-    #     marker_channel = Optional(PhysicalMarkerChannel)
+        amp_factor           = Required(float, default=1.0)
+        phase_skew           = Required(float, default=0.0)
+        I_channel_offset     = Required(float, default=0.0)
+        Q_channel_offset     = Required(float, default=0.0)
+        I_channel_amp_factor = Required(float, default=1.0)
+        Q_channel_amp_factor = Required(float, default=1.0)
 
     class ReceiverChannel(PhysicalChannel):
         '''
@@ -126,6 +159,13 @@ class ReceiverChannel(PhysicalChannel):
         '''
         triggering_channel = Optional(LogicalChannel)
         channel            = Optional(int)
+        stream_type        = Required(str, default="Raw", py_check=lambda x: x.lower() in["raw", "demodulated", "integrated", "averaged"])
+        if_freq            = Required(float, default=0.0)
+        kernel             = Optional(str)
+        kernel_bias        = Required(float, default=0.0)
+        threshold          = Required(float, default=0.0)
+        threshold_invert   = Required(bool, default=False)
+        digitizer          = Optional(Digitizer)
 
     def pulse_check(name):
         return name in ["constant", "gaussian", "drag", "gaussOn", "gaussOff", "dragGaussOn", "dragGaussOff",
@@ -220,4 +260,5 @@ def __init__(self, **kwargs):
     globals()["Edge"] = Edge
     globals()["MicrowaveSource"] = MicrowaveSource
     globals()["ChannelDatabase"] = ChannelDatabase
-    
\ No newline at end of file
+    globals()["Digitizer"] = Digitizer
+    globals()["AWG"] = AWG
\ No newline at end of file
diff --git a/QGL/__init__.py b/QGL/__init__.py
index e11ea869..eca7769b 100644
--- a/QGL/__init__.py
+++ b/QGL/__init__.py
@@ -1,5 +1,5 @@
-from .Channels import Qubit, Measurement, Edge, MicrowaveSource, ChannelDatabase
-from .ChannelLibraries import QubitFactory, MeasFactory, EdgeFactory, MarkerFactory, ChannelLibrary, channelLib, APS2, X6, new_qubit, set_control, set_measure, set_master, new_source
+from .Channels import Qubit, Measurement, Edge, MicrowaveSource, ChannelDatabase, AWG, Digitizer
+from .ChannelLibraries import QubitFactory, MeasFactory, EdgeFactory, MarkerFactory, ChannelLibrary, channelLib, new_APS2, new_X6, new_qubit, set_control, set_measure, set_master, new_source
 from .PulsePrimitives import *
 from .Compiler import compile_to_hardware, set_log_level
 from .PulseSequencer import align

From e1c99acb94085476538bf9709eb6c9ecf97063f6 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 20 Jun 2018 06:19:42 -0400
Subject: [PATCH 050/235] Tweaks to clearing, convenience functions, etc.

---
 QGL/ChannelLibraries.py | 148 +++++++++++++++++++++++-----------------
 QGL/Channels.py         |  20 ++++++
 2 files changed, 105 insertions(+), 63 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 1eeac1d4..55e9be21 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -54,30 +54,30 @@ def set_from_dict(obj, settings):
             except Exception as e:
                 print(f"{obj.label}: Error loading {prop_name} from config")
 
-def copy_objs(chans, srcs, new_channel_db):
-    new_chans       = []
-    new_srcs        = []
+def copy_objs(*entities, new_channel_db):
+    # Entities is a list of lists of entities of specific types
+    new_entities    = []
     old_to_new      = {}
     links_to_change = {}
 
-    for chan in chans:
-        c, links = copy_entity(chan, new_channel_db)
-        new_chans.append(c)
-        links_to_change[c] = links
-        old_to_new[c.label] = c
-
-    for src in srcs:
-        c, links = copy_entity(src, new_channel_db)
-        new_srcs.append(c)
-        links_to_change[c] = links
-        old_to_new[c.label] = c
+    for ent in entities:
+        new_ents = []
+        for obj in ent:
+            c, links = copy_entity(obj, new_channel_db)
+            new_ents.append(c)
+            links_to_change[c] = links
+            old_to_new[c.label] = c
+        new_entities.append(new_ents)
 
     for chan, link_info in links_to_change.items():
         for attr_name, link_name in link_info.items():
-            new = old_to_new[link_name]
+            if isinstance(link_name, pony.orm.core.Multiset):
+                new = [old_to_new[ln] for ln in link_name]
+            else:
+                new = old_to_new[link_name]
             setattr(chan, attr_name, new)
 
-    return new_chans, new_srcs
+    return new_entities
 
 def copy_entity(obj, new_channel_db):
     """Copy a pony entity instance"""
@@ -127,16 +127,11 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
         self.channelDict = {}
 
         # Check to see whether there is already a temp database
-        if "__temp__" in select(c.label for c in Channels.ChannelDatabase):
-            for cdb in select(d for d in Channels.ChannelDatabase if d.label == "__temp__"):
-                print("Trying to clear", cdb.label)
-                select(c for c in Channels.MicrowaveSource if c.channel_db == cdb).delete(bulk=True)
-                select(c for c in Channels.Channel if c.channel_db == cdb).delete(bulk=True)
-                commit()
-                select(d for d in Channels.ChannelDatabase if d == cdb).delete(bulk=True)
-                commit()
+        for cdb in select(d for d in Channels.ChannelDatabase if d.label == "__temp__"):
+            self.clear(channel_db=cdb, create_new=False)
 
         self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
+        commit()
 
         config.load_config()
 
@@ -149,9 +144,40 @@ def get_current_channels(self):
     def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
 
-    def list(self):
+    def ls(self):
         select((c.label, c.time, c.id) for c in Channels.ChannelDatabase if c.label != "__temp__").sort_by(1, 2).show()
 
+    def ent_by_type_name(self, name, show=False):
+        q = select(c for c in getattr(Channels,name) if c.label != "__temp__")
+        if show:
+            select(c.label for c in getattr(Channels,name) if c.label != "__temp__").sort_by(1).show()
+        else:
+            return {el.label: el for el in q}
+
+    def dig(self):
+        return self.ent_by_type_name("Digitizer")
+
+    def awg(self):
+        return self.ent_by_type_name("AWG")
+
+    def qubit(self):
+        return self.ent_by_type_name("Qubit")
+
+    def meas(self):
+        return self.ent_by_type_name("Measurement")
+
+    def ls_dig(self):
+        return self.ent_by_type_name("Digitizer", show=True)
+
+    def ls_awg(self):
+        return self.ent_by_type_name("AWG", show=True)
+
+    def ls_qubit(self):
+        return self.ent_by_type_name("Qubit", show=True)
+
+    def ls_meas(self):
+        return self.ent_by_type_name("Measurement", show=True)
+
     def load(self, name, index=1):
         """Load the latest instance for a particular name. Specifying index = 2 will select the second most recent instance """
         obj = list(select(c for c in Channels.ChannelDatabase if c.label==name).sort_by(desc(Channels.ChannelDatabase.time)))
@@ -161,32 +187,36 @@ def load_by_id(self, id_num):
         obj = select(c for c in Channels.ChannelDatabase if c.id==id_num).first()
         self.load_obj(obj)
 
-    def clear(self):
-        select(c for c in Channels.MicrowaveSource if c.channel_db == self.channelDatabase).delete(bulk=True)
-        select(c for c in Channels.Channel if c.channel_db == self.channelDatabase).delete(bulk=True)
-        self.channelDatabase.time  = datetime.datetime.now()
-        commit()
-        select(d for d in Channels.ChannelDatabase if d.label == "__temp__").delete(bulk=True)
-        commit()
-        self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
+    def clear(self, channel_db=None, create_new=True):
+        # If no database is specified, clear self.database
+        channel_db = channel_db if channel_db else self.channelDatabase
+        # First clear items that don't have Sets of other items
+        for ent in [Channels.MicrowaveSource, Channels.Channel, Channels.AWG, Channels.Digitizer]:
+            select(c for c in ent if c.channel_db == channel_db).delete(bulk=True)
+            commit()        
+        # Now clear items that do potentially have sets of items (which should be deleted)
+        for ent in [Channels.ChannelDatabase]:
+            select(d for d in ent if d.label == "__temp__").delete(bulk=True)
+            commit()
+        if create_new:
+            self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
+            commit()
 
     def load_obj(self, obj):
         commit()
         self.clear()
-        chans = list(obj.channels)
-        srcs  = list(obj.sources)
-        new_chans, new_srcs = copy_objs(chans, srcs, self.channelDatabase)
-
+        chans, srcs, awgs, digs = map(list, [obj.channels, obj.sources, obj.awgs, obj.digitizers])
+        copy_objs(chans, srcs, awgs, digs, new_channel_db=self.channelDatabase)
+        commit()
         self.update_channelDict()
 
     def save_as(self, name):
-        chans = list(self.channelDatabase.channels)
-        srcs  = list(self.channelDatabase.sources)
+        chans, srcs, awgs, digs = map(list, [self.channelDatabase.channels, self.channelDatabase.sources,
+                                            self.channelDatabase.awgs, self.channelDatabase.digitizers])
         commit()
         cd = Channels.ChannelDatabase(label=name, time=datetime.datetime.now())
-        new_chans, new_srcs = copy_objs(chans, srcs, cd)
-        cd.channels = new_chans
-        cd.sources  = new_srcs
+        new_chans, new_srcs, new_awgs, new_digs = copy_objs(chans, srcs, awgs, digs, new_channel_db=cd)
+        cd.channels, cd.sources, cd.awgs, cd.digitizers = new_chans, new_srcs, new_awgs, new_digs
         commit()
         
     #Dictionary methods
@@ -417,28 +447,14 @@ def load_from_library(self, return_only=False):
 # Convenience functions for generating and linking channels
 # TODO: move these to a shim layer shared by Auspex/QGL
 
-# class APS2(object):
-#     def __init__(self, label, address=None, delay=0.0):
-#         self.chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-#         self.m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-#         self.m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-#         self.m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-#         self.m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-        
-#         self.trigger_interval = None
-#         self.trigger_source   = "External"
-#         self.address          = address
-#         self.delay            = delay
-#         self.master           = False
-
 def new_APS2(label, address):
-    chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="new_APS2Pattern", channel_db=channelLib.channelDatabase)
+    chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
     m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
     m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
     m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
     m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
     
-    this_awg = Channels.AWG(label=label, address=address, channels=[chan12, m1, m2, m3, m4])
+    this_awg = Channels.AWG(label=label, address=address, channels=[chan12, m1, m2, m3, m4], channel_db=channelLib.channelDatabase)
     this_awg.trigger_source = "External"
     this_awg.address        = address
 
@@ -449,7 +465,7 @@ def new_X6(label, address):
     chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel_db=channelLib.channelDatabase)
     chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel_db=channelLib.channelDatabase)
     
-    this_dig = Channels.Digitizer(label=label, address=address, channels=[chan1, chan2])
+    this_dig = Channels.Digitizer(label=label, address=address, channels=[chan1, chan2], channel_db=channelLib.channelDatabase)
     this_dig.trigger_source = "External"
     this_dig.address        = address
 
@@ -458,10 +474,12 @@ def new_X6(label, address):
 
 def new_qubit(label):
     thing = Channels.Qubit(label=label, channel_db=channelLib.channelDatabase)
+    commit()
     return thing
 
 def new_source(label, source_type, address, power=-30.0):
     thing = Channels.MicrowaveSource(label=label, source_type=source_type, address=address, power=power, channel_db=channelLib.channelDatabase)
+    commit()
     return thing
 
 def set_control(qubit, awg, generator=None):
@@ -480,10 +498,9 @@ def set_control(qubit, awg, generator=None):
     qubit.phys_chan = phys_chan
     if generator:
         qubit.phys_chan.generator = generator
+    commit()
     
 def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
-    print(qubit, awg, dig)
-
     quads   = [c for c in awg.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
     markers = [c for c in awg.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
 
@@ -524,13 +541,18 @@ def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=Non
         gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=channelLib.channelDatabase)
         gate_chan.phys_chan = phys_gate_channel
         meas.gate_chan      = gate_chan
+    commit()
         
-def set_master(awg, trig_channel=2, pulse_length=1e-7):
+def set_master(awg, trig_channel, pulse_length=1e-7):
+    if not isinstance(trig_channel, Channels.PhysicalMarkerChannel):
+        raise ValueError("In set_master the trigger channel must be an instance of PhysicalMarkerChannel")
+   
     st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=channelLib.channelDatabase)
-    st.phys_chan = getattr(awg, f"m{trig_channel}")
+    st.phys_chan = trig_channel
     st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
     awg.master = True
     awg.trigger_source = "Internal"
+    commit()
 
 def QubitFactory(label, **kwargs):
     ''' Return a saved qubit channel or create a new one. '''
diff --git a/QGL/Channels.py b/QGL/Channels.py
index 64fe2910..f1ec2d8a 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -54,6 +54,10 @@ class ChannelDatabase(db.Entity):
         awgs       = Set("AWG", cascade_delete=True)
         digitizers = Set("Digitizer", cascade_delete=True)
         time       = Optional(datetime.datetime)
+        def __repr__(self):
+            return str(self)
+        def __str__(self):
+            return "{0}('{1}')".format(self.__class__.__name__, self.label)
 
     class MicrowaveSource(db.Entity):
         label           = Required(str)
@@ -62,6 +66,10 @@ class MicrowaveSource(db.Entity):
         power           = Optional(float)
         logical_channel = Optional("PhysicalChannel")
         channel_db      = Optional("ChannelDatabase")
+        def __repr__(self):
+            return str(self)
+        def __str__(self):
+            return "{0}('{1}')".format(self.__class__.__name__, self.label)
 
     class Digitizer(db.Entity):
         label           = Required(str)
@@ -76,6 +84,12 @@ class Digitizer(db.Entity):
         
         def get_chan(self, name):
             return self.channels.select(lambda x: x.label.endswith(name)).first()
+        def ch(self, name):
+            return self.get_chan(name)
+        def __repr__(self):
+            return str(self)
+        def __str__(self):
+            return "{0}('{1}')".format(self.__class__.__name__, self.label)
 
     class AWG(db.Entity):
         label            = Required(str)
@@ -89,6 +103,12 @@ class AWG(db.Entity):
 
         def get_chan(self, name):
             return self.channels.select(lambda x: x.label.endswith(name)).first()
+        def ch(self, name):
+            return self.get_chan(name)
+        def __repr__(self):
+            return str(self)
+        def __str__(self):
+            return "{0}('{1}')".format(self.__class__.__name__, self.label)
 
     class Channel(db.Entity):
         '''

From 0d370f1b87007c4e39695cc5dc40713df9d73a72 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Sun, 24 Jun 2018 21:11:02 -0400
Subject: [PATCH 051/235] Add quick qubit selection function to physical
 channels

---
 QGL/Channels.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/QGL/Channels.py b/QGL/Channels.py
index f1ec2d8a..669b5740 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -139,6 +139,10 @@ class PhysicalChannel(Channel):
         # marker_channel  = Optional("PhysicalMarkerChannel")
         awg             = Optional(AWG)
 
+        def q(self):
+            if isinstance(self.logical_channel, Qubit):
+                return self.logical_channel
+
     class LogicalChannel(Channel):
         '''
         The main class from which we will generate sequences.

From e65a5d314a2ff0dbbceb0499dcad86ccba037c2f Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Mon, 25 Jun 2018 13:24:50 -0400
Subject: [PATCH 052/235] Explicitly use "working" channel db rather than
 hiding "__temp__"

---
 QGL/ChannelLibraries.py | 27 +++++++++++++++++----------
 QGL/Compiler.py         | 13 ++++++++++---
 2 files changed, 27 insertions(+), 13 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 55e9be21..375d1496 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -105,6 +105,7 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
             channelLib.db.disconnect()
 
         config.load_db()
+        self.database_provider = "sqlite"
         if database_file:
             self.database_file = database_file
         elif config.db_file:
@@ -114,7 +115,7 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
 
         self.db = Database()
         Channels.define_entities(self.db)
-        self.db.bind('sqlite', filename=self.database_file, create_db=True)
+        self.db.bind(self.database_provider, filename=self.database_file, create_db=True)
         self.db.generate_mapping(create_tables=True)
 
         # Dirty trick: push the correct entity defs to the calling context
@@ -127,10 +128,16 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
         self.channelDict = {}
 
         # Check to see whether there is already a temp database
-        for cdb in select(d for d in Channels.ChannelDatabase if d.label == "__temp__"):
-            self.clear(channel_db=cdb, create_new=False)
-
-        self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
+        w_dbs = list(select(d for d in Channels.ChannelDatabase if d.label == "working"))
+        if len(w_dbs) > 1:
+            # self.clear(channel_db=cdb, create_new=False)
+            raise Exception("More than one working database exists!")
+        elif len(w_dbs) == 1:
+            self.channelDatabase = w_dbs[0]
+            commit()
+            self.update_channelDict()
+        elif len(w_dbs) == 0:
+            self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
         commit()
 
         config.load_config()
@@ -145,12 +152,12 @@ def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
 
     def ls(self):
-        select((c.label, c.time, c.id) for c in Channels.ChannelDatabase if c.label != "__temp__").sort_by(1, 2).show()
+        select((c.label, c.time, c.id) for c in Channels.ChannelDatabase).sort_by(1, 2).show()
 
     def ent_by_type_name(self, name, show=False):
-        q = select(c for c in getattr(Channels,name) if c.label != "__temp__")
+        q = select(c for c in getattr(Channels,name) if c.label == "working")
         if show:
-            select(c.label for c in getattr(Channels,name) if c.label != "__temp__").sort_by(1).show()
+            select(c.label for c in getattr(Channels,name) if c.label == "working").sort_by(1).show()
         else:
             return {el.label: el for el in q}
 
@@ -196,10 +203,10 @@ def clear(self, channel_db=None, create_new=True):
             commit()        
         # Now clear items that do potentially have sets of items (which should be deleted)
         for ent in [Channels.ChannelDatabase]:
-            select(d for d in ent if d.label == "__temp__").delete(bulk=True)
+            select(d for d in ent if d.label == "working").delete(bulk=True)
             commit()
         if create_new:
-            self.channelDatabase = Channels.ChannelDatabase(label="__temp__", time=datetime.datetime.now())
+            self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
             commit()
 
     def load_obj(self, obj):
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 717e9a4d..9a22d6fb 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -40,9 +40,9 @@
 logger = logging.getLogger(__name__)
 
 def map_logical_to_physical(wires):
-    # construct a mapping of physical channels to lists of logical channels
-    # (there will be more than one logical channel if multiple logical
-    # channels share a physical channel)
+    """construct a mapping of physical channels to lists of logical channels
+    (there will be more than one logical channel if multiple logical
+    channels share a physical channel)"""
     physicalChannels = {}
     for logicalChan in wires.keys():
         phys_chan = logicalChan.phys_chan
@@ -474,6 +474,12 @@ def compile_to_hardware(seqs,
     else:
         extra_meta = awg_metas
     # create meta output
+    db_info = {
+        'db_provider': ChannelLibraries.channelLib.database_provider,
+        'db_filename': ChannelLibraries.channelLib.database_file,
+        'library_name': 'working',
+        'library_id': ChannelLibraries.channelLib.channelDatabase.id
+    }
     if not axis_descriptor:
         axis_descriptor = [{
             'name': 'segment',
@@ -486,6 +492,7 @@ def compile_to_hardware(seqs,
         if wire.receiver_chan and n>0:
             receiver_measurements[wire.receiver_chan.label] = n
     meta = {
+        'database_info': db_info,
         'instruments': files,
         'num_sequences': len(seqs),
         'num_measurements': num_measurements,

From d5afc711657e30766284bf61dd9e3f6b834a17a8 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Mon, 25 Jun 2018 21:39:10 -0400
Subject: [PATCH 053/235] Added bbndb submodule

---
 .gitmodules | 3 +++
 QGL/bbndb   | 1 +
 2 files changed, 4 insertions(+)
 create mode 160000 QGL/bbndb

diff --git a/.gitmodules b/.gitmodules
index e69de29b..d0aadb96 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "QGL/bbndb"]
+	path = QGL/bbndb
+	url = git@github.com:bbn-q/bbndb
diff --git a/QGL/bbndb b/QGL/bbndb
new file mode 160000
index 00000000..cd508d77
--- /dev/null
+++ b/QGL/bbndb
@@ -0,0 +1 @@
+Subproject commit cd508d775ae4154a5bdae88af99a6d72760c63c5

From 1dee44cb5bc1b3820d8426a54d5eac7474677ab2 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 26 Jun 2018 09:28:34 -0400
Subject: [PATCH 054/235] Add requirements file and update setup.py

---
 .gitmodules      |  3 ---
 QGL/bbndb        |  1 -
 requirements.txt |  7 +++++++
 setup.py         | 21 ++++++++-------------
 4 files changed, 15 insertions(+), 17 deletions(-)
 delete mode 100644 .gitmodules
 delete mode 160000 QGL/bbndb
 create mode 100644 requirements.txt

diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index d0aadb96..00000000
--- a/.gitmodules
+++ /dev/null
@@ -1,3 +0,0 @@
-[submodule "QGL/bbndb"]
-	path = QGL/bbndb
-	url = git@github.com:bbn-q/bbndb
diff --git a/QGL/bbndb b/QGL/bbndb
deleted file mode 160000
index cd508d77..00000000
--- a/QGL/bbndb
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit cd508d775ae4154a5bdae88af99a6d72760c63c5
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 00000000..ee7ec4e7
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,7 @@
+bbndb >= 0.1
+numpy >= 1.11.1
+scipy >= 0.17.1
+networkx >= 1.11
+h5py >= 2.6.0
+bokeh >= 0.12.13
+jupyter >= 1.0.0
\ No newline at end of file
diff --git a/setup.py b/setup.py
index dee9e96b..c4db92c2 100644
--- a/setup.py
+++ b/setup.py
@@ -5,16 +5,11 @@
       url='https://github.com/BBN-Q/QGL',
       packages=find_packages(exclude=["tests"]),
       install_requires=[
-            "numpy >= 1.11.1",
-            "scipy >= 0.17.1",
-            "jupyter >= 1.0.0",
-            "atom >= 0.4.1",
-            "h5py >= 2.6.0",
-            "networkx >= 2.0",
-            "future >= 0.16",
-            "watchdog >= 0.8.3",
-            "bokeh >= 0.11",
-            "ruamel_yaml >= 0.11.14"
-      ],
-      extras_require={"gst": "pygsti>0.9.4"}
-)
+        "bbndb >= 0.1",
+        "numpy >= 1.11.1",
+        "scipy >= 0.17.1",
+        "networkx >= 1.11",
+        "h5py >= 2.6.0",
+        "bokeh >= 0.12.13",
+        # "pony >= 0.7.4", # This needs to be 0.7.4-dev
+    ])

From 95a4cc0019e1259125f6b63e2a5c6b21b68548b0 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 13 Jul 2018 12:04:25 -0400
Subject: [PATCH 055/235] Shifting to bbndb for channel entities

---
 QGL/ChannelLibraries.py |  19 ++-
 QGL/Channels.py         | 294 +++++-----------------------------------
 QGL/Compiler.py         |   6 +
 requirements.txt        |   1 -
 4 files changed, 54 insertions(+), 266 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 375d1496..7f23b5af 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -43,6 +43,7 @@
 from . import config
 from . import Channels
 from . import PulseShapes
+import bbndb
 
 channelLib = None
 
@@ -117,6 +118,7 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
         Channels.define_entities(self.db)
         self.db.bind(self.database_provider, filename=self.database_file, create_db=True)
         self.db.generate_mapping(create_tables=True)
+        bbndb.database = self.db
 
         # Dirty trick: push the correct entity defs to the calling context
         for var in ["Measurement","Qubit","Edge"]:
@@ -149,6 +151,7 @@ def get_current_channels(self):
         return list(self.channelDatabase.channels) + list(self.channelDatabase.sources)
 
     def update_channelDict(self):
+        commit()
         self.channelDict = {c.label: c for c in self.get_current_channels()}
 
     def ls(self):
@@ -461,19 +464,21 @@ def new_APS2(label, address):
     m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
     m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
     
-    this_awg = Channels.AWG(label=label, address=address, channels=[chan12, m1, m2, m3, m4], channel_db=channelLib.channelDatabase)
+    this_awg = Channels.AWG(label=label, model="APS2", address=address, channels=[chan12, m1, m2, m3, m4], channel_db=channelLib.channelDatabase)
     this_awg.trigger_source = "External"
     this_awg.address        = address
 
     commit()
     return this_awg
 
-def new_X6(label, address):
-    chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel_db=channelLib.channelDatabase)
-    chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel_db=channelLib.channelDatabase)
+def new_X6(label, address, dsp_channel=0, record_length=1024):
+    chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, dsp_channel=dsp_channel, channel_db=channelLib.channelDatabase)
+    chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, dsp_channel=dsp_channel, channel_db=channelLib.channelDatabase)
     
-    this_dig = Channels.Digitizer(label=label, address=address, channels=[chan1, chan2], channel_db=channelLib.channelDatabase)
+    this_dig = Channels.Digitizer(label=label, model="X6-1000M", address=address, channels=[chan1, chan2],
+                                  record_length=record_length, channel_db=channelLib.channelDatabase)
     this_dig.trigger_source = "External"
+    this_dig.stream_types   = "raw, demodulated, integrated, averaged"
     this_dig.address        = address
 
     commit()
@@ -484,8 +489,8 @@ def new_qubit(label):
     commit()
     return thing
 
-def new_source(label, source_type, address, power=-30.0):
-    thing = Channels.MicrowaveSource(label=label, source_type=source_type, address=address, power=power, channel_db=channelLib.channelDatabase)
+def new_source(label, model, address, power=-30.0):
+    thing = Channels.MicrowaveSource(label=label, model=model, address=address, power=power, channel_db=channelLib.channelDatabase)
     commit()
     return thing
 
diff --git a/QGL/Channels.py b/QGL/Channels.py
index 669b5740..2a240ee3 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -23,266 +23,44 @@
 
 from . import config
 from . import PulseShapes
-import numpy as np
-from math import tan, cos, pi
-from pony.orm import *
-from copy import deepcopy
-import datetime
+from bbndb import define_entities as def_ent
+from bbndb import qgl
 
 # Get these in global scope for module imports
-Channel = None
-PhysicalChannel = None
-LogicalChannel = None
+Channel                   = None
+PhysicalChannel           = None
+LogicalChannel            = None
 PhysicalQuadratureChannel = None
-PhysicalMarkerChannel = None
-LogicalMarkerChannel = None
-ReceiverChannel = None
-Measurement = None
-Qubit = None
-Edge = None
-MicrowaveSource = None
-ChannelDatabase = None
-Digitizer = None
-AWG = None
+PhysicalMarkerChannel     = None
+LogicalMarkerChannel      = None
+ReceiverChannel           = None
+Measurement               = None
+Qubit                     = None
+Edge                      = None
+MicrowaveSource           = None
+ChannelDatabase           = None
+Digitizer                 = None
+AWG                       = None
+
+# The main definitions have been moved to bbndb
+# to keep the schema consistent across Auspex and QGL
+# We retain this local framework in order to maintain
+# the paths for QGL primitives
 
 def define_entities(db):
-
-    class ChannelDatabase(db.Entity):
-        label      = Required(str)
-        channels   = Set("Channel", cascade_delete=True)
-        sources    = Set("MicrowaveSource", cascade_delete=True)
-        awgs       = Set("AWG", cascade_delete=True)
-        digitizers = Set("Digitizer", cascade_delete=True)
-        time       = Optional(datetime.datetime)
-        def __repr__(self):
-            return str(self)
-        def __str__(self):
-            return "{0}('{1}')".format(self.__class__.__name__, self.label)
-
-    class MicrowaveSource(db.Entity):
-        label           = Required(str)
-        source_type     = Required(str)
-        address         = Optional(str)
-        power           = Optional(float)
-        logical_channel = Optional("PhysicalChannel")
-        channel_db      = Optional("ChannelDatabase")
-        def __repr__(self):
-            return str(self)
-        def __str__(self):
-            return "{0}('{1}')".format(self.__class__.__name__, self.label)
-
-    class Digitizer(db.Entity):
-        label           = Required(str)
-        address         = Optional(str)
-        # stream_types    = Set(str)
-        channels        = Set("ReceiverChannel")
-        trigger_source  = Required(str, default="External", py_check=lambda x: x in ['External', 'Internal'])
-        channel_db      = Optional("ChannelDatabase")
-        # nbr_segments     = Required(int, default=1) # This should be automatic
-        # nbr_round_robins = Required(int, default=100) # This should be automatic
-        # acquire_mode     = Required(str,default="digitizer", py_check=lambda x: x in ['digitizer', 'averager'])
-        
-        def get_chan(self, name):
-            return self.channels.select(lambda x: x.label.endswith(name)).first()
-        def ch(self, name):
-            return self.get_chan(name)
-        def __repr__(self):
-            return str(self)
-        def __str__(self):
-            return "{0}('{1}')".format(self.__class__.__name__, self.label)
-
-    class AWG(db.Entity):
-        label            = Required(str)
-        address          = Optional(str)
-        channels         = Set("PhysicalChannel", reverse="awg")
-        trigger_interval = Required(float, default=100e-6)
-        trigger_source   = Required(str, default="External", py_check=lambda x: x in ['External', 'Internal'])
-        delay            = Required(float, default=0.0)
-        master           = Required(bool, default=False)
-        channel_db       = Optional("ChannelDatabase")
-
-        def get_chan(self, name):
-            return self.channels.select(lambda x: x.label.endswith(name)).first()
-        def ch(self, name):
-            return self.get_chan(name)
-        def __repr__(self):
-            return str(self)
-        def __str__(self):
-            return "{0}('{1}')".format(self.__class__.__name__, self.label)
-
-    class Channel(db.Entity):
-        '''
-        Every channel has a label and some printers.
-        '''
-        label      = Required(str)
-        channel_db = Optional("ChannelDatabase")
-
-        def __repr__(self):
-            return str(self)
-        def __str__(self):
-            return "{0}('{1}')".format(self.__class__.__name__, self.label)
-
-    class PhysicalChannel(Channel):
-        '''
-        The main class for actual AWG channels.
-        '''
-        instrument      = Optional(str) # i.e. the AWG or receiver
-        translator      = Optional(str)
-        generator       = Optional(MicrowaveSource, reverse="logical_channel")
-        sampling_rate   = Required(float, default=1.2e9)
-        delay           = Required(float, default=0.0)
-
-        # Required reverse connections
-        logical_channel = Optional("LogicalChannel")
-        # quad_channel_I  = Optional("PhysicalQuadratureChannel", reverse="I_channel")
-        # quad_channel_Q  = Optional("PhysicalQuadratureChannel", reverse="Q_channel")
-        # marker_channel  = Optional("PhysicalMarkerChannel")
-        awg             = Optional(AWG)
-
-        def q(self):
-            if isinstance(self.logical_channel, Qubit):
-                return self.logical_channel
-
-    class LogicalChannel(Channel):
-        '''
-        The main class from which we will generate sequences.
-        At some point it needs to be assigned to a physical channel.
-            frequency: modulation frequency of the channel (can be positive or negative)
-        '''
-        #During initilization we may just have a string reference to the channel
-        phys_chan     = Optional(PhysicalChannel)
-        frequency     = Required(float, default=0.0)
-        pulse_params  = Optional(Json, default={}) 
-        gate_chan     = Optional("LogicalMarkerChannel")
-        receiver_chan = Optional("ReceiverChannel")
-
-    class PhysicalMarkerChannel(PhysicalChannel):
-        '''
-        A digital output channel on an AWG.
-            gate_buffer: How much extra time should be added onto the beginning of a gating pulse
-            gate_min_width: The minimum marker pulse width
-        '''
-        gate_buffer    = Required(float, default=0.0)
-        gate_min_width = Required(float, default=0.0)
-        # phys_channel   = Optional(PhysicalChannel)
-
-    class PhysicalQuadratureChannel(PhysicalChannel):
-        '''
-        Something used to implement a standard qubit channel with two analog channels and a microwave gating channel.
-        '''
-        amp_factor           = Required(float, default=1.0)
-        phase_skew           = Required(float, default=0.0)
-        I_channel_offset     = Required(float, default=0.0)
-        Q_channel_offset     = Required(float, default=0.0)
-        I_channel_amp_factor = Required(float, default=1.0)
-        Q_channel_amp_factor = Required(float, default=1.0)
-
-    class ReceiverChannel(PhysicalChannel):
-        '''
-        A trigger input on a receiver.
-        '''
-        triggering_channel = Optional(LogicalChannel)
-        channel            = Optional(int)
-        stream_type        = Required(str, default="Raw", py_check=lambda x: x.lower() in["raw", "demodulated", "integrated", "averaged"])
-        if_freq            = Required(float, default=0.0)
-        kernel             = Optional(str)
-        kernel_bias        = Required(float, default=0.0)
-        threshold          = Required(float, default=0.0)
-        threshold_invert   = Required(bool, default=False)
-        digitizer          = Optional(Digitizer)
-
-    def pulse_check(name):
-        return name in ["constant", "gaussian", "drag", "gaussOn", "gaussOff", "dragGaussOn", "dragGaussOff",
-                       "tanh", "exp_decay", "autodyne", "arb_axis_drag"]
-        
-    class LogicalMarkerChannel(LogicalChannel):
-        '''
-        A class for digital channels for gating sources or triggering other things.
-        '''
-        meas_channel = Optional(LogicalChannel)
-        trig_channel = Optional("Measurement")
-
-        def __init__(self, **kwargs):
-            if "pulse_params" not in kwargs.keys():
-                kwargs["pulse_params"] =  {'shape_fun': "constant",'length': 10e-9}
-            super(LogicalMarkerChannel, self).__init__(**kwargs)
-
-    class Qubit(LogicalChannel):
-        '''
-        The main class for generating qubit pulses.  Effectively a logical "QuadratureChannel".
-            frequency: modulation frequency of the channel (can be positive or negative)
-        '''
-        edge_source = Optional("Edge", reverse="source")
-        edge_target = Optional("Edge", reverse="target")
-
-        def __init__(self, **kwargs):
-            if "pulse_params" not in kwargs.keys():
-                kwargs["pulse_params"] =  {'length': 20e-9,
-                                'piAmp': 1.0,
-                                'pi2Amp': 0.5,
-                                'shape_fun': "gaussian",
-                                'cutoff': 2,
-                                'drag_scaling': 0,
-                                'sigma': 5e-9}
-            super(Qubit, self).__init__(**kwargs)
-
-    class Measurement(LogicalChannel):
-        '''
-        A class for measurement channels.
-        Measurements are special because they can be different types:
-        autodyne which needs an IQ pair or hetero/homodyne which needs just a marker channel.
-            meas_type: Type of measurement (autodyne, homodyne)
-            autodyne_freq: use to bake the modulation into the pulse, so that it has constant phase
-            frequency: use to asssociate modulation with the channel
-        '''
-        meas_type     = Required(str, default='autodyne', py_check=lambda x: x in ['autodyne', 'homodyne'])
-        autodyne_freq = Required(float, default=0.0)
-        trig_chan     = Optional(LogicalMarkerChannel)
-
-        def __init__(self, **kwargs):
-            if "pulse_params" not in kwargs.keys():
-                kwargs["pulse_params"] =  {'length': 100e-9,
-                                    'amp': 1.0,
-                                    'shape_fun': "tanh",
-                                    'cutoff': 2,
-                                    'sigma': 1e-9}
-            super(Measurement, self).__init__(**kwargs)
-
-    class Edge(LogicalChannel):
-        '''
-        Defines an arc/directed edge between qubit vertices. If a device supports bi-directional
-        connectivity, that is represented with two independent Edges.
-
-        An Edge is also effectively an abstract channel, so it carries the same properties as a
-        Qubit channel.
-        '''
-        # allow string in source and target so that we can store a label or an object
-        source = Required(Qubit)
-        target = Required(Qubit)
-        
-        def __init__(self, **kwargs):
-            if "pulse_params" not in kwargs.keys():
-                kwargs["pulse_params"] =   {'length': 20e-9,
-                                            'amp': 1.0,
-                                            'phase': 0.0,
-                                            'shape_fun': "gaussian",
-                                            'cutoff': 2,
-                                            'drag_scaling': 0,
-                                            'sigma': 5e-9,
-                                            'riseFall': 20e-9}
-            super(Edge, self).__init__(**kwargs)
-
-    globals()["Channel"] = Channel
-    globals()["PhysicalChannel"] = PhysicalChannel
-    globals()["LogicalChannel"] = LogicalChannel
-    globals()["PhysicalQuadratureChannel"] = PhysicalQuadratureChannel
-    globals()["PhysicalMarkerChannel"] = PhysicalMarkerChannel
-    globals()["LogicalMarkerChannel"] = LogicalMarkerChannel
-    globals()["ReceiverChannel"] = ReceiverChannel
-    globals()["Measurement"] = Measurement
-    globals()["Qubit"] = Qubit
-    globals()["Edge"] = Edge
-    globals()["MicrowaveSource"] = MicrowaveSource
-    globals()["ChannelDatabase"] = ChannelDatabase
-    globals()["Digitizer"] = Digitizer
-    globals()["AWG"] = AWG
\ No newline at end of file
+    def_ent(db)
+
+    globals()["Channel"]                   = qgl.Channel
+    globals()["PhysicalChannel"]           = qgl.PhysicalChannel
+    globals()["LogicalChannel"]            = qgl.LogicalChannel
+    globals()["PhysicalQuadratureChannel"] = qgl.PhysicalQuadratureChannel
+    globals()["PhysicalMarkerChannel"]     = qgl.PhysicalMarkerChannel
+    globals()["LogicalMarkerChannel"]      = qgl.LogicalMarkerChannel
+    globals()["ReceiverChannel"]           = qgl.ReceiverChannel
+    globals()["Measurement"]               = qgl.Measurement
+    globals()["Qubit"]                     = qgl.Qubit
+    globals()["Edge"]                      = qgl.Edge
+    globals()["MicrowaveSource"]           = qgl.MicrowaveSource
+    globals()["ChannelDatabase"]           = qgl.ChannelDatabase
+    globals()["Digitizer"]                 = qgl.Digitizer
+    globals()["AWG"]                       = qgl.AWG
\ No newline at end of file
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 9a22d6fb..22efa16c 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -301,6 +301,7 @@ def collect_specializations(seqs):
 
 def compile_to_hardware(seqs,
                         fileName,
+                        library_version=None,
                         suffix='',
                         axis_descriptor=None,
                         add_slave_trigger=True,
@@ -309,6 +310,9 @@ def compile_to_hardware(seqs,
     '''
     Compiles 'seqs' to a hardware description and saves it to 'fileName'.
     Other inputs:
+        library_version (optional): string or ChannelLibrary instance to pack in the
+            metafile. This will be the version of the library loaded during program
+            execution. Default None uses the current working version.
         suffix (optional): string to append to end of fileName, e.g. with
             fileNames = 'test' and suffix = 'foo' might save to test-APSfoo.h5
         axis_descriptor (optional): a list of dictionaries describing the effective
@@ -497,6 +501,8 @@ def compile_to_hardware(seqs,
         'num_sequences': len(seqs),
         'num_measurements': num_measurements,
         'axis_descriptor': axis_descriptor,
+        'qubits': [c.label for c in channels if isinstance(c, Channels.Qubit)],
+        'measurements': [c.label for c in channels if isinstance(c, Channels.Measurement)], 
         'receivers': receiver_measurements
     }
     if extra_meta:
diff --git a/requirements.txt b/requirements.txt
index ee7ec4e7..e13f6dc7 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,4 +4,3 @@ scipy >= 0.17.1
 networkx >= 1.11
 h5py >= 2.6.0
 bokeh >= 0.12.13
-jupyter >= 1.0.0
\ No newline at end of file

From a0b213d8542695178c2bf234f204389f9643d772 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 18 Jul 2018 09:35:37 -0400
Subject: [PATCH 056/235] Added new_Alazar method

---
 QGL/ChannelLibraries.py | 17 +++++++++++++++--
 QGL/__init__.py         |  3 ++-
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 7f23b5af..a3cc7415 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -158,9 +158,9 @@ def ls(self):
         select((c.label, c.time, c.id) for c in Channels.ChannelDatabase).sort_by(1, 2).show()
 
     def ent_by_type_name(self, name, show=False):
-        q = select(c for c in getattr(Channels,name) if c.label == "working")
+        q = select(c for c in getattr(bbndb.qgl,name) if c.channel_db.label == "working")
         if show:
-            select(c.label for c in getattr(Channels,name) if c.label == "working").sort_by(1).show()
+            select(c.label for c in getattr(bbndb.qgl,name) if c.channel_db.label == "working").sort_by(1).show()
         else:
             return {el.label: el for el in q}
 
@@ -484,6 +484,19 @@ def new_X6(label, address, dsp_channel=0, record_length=1024):
     commit()
     return this_dig
 
+def new_Alazar(label, address, record_length=1024):
+    chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, channel_db=channelLib.channelDatabase)
+    chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, channel_db=channelLib.channelDatabase)
+
+    this_dig = Channels.Digitizer(label=label, model="AlazarATS9870", address=address, channels=[chan1, chan2],
+                                  record_length=record_length, channel_db=channelLib.channelDatabase)
+    this_dig.trigger_source = "External"
+    this_dig.stream_types   = "raw"
+    this_dig.address        = address
+
+    commit()
+    return this_dig
+
 def new_qubit(label):
     thing = Channels.Qubit(label=label, channel_db=channelLib.channelDatabase)
     commit()
diff --git a/QGL/__init__.py b/QGL/__init__.py
index eca7769b..99081cde 100644
--- a/QGL/__init__.py
+++ b/QGL/__init__.py
@@ -1,5 +1,6 @@
 from .Channels import Qubit, Measurement, Edge, MicrowaveSource, ChannelDatabase, AWG, Digitizer
-from .ChannelLibraries import QubitFactory, MeasFactory, EdgeFactory, MarkerFactory, ChannelLibrary, channelLib, new_APS2, new_X6, new_qubit, set_control, set_measure, set_master, new_source
+from .ChannelLibraries import QubitFactory, MeasFactory, EdgeFactory, MarkerFactory, ChannelLibrary, channelLib
+from .ChannelLibraries import new_APS2, new_X6, new_Alazar, new_qubit, set_control, set_measure, set_master, new_source
 from .PulsePrimitives import *
 from .Compiler import compile_to_hardware, set_log_level
 from .PulseSequencer import align

From 6797bb4b93c24f2ff78ee3d6115d543b7cebe0ee Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 18 Jul 2018 11:17:43 -0400
Subject: [PATCH 057/235] Setting any channel attribute now invalidates the
 memoize cache

---
 QGL/ChannelLibraries.py | 32 ++++++++++++++++----------------
 QGL/Channels.py         |  6 +++---
 QGL/Compiler.py         |  5 +++--
 QGL/PulsePrimitives.py  |  4 ++++
 4 files changed, 26 insertions(+), 21 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index a3cc7415..b7b81cb6 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -43,6 +43,7 @@
 from . import config
 from . import Channels
 from . import PulseShapes
+from .PulsePrimitives import clear_pulse_cache
 import bbndb
 
 channelLib = None
@@ -91,7 +92,7 @@ def copy_entity(obj, new_channel_db):
             obj_attr = getattr(obj, attr.name)
             if hasattr(obj_attr, "id"):
                 kwargs.pop(attr.name)
-                links[attr.name] = obj_attr.label 
+                links[attr.name] = obj_attr.label
 
     kwargs["channel_db"] = new_channel_db
     return obj.__class__(**kwargs), links
@@ -115,7 +116,7 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
             self.database_file = ":memory:"
 
         self.db = Database()
-        Channels.define_entities(self.db)
+        Channels.define_entities(self.db, cache_callback=clear_pulse_cache)
         self.db.bind(self.database_provider, filename=self.database_file, create_db=True)
         self.db.generate_mapping(create_tables=True)
         bbndb.database = self.db
@@ -125,7 +126,7 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
             inspect.stack()[1][0].f_globals[var] = getattr(Channels, var)
 
         self.connectivityG = nx.DiGraph()
-        
+
         # This is still somewhere legacy QGL behavior. Massage db into dict for lookup.
         self.channelDict = {}
 
@@ -203,7 +204,7 @@ def clear(self, channel_db=None, create_new=True):
         # First clear items that don't have Sets of other items
         for ent in [Channels.MicrowaveSource, Channels.Channel, Channels.AWG, Channels.Digitizer]:
             select(c for c in ent if c.channel_db == channel_db).delete(bulk=True)
-            commit()        
+            commit()
         # Now clear items that do potentially have sets of items (which should be deleted)
         for ent in [Channels.ChannelDatabase]:
             select(d for d in ent if d.label == "working").delete(bulk=True)
@@ -228,7 +229,7 @@ def save_as(self, name):
         new_chans, new_srcs, new_awgs, new_digs = copy_objs(chans, srcs, awgs, digs, new_channel_db=cd)
         cd.channels, cd.sources, cd.awgs, cd.digitizers = new_chans, new_srcs, new_awgs, new_digs
         commit()
-        
+
     #Dictionary methods
     def __getitem__(self, key):
         return self.channelDict[key]
@@ -463,7 +464,7 @@ def new_APS2(label, address):
     m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
     m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
     m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-    
+
     this_awg = Channels.AWG(label=label, model="APS2", address=address, channels=[chan12, m1, m2, m3, m4], channel_db=channelLib.channelDatabase)
     this_awg.trigger_source = "External"
     this_awg.address        = address
@@ -474,7 +475,7 @@ def new_APS2(label, address):
 def new_X6(label, address, dsp_channel=0, record_length=1024):
     chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, dsp_channel=dsp_channel, channel_db=channelLib.channelDatabase)
     chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, dsp_channel=dsp_channel, channel_db=channelLib.channelDatabase)
-    
+
     this_dig = Channels.Digitizer(label=label, model="X6-1000M", address=address, channels=[chan1, chan2],
                                   record_length=record_length, channel_db=channelLib.channelDatabase)
     this_dig.trigger_source = "External"
@@ -524,7 +525,7 @@ def set_control(qubit, awg, generator=None):
     if generator:
         qubit.phys_chan.generator = generator
     commit()
-    
+
 def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
     quads   = [c for c in awg.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
     markers = [c for c in awg.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
@@ -542,14 +543,14 @@ def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=Non
     meas.phys_chan = phys_chan
     if generator:
         meas.phys_chan.generator = generator
-    
+
     phys_trig_channel = trig_channel if trig_channel else awg.get_chan("12m1")
 
     trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}", channel_db=channelLib.channelDatabase)
     trig_chan.phys_chan    = phys_trig_channel
     trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
     meas.trig_chan         = trig_chan
-    
+
     if isinstance(dig, Channels.Digitizer) and len(dig.channels) > 1:
         raise ValueError("In set_measure the Digitizer must have a single receiver channel or a specific channel must be passed instead")
     elif isinstance(dig, Channels.Digitizer) and len(dig.channels) == 1:
@@ -567,11 +568,11 @@ def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=Non
         gate_chan.phys_chan = phys_gate_channel
         meas.gate_chan      = gate_chan
     commit()
-        
+
 def set_master(awg, trig_channel, pulse_length=1e-7):
     if not isinstance(trig_channel, Channels.PhysicalMarkerChannel):
         raise ValueError("In set_master the trigger channel must be an instance of PhysicalMarkerChannel")
-   
+
     st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=channelLib.channelDatabase)
     st.phys_chan = trig_channel
     st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
@@ -583,15 +584,15 @@ def QubitFactory(label, **kwargs):
     ''' Return a saved qubit channel or create a new one. '''
     # TODO: this will just get the first entry in the whole damned DB!
     # thing = select(el for el in Channels.Qubit if el.label==label).first()
-    thing = {c.label: c for c in channelLib.get_current_channels()}[label]
+    thing = {c.label: c for c in channelLib.get_current_channels() if isinstance(c, Channels.Qubit)}[label]
     if thing:
         return thing
     else:
         return Channels.Qubit(label=label, **kwargs)
-    
+
 def MeasFactory(label, **kwargs):
     ''' Return a saved measurement channel or create a new one. '''
-    thing = {c.label: c for c in channelLib.get_current_channels()}[label]
+    thing = {c.label: c for c in channelLib.get_current_channels() if isinstance(c, Channels.Measurement)}[label]
     if thing:
         return thing
     else:
@@ -613,4 +614,3 @@ def EdgeFactory(source, target):
     else:
         raise ValueError('Edge {0} not found in connectivity graph'.format((
             source, target)))
-
diff --git a/QGL/Channels.py b/QGL/Channels.py
index 2a240ee3..abb1a6c2 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -47,8 +47,8 @@
 # We retain this local framework in order to maintain
 # the paths for QGL primitives
 
-def define_entities(db):
-    def_ent(db)
+def define_entities(db, cache_callback=None):
+    def_ent(db, cache_callback=cache_callback)
 
     globals()["Channel"]                   = qgl.Channel
     globals()["PhysicalChannel"]           = qgl.PhysicalChannel
@@ -63,4 +63,4 @@ def define_entities(db):
     globals()["MicrowaveSource"]           = qgl.MicrowaveSource
     globals()["ChannelDatabase"]           = qgl.ChannelDatabase
     globals()["Digitizer"]                 = qgl.Digitizer
-    globals()["AWG"]                       = qgl.AWG
\ No newline at end of file
+    globals()["AWG"]                       = qgl.AWG
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 22efa16c..3ee00996 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -30,7 +30,7 @@
 from . import Channels
 from . import ChannelLibraries
 from . import PulseShapes
-from .PulsePrimitives import Id
+from .PulsePrimitives import Id, clear_pulse_cache
 from .PulseSequencer import Pulse, PulseBlock, CompositePulse
 from . import ControlFlow
 from . import BlockLabel
@@ -323,6 +323,7 @@ def compile_to_hardware(seqs,
         tdm_seq (optional): compile for TDM
     '''
     ChannelLibraries.channelLib.update_channelDict()
+    # clear_pulse_cache()
 
     logger.debug("Compiling %d sequence(s)", len(seqs))
 
@@ -502,7 +503,7 @@ def compile_to_hardware(seqs,
         'num_measurements': num_measurements,
         'axis_descriptor': axis_descriptor,
         'qubits': [c.label for c in channels if isinstance(c, Channels.Qubit)],
-        'measurements': [c.label for c in channels if isinstance(c, Channels.Measurement)], 
+        'measurements': [c.label for c in channels if isinstance(c, Channels.Measurement)],
         'receivers': receiver_measurements
     }
     if extra_meta:
diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index 59d48099..538f6714 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -46,6 +46,9 @@ def cacheWrap(*args, **kwargs):
         key = (pulseFunc, args)
         if key not in _memoize.cache:
             _memoize.cache[key] = pulseFunc(*args)
+            print("Caching", pulseFunc)
+        else:
+            print("Recalling", pulseFunc)
         return _memoize.cache[key]
 
     return cacheWrap
@@ -757,6 +760,7 @@ def _MEAS(qubit, **kwargs):
         params['frequency'] = measChan.autodyne_freq
         params['baseShape'] = params.pop('shape_fun')
         params['shape_fun'] = PulseShapes.autodyne
+    print(params)
     amp = params.pop('amp')
     ignoredStrParams = ['phase', 'frameChange']
     if 'amp' not in kwargs:

From 492de567efe5d74be0e1619b972792522264a9da Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 18 Jul 2018 17:35:55 -0400
Subject: [PATCH 058/235] Remove overly verbose code from aed6222

---
 QGL/PulsePrimitives.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index 538f6714..59d48099 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -46,9 +46,6 @@ def cacheWrap(*args, **kwargs):
         key = (pulseFunc, args)
         if key not in _memoize.cache:
             _memoize.cache[key] = pulseFunc(*args)
-            print("Caching", pulseFunc)
-        else:
-            print("Recalling", pulseFunc)
         return _memoize.cache[key]
 
     return cacheWrap
@@ -760,7 +757,6 @@ def _MEAS(qubit, **kwargs):
         params['frequency'] = measChan.autodyne_freq
         params['baseShape'] = params.pop('shape_fun')
         params['shape_fun'] = PulseShapes.autodyne
-    print(params)
     amp = params.pop('amp')
     ignoredStrParams = ['phase', 'frameChange']
     if 'amp' not in kwargs:

From dfef1cfe6e57dce828d0c54f57dbece2e9b5edda Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 19 Jul 2018 21:39:51 -0400
Subject: [PATCH 059/235] Created wrapper to convert func args that are
 entities into unique IDs to avoid crossing db_sessions

---
 QGL/ChannelLibraries.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index b7b81cb6..1d2e2a23 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -37,6 +37,7 @@
 import datetime
 import importlib
 import inspect
+from functools import wraps
 from pony.orm import *
 import networkx as nx
 
@@ -47,6 +48,21 @@
 import bbndb
 
 channelLib = None
+db = None
+
+def localize_db_objects(f):
+    """Since we can't mix db objects from separate sessions, re-fetch entities by their unique IDs"""
+    @wraps(f)
+    def wrapper(*args, **kwargs):
+        global db
+        with db_session:
+            args_info    = [(type(arg), arg.id) if isinstance(arg, db.Entity) else (arg, None) for arg in args]
+            kwargs_info  = {k: (type(v), v.id) if isinstance(v, db.Entity) else (v, None) for k, v in kwargs.items()}
+        with db_session:
+            new_args   = [c[i] if i else c for c, i in args_info]
+            new_kwargs = {k: v[0][v[1]] if v[1] else v[0] for k,v in kwargs_info.items()}
+            return f(*new_args, **new_kwargs)
+    return wrapper
 
 def set_from_dict(obj, settings):
     for prop_name in obj.to_dict().keys():

From ccc4a1dda0e3e0fc241fd970caf0d302eea50acd Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 19 Jul 2018 21:40:24 -0400
Subject: [PATCH 060/235] Convert channel library to properly using db_sessions
 for non-interactive pony use

---
 QGL/ChannelLibraries.py | 112 +++++++++++++++++++++++++---------------
 1 file changed, 70 insertions(+), 42 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 1d2e2a23..d16b7c93 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -72,6 +72,7 @@ def set_from_dict(obj, settings):
             except Exception as e:
                 print(f"{obj.label}: Error loading {prop_name} from config")
 
+@db_session
 def copy_objs(*entities, new_channel_db):
     # Entities is a list of lists of entities of specific types
     new_entities    = []
@@ -97,6 +98,7 @@ def copy_objs(*entities, new_channel_db):
 
     return new_entities
 
+@db_session
 def copy_entity(obj, new_channel_db):
     """Copy a pony entity instance"""
     kwargs = {a.name: getattr(obj, a.name) for a in obj._attrs_ if a.name not in ["id", "classtype"]}
@@ -118,7 +120,7 @@ class ChannelLibrary(object):
     def __init__(self, database_file=None, channelDict={}, **kwargs):
         """Create the channel library."""
 
-        global channelLib
+        global channelLib, db
         if channelLib is not None:
             channelLib.db.disconnect()
 
@@ -131,11 +133,11 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
         else:
             self.database_file = ":memory:"
 
-        self.db = Database()
-        Channels.define_entities(self.db, cache_callback=clear_pulse_cache)
-        self.db.bind(self.database_provider, filename=self.database_file, create_db=True)
-        self.db.generate_mapping(create_tables=True)
-        bbndb.database = self.db
+        db = Database()
+        Channels.define_entities(db, cache_callback=clear_pulse_cache)
+        db.bind(self.database_provider, filename=self.database_file, create_db=True)
+        db.generate_mapping(create_tables=True)
+        bbndb.database = db
 
         # Dirty trick: push the correct entity defs to the calling context
         for var in ["Measurement","Qubit","Edge"]:
@@ -147,33 +149,39 @@ def __init__(self, database_file=None, channelDict={}, **kwargs):
         self.channelDict = {}
 
         # Check to see whether there is already a temp database
-        w_dbs = list(select(d for d in Channels.ChannelDatabase if d.label == "working"))
-        if len(w_dbs) > 1:
-            # self.clear(channel_db=cdb, create_new=False)
-            raise Exception("More than one working database exists!")
-        elif len(w_dbs) == 1:
-            self.channelDatabase = w_dbs[0]
-            commit()
-            self.update_channelDict()
-        elif len(w_dbs) == 0:
-            self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
-        commit()
+        with db_session:
+            w_dbs = list(select(d for d in Channels.ChannelDatabase if d.label == "working"))
+            if len(w_dbs) > 1:
+                # self.clear(channel_db=cdb, create_new=False)
+                raise Exception("More than one working database exists!")
+            elif len(w_dbs) == 1:
+                self.channelDatabase = w_dbs[0]
+                commit()
+                self.update_channelDict()
+            elif len(w_dbs) == 0:
+                self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
+            # commit()
 
         config.load_config()
 
         # Update the global reference
         channelLib = self
 
+    @db_session
     def get_current_channels(self):
-        return list(self.channelDatabase.channels) + list(self.channelDatabase.sources)
+        cdb = Channels.ChannelDatabase[self.channelDatabase.id] # Can't use external object
+        return list(cdb.channels) + list(cdb.sources)
 
+    @db_session
     def update_channelDict(self):
         commit()
         self.channelDict = {c.label: c for c in self.get_current_channels()}
 
+    @db_session
     def ls(self):
         select((c.label, c.time, c.id) for c in Channels.ChannelDatabase).sort_by(1, 2).show()
 
+    @db_session
     def ent_by_type_name(self, name, show=False):
         q = select(c for c in getattr(bbndb.qgl,name) if c.channel_db.label == "working")
         if show:
@@ -205,15 +213,18 @@ def ls_qubit(self):
     def ls_meas(self):
         return self.ent_by_type_name("Measurement", show=True)
 
+    @db_session
     def load(self, name, index=1):
         """Load the latest instance for a particular name. Specifying index = 2 will select the second most recent instance """
         obj = list(select(c for c in Channels.ChannelDatabase if c.label==name).sort_by(desc(Channels.ChannelDatabase.time)))
         self.load_obj(obj[-index])
 
+    @db_session
     def load_by_id(self, id_num):
         obj = select(c for c in Channels.ChannelDatabase if c.id==id_num).first()
         self.load_obj(obj)
 
+    @db_session
     def clear(self, channel_db=None, create_new=True):
         # If no database is specified, clear self.database
         channel_db = channel_db if channel_db else self.channelDatabase
@@ -229,6 +240,7 @@ def clear(self, channel_db=None, create_new=True):
             self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
             commit()
 
+    @db_session
     def load_obj(self, obj):
         commit()
         self.clear()
@@ -237,6 +249,7 @@ def load_obj(self, obj):
         commit()
         self.update_channelDict()
 
+    @db_session
     def save_as(self, name):
         chans, srcs, awgs, digs = map(list, [self.channelDatabase.channels, self.channelDatabase.sources,
                                             self.channelDatabase.awgs, self.channelDatabase.digitizers])
@@ -265,6 +278,7 @@ def keys(self):
     def values(self):
         return self.channelDict.values()
 
+    @db_session
     def build_connectivity_graph(self):
         # build connectivity graph
 <<<<<<< HEAD
@@ -474,26 +488,30 @@ def load_from_library(self, return_only=False):
 # Convenience functions for generating and linking channels
 # TODO: move these to a shim layer shared by Auspex/QGL
 
+@db_session
 def new_APS2(label, address):
-    chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-    m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-    m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-    m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-    m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=channelLib.channelDatabase)
-
-    this_awg = Channels.AWG(label=label, model="APS2", address=address, channels=[chan12, m1, m2, m3, m4], channel_db=channelLib.channelDatabase)
+    cdb    = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
+    chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=cdb)
+    m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=cdb)
+    m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=cdb)
+    m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=cdb)
+    m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=cdb)
+
+    this_awg = Channels.AWG(label=label, model="APS2", address=address, channels=[chan12, m1, m2, m3, m4], channel_db=cdb)
     this_awg.trigger_source = "External"
     this_awg.address        = address
 
     commit()
     return this_awg
 
+@db_session
 def new_X6(label, address, dsp_channel=0, record_length=1024):
-    chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, dsp_channel=dsp_channel, channel_db=channelLib.channelDatabase)
-    chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, dsp_channel=dsp_channel, channel_db=channelLib.channelDatabase)
+    cdb   = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
+    chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, dsp_channel=dsp_channel, channel_db=cdb)
+    chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, dsp_channel=dsp_channel, channel_db=cdb)
 
     this_dig = Channels.Digitizer(label=label, model="X6-1000M", address=address, channels=[chan1, chan2],
-                                  record_length=record_length, channel_db=channelLib.channelDatabase)
+                                  record_length=record_length, channel_db=cdb)
     this_dig.trigger_source = "External"
     this_dig.stream_types   = "raw, demodulated, integrated, averaged"
     this_dig.address        = address
@@ -501,12 +519,14 @@ def new_X6(label, address, dsp_channel=0, record_length=1024):
     commit()
     return this_dig
 
+@db_session
 def new_Alazar(label, address, record_length=1024):
-    chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, channel_db=channelLib.channelDatabase)
-    chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, channel_db=channelLib.channelDatabase)
+    cdb   = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
+    chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, channel_db=cdb)
+    chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, channel_db=cdb)
 
     this_dig = Channels.Digitizer(label=label, model="AlazarATS9870", address=address, channels=[chan1, chan2],
-                                  record_length=record_length, channel_db=channelLib.channelDatabase)
+                                  record_length=record_length, channel_db=cdb)
     this_dig.trigger_source = "External"
     this_dig.stream_types   = "raw"
     this_dig.address        = address
@@ -514,16 +534,19 @@ def new_Alazar(label, address, record_length=1024):
     commit()
     return this_dig
 
+@db_session
 def new_qubit(label):
-    thing = Channels.Qubit(label=label, channel_db=channelLib.channelDatabase)
-    commit()
+    cdb   = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
+    thing = Channels.Qubit(label=label, channel_db=cdb)
     return thing
 
+@db_session
 def new_source(label, model, address, power=-30.0):
-    thing = Channels.MicrowaveSource(label=label, model=model, address=address, power=power, channel_db=channelLib.channelDatabase)
-    commit()
+    cdb   = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
+    thing = Channels.MicrowaveSource(label=label, model=model, address=address, power=power, channel_db=cdb)
     return thing
 
+@localize_db_objects
 def set_control(qubit, awg, generator=None):
     quads   = [c for c in awg.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
     markers = [c for c in awg.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
@@ -540,9 +563,10 @@ def set_control(qubit, awg, generator=None):
     qubit.phys_chan = phys_chan
     if generator:
         qubit.phys_chan.generator = generator
-    commit()
 
+@localize_db_objects
 def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
+    cdb     = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
     quads   = [c for c in awg.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
     markers = [c for c in awg.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
 
@@ -555,14 +579,14 @@ def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=Non
     else:
         raise ValueError("In set_measure the AWG must have a single quadrature channel or a specific channel must be passed instead")
 
-    meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=channelLib.channelDatabase)
+    meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=cdb)
     meas.phys_chan = phys_chan
     if generator:
         meas.phys_chan.generator = generator
 
     phys_trig_channel = trig_channel if trig_channel else awg.get_chan("12m1")
 
-    trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}", channel_db=channelLib.channelDatabase)
+    trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}", channel_db=cdb)
     trig_chan.phys_chan    = phys_trig_channel
     trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
     meas.trig_chan         = trig_chan
@@ -580,22 +604,23 @@ def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=Non
 
     if gate:
         phys_gate_channel   = gate_channel if gate_channel else awg.get_chan("12m2")
-        gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=channelLib.channelDatabase)
+        gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=cdb)
         gate_chan.phys_chan = phys_gate_channel
         meas.gate_chan      = gate_chan
-    commit()
 
+@localize_db_objects
 def set_master(awg, trig_channel, pulse_length=1e-7):
     if not isinstance(trig_channel, Channels.PhysicalMarkerChannel):
         raise ValueError("In set_master the trigger channel must be an instance of PhysicalMarkerChannel")
 
-    st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=channelLib.channelDatabase)
+    cdb = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
+    st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=cdb)
     st.phys_chan = trig_channel
     st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
     awg.master = True
     awg.trigger_source = "Internal"
-    commit()
 
+@db_session
 def QubitFactory(label, **kwargs):
     ''' Return a saved qubit channel or create a new one. '''
     # TODO: this will just get the first entry in the whole damned DB!
@@ -606,6 +631,7 @@ def QubitFactory(label, **kwargs):
     else:
         return Channels.Qubit(label=label, **kwargs)
 
+@db_session
 def MeasFactory(label, **kwargs):
     ''' Return a saved measurement channel or create a new one. '''
     thing = {c.label: c for c in channelLib.get_current_channels() if isinstance(c, Channels.Measurement)}[label]
@@ -614,6 +640,7 @@ def MeasFactory(label, **kwargs):
     else:
         return Channels.Measurement(label=label, **kwargs)
 
+@db_session
 def MarkerFactory(label, **kwargs):
     ''' Return a saved Marker channel or create a new one. '''
     thing = {c.label: c for c in channelLib.get_current_channels()}[label]
@@ -622,6 +649,7 @@ def MarkerFactory(label, **kwargs):
     else:
         return Channels.LogicalMarkerChannel(label=label, **kwargs)
 
+@db_session
 def EdgeFactory(source, target):
     if channelLib.connectivityG.has_edge(source, target):
         return channelLib.connectivityG[source][target]['channel']

From a508cfd678bdfc8f8fb79e66a6424542a9ee4620 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 19 Sep 2018 11:42:39 -0400
Subject: [PATCH 061/235] Frequency now required for sources

---
 QGL/ChannelLibraries.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index d16b7c93..41bbe8c8 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -541,9 +541,9 @@ def new_qubit(label):
     return thing
 
 @db_session
-def new_source(label, model, address, power=-30.0):
+def new_source(label, model, address, power=-30.0, frequency=5.0e9):
     cdb   = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
-    thing = Channels.MicrowaveSource(label=label, model=model, address=address, power=power, channel_db=cdb)
+    thing = Channels.MicrowaveSource(label=label, model=model, address=address, power=power, frequency=frequency, channel_db=cdb)
     return thing
 
 @localize_db_objects

From dd709e2d1e52a67bef201afcb59bbf4d7c2b63b7 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 2 Oct 2018 21:49:06 -0400
Subject: [PATCH 062/235] Add transceiver object and rename AWG->transmitter,
 dig->receiver

---
 QGL/ChannelLibraries.py | 141 ++++++++++++++++++++++------------------
 QGL/Channels.py         |  10 +--
 QGL/__init__.py         |   4 +-
 3 files changed, 87 insertions(+), 68 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 41bbe8c8..81f54d12 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -39,6 +39,7 @@
 import inspect
 from functools import wraps
 from pony.orm import *
+import numpy as np
 import networkx as nx
 
 from . import config
@@ -189,25 +190,25 @@ def ent_by_type_name(self, name, show=False):
         else:
             return {el.label: el for el in q}
 
-    def dig(self):
-        return self.ent_by_type_name("Digitizer")
+    def receivers(self):
+        return self.ent_by_type_name("Receiver")
 
-    def awg(self):
-        return self.ent_by_type_name("AWG")
+    def transmitter(self):
+        return self.ent_by_type_name("Transmitter")
 
-    def qubit(self):
+    def qubits(self):
         return self.ent_by_type_name("Qubit")
 
     def meas(self):
         return self.ent_by_type_name("Measurement")
 
-    def ls_dig(self):
-        return self.ent_by_type_name("Digitizer", show=True)
+    def ls_receivers(self):
+        return self.ent_by_type_name("Receiver", show=True)
 
-    def ls_awg(self):
-        return self.ent_by_type_name("AWG", show=True)
+    def ls_transmitters(self):
+        return self.ent_by_type_name("Transmitter", show=True)
 
-    def ls_qubit(self):
+    def ls_qubits(self):
         return self.ent_by_type_name("Qubit", show=True)
 
     def ls_meas(self):
@@ -229,7 +230,7 @@ def clear(self, channel_db=None, create_new=True):
         # If no database is specified, clear self.database
         channel_db = channel_db if channel_db else self.channelDatabase
         # First clear items that don't have Sets of other items
-        for ent in [Channels.MicrowaveSource, Channels.Channel, Channels.AWG, Channels.Digitizer]:
+        for ent in [Channels.MicrowaveSource, Channels.Channel, Channels.Transmitter, Channels.Receiver, Channels.Transceiver]:
             select(c for c in ent if c.channel_db == channel_db).delete(bulk=True)
             commit()
         # Now clear items that do potentially have sets of items (which should be deleted)
@@ -244,19 +245,20 @@ def clear(self, channel_db=None, create_new=True):
     def load_obj(self, obj):
         commit()
         self.clear()
-        chans, srcs, awgs, digs = map(list, [obj.channels, obj.sources, obj.awgs, obj.digitizers])
-        copy_objs(chans, srcs, awgs, digs, new_channel_db=self.channelDatabase)
+        chans, srcs, d2as, a2ds, trans = map(list, [obj.channels, obj.sources, obj.transmitters, obj.receivers, obj.transceivers])
+        copy_objs(chans, srcs, d2as, a2ds, trans, new_channel_db=self.channelDatabase)
         commit()
         self.update_channelDict()
 
     @db_session
     def save_as(self, name):
-        chans, srcs, awgs, digs = map(list, [self.channelDatabase.channels, self.channelDatabase.sources,
-                                            self.channelDatabase.awgs, self.channelDatabase.digitizers])
+        chans, srcs, d2as, a2dsm, trans = map(list, [self.channelDatabase.channels, self.channelDatabase.sources,
+                                            self.channelDatabase.transmitters, self.channelDatabase.receivers,
+                                            self.channelDatabase.transceivers])
         commit()
         cd = Channels.ChannelDatabase(label=name, time=datetime.datetime.now())
-        new_chans, new_srcs, new_awgs, new_digs = copy_objs(chans, srcs, awgs, digs, new_channel_db=cd)
-        cd.channels, cd.sources, cd.awgs, cd.digitizers = new_chans, new_srcs, new_awgs, new_digs
+        new_chans, new_srcs, new_d2as, new_a2ds, new_trans = copy_objs(chans, srcs, d2as, a2ds, trans, new_channel_db=cd)
+        cd.channels, cd.sources, cd.transmitters, cd.receivers, cd.transceivers = new_chans, new_srcs, new_d2as, new_a2ds, new_trans
         commit()
 
     #Dictionary methods
@@ -497,12 +499,23 @@ def new_APS2(label, address):
     m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=cdb)
     m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=cdb)
 
-    this_awg = Channels.AWG(label=label, model="APS2", address=address, channels=[chan12, m1, m2, m3, m4], channel_db=cdb)
-    this_awg.trigger_source = "External"
-    this_awg.address        = address
+    this_transmitter = Channels.Transmitter(label=label, model="APS2", address=address, channels=[chan12, m1, m2, m3, m4], channel_db=cdb)
+    this_transmitter.trigger_source = "External"
+    this_transmitter.address        = address
 
     commit()
-    return this_awg
+    return this_transmitter
+
+@db_session
+def new_APS2_rack(label, num, start_address):
+    cdb              = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
+    address_start    = ".".join(start_address.split(".")[:3])
+    address_end      = int(start_address.split(".")[-1])
+    transmitters     = [new_APS2(f"{label}_U{i}", f"{address_start}.{address_end+i}") for i in range(1,num+1)]
+    this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", transmitters=transmitters, channel_db=cdb)
+
+    commit()
+    return this_transceiver
 
 @db_session
 def new_X6(label, address, dsp_channel=0, record_length=1024):
@@ -510,14 +523,18 @@ def new_X6(label, address, dsp_channel=0, record_length=1024):
     chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, dsp_channel=dsp_channel, channel_db=cdb)
     chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, dsp_channel=dsp_channel, channel_db=cdb)
 
-    this_dig = Channels.Digitizer(label=label, model="X6-1000M", address=address, channels=[chan1, chan2],
+    this_receiver = Channels.Receiver(label=label, model="X6-1000M", address=address, channels=[chan1, chan2],
                                   record_length=record_length, channel_db=cdb)
-    this_dig.trigger_source = "External"
-    this_dig.stream_types   = "raw, demodulated, integrated, averaged"
-    this_dig.address        = address
+    this_receiver.trigger_source = "External"
+    this_receiver.stream_types   = "raw, demodulated, integrated"
+    this_receiver.address        = address
+
+    # Add a default kernel
+    chan1.kernel = np.ones(record_length, dtype=np.complex).tobytes()
+    chan2.kernel = np.ones(record_length, dtype=np.complex).tobytes()
 
     commit()
-    return this_dig
+    return this_receiver
 
 @db_session
 def new_Alazar(label, address, record_length=1024):
@@ -525,14 +542,14 @@ def new_Alazar(label, address, record_length=1024):
     chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, channel_db=cdb)
     chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, channel_db=cdb)
 
-    this_dig = Channels.Digitizer(label=label, model="AlazarATS9870", address=address, channels=[chan1, chan2],
+    this_receiver = Channels.Receiver(label=label, model="AlazarATS9870", address=address, channels=[chan1, chan2],
                                   record_length=record_length, channel_db=cdb)
-    this_dig.trigger_source = "External"
-    this_dig.stream_types   = "raw"
-    this_dig.address        = address
+    this_receiver.trigger_source = "External"
+    this_receiver.stream_types   = "raw"
+    this_receiver.address        = address
 
     commit()
-    return this_dig
+    return this_receiver
 
 @db_session
 def new_qubit(label):
@@ -547,69 +564,69 @@ def new_source(label, model, address, power=-30.0, frequency=5.0e9):
     return thing
 
 @localize_db_objects
-def set_control(qubit, awg, generator=None):
-    quads   = [c for c in awg.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
-    markers = [c for c in awg.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
+def set_control(qubit, transmitter, generator=None):
+    quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
+    markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
 
-    if isinstance(awg, Channels.AWG) and len(quads) > 1:
-        raise ValueError("In set_control the AWG must have a single quadrature channel or a specific channel must be passed instead")
-    elif isinstance(awg, Channels.AWG) and len(quads) == 1:
+    if isinstance(transmitter, Channels.Transmitter) and len(quads) > 1:
+        raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+    elif isinstance(transmitter, Channels.Transmitter) and len(quads) == 1:
         phys_chan = quads[0]
-    elif isinstance(awg, Channels.PhysicalQuadratureChannel):
-        phys_chan = awg
+    elif isinstance(transmitter, Channels.PhysicalQuadratureChannel):
+        phys_chan = transmitter
     else:
-        raise ValueError("In set_control the AWG must have a single quadrature channel or a specific channel must be passed instead")
+        raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
     qubit.phys_chan = phys_chan
     if generator:
         qubit.phys_chan.generator = generator
 
 @localize_db_objects
-def set_measure(qubit, awg, dig, generator=None, dig_channel=1, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
+def set_measure(qubit, transmitter, receivers, generator=None, receivers_channel=1, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
     cdb     = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
-    quads   = [c for c in awg.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
-    markers = [c for c in awg.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
+    quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
+    markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
 
-    if isinstance(awg, Channels.AWG) and len(quads) > 1:
-        raise ValueError("In set_measure the AWG must have a single quadrature channel or a specific channel must be passed instead")
-    elif isinstance(awg, Channels.AWG) and len(quads) == 1:
+    if isinstance(transmitter, Channels.Transmitter) and len(quads) > 1:
+        raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+    elif isinstance(transmitter, Channels.Transmitter) and len(quads) == 1:
         phys_chan = quads[0]
-    elif isinstance(awg, Channels.PhysicalQuadratureChannel):
-        phys_chan = awg
+    elif isinstance(transmitter, Channels.PhysicalQuadratureChannel):
+        phys_chan = transmitter
     else:
-        raise ValueError("In set_measure the AWG must have a single quadrature channel or a specific channel must be passed instead")
+        raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
     meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=cdb)
     meas.phys_chan = phys_chan
     if generator:
         meas.phys_chan.generator = generator
 
-    phys_trig_channel = trig_channel if trig_channel else awg.get_chan("12m1")
+    phys_trig_channel = trig_channel if trig_channel else transmitter.get_chan("12m1")
 
-    trig_chan              = Channels.LogicalMarkerChannel(label=f"digTrig-{qubit.label}", channel_db=cdb)
+    trig_chan              = Channels.LogicalMarkerChannel(label=f"receiversTrig-{qubit.label}", channel_db=cdb)
     trig_chan.phys_chan    = phys_trig_channel
     trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
     meas.trig_chan         = trig_chan
 
-    if isinstance(dig, Channels.Digitizer) and len(dig.channels) > 1:
-        raise ValueError("In set_measure the Digitizer must have a single receiver channel or a specific channel must be passed instead")
-    elif isinstance(dig, Channels.Digitizer) and len(dig.channels) == 1:
-        rcv_chan = dig.channels[0]
-    elif isinstance(dig, Channels.ReceiverChannel):
-        rcv_chan = dig
+    if isinstance(receivers, Channels.Receiver) and len(receivers.channels) > 1:
+        raise ValueError("In set_measure the Receiver must have a single receiver channel or a specific channel must be passed instead")
+    elif isinstance(receivers, Channels.Receiver) and len(receivers.channels) == 1:
+        rcv_chan = receivers.channels[0]
+    elif isinstance(receivers, Channels.ReceiverChannel):
+        rcv_chan = receivers
     else:
-        raise ValueError("In set_measure the AWG must have a single quadrature channel or a specific channel must be passed instead")
+        raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
     meas.receiver_chan = rcv_chan
 
     if gate:
-        phys_gate_channel   = gate_channel if gate_channel else awg.get_chan("12m2")
+        phys_gate_channel   = gate_channel if gate_channel else transmitter.get_chan("12m2")
         gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=cdb)
         gate_chan.phys_chan = phys_gate_channel
         meas.gate_chan      = gate_chan
 
 @localize_db_objects
-def set_master(awg, trig_channel, pulse_length=1e-7):
+def set_master(transmitter, trig_channel, pulse_length=1e-7):
     if not isinstance(trig_channel, Channels.PhysicalMarkerChannel):
         raise ValueError("In set_master the trigger channel must be an instance of PhysicalMarkerChannel")
 
@@ -617,8 +634,8 @@ def set_master(awg, trig_channel, pulse_length=1e-7):
     st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=cdb)
     st.phys_chan = trig_channel
     st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
-    awg.master = True
-    awg.trigger_source = "Internal"
+    transmitter.master = True
+    transmitter.trigger_source = "Internal"
 
 @db_session
 def QubitFactory(label, **kwargs):
diff --git a/QGL/Channels.py b/QGL/Channels.py
index abb1a6c2..2e1a2a8c 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -39,8 +39,9 @@
 Edge                      = None
 MicrowaveSource           = None
 ChannelDatabase           = None
-Digitizer                 = None
-AWG                       = None
+Receiver                  = None
+Transmitter               = None
+Transceiver               = None
 
 # The main definitions have been moved to bbndb
 # to keep the schema consistent across Auspex and QGL
@@ -62,5 +63,6 @@ def define_entities(db, cache_callback=None):
     globals()["Edge"]                      = qgl.Edge
     globals()["MicrowaveSource"]           = qgl.MicrowaveSource
     globals()["ChannelDatabase"]           = qgl.ChannelDatabase
-    globals()["Digitizer"]                 = qgl.Digitizer
-    globals()["AWG"]                       = qgl.AWG
+    globals()["Receiver"]                  = qgl.Receiver
+    globals()["Transmitter"]               = qgl.Transmitter
+    globals()["Transceiver"]               = qgl.Transceiver
diff --git a/QGL/__init__.py b/QGL/__init__.py
index 99081cde..b82dc058 100644
--- a/QGL/__init__.py
+++ b/QGL/__init__.py
@@ -1,6 +1,6 @@
-from .Channels import Qubit, Measurement, Edge, MicrowaveSource, ChannelDatabase, AWG, Digitizer
+from .Channels import Qubit, Measurement, Edge, MicrowaveSource, ChannelDatabase, Transmitter, Receiver, Transceiver
 from .ChannelLibraries import QubitFactory, MeasFactory, EdgeFactory, MarkerFactory, ChannelLibrary, channelLib
-from .ChannelLibraries import new_APS2, new_X6, new_Alazar, new_qubit, set_control, set_measure, set_master, new_source
+from .ChannelLibraries import new_APS2, new_X6, new_APS2_rack, new_Alazar, new_qubit, set_control, set_measure, set_master, new_source
 from .PulsePrimitives import *
 from .Compiler import compile_to_hardware, set_log_level
 from .PulseSequencer import align

From 99d30b87a39c4d8eb1b13c6a5092b9c6708e2a37 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 9 Oct 2018 17:21:54 -0400
Subject: [PATCH 063/235] Preliminary functionality moving to sqlalchemy from
 pony (sigh of relief)

---
 QGL/ChannelLibraries.py | 436 ++++++++++++++++++----------------------
 QGL/Channels.py         |  44 +---
 QGL/Compiler.py         |   4 +-
 QGL/__init__.py         |   4 +-
 QGL/config.py           |  11 +-
 5 files changed, 208 insertions(+), 291 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 81f54d12..1f62d3ac 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -38,34 +38,33 @@
 import importlib
 import inspect
 from functools import wraps
-from pony.orm import *
 import numpy as np
 import networkx as nx
+ 
+import bbndb
 
 from . import config
 from . import Channels
 from . import PulseShapes
 from .PulsePrimitives import clear_pulse_cache
-import bbndb
 
 channelLib = None
-db = None
-
-def localize_db_objects(f):
-    """Since we can't mix db objects from separate sessions, re-fetch entities by their unique IDs"""
-    @wraps(f)
-    def wrapper(*args, **kwargs):
-        global db
-        with db_session:
-            args_info    = [(type(arg), arg.id) if isinstance(arg, db.Entity) else (arg, None) for arg in args]
-            kwargs_info  = {k: (type(v), v.id) if isinstance(v, db.Entity) else (v, None) for k, v in kwargs.items()}
-        with db_session:
-            new_args   = [c[i] if i else c for c, i in args_info]
-            new_kwargs = {k: v[0][v[1]] if v[1] else v[0] for k,v in kwargs_info.items()}
-            return f(*new_args, **new_kwargs)
-    return wrapper
-
-def set_from_dict(obj, settings):
+
+# def localize_db_objects(f):
+    # """Since we can't mix db objects from separate sessions, re-fetch entities by their unique IDs"""
+    # @wraps(f)
+    # def wrapper(*args, **kwargs):
+    #     global db
+    #     with db_session:
+    #         args_info    = [(type(arg), arg.id) if isinstance(arg, db.Entity) else (arg, None) for arg in args]
+    #         kwargs_info  = {k: (type(v), v.id) if isinstance(v, db.Entity) else (v, None) for k, v in kwargs.items()}
+    #     with db_session:
+    #         new_args   = [c[i] if i else c for c, i in args_info]
+    #         new_kwargs = {k: v[0][v[1]] if v[1] else v[0] for k,v in kwargs_info.items()}
+    #         return f(*new_args, **new_kwargs)
+    # return wrapper
+
+def set_from_dict(self, obj, settings):
     for prop_name in obj.to_dict().keys():
         if prop_name in settings.keys():
             try:
@@ -73,7 +72,6 @@ def set_from_dict(obj, settings):
             except Exception as e:
                 print(f"{obj.label}: Error loading {prop_name} from config")
 
-@db_session
 def copy_objs(*entities, new_channel_db):
     # Entities is a list of lists of entities of specific types
     new_entities    = []
@@ -99,7 +97,6 @@ def copy_objs(*entities, new_channel_db):
 
     return new_entities
 
-@db_session
 def copy_entity(obj, new_channel_db):
     """Copy a pony entity instance"""
     kwargs = {a.name: getattr(obj, a.name) for a in obj._attrs_ if a.name not in ["id", "classtype"]}
@@ -118,71 +115,57 @@ def copy_entity(obj, new_channel_db):
 
 class ChannelLibrary(object):
 
-    def __init__(self, database_file=None, channelDict={}, **kwargs):
+    def __init__(self, db_resource_name=None):
         """Create the channel library."""
 
-        global channelLib, db
-        if channelLib is not None:
-            channelLib.db.disconnect()
+        global channelLib
 
-        config.load_db()
-        self.database_provider = "sqlite"
-        if database_file:
-            self.database_file = database_file
-        elif config.db_file:
-            self.database_file = config.db_file
-        else:
-            self.database_file = ":memory:"
+        self.db_provider = "sqlite"
+        self.db_resource_name = ":memory:"
 
-        db = Database()
-        Channels.define_entities(db, cache_callback=clear_pulse_cache)
-        db.bind(self.database_provider, filename=self.database_file, create_db=True)
-        db.generate_mapping(create_tables=True)
-        bbndb.database = db
-
-        # Dirty trick: push the correct entity defs to the calling context
-        for var in ["Measurement","Qubit","Edge"]:
-            inspect.stack()[1][0].f_globals[var] = getattr(Channels, var)
+        if bbndb.engine:
+            # Use current db
+            self.db = bbndb.engine
+        else:
+            
+            if db_resource_name:
+                self.db_resource_name = db_resource_name
+            elif config.load_db():
+                self.db_resource_name = config.load_db()
+
+            self.db = bbndb.engine = bbndb.create_engine(f'{self.db_provider}:///{self.db_resource_name}', echo=False)
+        
+        bbndb.Base.metadata.create_all(bbndb.engine)
+        bbndb.Session.configure(bind=bbndb.engine)
+        self.Session = bbndb.Session
+        self.session = self.Session()
 
         self.connectivityG = nx.DiGraph()
 
-        # This is still somewhere legacy QGL behavior. Massage db into dict for lookup.
-        self.channelDict = {}
-
         # Check to see whether there is already a temp database
-        with db_session:
-            w_dbs = list(select(d for d in Channels.ChannelDatabase if d.label == "working"))
-            if len(w_dbs) > 1:
-                # self.clear(channel_db=cdb, create_new=False)
-                raise Exception("More than one working database exists!")
-            elif len(w_dbs) == 1:
-                self.channelDatabase = w_dbs[0]
-                commit()
-                self.update_channelDict()
-            elif len(w_dbs) == 0:
-                self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
-            # commit()
-
-        config.load_config()
+        working_dbs = self.session.query(Channels.ChannelDatabase).filter_by(label="working").all()
+        if len(working_dbs) > 1:
+            raise Exception("More than one working database exists!")
+        elif len(working_dbs) == 1:
+            self.channelDatabase = working_dbs[0]
+        elif len(working_dbs) == 0:
+            self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
+            self.session.add(self.channelDatabase)
+
+        self.update_channelDict()
 
         # Update the global reference
         channelLib = self
 
-    @db_session
     def get_current_channels(self):
-        cdb = Channels.ChannelDatabase[self.channelDatabase.id] # Can't use external object
-        return list(cdb.channels) + list(cdb.sources)
+        return self.channelDatabase.channels + self.channelDatabase.generators
 
-    @db_session
     def update_channelDict(self):
-        commit()
         self.channelDict = {c.label: c for c in self.get_current_channels()}
 
-    @db_session
     def ls(self):
         select((c.label, c.time, c.id) for c in Channels.ChannelDatabase).sort_by(1, 2).show()
 
-    @db_session
     def ent_by_type_name(self, name, show=False):
         q = select(c for c in getattr(bbndb.qgl,name) if c.channel_db.label == "working")
         if show:
@@ -214,52 +197,40 @@ def ls_qubits(self):
     def ls_meas(self):
         return self.ent_by_type_name("Measurement", show=True)
 
-    @db_session
     def load(self, name, index=1):
         """Load the latest instance for a particular name. Specifying index = 2 will select the second most recent instance """
         obj = list(select(c for c in Channels.ChannelDatabase if c.label==name).sort_by(desc(Channels.ChannelDatabase.time)))
         self.load_obj(obj[-index])
 
-    @db_session
     def load_by_id(self, id_num):
         obj = select(c for c in Channels.ChannelDatabase if c.id==id_num).first()
         self.load_obj(obj)
 
-    @db_session
     def clear(self, channel_db=None, create_new=True):
         # If no database is specified, clear self.database
         channel_db = channel_db if channel_db else self.channelDatabase
         # First clear items that don't have Sets of other items
         for ent in [Channels.MicrowaveSource, Channels.Channel, Channels.Transmitter, Channels.Receiver, Channels.Transceiver]:
             select(c for c in ent if c.channel_db == channel_db).delete(bulk=True)
-            commit()
         # Now clear items that do potentially have sets of items (which should be deleted)
         for ent in [Channels.ChannelDatabase]:
             select(d for d in ent if d.label == "working").delete(bulk=True)
-            commit()
         if create_new:
-            self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
-            commit()
+            print("created new database with id", self.channelDatabase.id)
+        channelLib = self
 
-    @db_session
     def load_obj(self, obj):
-        commit()
         self.clear()
         chans, srcs, d2as, a2ds, trans = map(list, [obj.channels, obj.sources, obj.transmitters, obj.receivers, obj.transceivers])
         copy_objs(chans, srcs, d2as, a2ds, trans, new_channel_db=self.channelDatabase)
-        commit()
         self.update_channelDict()
 
-    @db_session
     def save_as(self, name):
         chans, srcs, d2as, a2dsm, trans = map(list, [self.channelDatabase.channels, self.channelDatabase.sources,
                                             self.channelDatabase.transmitters, self.channelDatabase.receivers,
                                             self.channelDatabase.transceivers])
-        commit()
-        cd = Channels.ChannelDatabase(label=name, time=datetime.datetime.now())
         new_chans, new_srcs, new_d2as, new_a2ds, new_trans = copy_objs(chans, srcs, d2as, a2ds, trans, new_channel_db=cd)
         cd.channels, cd.sources, cd.transmitters, cd.receivers, cd.transceivers = new_chans, new_srcs, new_d2as, new_a2ds, new_trans
-        commit()
 
     #Dictionary methods
     def __getitem__(self, key):
@@ -280,7 +251,6 @@ def keys(self):
     def values(self):
         return self.channelDict.values()
 
-    @db_session
     def build_connectivity_graph(self):
         # build connectivity graph
 <<<<<<< HEAD
@@ -487,158 +457,149 @@ def load_from_library(self, return_only=False):
             self.connectivityG[chan.source][chan.target]['channel'] = chan
 >>>>>>> Ditch atom, move to Pony.orm for all channel library objects.
 
-# Convenience functions for generating and linking channels
-# TODO: move these to a shim layer shared by Auspex/QGL
-
-@db_session
-def new_APS2(label, address):
-    cdb    = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
-    chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=cdb)
-    m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=cdb)
-    m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=cdb)
-    m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=cdb)
-    m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=cdb)
-
-    this_transmitter = Channels.Transmitter(label=label, model="APS2", address=address, channels=[chan12, m1, m2, m3, m4], channel_db=cdb)
-    this_transmitter.trigger_source = "External"
-    this_transmitter.address        = address
-
-    commit()
-    return this_transmitter
-
-@db_session
-def new_APS2_rack(label, num, start_address):
-    cdb              = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
-    address_start    = ".".join(start_address.split(".")[:3])
-    address_end      = int(start_address.split(".")[-1])
-    transmitters     = [new_APS2(f"{label}_U{i}", f"{address_start}.{address_end+i}") for i in range(1,num+1)]
-    this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", transmitters=transmitters, channel_db=cdb)
-
-    commit()
-    return this_transceiver
-
-@db_session
-def new_X6(label, address, dsp_channel=0, record_length=1024):
-    cdb   = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
-    chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, dsp_channel=dsp_channel, channel_db=cdb)
-    chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, dsp_channel=dsp_channel, channel_db=cdb)
-
-    this_receiver = Channels.Receiver(label=label, model="X6-1000M", address=address, channels=[chan1, chan2],
-                                  record_length=record_length, channel_db=cdb)
-    this_receiver.trigger_source = "External"
-    this_receiver.stream_types   = "raw, demodulated, integrated"
-    this_receiver.address        = address
-
-    # Add a default kernel
-    chan1.kernel = np.ones(record_length, dtype=np.complex).tobytes()
-    chan2.kernel = np.ones(record_length, dtype=np.complex).tobytes()
-
-    commit()
-    return this_receiver
-
-@db_session
-def new_Alazar(label, address, record_length=1024):
-    cdb   = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
-    chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, channel_db=cdb)
-    chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, channel_db=cdb)
-
-    this_receiver = Channels.Receiver(label=label, model="AlazarATS9870", address=address, channels=[chan1, chan2],
-                                  record_length=record_length, channel_db=cdb)
-    this_receiver.trigger_source = "External"
-    this_receiver.stream_types   = "raw"
-    this_receiver.address        = address
-
-    commit()
-    return this_receiver
-
-@db_session
-def new_qubit(label):
-    cdb   = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
-    thing = Channels.Qubit(label=label, channel_db=cdb)
-    return thing
-
-@db_session
-def new_source(label, model, address, power=-30.0, frequency=5.0e9):
-    cdb   = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
-    thing = Channels.MicrowaveSource(label=label, model=model, address=address, power=power, frequency=frequency, channel_db=cdb)
-    return thing
-
-@localize_db_objects
-def set_control(qubit, transmitter, generator=None):
-    quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
-    markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
-
-    if isinstance(transmitter, Channels.Transmitter) and len(quads) > 1:
-        raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
-    elif isinstance(transmitter, Channels.Transmitter) and len(quads) == 1:
-        phys_chan = quads[0]
-    elif isinstance(transmitter, Channels.PhysicalQuadratureChannel):
-        phys_chan = transmitter
-    else:
-        raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
-
-    qubit.phys_chan = phys_chan
-    if generator:
-        qubit.phys_chan.generator = generator
-
-@localize_db_objects
-def set_measure(qubit, transmitter, receivers, generator=None, receivers_channel=1, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
-    cdb     = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
-    quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
-    markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
-
-    if isinstance(transmitter, Channels.Transmitter) and len(quads) > 1:
-        raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
-    elif isinstance(transmitter, Channels.Transmitter) and len(quads) == 1:
-        phys_chan = quads[0]
-    elif isinstance(transmitter, Channels.PhysicalQuadratureChannel):
-        phys_chan = transmitter
-    else:
-        raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
-
-    meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=cdb)
-    meas.phys_chan = phys_chan
-    if generator:
-        meas.phys_chan.generator = generator
-
-    phys_trig_channel = trig_channel if trig_channel else transmitter.get_chan("12m1")
-
-    trig_chan              = Channels.LogicalMarkerChannel(label=f"receiversTrig-{qubit.label}", channel_db=cdb)
-    trig_chan.phys_chan    = phys_trig_channel
-    trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
-    meas.trig_chan         = trig_chan
-
-    if isinstance(receivers, Channels.Receiver) and len(receivers.channels) > 1:
-        raise ValueError("In set_measure the Receiver must have a single receiver channel or a specific channel must be passed instead")
-    elif isinstance(receivers, Channels.Receiver) and len(receivers.channels) == 1:
-        rcv_chan = receivers.channels[0]
-    elif isinstance(receivers, Channels.ReceiverChannel):
-        rcv_chan = receivers
-    else:
-        raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
-
-    meas.receiver_chan = rcv_chan
-
-    if gate:
-        phys_gate_channel   = gate_channel if gate_channel else transmitter.get_chan("12m2")
-        gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=cdb)
-        gate_chan.phys_chan = phys_gate_channel
-        meas.gate_chan      = gate_chan
-
-@localize_db_objects
-def set_master(transmitter, trig_channel, pulse_length=1e-7):
-    if not isinstance(trig_channel, Channels.PhysicalMarkerChannel):
-        raise ValueError("In set_master the trigger channel must be an instance of PhysicalMarkerChannel")
-
-    cdb = Channels.ChannelDatabase[channelLib.channelDatabase.id] # Can't use external object
-    st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=cdb)
-    st.phys_chan = trig_channel
-    st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
-    transmitter.master = True
-    transmitter.trigger_source = "Internal"
-
-@db_session
-def QubitFactory(label, **kwargs):
+    # # Convenience functions for generating and linking channels
+    # # TODO: move these to a shim layer shared by Auspex/QGL
+    # def sessionify(func):
+    #     @wraps(func)
+    #     def without_session(*args, **kwargs):
+    #         return func(channelLib.session, *args, **kwargs)
+    #     return without_session
+
+    def new_APS2(self, label, address):
+        chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+
+        this_transmitter = Channels.Transmitter(label=label, model="APS2", address=address, channels=[chan12, m1, m2, m3, m4], channel_db=self.channelDatabase)
+        this_transmitter.trigger_source = "external"
+        this_transmitter.address        = address
+
+        self.session.add(this_transmitter)
+        return this_transmitter
+
+    def new_APS2_rack(self, label, num, start_address):
+        address_start    = ".".join(start_address.split(".")[:3])
+        address_end      = int(start_address.split(".")[-1])
+        transmitters     = [new_APS2(f"{label}_U{i}", f"{address_start}.{address_end+i}") for i in range(1,num+1)]
+        this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", transmitters=transmitters, channel_db=self.channelDatabase)
+
+        self.session.add(this_transceiver)
+        return this_transceiver
+
+    def new_X6(self, label, address, dsp_channel=0, record_length=1024):
+        chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, dsp_channel=dsp_channel, channel_db=self.channelDatabase)
+        chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, dsp_channel=dsp_channel, channel_db=self.channelDatabase)
+
+        this_receiver = Channels.Receiver(label=label, model="X6-1000M", address=address, channels=[chan1, chan2],
+                                      record_length=record_length, channel_db=self.channelDatabase)
+        this_receiver.trigger_source = "external"
+        this_receiver.stream_types   = "raw, demodulated, integrated"
+        this_receiver.address        = address
+
+        # Add a default kernel
+        chan1.kernel = np.ones(record_length, dtype=np.complex).tobytes()
+        chan2.kernel = np.ones(record_length, dtype=np.complex).tobytes()
+
+        self.session.add(this_receiver)
+        return this_receiver
+
+    def new_Alazar(self, label, address, record_length=1024):
+        chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, channel_db=self.channelDatabase)
+        chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, channel_db=self.channelDatabase)
+
+        this_receiver = Channels.Receiver(label=label, model="AlazarATS9870", address=address, channels=[chan1, chan2],
+                                      record_length=record_length, channel_db=self.channelDatabase)
+        this_receiver.trigger_source = "external"
+        this_receiver.stream_types   = "raw"
+        this_receiver.address        = address
+
+        self.session.add(this_receiver)
+        return this_receiver
+
+    def new_qubit(self, label):
+        thing = Channels.Qubit(label=label, channel_db=self.channelDatabase)
+        self.session.add(thing)
+        return thing
+
+    def new_source(self, label, model, address, power=-30.0, frequency=5.0e9):
+        thing = Channels.MicrowaveSource(label=label, model=model, address=address, power=power, frequency=frequency, channel_db=self.channelDatabase)
+        self.session.add(thing)
+        return thing
+
+    # @localize_db_objects
+    def set_control(self, qubit, transmitter, generator=None):
+        quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
+        markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
+
+        if isinstance(transmitter, Channels.Transmitter) and len(quads) > 1:
+            raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+        elif isinstance(transmitter, Channels.Transmitter) and len(quads) == 1:
+            phys_chan = quads[0]
+        elif isinstance(transmitter, Channels.PhysicalQuadratureChannel):
+            phys_chan = transmitter
+        else:
+            raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+
+        qubit.phys_chan = phys_chan
+        if generator:
+            qubit.phys_chan.generator = generator
+
+    # @localize_db_objects
+    def set_measure(self, qubit, transmitter, receivers, generator=None, receivers_channel=1, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
+        quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
+        markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
+
+        if isinstance(transmitter, Channels.Transmitter) and len(quads) > 1:
+            raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+        elif isinstance(transmitter, Channels.Transmitter) and len(quads) == 1:
+            phys_chan = quads[0]
+        elif isinstance(transmitter, Channels.PhysicalQuadratureChannel):
+            phys_chan = transmitter
+        else:
+            raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+
+        meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=self.channelDatabase)
+        meas.phys_chan = phys_chan
+        if generator:
+            meas.phys_chan.generator = generator
+
+        phys_trig_channel = trig_channel if trig_channel else transmitter.get_chan("12m1")
+
+        trig_chan              = Channels.LogicalMarkerChannel(label=f"receiversTrig-{qubit.label}", channel_db=self.channelDatabase)
+        trig_chan.phys_chan    = phys_trig_channel
+        trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
+        meas.trig_chan         = trig_chan
+
+        if isinstance(receivers, Channels.Receiver) and len(receivers.channels) > 1:
+            raise ValueError("In set_measure the Receiver must have a single receiver channel or a specific channel must be passed instead")
+        elif isinstance(receivers, Channels.Receiver) and len(receivers.channels) == 1:
+            rcv_chan = receivers.channels[0]
+        elif isinstance(receivers, Channels.ReceiverChannel):
+            rcv_chan = receivers
+        else:
+            raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+
+        meas.receiver_chan = rcv_chan
+
+        if gate:
+            phys_gate_channel   = gate_channel if gate_channel else transmitter.get_chan("12m2")
+            gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=self.channelDatabase)
+            gate_chan.phys_chan = phys_gate_channel
+            meas.gate_chan      = gate_chan
+
+    def set_master(self, transmitter, trig_channel, pulse_length=1e-7):
+        if not isinstance(trig_channel, Channels.PhysicalMarkerChannel):
+            raise ValueError("In set_master the trigger channel must be an instance of PhysicalMarkerChannel")
+
+        st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=self.channelDatabase)
+        st.phys_chan = trig_channel
+        st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
+        transmitter.master = True
+        transmitter.trigger_source = "internal"
+
+def QubitFactory(self, label, **kwargs):
     ''' Return a saved qubit channel or create a new one. '''
     # TODO: this will just get the first entry in the whole damned DB!
     # thing = select(el for el in Channels.Qubit if el.label==label).first()
@@ -648,8 +609,7 @@ def QubitFactory(label, **kwargs):
     else:
         return Channels.Qubit(label=label, **kwargs)
 
-@db_session
-def MeasFactory(label, **kwargs):
+def MeasFactory(self, label, **kwargs):
     ''' Return a saved measurement channel or create a new one. '''
     thing = {c.label: c for c in channelLib.get_current_channels() if isinstance(c, Channels.Measurement)}[label]
     if thing:
@@ -657,8 +617,7 @@ def MeasFactory(label, **kwargs):
     else:
         return Channels.Measurement(label=label, **kwargs)
 
-@db_session
-def MarkerFactory(label, **kwargs):
+def MarkerFactory(self, label, **kwargs):
     ''' Return a saved Marker channel or create a new one. '''
     thing = {c.label: c for c in channelLib.get_current_channels()}[label]
     if thing:
@@ -666,8 +625,7 @@ def MarkerFactory(label, **kwargs):
     else:
         return Channels.LogicalMarkerChannel(label=label, **kwargs)
 
-@db_session
-def EdgeFactory(source, target):
+def EdgeFactory(self, source, target):
     if channelLib.connectivityG.has_edge(source, target):
         return channelLib.connectivityG[source][target]['channel']
     elif channelLib.connectivityG.has_edge(target, source):
diff --git a/QGL/Channels.py b/QGL/Channels.py
index 2e1a2a8c..1c9807d4 100644
--- a/QGL/Channels.py
+++ b/QGL/Channels.py
@@ -23,46 +23,4 @@
 
 from . import config
 from . import PulseShapes
-from bbndb import define_entities as def_ent
-from bbndb import qgl
-
-# Get these in global scope for module imports
-Channel                   = None
-PhysicalChannel           = None
-LogicalChannel            = None
-PhysicalQuadratureChannel = None
-PhysicalMarkerChannel     = None
-LogicalMarkerChannel      = None
-ReceiverChannel           = None
-Measurement               = None
-Qubit                     = None
-Edge                      = None
-MicrowaveSource           = None
-ChannelDatabase           = None
-Receiver                  = None
-Transmitter               = None
-Transceiver               = None
-
-# The main definitions have been moved to bbndb
-# to keep the schema consistent across Auspex and QGL
-# We retain this local framework in order to maintain
-# the paths for QGL primitives
-
-def define_entities(db, cache_callback=None):
-    def_ent(db, cache_callback=cache_callback)
-
-    globals()["Channel"]                   = qgl.Channel
-    globals()["PhysicalChannel"]           = qgl.PhysicalChannel
-    globals()["LogicalChannel"]            = qgl.LogicalChannel
-    globals()["PhysicalQuadratureChannel"] = qgl.PhysicalQuadratureChannel
-    globals()["PhysicalMarkerChannel"]     = qgl.PhysicalMarkerChannel
-    globals()["LogicalMarkerChannel"]      = qgl.LogicalMarkerChannel
-    globals()["ReceiverChannel"]           = qgl.ReceiverChannel
-    globals()["Measurement"]               = qgl.Measurement
-    globals()["Qubit"]                     = qgl.Qubit
-    globals()["Edge"]                      = qgl.Edge
-    globals()["MicrowaveSource"]           = qgl.MicrowaveSource
-    globals()["ChannelDatabase"]           = qgl.ChannelDatabase
-    globals()["Receiver"]                  = qgl.Receiver
-    globals()["Transmitter"]               = qgl.Transmitter
-    globals()["Transceiver"]               = qgl.Transceiver
+from bbndb.qgl import *
\ No newline at end of file
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 3ee00996..ec17af38 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -480,8 +480,8 @@ def compile_to_hardware(seqs,
         extra_meta = awg_metas
     # create meta output
     db_info = {
-        'db_provider': ChannelLibraries.channelLib.database_provider,
-        'db_filename': ChannelLibraries.channelLib.database_file,
+        'db_provider': ChannelLibraries.channelLib.db_provider,
+        'db_resource_name': ChannelLibraries.channelLib.db_resource_name,
         'library_name': 'working',
         'library_id': ChannelLibraries.channelLib.channelDatabase.id
     }
diff --git a/QGL/__init__.py b/QGL/__init__.py
index b82dc058..aa06418c 100644
--- a/QGL/__init__.py
+++ b/QGL/__init__.py
@@ -1,6 +1,6 @@
-from .Channels import Qubit, Measurement, Edge, MicrowaveSource, ChannelDatabase, Transmitter, Receiver, Transceiver
+from .Channels import Qubit, Measurement, Edge, Generator, ChannelDatabase, Transmitter, Receiver, Transceiver
 from .ChannelLibraries import QubitFactory, MeasFactory, EdgeFactory, MarkerFactory, ChannelLibrary, channelLib
-from .ChannelLibraries import new_APS2, new_X6, new_APS2_rack, new_Alazar, new_qubit, set_control, set_measure, set_master, new_source
+# from .ChannelLibraries import new_APS2, new_X6, new_APS2_rack, new_Alazar, new_qubit, set_control, set_measure, set_master, new_source
 from .PulsePrimitives import *
 from .Compiler import compile_to_hardware, set_log_level
 from .PulseSequencer import align
diff --git a/QGL/config.py b/QGL/config.py
index eaeb6322..c21dd560 100644
--- a/QGL/config.py
+++ b/QGL/config.py
@@ -6,13 +6,13 @@
 import importlib
 
 # Where to store AWG data
-AWGDir         = None
+AWGDir           = None
 
 # The db file, where the channel libraries are stored
-db_file        = None
+db_resource_name = None
 
 # The config file (executed upon channel library loading)
-config_file    = None
+config_file      = None
 
 # plotting options
 plotBackground = '#EAEAF2'
@@ -36,6 +36,7 @@ def load_config():
             raise Exception(f"Could not import/execute the BBN_CONFIG {os.getenv('BBN_CONFIG')}")
             
 def load_db():
-    global db_file
+    global db_resource_name
     if os.getenv('BBN_DB'):
-        db_file = os.getenv("BBN_DB")
\ No newline at end of file
+        db_resource_name = os.getenv("BBN_DB")
+    return db_resource_name
\ No newline at end of file

From 352b23c4eb866493fbf1e5a8ca272518442b892c Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 9 Oct 2018 22:05:56 -0400
Subject: [PATCH 064/235] Fix queries for channel db

---
 QGL/ChannelLibraries.py | 53 ++++++++++++++++++++++++++++-------------
 1 file changed, 36 insertions(+), 17 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 1f62d3ac..4a369eb2 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -143,7 +143,8 @@ def __init__(self, db_resource_name=None):
         self.connectivityG = nx.DiGraph()
 
         # Check to see whether there is already a temp database
-        working_dbs = self.session.query(Channels.ChannelDatabase).filter_by(label="working").all()
+        working_dbs = self.query(Channels.ChannelDatabase, label="working").all()
+        # working_dbs = self.session.query(Channels.ChannelDatabase).filter_by(label="working").all()
         if len(working_dbs) > 1:
             raise Exception("More than one working database exists!")
         elif len(working_dbs) == 1:
@@ -157,6 +158,9 @@ def __init__(self, db_resource_name=None):
         # Update the global reference
         channelLib = self
 
+    def query(self, obj_type, **kwargs):
+        return self.session.query(obj_type).filter_by(**kwargs)
+
     def get_current_channels(self):
         return self.channelDatabase.channels + self.channelDatabase.generators
 
@@ -164,38 +168,47 @@ def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
 
     def ls(self):
-        select((c.label, c.time, c.id) for c in Channels.ChannelDatabase).sort_by(1, 2).show()
-
-    def ent_by_type_name(self, name, show=False):
-        q = select(c for c in getattr(bbndb.qgl,name) if c.channel_db.label == "working")
+        cdb = Channels.ChannelDatabase
+        q = self.session.query(cdb.label, cdb.time, cdb.id).\
+            order_by(Channels.ChannelDatabase.id, Channels.ChannelDatabase.label).all()
+        # select((c.label, c.time, c.id) for c in Channels.ChannelDatabase).sort_by(1, 2).show()
+        for i, (label, time, id) in enumerate(q):
+                print(f"[{id}] ({time}) -> {label}")
+
+    def ent_by_type(self, obj_type, show=False):
+        q = self.session.query(obj_type).filter(obj_type.channel_db.has(label="working")).order_by(obj_type.label).all()
         if show:
-            select(c.label for c in getattr(bbndb.qgl,name) if c.channel_db.label == "working").sort_by(1).show()
+            for i, el in enumerate(q):
+                print(f"[{i}] -> {el.label}")
         else:
-            return {el.label: el for el in q}
+            return q
 
     def receivers(self):
-        return self.ent_by_type_name("Receiver")
+        return self.ent_by_type(Channels.Receiver)
+
+    def transmitters(self):
+        return self.ent_by_type(Channels.Transmitter)
 
-    def transmitter(self):
-        return self.ent_by_type_name("Transmitter")
+    def transceivers(self):
+        return self.ent_by_type(Channels.Transceiver)
 
     def qubits(self):
-        return self.ent_by_type_name("Qubit")
+        return self.ent_by_type(Channels.Qubit)
 
     def meas(self):
-        return self.ent_by_type_name("Measurement")
+        return self.ent_by_type(Channels.Measurement)
 
     def ls_receivers(self):
-        return self.ent_by_type_name("Receiver", show=True)
+        return self.ent_by_type(Channels.Receiver, show=True)
 
     def ls_transmitters(self):
-        return self.ent_by_type_name("Transmitter", show=True)
+        return self.ent_by_type(Channels.Transmitter, show=True)
 
     def ls_qubits(self):
-        return self.ent_by_type_name("Qubit", show=True)
+        return self.ent_by_type(Channels.Qubit, show=True)
 
-    def ls_meas(self):
-        return self.ent_by_type_name("Measurement", show=True)
+    def ls_measurements(self):
+        return self.ent_by_type(Channels.Measurement, show=True)
 
     def load(self, name, index=1):
         """Load the latest instance for a particular name. Specifying index = 2 will select the second most recent instance """
@@ -225,6 +238,12 @@ def load_obj(self, obj):
         copy_objs(chans, srcs, d2as, a2ds, trans, new_channel_db=self.channelDatabase)
         self.update_channelDict()
 
+    def save(self):
+        self.session.commit()
+
+    def discard_changes(self):
+        self.session.rollback()
+
     def save_as(self, name):
         chans, srcs, d2as, a2dsm, trans = map(list, [self.channelDatabase.channels, self.channelDatabase.sources,
                                             self.channelDatabase.transmitters, self.channelDatabase.receivers,

From 64cca256c3b480558b9e0ff7fa486e28b89d054f Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 9 Oct 2018 22:22:10 -0400
Subject: [PATCH 065/235] Fix Factories in ChannelLibraries

---
 QGL/ChannelLibraries.py | 49 +++++++++++++++++++++--------------------
 1 file changed, 25 insertions(+), 24 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 4a369eb2..575d28db 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -476,14 +476,6 @@ def load_from_library(self, return_only=False):
             self.connectivityG[chan.source][chan.target]['channel'] = chan
 >>>>>>> Ditch atom, move to Pony.orm for all channel library objects.
 
-    # # Convenience functions for generating and linking channels
-    # # TODO: move these to a shim layer shared by Auspex/QGL
-    # def sessionify(func):
-    #     @wraps(func)
-    #     def without_session(*args, **kwargs):
-    #         return func(channelLib.session, *args, **kwargs)
-    #     return without_session
-
     def new_APS2(self, label, address):
         chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
         m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
@@ -618,33 +610,42 @@ def set_master(self, transmitter, trig_channel, pulse_length=1e-7):
         transmitter.master = True
         transmitter.trigger_source = "internal"
 
-def QubitFactory(self, label, **kwargs):
+def QubitFactory(label, **kwargs):
     ''' Return a saved qubit channel or create a new one. '''
     # TODO: this will just get the first entry in the whole damned DB!
     # thing = select(el for el in Channels.Qubit if el.label==label).first()
-    thing = {c.label: c for c in channelLib.get_current_channels() if isinstance(c, Channels.Qubit)}[label]
-    if thing:
-        return thing
+    q = channelLib.session.query(Channels.Qubit).filter(Channels.Qubit.label==label).all()
+    # thing = {c.label: c for c in channelLib.get_current_channels() if isinstance(c, Channels.Qubit)}[label]
+    if len(q) == 1:
+        return q[0]
     else:
-        return Channels.Qubit(label=label, **kwargs)
+        c = Channels.Qubit(label=label, channel_db=channelLib.channelDatabase, **kwargs)
+        channelLib.session.add(c)
+        return c
 
-def MeasFactory(self, label, **kwargs):
+def MeasFactory(label, **kwargs):
     ''' Return a saved measurement channel or create a new one. '''
-    thing = {c.label: c for c in channelLib.get_current_channels() if isinstance(c, Channels.Measurement)}[label]
-    if thing:
-        return thing
+    q = channelLib.session.query(Channels.Measurement).filter(Channels.Measurement.label==label).all()
+    # thing = {c.label: c for c in channelLib.get_current_channels() if isinstance(c, Channels.Measurement)}[label]
+    if len(q) == 1:
+        return q[0]
     else:
-        return Channels.Measurement(label=label, **kwargs)
+        c = Channels.Measurement(label=label, channel_db=channelLib.channelDatabase, **kwargs)
+        channelLib.session.add(c)
+        return c
 
-def MarkerFactory(self, label, **kwargs):
+def MarkerFactory(label, **kwargs):
     ''' Return a saved Marker channel or create a new one. '''
-    thing = {c.label: c for c in channelLib.get_current_channels()}[label]
-    if thing:
-        return thing
+    q = channelLib.session.query(Channels.LogicalMarkerChannel).filter(Channels.LogicalMarkerChannel.label==label).all()
+    # thing = {c.label: c for c in channelLib.get_current_channels()}[label]
+    if len(q) == 1:
+        return q[0]
     else:
-        return Channels.LogicalMarkerChannel(label=label, **kwargs)
+        c = Channels.LogicalMarkerChannel(label=label, channel_db=channelLib.channelDatabase, **kwargs)
+        channelLib.session.add(c)
+        return c
 
-def EdgeFactory(self, source, target):
+def EdgeFactory(source, target):
     if channelLib.connectivityG.has_edge(source, target):
         return channelLib.connectivityG[source][target]['channel']
     elif channelLib.connectivityG.has_edge(target, source):

From c3279f6b7c99f624e779196431a92b4f40fb0ba7 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 11 Oct 2018 09:51:57 -0400
Subject: [PATCH 066/235] Clearing now functioning properly, working on copy,
 load

---
 QGL/ChannelLibraries.py | 329 +++++++++-------------------------------
 1 file changed, 73 insertions(+), 256 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 575d28db..995191ac 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -40,7 +40,7 @@
 from functools import wraps
 import numpy as np
 import networkx as nx
- 
+
 import bbndb
 
 from . import config
@@ -48,21 +48,20 @@
 from . import PulseShapes
 from .PulsePrimitives import clear_pulse_cache
 
+from sqlalchemy.orm.session import make_transient
+
 channelLib = None
 
-# def localize_db_objects(f):
-    # """Since we can't mix db objects from separate sessions, re-fetch entities by their unique IDs"""
-    # @wraps(f)
-    # def wrapper(*args, **kwargs):
-    #     global db
-    #     with db_session:
-    #         args_info    = [(type(arg), arg.id) if isinstance(arg, db.Entity) else (arg, None) for arg in args]
-    #         kwargs_info  = {k: (type(v), v.id) if isinstance(v, db.Entity) else (v, None) for k, v in kwargs.items()}
-    #     with db_session:
-    #         new_args   = [c[i] if i else c for c, i in args_info]
-    #         new_kwargs = {k: v[0][v[1]] if v[1] else v[0] for k,v in kwargs_info.items()}
-    #         return f(*new_args, **new_kwargs)
-    # return wrapper
+def check_session_dirty(f):
+    """Since we can't mix db objects from separate sessions, re-fetch entities by their unique IDs"""
+    @wraps(f)
+    def wrapper(cls, *args, **kwargs):
+        if not 'force' in kwargs and kwargs['force']:
+            if len(cls.session.dirty | cls.session.new) != 0:
+                kwargs.pop('force')
+                raise Exception("Uncommitted transactions for working database. Either use force=True or commit/revert your changes.")
+        return f(cls, *args, **kwargs)
+    return wrapper
 
 def set_from_dict(self, obj, settings):
     for prop_name in obj.to_dict().keys():
@@ -72,7 +71,7 @@ def set_from_dict(self, obj, settings):
             except Exception as e:
                 print(f"{obj.label}: Error loading {prop_name} from config")
 
-def copy_objs(*entities, new_channel_db):
+def copy_objs(entities, new_channel_db, session):
     # Entities is a list of lists of entities of specific types
     new_entities    = []
     old_to_new      = {}
@@ -81,7 +80,7 @@ def copy_objs(*entities, new_channel_db):
     for ent in entities:
         new_ents = []
         for obj in ent:
-            c, links = copy_entity(obj, new_channel_db)
+            c, links = copy_entity(obj, new_channel_db, session)
             new_ents.append(c)
             links_to_change[c] = links
             old_to_new[c.label] = c
@@ -89,29 +88,44 @@ def copy_objs(*entities, new_channel_db):
 
     for chan, link_info in links_to_change.items():
         for attr_name, link_name in link_info.items():
-            if isinstance(link_name, pony.orm.core.Multiset):
+            if isinstance(link_name, list):
                 new = [old_to_new[ln] for ln in link_name]
             else:
                 new = old_to_new[link_name]
             setattr(chan, attr_name, new)
 
+    session.add_all(entities + [new_channel_db])
     return new_entities
 
-def copy_entity(obj, new_channel_db):
+def copy_entity(obj, new_channel_db, session):
     """Copy a pony entity instance"""
-    kwargs = {a.name: getattr(obj, a.name) for a in obj._attrs_ if a.name not in ["id", "classtype"]}
+    rel_vals = {}
+
+    # Make a copy of the relationships
+    for rel_name in obj.__mapper__.relationships.keys():
+        attr = getattr(obj, rel_name)
+        print("examining", rel_name, attr.__class__)
+        if isinstance(attr, list):
+            print("adding", rel_name)
+            rel_vals[rel_name] = attr.copy()
+
+    # Expire these relationships from the session
+    session.expire(b)
+
+    # Make the object instances transient
+    make_transient(obj)
 
-    # Extract any links to other entities
-    links = {}
-    for attr in obj._attrs_:
-        if attr.name not in ["channel_db"]:
-            obj_attr = getattr(obj, attr.name)
-            if hasattr(obj_attr, "id"):
-                kwargs.pop(attr.name)
-                links[attr.name] = obj_attr.label
+    # Restore the old links
+    for rel_name, rel_val in rel_vals.items():
+        setattr(obj, rel_name, rel_val)
 
-    kwargs["channel_db"] = new_channel_db
-    return obj.__class__(**kwargs), links
+    # Reset the id and channel db
+    obj.id = None
+    obj.channel_db = new_channel_db
+
+    session.add(obj)
+
+    return obj, rel_vals
 
 class ChannelLibrary(object):
 
@@ -127,14 +141,14 @@ def __init__(self, db_resource_name=None):
             # Use current db
             self.db = bbndb.engine
         else:
-            
+
             if db_resource_name:
                 self.db_resource_name = db_resource_name
             elif config.load_db():
                 self.db_resource_name = config.load_db()
 
             self.db = bbndb.engine = bbndb.create_engine(f'{self.db_provider}:///{self.db_resource_name}', echo=False)
-        
+
         bbndb.Base.metadata.create_all(bbndb.engine)
         bbndb.Session.configure(bind=bbndb.engine)
         self.Session = bbndb.Session
@@ -152,6 +166,7 @@ def __init__(self, db_resource_name=None):
         elif len(working_dbs) == 0:
             self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
             self.session.add(self.channelDatabase)
+            self.session.commit()
 
         self.update_channelDict()
 
@@ -171,7 +186,6 @@ def ls(self):
         cdb = Channels.ChannelDatabase
         q = self.session.query(cdb.label, cdb.time, cdb.id).\
             order_by(Channels.ChannelDatabase.id, Channels.ChannelDatabase.label).all()
-        # select((c.label, c.time, c.id) for c in Channels.ChannelDatabase).sort_by(1, 2).show()
         for i, (label, time, id) in enumerate(q):
                 print(f"[{id}] ({time}) -> {label}")
 
@@ -210,46 +224,51 @@ def ls_qubits(self):
     def ls_measurements(self):
         return self.ent_by_type(Channels.Measurement, show=True)
 
+    @check_session_dirty
     def load(self, name, index=1):
         """Load the latest instance for a particular name. Specifying index = 2 will select the second most recent instance """
-        obj = list(select(c for c in Channels.ChannelDatabase if c.label==name).sort_by(desc(Channels.ChannelDatabase.time)))
-        self.load_obj(obj[-index])
+        cdb = Channels.ChannelDatabase
+        items = self.session.query(cdb).filter(cdb.label==name).order_by(cdb.time.desc()).all()
+        self.load_obj(items[-index])
 
+    @check_session_dirty
     def load_by_id(self, id_num):
-        obj = select(c for c in Channels.ChannelDatabase if c.id==id_num).first()
-        self.load_obj(obj)
+        cdb = Channels.ChannelDatabase
+        item = self.session.query(cdb).filter(cdb.id==id_num).first()
+        self.load_obj(item)
 
     def clear(self, channel_db=None, create_new=True):
         # If no database is specified, clear self.database
         channel_db = channel_db if channel_db else self.channelDatabase
-        # First clear items that don't have Sets of other items
-        for ent in [Channels.MicrowaveSource, Channels.Channel, Channels.Transmitter, Channels.Receiver, Channels.Transceiver]:
-            select(c for c in ent if c.channel_db == channel_db).delete(bulk=True)
-        # Now clear items that do potentially have sets of items (which should be deleted)
-        for ent in [Channels.ChannelDatabase]:
-            select(d for d in ent if d.label == "working").delete(bulk=True)
+
+        self.session.delete(channel_db)
+        self.session.commit()
+
         if create_new:
-            print("created new database with id", self.channelDatabase.id)
+            self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
+            self.session.add(self.channelDatabase)
+            self.session.commit()
         channelLib = self
 
     def load_obj(self, obj):
         self.clear()
-        chans, srcs, d2as, a2ds, trans = map(list, [obj.channels, obj.sources, obj.transmitters, obj.receivers, obj.transceivers])
-        copy_objs(chans, srcs, d2as, a2ds, trans, new_channel_db=self.channelDatabase)
+        chans, srcs, d2as, a2ds, trans = map(list, [obj.channels, obj.generators, obj.transmitters, obj.receivers, obj.transceivers])
+        copy_objs([chans, srcs, d2as, a2ds, trans], self.channelDatabase, self.session)
         self.update_channelDict()
 
-    def save(self):
+    def commit(self):
         self.session.commit()
 
-    def discard_changes(self):
+    def revert(self):
         self.session.rollback()
 
     def save_as(self, name):
-        chans, srcs, d2as, a2dsm, trans = map(list, [self.channelDatabase.channels, self.channelDatabase.sources,
+        self.commit()
+        chans, srcs, d2as, a2ds, trans = map(list, [self.channelDatabase.channels, self.channelDatabase.generators,
                                             self.channelDatabase.transmitters, self.channelDatabase.receivers,
                                             self.channelDatabase.transceivers])
-        new_chans, new_srcs, new_d2as, new_a2ds, new_trans = copy_objs(chans, srcs, d2as, a2ds, trans, new_channel_db=cd)
-        cd.channels, cd.sources, cd.transmitters, cd.receivers, cd.transceivers = new_chans, new_srcs, new_d2as, new_a2ds, new_trans
+        new_chans, new_srcs, new_d2as, new_a2ds, new_trans = copy_objs([chans, srcs, d2as, a2ds, trans], cd, self.session)
+        cd.channels, cd.generators, cd.transmitters, cd.receivers, cd.transceivers = new_chans, new_srcs, new_d2as, new_a2ds, new_trans
 
     #Dictionary methods
     def __getitem__(self, key):
@@ -272,206 +291,11 @@ def values(self):
 
     def build_connectivity_graph(self):
         # build connectivity graph
-<<<<<<< HEAD
-        self.connectivityG.clear()
-        for chan in self.channelDict.values():
-            if isinstance(chan,
-                          Channels.Qubit) and chan not in self.connectivityG:
-                self.connectivityG.add_node(chan)
-        for chan in self.channelDict.values():
-            if isinstance(chan, Channels.Edge):
-                self.connectivityG.add_edge(chan.source, chan.target)
-                self.connectivityG[chan.source][chan.target]['channel'] = chan
-
-    def load_from_library(self, return_only=False):
-        """Loads the YAML library, creates the QGL objects, and returns a list of the visited filenames
-        for the filewatcher."""
-        if not self.library_file:
-            return
-        try:
-            with open(self.library_file, 'r') as FID:
-                loader = config.Loader(FID)
-                try:
-                    tmpLib = loader.get_single_data()
-                    filenames = loader.filenames
-                finally:
-                    loader.dispose()
-
-            # Check to see if we have the mandatory sections
-            for section in ['instruments', 'qubits']: #, 'filters']:
-                if section not in tmpLib.keys():
-                    raise ValueError("{} section not present in config file {}.".format(section, self.library_file))
-
-            instr_dict   = tmpLib['instruments']
-            qubit_dict   = tmpLib['qubits']
-            # filter_dict  = tmpLib['filters']
-            trigger_dict = tmpLib.get('markers', {}) # This section is optional
-            edge_dict    = tmpLib.get('edges', {}) # This section is optional
-            master_awgs  = []
-
-            # Construct the channel library
-            channel_dict = {}
-            marker_lens = {}
-
-            for name, instr in instr_dict.items():
-                if "tx_channels" in instr.keys():
-                    for chan_name, channel in instr["tx_channels"].items():
-                        if channel is None:
-                            params = {}
-                        else:
-                            params = {k: v for k,v in channel.items() if k in Channels.PhysicalQuadratureChannel.__atom_members__.keys()}
-                        params["label"] = name + "-" + chan_name
-                        params["instrument"] = name
-                        params["translator"] = instr["type"] + "Pattern"
-                        params["__module__"] = "QGL.Channels"
-                        params["__class__"]  = "PhysicalQuadratureChannel"
-                        channel_dict[params["label"]] = params
-                if "rx_channels" in instr.keys():
-                    for chan_name, channel in instr["rx_channels"].items():
-                        if channel is None:
-                            params = {}
-                        else:
-                            params = {k: v for k,v in channel.items() if k in Channels.PhysicalMarkerChannel.__atom_members__.keys()}
-                        params["label"] = name + "-" + chan_name
-                        params["instrument"] = name
-                        params["translator"] = instr["type"] + "Pattern"
-                        params["__module__"] = "QGL.Channels"
-                        params["__class__"]  = "PhysicalMarkerChannel"
-                        channel_dict[params["label"]] = params
-                if "markers" in instr.keys():
-                    for mark_name, marker in instr["markers"].items():
-                        if marker is None:
-                            params = {}
-                        else:
-                            params = {k: v for k,v in marker.items() if k in Channels.PhysicalMarkerChannel.__atom_members__.keys()}
-                        params["label"] = name + "-" + mark_name
-                        params["instrument"] = name
-                        params["translator"] = instr["type"] + "Pattern"
-                        params["__module__"] = "QGL.Channels"
-                        params["__class__"]  = "PhysicalMarkerChannel"
-                        if "length" in marker.keys():
-                            marker_lens[params["label"]] = marker["length"]
-                        channel_dict[params["label"]] = params
-                if "master" in instr.keys() and instr["master"]:
-                    if instr['type'] != 'TDM':
-                        slave_chan = instr["slave_trig"] if "slave_trig" in instr.keys() else "slave"
-                        master_awgs.append(name + "-" + slave_chan)
-                    else:
-                        master_awgs.append(name)
-                # Eventually we should support multiple masters...
-                if "slave_trig" in instr.keys():
-                    params = {}
-                    params["label"]        = "slave_trig"
-                    params["phys_chan"]    = name + "-" + instr["slave_trig"]
-                    if params["phys_chan"] in marker_lens.keys():
-                        length = marker_lens[params["phys_chan"]]
-                    else:
-                        length = 1e-7
-                    params["pulse_params"] = {"length": length, "shape_fun": "constant"}
-                    params["__module__"]   = "QGL.Channels"
-                    params["__class__"]    = "LogicalMarkerChannel"
-                    channel_dict[params["label"]] = params
-
-            # Establish the slave trigger, assuming for now that we have a single
-            # APS master. This might change later.
-            if len(master_awgs) > 1:
-                raise ValueError("More than one AWG is marked as master.")
-            # elif len(master_awgs) == 1  and instr_dict[master_awgs[0].split('-')[0]]['type'] != 'TDM':
-            #     params = {}
-            #     params["label"]       = "slave_trig"
-            #     params["phys_chan"]    = master_awgs[0]
-            #     if params["phys_chan"] in marker_lens.keys():
-            #         length = marker_lens[params["phys_chan"]]
-            #     else:
-            #         length = 1e-7
-            #     params["pulse_params"] = {"length": length, "shape_fun": "constant"}
-            #     params["__module__"]  = "QGL.Channels"
-            #     params["__class__"]   = "LogicalMarkerChannel"
-            #     channel_dict[params["label"]] = params
-
-            # for name, filt in filter_dict.items():
-            #     if "StreamSelector" in filt["type"]:
-            #         params = {k: v for k,v in filt.items() if k in Channels.ReceiverChannel.__atom_members__.keys()}
-            #         params["label"]      = "RecvChan-" + name # instr_dict[filt["instrument"]]["name"] + "-" + name
-            #         params["channel"]    = str(params["channel"]) # Convert to a string
-            #         params["instrument"] = filt["source"]
-            #         params["__module__"] = "QGL.Channels"
-            #         params["__class__"]  = "ReceiverChannel"
-            #         if "source" not in filt.keys():
-            #             raise ValueError("No instrument (source) specified for Stream Selector")
-            #         if filt["source"] not in instr_dict.keys() and filt["source"] not in channel_dict.keys():
-            #             raise ValueError("Stream Selector source {} not found among list of instruments.".format(filt["source"]))
-            #         params["instrument"] = filt["source"]
-
-            #         channel_dict[params["label"]] = params
-
-            for name, qubit in qubit_dict.items():
-                # Create a stream selector
-                rcv_inst, rcv_chan, rcv_stream = qubit["measure"]["receiver"].split()
-                rcv_params = {}
-                rcv_params["label"]      = "RecvChan-" + name + "-SS"
-                rcv_params["channel"]    = str(rcv_chan)
-                rcv_params["instrument"] = rcv_inst
-                rcv_params["__module__"] = "QGL.Channels"
-                rcv_params["__class__"]  = "ReceiverChannel"
-                channel_dict[rcv_params["label"]] = rcv_params
-
-                # Create the Qubits
-                if len(qubit["control"]["AWG"].split()) != 2:
-                    print("Control AWG specification for {} ({}) must have a device, channel".format(name, qubit["control"]["AWG"]))
-                    raise ValueError("Control AWG specification for {} ({}) must have a device, channel".format(name, qubit["control"]["AWG"]))
-                ctrl_instr, ctrl_chan = qubit["control"]["AWG"].split()
-                params = {k: v for k,v in qubit["control"].items() if k in Channels.Qubit.__atom_members__.keys()}
-                params["label"]      = name
-                params["phys_chan"]   = ctrl_instr + "-" + ctrl_chan 
-                params["__module__"] = "QGL.Channels"
-                params["__class__"]  = "Qubit"
-                channel_dict[params["label"]] = params
-                if 'generator' in qubit["control"].keys():
-                    channel_dict[params["phys_chan"]]["generator"] = qubit["control"]["generator"]
-
-                # Create the measurements
-                if len(qubit["measure"]["AWG"].split()) != 2:
-                    print("Measurement AWG specification for {} ({}) must have a device, channel".format(name, qubit["measure"]["AWG"]))
-                    raise ValueError("Measurement AWG specification for {} ({}) must have a device, channel".format(name, qubit["measure"]["AWG"]))
-                meas_instr, meas_chan = qubit["measure"]["AWG"].split()
-                params = {k: v for k,v in qubit["measure"].items() if k in Channels.Measurement.__atom_members__.keys()}
-                params["label"]        = "M-{}".format(name)
-                # parse the digitizer trigger from the marker dictionary, if available. If not, expected in the form Instr Ch
-                dig_trig = trigger_dict.get(qubit["measure"]["trigger"], qubit["measure"]["trigger"]) if trigger_dict else qubit["measure"]["trigger"]
-                params["trig_chan"]     = "digTrig-" + dig_trig
-                params["phys_chan"]     = meas_instr + "-" + meas_chan
-                params["meas_type"]     = "autodyne"
-                params["receiver_chan"] = rcv_params["label"]
-                params["__module__"]   = "QGL.Channels"
-                params["__class__"]    = "Measurement"
-                channel_dict[params["label"]] = params
-                if 'generator' in qubit["measure"].keys():
-                    channel_dict[params["phys_chan"]]["generator"] = qubit["measure"]["generator"]
-
-                # Create the receiver channels
-                if "receiver" in qubit["measure"].keys():
-                    if len(qubit["measure"]["receiver"].split()) != 3:
-                        print("Receiver specification for {} ({}) must have an instrument name, physical channel, and stream".format(name, qubit["measure"]["receiver"]))
-                        raise ValueError("Receiver specification for {} ({}) must have a stream selector".format(name, qubit["measure"]["receiver"]))
-                    phys_instr, phys_marker = dig_trig.split()
-                    params = {}
-                    params["label"]        = "digTrig-" + dig_trig
-                    params["phys_chan"]     = phys_instr + "-" + phys_marker
-                    if params["phys_chan"] in marker_lens.keys():
-                        length = marker_lens[params["phys_chan"]]
-                    else:
-                        length = 3e-7
-                    params["pulse_params"]  = {"length": length, "shape_fun": "constant"}
-                    params["__module__"]   = "QGL.Channels"
-                    params["__class__"]    = "LogicalMarkerChannel"
-                    # Don't duplicate triggers to the same digitizer
-                    if params["label"] not in channel_dict.keys():
-                        channel_dict[params["label"]] = params
-=======
         for chan in select(q for q in Channels.Qubit if q not in self.connectivityG):
+=======
+        for chan in self.session.query(Channels.Qubit).filter(Channels.Qubit not in self.connectivityG).all():
             self.connectivityG.add_node(chan)
-        for chan in select(e for e in Channels.Edge):
+        for chan in self.session.query(Channels.Edge): #select(e for e in Channels.Edge):
             self.connectivityG.add_edge(chan.source, chan.target)
             self.connectivityG[chan.source][chan.target]['channel'] = chan
 >>>>>>> Ditch atom, move to Pony.orm for all channel library objects.
@@ -535,11 +359,10 @@ def new_qubit(self, label):
         return thing
 
     def new_source(self, label, model, address, power=-30.0, frequency=5.0e9):
-        thing = Channels.MicrowaveSource(label=label, model=model, address=address, power=power, frequency=frequency, channel_db=self.channelDatabase)
+        thing = Channels.Generator(label=label, model=model, address=address, power=power, frequency=frequency, channel_db=self.channelDatabase)
         self.session.add(thing)
         return thing
 
-    # @localize_db_objects
     def set_control(self, qubit, transmitter, generator=None):
         quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
         markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
@@ -557,7 +380,6 @@ def set_control(self, qubit, transmitter, generator=None):
         if generator:
             qubit.phys_chan.generator = generator
 
-    # @localize_db_objects
     def set_measure(self, qubit, transmitter, receivers, generator=None, receivers_channel=1, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
         quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
         markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
@@ -612,10 +434,7 @@ def set_master(self, transmitter, trig_channel, pulse_length=1e-7):
 
 def QubitFactory(label, **kwargs):
     ''' Return a saved qubit channel or create a new one. '''
-    # TODO: this will just get the first entry in the whole damned DB!
-    # thing = select(el for el in Channels.Qubit if el.label==label).first()
     q = channelLib.session.query(Channels.Qubit).filter(Channels.Qubit.label==label).all()
-    # thing = {c.label: c for c in channelLib.get_current_channels() if isinstance(c, Channels.Qubit)}[label]
     if len(q) == 1:
         return q[0]
     else:
@@ -626,7 +445,6 @@ def QubitFactory(label, **kwargs):
 def MeasFactory(label, **kwargs):
     ''' Return a saved measurement channel or create a new one. '''
     q = channelLib.session.query(Channels.Measurement).filter(Channels.Measurement.label==label).all()
-    # thing = {c.label: c for c in channelLib.get_current_channels() if isinstance(c, Channels.Measurement)}[label]
     if len(q) == 1:
         return q[0]
     else:
@@ -637,7 +455,6 @@ def MeasFactory(label, **kwargs):
 def MarkerFactory(label, **kwargs):
     ''' Return a saved Marker channel or create a new one. '''
     q = channelLib.session.query(Channels.LogicalMarkerChannel).filter(Channels.LogicalMarkerChannel.label==label).all()
-    # thing = {c.label: c for c in channelLib.get_current_channels()}[label]
     if len(q) == 1:
         return q[0]
     else:

From f79129f925a9efc97824f0b1e7209735397bbf95 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 11 Oct 2018 22:16:57 -0400
Subject: [PATCH 067/235] Move to cleaner deep copy and fix up saving channel
 dbs

---
 QGL/ChannelLibraries.py | 158 ++++++++++++++++++++++------------------
 1 file changed, 88 insertions(+), 70 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 995191ac..c5ecf172 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -49,6 +49,7 @@
 from .PulsePrimitives import clear_pulse_cache
 
 from sqlalchemy.orm.session import make_transient
+from sqlalchemy.pool import StaticPool
 
 channelLib = None
 
@@ -63,69 +64,84 @@ def wrapper(cls, *args, **kwargs):
         return f(cls, *args, **kwargs)
     return wrapper
 
-def set_from_dict(self, obj, settings):
-    for prop_name in obj.to_dict().keys():
-        if prop_name in settings.keys():
-            try:
-                setattr(obj, prop_name, settings[prop_name])
-            except Exception as e:
-                print(f"{obj.label}: Error loading {prop_name} from config")
-
-def copy_objs(entities, new_channel_db, session):
-    # Entities is a list of lists of entities of specific types
-    new_entities    = []
-    old_to_new      = {}
-    links_to_change = {}
-
-    for ent in entities:
-        new_ents = []
-        for obj in ent:
-            c, links = copy_entity(obj, new_channel_db, session)
-            new_ents.append(c)
-            links_to_change[c] = links
-            old_to_new[c.label] = c
-        new_entities.append(new_ents)
-
-    for chan, link_info in links_to_change.items():
-        for attr_name, link_name in link_info.items():
-            if isinstance(link_name, list):
-                new = [old_to_new[ln] for ln in link_name]
-            else:
-                new = old_to_new[link_name]
-            setattr(chan, attr_name, new)
-
-    session.add_all(entities + [new_channel_db])
-    return new_entities
-
-def copy_entity(obj, new_channel_db, session):
-    """Copy a pony entity instance"""
-    rel_vals = {}
-
-    # Make a copy of the relationships
-    for rel_name in obj.__mapper__.relationships.keys():
-        attr = getattr(obj, rel_name)
-        print("examining", rel_name, attr.__class__)
-        if isinstance(attr, list):
-            print("adding", rel_name)
-            rel_vals[rel_name] = attr.copy()
-
-    # Expire these relationships from the session
-    session.expire(b)
-
-    # Make the object instances transient
-    make_transient(obj)
-
-    # Restore the old links
-    for rel_name, rel_val in rel_vals.items():
-        setattr(obj, rel_name, rel_val)
-
-    # Reset the id and channel db
-    obj.id = None
-    obj.channel_db = new_channel_db
-
-    session.add(obj)
-
-    return obj, rel_vals
+# def set_from_dict(self, obj, settings):
+#     for prop_name in obj.to_dict().keys():
+#         if prop_name in settings.keys():
+#             try:
+#                 setattr(obj, prop_name, settings[prop_name])
+#             except Exception as e:
+#                 print(f"{obj.label}: Error loading {prop_name} from config")
+
+
+# def copy_objs(entities, new_channel_db, session):
+#     # Entities is a list of lists of entities of specific types
+#     new_entities    = []
+#     old_to_new      = {}
+#     links_to_change = {}
+
+#     for ent in entities:
+#         new_ents = []
+#         for obj in ent:
+#             c, links = copy_entity(obj, new_channel_db, session)
+#             new_ents.append(c)
+#             links_to_change[c] = links
+#             old_to_new[c.label] = c
+#         new_entities.append(new_ents)
+#     # import ipdb; ipdb.set_trace()
+#     # for chan, link_info in links_to_change.items():
+#     #     for attr_name, link_name in link_info.items():
+#     #         if isinstance(link_name, list):
+#     #             new = [old_to_new[ln] for ln in link_name]
+#     #         else:
+#     #             new = old_to_new[link_name]
+#     #         setattr(chan, attr_name, new)
+#     # import ipdb; ipdb.set_trace()
+#     for ents in new_entities:
+#         session.add_all(ents)
+#     session.add(new_channel_db)
+#     return new_entities
+
+# def copy_entity(obj, new_channel_db, session):
+#     """Copy a pony entity instance"""
+#     rel_vals = {}
+#     to_relink = []
+
+#     # Make a copy of the relationships
+#     print("Copying object", obj.label)
+#     for rel_name in obj.__mapper__.attrs.keys():
+#         attr = getattr(obj, rel_name)
+#         # print("\texamining", rel_name, attr.__class__)
+#         if isinstance(attr, list):
+#             rel_vals[rel_name] = attr.copy()
+#             # to_relink.append(rel_name)
+#         else:
+#             rel_vals[rel_name] = attr
+
+#     # for rel_name in obj.__mapper__.attrs.keys():
+
+#     # Expire these relationships from the session
+#     # print("to_relink", to_relink)
+#     # session.expire(obj, to_relink)
+#     # print("\tNew label", obj.label)
+
+#     # Make the object instances transient
+#     make_transient(obj)
+#     # print("\tNew label", obj.label)
+
+#     # Restore the old links
+#     for rel_name, rel_val in rel_vals.items():
+#         # print("\tsetting", rel_name, rel_val)
+#         setattr(obj, rel_name, rel_val)
+#     # print("\tNew label", obj.label)
+
+#     # Reset the id and channel db
+#     obj.id = None
+#     obj.channel_db = new_channel_db
+#     # print("\tNew label", obj.label)
+
+#     session.add(obj)
+
+#     return obj, rel_vals
 
 class ChannelLibrary(object):
 
@@ -147,7 +163,10 @@ def __init__(self, db_resource_name=None):
             elif config.load_db():
                 self.db_resource_name = config.load_db()
 
-            self.db = bbndb.engine = bbndb.create_engine(f'{self.db_provider}:///{self.db_resource_name}', echo=False)
+            self.db = bbndb.engine = bbndb.create_engine(f'{self.db_provider}:///{self.db_resource_name}',
+                                                            connect_args={'check_same_thread':False},
+                                                            poolclass=StaticPool,
+                                                            echo=False)
 
         bbndb.Base.metadata.create_all(bbndb.engine)
         bbndb.Session.configure(bind=bbndb.engine)
@@ -264,11 +283,10 @@ def revert(self):
 
     def save_as(self, name):
         self.commit()
-        chans, srcs, d2as, a2ds, trans = map(list, [self.channelDatabase.channels, self.channelDatabase.generators,
-                                            self.channelDatabase.transmitters, self.channelDatabase.receivers,
-                                            self.channelDatabase.transceivers])
-        new_chans, new_srcs, new_d2as, new_a2ds, new_trans = copy_objs([chans, srcs, d2as, a2ds, trans], cd, self.session)
-        cd.channels, cd.generators, cd.transmitters, cd.receivers, cd.transceivers = new_chans, new_srcs, new_d2as, new_a2ds, new_trans
+        new_channelDatabase = bbndb.deepcopy_sqla_object(self.channelDatabase, self.session)
+        new_channelDatabase.label = name
+        new_channelDatabase.time = datetime.datetime.now()
+        self.commit()
 
     #Dictionary methods
     def __getitem__(self, key):
@@ -380,7 +398,7 @@ def set_control(self, qubit, transmitter, generator=None):
         if generator:
             qubit.phys_chan.generator = generator
 
-    def set_measure(self, qubit, transmitter, receivers, generator=None, receivers_channel=1, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
+    def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
         quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
         markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
 

From 7feae774c953f5831aeda1dd9248390f69d45dc6 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 11 Oct 2018 22:31:06 -0400
Subject: [PATCH 068/235] Saving and loading appear to be working again

---
 QGL/ChannelLibraries.py | 97 ++++-------------------------------------
 1 file changed, 8 insertions(+), 89 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index c5ecf172..56ccd3ad 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -8,7 +8,7 @@
 Original Author: Colm Ryan
 Modified By: Graham Rowlands
 
-Copyright 2016 Raytheon BBN Technologies
+Copyright 2016-2018 Raytheon BBN Technologies
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -57,92 +57,12 @@ def check_session_dirty(f):
     """Since we can't mix db objects from separate sessions, re-fetch entities by their unique IDs"""
     @wraps(f)
     def wrapper(cls, *args, **kwargs):
-        if not 'force' in kwargs and kwargs['force']:
-            if len(cls.session.dirty | cls.session.new) != 0:
-                kwargs.pop('force')
-                raise Exception("Uncommitted transactions for working database. Either use force=True or commit/revert your changes.")
-        return f(cls, *args, **kwargs)
+        if 'force' in kwargs and kwargs['force']:
+            return f(cls, *args, **kwargs)
+        elif len(cls.session.dirty | cls.session.new) != 0:
+            raise Exception("Uncommitted transactions for working database. Either use force=True or commit/revert your changes.")
     return wrapper
 
-# def set_from_dict(self, obj, settings):
-#     for prop_name in obj.to_dict().keys():
-#         if prop_name in settings.keys():
-#             try:
-#                 setattr(obj, prop_name, settings[prop_name])
-#             except Exception as e:
-#                 print(f"{obj.label}: Error loading {prop_name} from config")
-
-
-# def copy_objs(entities, new_channel_db, session):
-#     # Entities is a list of lists of entities of specific types
-#     new_entities    = []
-#     old_to_new      = {}
-#     links_to_change = {}
-
-#     for ent in entities:
-#         new_ents = []
-#         for obj in ent:
-#             c, links = copy_entity(obj, new_channel_db, session)
-#             new_ents.append(c)
-#             links_to_change[c] = links
-#             old_to_new[c.label] = c
-#         new_entities.append(new_ents)
-#     # import ipdb; ipdb.set_trace()
-#     # for chan, link_info in links_to_change.items():
-#     #     for attr_name, link_name in link_info.items():
-#     #         if isinstance(link_name, list):
-#     #             new = [old_to_new[ln] for ln in link_name]
-#     #         else:
-#     #             new = old_to_new[link_name]
-#     #         setattr(chan, attr_name, new)
-#     # import ipdb; ipdb.set_trace()
-#     for ents in new_entities:
-#         session.add_all(ents)
-#     session.add(new_channel_db)
-#     return new_entities
-
-# def copy_entity(obj, new_channel_db, session):
-#     """Copy a pony entity instance"""
-#     rel_vals = {}
-#     to_relink = []
-
-#     # Make a copy of the relationships
-#     print("Copying object", obj.label)
-#     for rel_name in obj.__mapper__.attrs.keys():
-#         attr = getattr(obj, rel_name)
-#         # print("\texamining", rel_name, attr.__class__)
-#         if isinstance(attr, list):
-#             rel_vals[rel_name] = attr.copy()
-#             # to_relink.append(rel_name)
-#         else:
-#             rel_vals[rel_name] = attr
-
-#     # for rel_name in obj.__mapper__.attrs.keys():
-
-#     # Expire these relationships from the session
-#     # print("to_relink", to_relink)
-#     # session.expire(obj, to_relink)
-#     # print("\tNew label", obj.label)
-
-#     # Make the object instances transient
-#     make_transient(obj)
-#     # print("\tNew label", obj.label)
-
-#     # Restore the old links
-#     for rel_name, rel_val in rel_vals.items():
-#         # print("\tsetting", rel_name, rel_val)
-#         setattr(obj, rel_name, rel_val)
-#     # print("\tNew label", obj.label)
-
-#     # Reset the id and channel db
-#     obj.id = None
-#     obj.channel_db = new_channel_db
-#     # print("\tNew label", obj.label)
-
-#     session.add(obj)
-
-#     return obj, rel_vals
-
 class ChannelLibrary(object):
 
     def __init__(self, db_resource_name=None):
@@ -177,7 +97,6 @@ def __init__(self, db_resource_name=None):
 
         # Check to see whether there is already a temp database
         working_dbs = self.query(Channels.ChannelDatabase, label="working").all()
-        # working_dbs = self.session.query(Channels.ChannelDatabase).filter_by(label="working").all()
         if len(working_dbs) > 1:
             raise Exception("More than one working database exists!")
         elif len(working_dbs) == 1:
@@ -270,9 +189,9 @@ def clear(self, channel_db=None, create_new=True):
         channelLib = self
 
     def load_obj(self, obj):
-        self.clear()
-        chans, srcs, d2as, a2ds, trans = map(list, [obj.channels, obj.generators, obj.transmitters, obj.receivers, obj.transceivers])
-        copy_objs([chans, srcs, d2as, a2ds, trans], self.channelDatabase, self.session)
+        self.clear(create_new=False)
+        self.channelDatabase = bbndb.deepcopy_sqla_object(obj, self.session)
+        self.channelDatabase.label = "working"
         self.update_channelDict()
 
     def commit(self):

From 4fc5cfd2d81c093f871f7eea5d7eda58fddf9653 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 11 Oct 2018 23:20:55 -0400
Subject: [PATCH 069/235] Compatibility of compiler with new SQLAlchemy

---
 QGL/ChannelLibraries.py | 7 +++++--
 QGL/PatternUtils.py     | 2 +-
 QGL/config.py           | 2 +-
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 56ccd3ad..338766cf 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -3,7 +3,7 @@
 real channels.
 
 Split from Channels.py on Jan 14, 2016.
-Moved to pony ORM from atom June 1, 2018
+Moved to SQLAlchemy ORM from atom 2018
 
 Original Author: Colm Ryan
 Modified By: Graham Rowlands
@@ -125,7 +125,8 @@ def ls(self):
         q = self.session.query(cdb.label, cdb.time, cdb.id).\
             order_by(Channels.ChannelDatabase.id, Channels.ChannelDatabase.label).all()
         for i, (label, time, id) in enumerate(q):
-                print(f"[{id}] ({time}) -> {label}")
+                t = time.strftime("(%Y) %b. %d @ %I:%M:%S %p")
+                print(f"[{id}] {t} -> {label}")
 
     def ent_by_type(self, obj_type, show=False):
         q = self.session.query(obj_type).filter(obj_type.channel_db.has(label="working")).order_by(obj_type.label).all()
@@ -201,6 +202,8 @@ def revert(self):
         self.session.rollback()
 
     def save_as(self, name):
+        if name == "working":
+            raise ValueError("Cannot save as `working` since that is the default working environment name...")
         self.commit()
         new_channelDatabase = bbndb.deepcopy_sqla_object(self.channelDatabase, self.session)
         new_channelDatabase.label = name
diff --git a/QGL/PatternUtils.py b/QGL/PatternUtils.py
index 9748b35d..a718082a 100644
--- a/QGL/PatternUtils.py
+++ b/QGL/PatternUtils.py
@@ -202,7 +202,7 @@ def add_digitizer_trigger(seqs):
             #find corresponding digitizer trigger
             chanlist = list(flatten([seq[ct].channel]))
             for chan in chanlist:
-                if hasattr(chan, 'trig_chan'):
+                if hasattr(chan, 'trig_chan') and chan.trig_chan is not None:
                     trig_chan = chan.trig_chan
                     if not (hasattr(seq[ct], 'pulses') and
                             trig_chan in seq[ct].pulses.keys()):
diff --git a/QGL/config.py b/QGL/config.py
index c21dd560..18ca79c5 100644
--- a/QGL/config.py
+++ b/QGL/config.py
@@ -12,7 +12,7 @@
 db_resource_name = None
 
 # The config file (executed upon channel library loading)
-config_file      = None
+# config_file      = None
 
 # plotting options
 plotBackground = '#EAEAF2'

From 4949158eab155226bffb25fd183a0cc748e9beda Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 15 Nov 2018 17:05:09 -0500
Subject: [PATCH 070/235] Fix saving and loading and interactions with
 QubitFactory etc.

---
 QGL/ChannelLibraries.py | 80 +++++++++++++++++++++++------------------
 QGL/Compiler.py         |  2 +-
 2 files changed, 46 insertions(+), 36 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 338766cf..f94cc74a 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -57,9 +57,14 @@ def check_session_dirty(f):
     """Since we can't mix db objects from separate sessions, re-fetch entities by their unique IDs"""
     @wraps(f)
     def wrapper(cls, *args, **kwargs):
-        if 'force' in kwargs and kwargs['force']:
+        if (len(cls.session.dirty | cls.session.new)) == 0:
+            if 'force' in kwargs:
+                kwargs.pop('force')
             return f(cls, *args, **kwargs)
-        elif len(cls.session.dirty | cls.session.new) != 0:
+        elif 'force' in kwargs and kwargs['force']:
+            kwargs.pop('force')
+            return f(cls, *args, **kwargs)
+        else:
             raise Exception("Uncommitted transactions for working database. Either use force=True or commit/revert your changes.")
     return wrapper
 
@@ -91,7 +96,7 @@ def __init__(self, db_resource_name=None):
         bbndb.Base.metadata.create_all(bbndb.engine)
         bbndb.Session.configure(bind=bbndb.engine)
         self.Session = bbndb.Session
-        self.session = self.Session()
+        bbndb.session = self.session = self.Session()
 
         self.connectivityG = nx.DiGraph()
 
@@ -103,7 +108,7 @@ def __init__(self, db_resource_name=None):
             self.channelDatabase = working_dbs[0]
         elif len(working_dbs) == 0:
             self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
-            self.session.add(self.channelDatabase)
+            self.add_and_update_dict(self.channelDatabase)
             self.session.commit()
 
         self.update_channelDict()
@@ -185,7 +190,7 @@ def clear(self, channel_db=None, create_new=True):
 
         if create_new:
             self.channelDatabase = Channels.ChannelDatabase(label="working", time=datetime.datetime.now())
-            self.session.add(self.channelDatabase)
+            self.add_and_update_dict(self.channelDatabase)
             self.session.commit()
         channelLib = self
 
@@ -193,10 +198,12 @@ def load_obj(self, obj):
         self.clear(create_new=False)
         self.channelDatabase = bbndb.deepcopy_sqla_object(obj, self.session)
         self.channelDatabase.label = "working"
+        self.session.commit()
         self.update_channelDict()
 
     def commit(self):
         self.session.commit()
+        self.update_channelDict()
 
     def revert(self):
         self.session.rollback()
@@ -210,6 +217,10 @@ def save_as(self, name):
         new_channelDatabase.time = datetime.datetime.now()
         self.commit()
 
+    def add_and_update_dict(self, el):
+        self.session.add(el)
+        self.update_channelDict()
+
     #Dictionary methods
     def __getitem__(self, key):
         return self.channelDict[key]
@@ -251,7 +262,7 @@ def new_APS2(self, label, address):
         this_transmitter.trigger_source = "external"
         this_transmitter.address        = address
 
-        self.session.add(this_transmitter)
+        self.add_and_update_dict(this_transmitter)
         return this_transmitter
 
     def new_APS2_rack(self, label, num, start_address):
@@ -260,7 +271,7 @@ def new_APS2_rack(self, label, num, start_address):
         transmitters     = [new_APS2(f"{label}_U{i}", f"{address_start}.{address_end+i}") for i in range(1,num+1)]
         this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", transmitters=transmitters, channel_db=self.channelDatabase)
 
-        self.session.add(this_transceiver)
+        self.add_and_update_dict(this_transceiver)
         return this_transceiver
 
     def new_X6(self, label, address, dsp_channel=0, record_length=1024):
@@ -277,7 +288,7 @@ def new_X6(self, label, address, dsp_channel=0, record_length=1024):
         chan1.kernel = np.ones(record_length, dtype=np.complex).tobytes()
         chan2.kernel = np.ones(record_length, dtype=np.complex).tobytes()
 
-        self.session.add(this_receiver)
+        self.add_and_update_dict(this_receiver)
         return this_receiver
 
     def new_Alazar(self, label, address, record_length=1024):
@@ -290,17 +301,17 @@ def new_Alazar(self, label, address, record_length=1024):
         this_receiver.stream_types   = "raw"
         this_receiver.address        = address
 
-        self.session.add(this_receiver)
+        self.add_and_update_dict(this_receiver)
         return this_receiver
 
-    def new_qubit(self, label):
-        thing = Channels.Qubit(label=label, channel_db=self.channelDatabase)
-        self.session.add(thing)
+    def new_qubit(self, label, **kwargs):
+        thing = Channels.Qubit(label=label, channel_db=self.channelDatabase, **kwargs)
+        self.add_and_update_dict(thing)
         return thing
 
     def new_source(self, label, model, address, power=-30.0, frequency=5.0e9):
         thing = Channels.Generator(label=label, model=model, address=address, power=power, frequency=frequency, channel_db=self.channelDatabase)
-        self.session.add(thing)
+        self.add_and_update_dict(thing)
         return thing
 
     def set_control(self, qubit, transmitter, generator=None):
@@ -344,6 +355,7 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
         trig_chan.phys_chan    = phys_trig_channel
         trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
         meas.trig_chan         = trig_chan
+        qubit.measure_chan     = meas
 
         if isinstance(receivers, Channels.Receiver) and len(receivers.channels) > 1:
             raise ValueError("In set_measure the Receiver must have a single receiver channel or a specific channel must be passed instead")
@@ -372,35 +384,33 @@ def set_master(self, transmitter, trig_channel, pulse_length=1e-7):
         transmitter.master = True
         transmitter.trigger_source = "internal"
 
-def QubitFactory(label, **kwargs):
-    ''' Return a saved qubit channel or create a new one. '''
-    q = channelLib.session.query(Channels.Qubit).filter(Channels.Qubit.label==label).all()
-    if len(q) == 1:
-        return q[0]
+def QubitFactory(label):
+    ''' Return a saved qubit channel'''
+    cs = [c for c in channelLib.channelDatabase.channels if c.label==label]
+    # q = channelLib.session.query(Channels.Qubit).filter(Channels.Qubit.label==label and Channels.Qubit.channel_db==channelLib.channelDatabase).all()
+    if len(cs) == 1:
+        return cs[0]
     else:
-        c = Channels.Qubit(label=label, channel_db=channelLib.channelDatabase, **kwargs)
-        channelLib.session.add(c)
-        return c
+        raise Exception(f"Expected to find a single qubit {label} but found {len(cs)} qubits with the same label instead.")
 
-def MeasFactory(label, **kwargs):
+def MeasFactory(label):
     ''' Return a saved measurement channel or create a new one. '''
-    q = channelLib.session.query(Channels.Measurement).filter(Channels.Measurement.label==label).all()
-    if len(q) == 1:
-        return q[0]
+    cs = [c for c in channelLib.channelDatabase.channels if c.label==label]
+    # q = channelLib.session.query(Channels.Qubit).filter(Channels.Qubit.label==label and Channels.Qubit.channel_db==channelLib.channelDatabase).all()
+    if len(cs) == 1:
+        return cs[0]
     else:
-        c = Channels.Measurement(label=label, channel_db=channelLib.channelDatabase, **kwargs)
-        channelLib.session.add(c)
-        return c
+        raise Exception(f"Expected to find a single measurement {label} but found {len(cs)} measurements with the same label instead.")
 
-def MarkerFactory(label, **kwargs):
+def MarkerFactory(label):
     ''' Return a saved Marker channel or create a new one. '''
-    q = channelLib.session.query(Channels.LogicalMarkerChannel).filter(Channels.LogicalMarkerChannel.label==label).all()
-    if len(q) == 1:
-        return q[0]
+    cs = [c for c in channelLib.channelDatabase.channels if c.label==label]
+    # q = channelLib.session.query(Channels.Qubit).filter(Channels.Qubit.label==label and Channels.Qubit.channel_db==channelLib.channelDatabase).all()
+    if len(cs) == 1:
+        return cs[0]
     else:
-        c = Channels.LogicalMarkerChannel(label=label, channel_db=channelLib.channelDatabase, **kwargs)
-        channelLib.session.add(c)
-        return c
+        raise Exception(f"Expected to find a single marker {label} but found {len(cs)} markers with the same label instead.")
+
 
 def EdgeFactory(source, target):
     if channelLib.connectivityG.has_edge(source, target):
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index ec17af38..782c08c3 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -47,7 +47,7 @@ def map_logical_to_physical(wires):
     for logicalChan in wires.keys():
         phys_chan = logicalChan.phys_chan
         if not phys_chan:
-            raise ValueError("LogicalChannel {} does not have a PhysicalChannel".format(phys_chan))
+            raise ValueError("LogicalChannel {} does not have a PhysicalChannel".format(logicalChan))
         if phys_chan not in physicalChannels:
             physicalChannels[phys_chan] = [logicalChan]
         else:

From 1a5a8f0da3e7048d43915bc1435560c8280e7411 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 16 Nov 2018 13:15:35 -0500
Subject: [PATCH 071/235] Clear pulse cache before recompiling, otherwise DB
 updates fall on deaf ears

---
 QGL/Compiler.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 782c08c3..a21a9df0 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -323,7 +323,7 @@ def compile_to_hardware(seqs,
         tdm_seq (optional): compile for TDM
     '''
     ChannelLibraries.channelLib.update_channelDict()
-    # clear_pulse_cache()
+    clear_pulse_cache()
 
     logger.debug("Compiling %d sequence(s)", len(seqs))
 

From 4418a7b5945be02bdaab454c3c8ae63fac49ab79 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 16 Nov 2018 13:16:16 -0500
Subject: [PATCH 072/235] Add checking for duplicates and dirty session

---
 QGL/ChannelLibraries.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index f94cc74a..0b8ad87b 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -68,6 +68,16 @@ def wrapper(cls, *args, **kwargs):
             raise Exception("Uncommitted transactions for working database. Either use force=True or commit/revert your changes.")
     return wrapper
 
+def check_for_duplicates(f):
+    """Since we can't mix db objects from separate sessions, re-fetch entities by their unique IDs"""
+    @wraps(f)
+    def wrapper(cls, label, *args, **kwargs):
+        if label in cls.channelDict:
+            raise ValueError(f"Cannot create {label}: a channel with the same name already exists.")
+        else:
+            return f(cls, label, *args, **kwargs)  
+    return wrapper
+
 class ChannelLibrary(object):
 
     def __init__(self, db_resource_name=None):
@@ -208,6 +218,7 @@ def commit(self):
     def revert(self):
         self.session.rollback()
 
+    @check_session_dirty
     def save_as(self, name):
         if name == "working":
             raise ValueError("Cannot save as `working` since that is the default working environment name...")
@@ -251,6 +262,7 @@ def build_connectivity_graph(self):
             self.connectivityG[chan.source][chan.target]['channel'] = chan
 >>>>>>> Ditch atom, move to Pony.orm for all channel library objects.
 
+    @check_for_duplicates
     def new_APS2(self, label, address):
         chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
         m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
@@ -265,6 +277,7 @@ def new_APS2(self, label, address):
         self.add_and_update_dict(this_transmitter)
         return this_transmitter
 
+    @check_for_duplicates
     def new_APS2_rack(self, label, num, start_address):
         address_start    = ".".join(start_address.split(".")[:3])
         address_end      = int(start_address.split(".")[-1])
@@ -274,6 +287,7 @@ def new_APS2_rack(self, label, num, start_address):
         self.add_and_update_dict(this_transceiver)
         return this_transceiver
 
+    @check_for_duplicates
     def new_X6(self, label, address, dsp_channel=0, record_length=1024):
         chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, dsp_channel=dsp_channel, channel_db=self.channelDatabase)
         chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, dsp_channel=dsp_channel, channel_db=self.channelDatabase)
@@ -291,6 +305,7 @@ def new_X6(self, label, address, dsp_channel=0, record_length=1024):
         self.add_and_update_dict(this_receiver)
         return this_receiver
 
+    @check_for_duplicates
     def new_Alazar(self, label, address, record_length=1024):
         chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, channel_db=self.channelDatabase)
         chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, channel_db=self.channelDatabase)
@@ -304,11 +319,13 @@ def new_Alazar(self, label, address, record_length=1024):
         self.add_and_update_dict(this_receiver)
         return this_receiver
 
+    @check_for_duplicates
     def new_qubit(self, label, **kwargs):
         thing = Channels.Qubit(label=label, channel_db=self.channelDatabase, **kwargs)
         self.add_and_update_dict(thing)
         return thing
 
+    @check_for_duplicates
     def new_source(self, label, model, address, power=-30.0, frequency=5.0e9):
         thing = Channels.Generator(label=label, model=model, address=address, power=power, frequency=frequency, channel_db=self.channelDatabase)
         self.add_and_update_dict(thing)

From d81b5f812684f0b1e15a9a1fcb3d32cffb75849c Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 16 Nov 2018 13:16:53 -0500
Subject: [PATCH 073/235] Update channel lib automatically when loading
 factories

---
 QGL/ChannelLibraries.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 0b8ad87b..749d2056 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -403,6 +403,7 @@ def set_master(self, transmitter, trig_channel, pulse_length=1e-7):
 
 def QubitFactory(label):
     ''' Return a saved qubit channel'''
+    channelLib.update_channelDict()
     cs = [c for c in channelLib.channelDatabase.channels if c.label==label]
     # q = channelLib.session.query(Channels.Qubit).filter(Channels.Qubit.label==label and Channels.Qubit.channel_db==channelLib.channelDatabase).all()
     if len(cs) == 1:
@@ -412,6 +413,7 @@ def QubitFactory(label):
 
 def MeasFactory(label):
     ''' Return a saved measurement channel or create a new one. '''
+    channelLib.update_channelDict()
     cs = [c for c in channelLib.channelDatabase.channels if c.label==label]
     # q = channelLib.session.query(Channels.Qubit).filter(Channels.Qubit.label==label and Channels.Qubit.channel_db==channelLib.channelDatabase).all()
     if len(cs) == 1:
@@ -422,14 +424,15 @@ def MeasFactory(label):
 def MarkerFactory(label):
     ''' Return a saved Marker channel or create a new one. '''
     cs = [c for c in channelLib.channelDatabase.channels if c.label==label]
+    channelLib.update_channelDict()
     # q = channelLib.session.query(Channels.Qubit).filter(Channels.Qubit.label==label and Channels.Qubit.channel_db==channelLib.channelDatabase).all()
     if len(cs) == 1:
         return cs[0]
     else:
         raise Exception(f"Expected to find a single marker {label} but found {len(cs)} markers with the same label instead.")
 
-
 def EdgeFactory(source, target):
+    channelLib.update_channelDict()
     if channelLib.connectivityG.has_edge(source, target):
         return channelLib.connectivityG[source][target]['channel']
     elif channelLib.connectivityG.has_edge(target, source):

From 7fa03ea219bf8b0ab2e740bb06c558a23a9045ac Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 16 Nov 2018 16:02:00 -0500
Subject: [PATCH 074/235] Pretty printing filter channel library versions

---
 QGL/ChannelLibraries.py | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 749d2056..fdb82599 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -50,6 +50,7 @@
 
 from sqlalchemy.orm.session import make_transient
 from sqlalchemy.pool import StaticPool
+from IPython.display import HTML, display
 
 channelLib = None
 
@@ -130,7 +131,13 @@ def query(self, obj_type, **kwargs):
         return self.session.query(obj_type).filter_by(**kwargs)
 
     def get_current_channels(self):
-        return self.channelDatabase.channels + self.channelDatabase.generators
+        return (self.channelDatabase.channels + 
+               self.channelDatabase.generators + 
+               self.channelDatabase.transmitters + 
+               self.channelDatabase.receivers + 
+               self.channelDatabase.transceivers + 
+               self.channelDatabase.instruments + 
+               self.channelDatabase.processors)
 
     def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
@@ -139,9 +146,12 @@ def ls(self):
         cdb = Channels.ChannelDatabase
         q = self.session.query(cdb.label, cdb.time, cdb.id).\
             order_by(Channels.ChannelDatabase.id, Channels.ChannelDatabase.label).all()
+        table_code = ""        
         for i, (label, time, id) in enumerate(q):
-                t = time.strftime("(%Y) %b. %d @ %I:%M:%S %p")
-                print(f"[{id}] {t} -> {label}")
+            y, d, t = map(time.strftime, ["%Y", "%b. %d", "%I:%M:%S %p"])
+            # t = time.strftime("(%Y) %b. %d @ %I:%M:%S %p")
+            table_code += f"<tr><td>{id}</td><td>{y}</td><td>{d}</td><td>{t}</td><td>{label}</td></tr>"
+        display(HTML(f"<table><tr><th>id</th><th>Year</th><th>Date</th><th>Time</th><th>Name</th></tr><tr>{table_code}</tr></table>"))
 
     def ent_by_type(self, obj_type, show=False):
         q = self.session.query(obj_type).filter(obj_type.channel_db.has(label="working")).order_by(obj_type.label).all()

From e76e1a5343e3b029a68ed78eb36daa6e245490b9 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Mon, 19 Nov 2018 10:23:58 -0500
Subject: [PATCH 075/235] Added ability to delete channel library versions

---
 QGL/ChannelLibraries.py | 16 ++++++++++++++--
 README.md               |  9 +--------
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index fdb82599..f6adb63e 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -197,8 +197,7 @@ def load(self, name, index=1):
 
     @check_session_dirty
     def load_by_id(self, id_num):
-        cdb = Channels.ChannelDatabase
-        item = self.session.query(cdb).filter(cdb.id==id_num).first()
+        item = self.session.query(Channels.ChannelDatabase).filter_by(id=id_num).first()
         self.load_obj(item)
 
     def clear(self, channel_db=None, create_new=True):
@@ -214,6 +213,19 @@ def clear(self, channel_db=None, create_new=True):
             self.session.commit()
         channelLib = self
 
+    def rm(self, library_name, keep_id=-1):
+        """Remove the channel library named `library_name`. If no `keep_version` is specified then
+        all versions are removed. Otherwise """
+        cdb = Channels.ChannelDatabase
+        items = self.session.query(cdb).filter(cdb.label==library_name and cdb.id!=keep_id).all()
+        for item in items:
+            self.session.delete(item)
+
+    def rm_by_id(self, id):
+        """Remove the channel library with id `id`"""
+        item = self.session.query(Channels.ChannelDatabase).filter_by(id=id_num).first()
+        self.session.delete(item)
+
     def load_obj(self, obj):
         self.clear(create_new=False)
         self.channelDatabase = bbndb.deepcopy_sqla_object(obj, self.session)
diff --git a/README.md b/README.md
index 57b51930..974fdbdd 100644
--- a/README.md
+++ b/README.md
@@ -54,16 +54,9 @@ The QGL config file will be created the first time you run `import QGL` or `from
 
 ## Dependencies
 * Python 2.7 or 3.4+
-* JSONLibraryUtils (https://github.com/BBN-Q/JSONLibraryUtils, integrated as a Git submodule)
 * Numpy/Scipy
-* Nucleic atom (from ecpy channel for Python 3)
 * h5py
-* watchdog
 * Bokeh 0.11
 * networkx 2.0
 * iPython/Jupyter 4.0 (only for Jupyter notebooks)
-* ruamel_yaml
-
-## UnitTest data support
-This repository uses the Git Large File Storage (LFS) extension to manage a few
-UnitTest data files (see https://git-lfs.github.com/).
+* bbndb

From be6e5385947285922faf37f47d84ff02a130ee3c Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 7 Dec 2018 09:40:23 -0500
Subject: [PATCH 076/235] Fix timing for connectivity building

---
 QGL/ChannelLibraries.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index f6adb63e..9b18ea3c 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -141,6 +141,7 @@ def get_current_channels(self):
 
     def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
+        self.build_connectivity_graph()
 
     def ls(self):
         cdb = Channels.ChannelDatabase
@@ -251,7 +252,10 @@ def save_as(self, name):
         self.commit()
 
     def add_and_update_dict(self, el):
-        self.session.add(el)
+        if isinstance(el, list):
+            self.session.add_all(el)
+        else:
+            self.session.add(el)
         self.update_channelDict()
 
     #Dictionary methods
@@ -303,7 +307,7 @@ def new_APS2(self, label, address):
     def new_APS2_rack(self, label, num, start_address):
         address_start    = ".".join(start_address.split(".")[:3])
         address_end      = int(start_address.split(".")[-1])
-        transmitters     = [new_APS2(f"{label}_U{i}", f"{address_start}.{address_end+i}") for i in range(1,num+1)]
+        transmitters     = [self.new_APS2(f"{label}_U{i}", f"{address_start}.{address_end+i}") for i in range(1,num+1)]
         this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", transmitters=transmitters, channel_db=self.channelDatabase)
 
         self.add_and_update_dict(this_transceiver)
@@ -370,6 +374,14 @@ def set_control(self, qubit, transmitter, generator=None):
         if generator:
             qubit.phys_chan.generator = generator
 
+    def set_qubit_connectivity(self, graph):
+        """
+        Graph is a networkx DiGraph consisting of edges (source qubit, target qubit)
+        """
+        new_edges = [Channels.Edge(label=f"{source.label}->{target.label}", source=source, target=target) for source, target in graph.edges()]
+        self.add_and_update_dict(new_edges)
+        return new_edges
+
     def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
         quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
         markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]

From 61c4cf31cdd32af49b46d401c0f1e1248514e93d Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 11 Dec 2018 11:09:41 -0500
Subject: [PATCH 077/235] Now properly adding all new objects to the session.

---
 QGL/ChannelLibraries.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 9b18ea3c..abe7168f 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -373,6 +373,7 @@ def set_control(self, qubit, transmitter, generator=None):
         qubit.phys_chan = phys_chan
         if generator:
             qubit.phys_chan.generator = generator
+        self.update_channelDict()
 
     def set_qubit_connectivity(self, graph):
         """
@@ -418,12 +419,14 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
             raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
         meas.receiver_chan = rcv_chan
+        self.add_and_update_dict([meas, trig_chan])
 
         if gate:
             phys_gate_channel   = gate_channel if gate_channel else transmitter.get_chan("12m2")
             gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=self.channelDatabase)
             gate_chan.phys_chan = phys_gate_channel
             meas.gate_chan      = gate_chan
+            self.add_and_update_dict([gate_chan])
 
     def set_master(self, transmitter, trig_channel, pulse_length=1e-7):
         if not isinstance(trig_channel, Channels.PhysicalMarkerChannel):
@@ -434,6 +437,7 @@ def set_master(self, transmitter, trig_channel, pulse_length=1e-7):
         st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
         transmitter.master = True
         transmitter.trigger_source = "internal"
+        self.add_and_update_dict([st])
 
 def QubitFactory(label):
     ''' Return a saved qubit channel'''

From 5fd7a903caec83ef615c2ca14f3e31573af7277c Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 19 Dec 2018 16:39:49 -0500
Subject: [PATCH 078/235] Replace historical channel naming convention ch12->
 ch1, ch12m2->m2 etc.

---
 QGL/ChannelLibraries.py    | 16 ++++++++--------
 QGL/Compiler.py            |  3 ++-
 QGL/drivers/APS2Pattern.py | 22 +++++++++++-----------
 3 files changed, 21 insertions(+), 20 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index abe7168f..90306e98 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -290,13 +290,13 @@ def build_connectivity_graph(self):
 
     @check_for_duplicates
     def new_APS2(self, label, address):
-        chan12 = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
-        m1     = Channels.PhysicalMarkerChannel(label=f"{label}-12m1", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
-        m2     = Channels.PhysicalMarkerChannel(label=f"{label}-12m2", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
-        m3     = Channels.PhysicalMarkerChannel(label=f"{label}-12m3", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
-        m4     = Channels.PhysicalMarkerChannel(label=f"{label}-12m4", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        chan1  = Channels.PhysicalQuadratureChannel(label=f"{label}-1", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m1     = Channels.PhysicalMarkerChannel(label=f"{label}-m1", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m2     = Channels.PhysicalMarkerChannel(label=f"{label}-m2", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m3     = Channels.PhysicalMarkerChannel(label=f"{label}-m3", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m4     = Channels.PhysicalMarkerChannel(label=f"{label}-m4", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
 
-        this_transmitter = Channels.Transmitter(label=label, model="APS2", address=address, channels=[chan12, m1, m2, m3, m4], channel_db=self.channelDatabase)
+        this_transmitter = Channels.Transmitter(label=label, model="APS2", address=address, channels=[chan1, m1, m2, m3, m4], channel_db=self.channelDatabase)
         this_transmitter.trigger_source = "external"
         this_transmitter.address        = address
 
@@ -401,7 +401,7 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
         if generator:
             meas.phys_chan.generator = generator
 
-        phys_trig_channel = trig_channel if trig_channel else transmitter.get_chan("12m1")
+        phys_trig_channel = trig_channel if trig_channel else transmitter.get_chan("m1")
 
         trig_chan              = Channels.LogicalMarkerChannel(label=f"receiversTrig-{qubit.label}", channel_db=self.channelDatabase)
         trig_chan.phys_chan    = phys_trig_channel
@@ -422,7 +422,7 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
         self.add_and_update_dict([meas, trig_chan])
 
         if gate:
-            phys_gate_channel   = gate_channel if gate_channel else transmitter.get_chan("12m2")
+            phys_gate_channel   = gate_channel if gate_channel else transmitter.get_chan("m2")
             gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=self.channelDatabase)
             gate_chan.phys_chan = phys_gate_channel
             meas.gate_chan      = gate_chan
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index a21a9df0..115338de 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -276,7 +276,8 @@ def bundle_wires(physWires, wfs):
     awgData = setup_awg_channels(physWires.keys())
     for chan in physWires.keys():
         _, awgChan = chan.label.rsplit('-', 1)
-        awgChan = 'ch' + awgChan
+        if awgChan[0] != 'm':
+            awgChan = 'ch' + awgChan
         awgData[chan.instrument][awgChan]['linkList'] = physWires[chan]
         awgData[chan.instrument][awgChan]['wfLib'] = wfs[chan]
         if hasattr(chan, 'correctionT'):
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 1f174564..4291e34d 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -106,7 +106,7 @@
 SEQFILE_PER_CHANNEL = False
 
 def get_empty_channel_set():
-    return {'ch12': {}, 'ch12m1': {}, 'ch12m2': {}, 'ch12m3': {}, 'ch12m4': {}}
+    return {'ch1': {}, 'm1': {}, 'm2': {}, 'm3': {}, 'm4': {}}
 
 
 def get_seq_file_extension():
@@ -1024,11 +1024,11 @@ def write_sequence_file(awgData, fileName):
     Main function to pack channel sequences into an APS2 h5 file.
     '''
     # Convert QGL IR into a representation that is closer to the hardware.
-    awgData['ch12']['linkList'], wfLib = preprocess(
-        awgData['ch12']['linkList'], awgData['ch12']['wfLib'])
+    awgData['ch1']['linkList'], wfLib = preprocess(
+        awgData['ch1']['linkList'], awgData['ch1']['wfLib'])
 
     # compress marker data
-    for field in ['ch12m1', 'ch12m2', 'ch12m3', 'ch12m4']:
+    for field in ['m1', 'm2', 'm3', 'm4']:
         if 'linkList' in awgData[field].keys():
             PatternUtils.convert_lengths_to_samples(awgData[field]['linkList'],
                                                     SAMPLING_RATE, 1,
@@ -1041,10 +1041,10 @@ def write_sequence_file(awgData, fileName):
     wfInfo = []
     wfInfo.append(create_wf_vector({key: wf.real
                                     for key, wf in wfLib.items()}, awgData[
-                                        'ch12']['linkList']))
+                                        'ch1']['linkList']))
     wfInfo.append(create_wf_vector({key: wf.imag
                                     for key, wf in wfLib.items()}, awgData[
-                                        'ch12']['linkList']))
+                                        'ch1']['linkList']))
 
     if SAVE_WF_OFFSETS:
         #create a set of all waveform signatures in offset dictionaries
@@ -1055,7 +1055,7 @@ def write_sequence_file(awgData, fileName):
             wf_sigs |= set(offset_dict.keys())
         #create dictionary linking entry labels (that's what we'll have later) with offsets
         offsets = {}
-        for seq in awgData['ch12']['linkList']:
+        for seq in awgData['ch1']['linkList']:
             for entry in seq:
                 if len(wf_sigs) == 0:
                     break
@@ -1079,7 +1079,7 @@ def write_sequence_file(awgData, fileName):
 
     # build instruction vector
     seq_data = [awgData[s]['linkList']
-                for s in ['ch12', 'ch12m1', 'ch12m2', 'ch12m3', 'ch12m4']]
+                for s in ['ch1', 'm1', 'm2', 'm3', 'm4']]
     instructions = create_instr_data(seq_data, wfInfo[0][1], wfInfo[0][2])
 
     #Open the HDF5 file
@@ -1114,10 +1114,10 @@ def write_sequence_file(awgData, fileName):
 def read_sequence_file(fileName):
     """
     Reads a HDF5 sequence file and returns a dictionary of lists.
-    Dictionary keys are channel strings such as ch1, ch12m1
+    Dictionary keys are channel strings such as ch1, m1
     Lists are or tuples of time-amplitude pairs (time, output)
     """
-    chanStrs = ['ch1', 'ch2', 'ch12m1', 'ch12m2', 'ch12m3', 'ch12m4',
+    chanStrs = ['ch1', 'ch2', 'm1', 'm2', 'm3', 'm4',
                 'mod_phase']
     seqs = {ch: [] for ch in chanStrs}
 
@@ -1189,7 +1189,7 @@ def start_new_seq():
                                 seqs[chan][-1].append((1, sample))
 
             elif instr.opcode == MARKER:
-                chan = 'ch12m' + str(((instr.header >> 2) & 0x3) + 1)
+                chan = 'm' + str(((instr.header >> 2) & 0x3) + 1)
                 count = instr.payload & 0xffffffff
                 count = (count + 1) * ADDRESS_UNIT
                 state = (instr.payload >> 32) & 0x1

From 72582af642d091ad4c17dd8733eaabd962dcaef6 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matthew.e.ware@gmail.com>
Date: Fri, 25 Jan 2019 14:34:01 -0500
Subject: [PATCH 079/235] X6 and TDM compatibility. -- GER, GJR

---
 QGL/ChannelLibraries.py     | 97 ++++++++++++++++++++++++++-----------
 QGL/PulseSequencePlotter.py | 12 ++---
 2 files changed, 74 insertions(+), 35 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 90306e98..f7aecd7e 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -38,6 +38,7 @@
 import importlib
 import inspect
 from functools import wraps
+import itertools
 import numpy as np
 import networkx as nx
 
@@ -76,7 +77,7 @@ def wrapper(cls, label, *args, **kwargs):
         if label in cls.channelDict:
             raise ValueError(f"Cannot create {label}: a channel with the same name already exists.")
         else:
-            return f(cls, label, *args, **kwargs)  
+            return f(cls, label, *args, **kwargs)
     return wrapper
 
 class ChannelLibrary(object):
@@ -131,12 +132,12 @@ def query(self, obj_type, **kwargs):
         return self.session.query(obj_type).filter_by(**kwargs)
 
     def get_current_channels(self):
-        return (self.channelDatabase.channels + 
-               self.channelDatabase.generators + 
-               self.channelDatabase.transmitters + 
-               self.channelDatabase.receivers + 
-               self.channelDatabase.transceivers + 
-               self.channelDatabase.instruments + 
+        return (self.channelDatabase.channels +
+               self.channelDatabase.generators +
+               self.channelDatabase.transmitters +
+               self.channelDatabase.receivers +
+               self.channelDatabase.transceivers +
+               self.channelDatabase.instruments +
                self.channelDatabase.processors)
 
     def update_channelDict(self):
@@ -147,7 +148,7 @@ def ls(self):
         cdb = Channels.ChannelDatabase
         q = self.session.query(cdb.label, cdb.time, cdb.id).\
             order_by(Channels.ChannelDatabase.id, Channels.ChannelDatabase.label).all()
-        table_code = ""        
+        table_code = ""
         for i, (label, time, id) in enumerate(q):
             y, d, t = map(time.strftime, ["%Y", "%b. %d", "%I:%M:%S %p"])
             # t = time.strftime("(%Y) %b. %d @ %I:%M:%S %p")
@@ -304,29 +305,52 @@ def new_APS2(self, label, address):
         return this_transmitter
 
     @check_for_duplicates
-    def new_APS2_rack(self, label, num, start_address):
-        address_start    = ".".join(start_address.split(".")[:3])
-        address_end      = int(start_address.split(".")[-1])
-        transmitters     = [self.new_APS2(f"{label}_U{i}", f"{address_start}.{address_end+i}") for i in range(1,num+1)]
+    def new_TDM(self, label, address):
+        return Channels.Processor(label=label, model="TDM", address=address, trigger_interval=250e-6)
+
+    @check_for_duplicates
+    def new_APS2_rack(self, label, num, start_address, tdm_ip=None):
+        address_start = ".".join(start_address.split(".")[:3])
+        address_end   = int(start_address.split(".")[-1])
+        transmitters  = [self.new_APS2(f"{label}_U{i}", f"{address_start}.{address_end+i}") for i in range(1,num+1)]
+
         this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", transmitters=transmitters, channel_db=self.channelDatabase)
+        for t in transmitters:
+            t.transceiver = this_transceiver
+
+        if tdm_ip:
+            tdm = self.new_TDM(f"{label}_TDM", tdm_ip)
+            this_transceiver.processors = [tdm]
+            for t in transmitters:
+                t.trigger_source = 'system'
 
         self.add_and_update_dict(this_transceiver)
         return this_transceiver
 
     @check_for_duplicates
     def new_X6(self, label, address, dsp_channel=0, record_length=1024):
-        chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, dsp_channel=dsp_channel, channel_db=self.channelDatabase)
-        chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, dsp_channel=dsp_channel, channel_db=self.channelDatabase)
 
-        this_receiver = Channels.Receiver(label=label, model="X6-1000M", address=address, channels=[chan1, chan2],
+        phys_channels = (1, 2)
+        dsp_channels = (1, 2)
+        stream_types = ("raw", "demodulated", "integrated")
+
+        chans = []
+
+        for p, d, s in itertools.product(phys_channels, dsp_channels, stream_types):
+            chans.append(Channels.ReceiverChannel(label=f"RecvChan-{label}-{s}-{d}-{p}",
+                            channel=p, dsp_channel=d, stream_type=s,
+                            channel_db=self.channelDatabase))
+
+        this_receiver = Channels.Receiver(label=label, model="X6-1000M", address=address, channels=chans,
                                       record_length=record_length, channel_db=self.channelDatabase)
         this_receiver.trigger_source = "external"
         this_receiver.stream_types   = "raw, demodulated, integrated"
         this_receiver.address        = address
 
         # Add a default kernel
-        chan1.kernel = np.ones(record_length, dtype=np.complex).tobytes()
-        chan2.kernel = np.ones(record_length, dtype=np.complex).tobytes()
+        for chan in chans:
+            if chan.stream_type is "integrated":
+                chan.kernel = np.ones(record_length, dtype=np.complex).tobytes()
 
         self.add_and_update_dict(this_receiver)
         return this_receiver
@@ -352,8 +376,10 @@ def new_qubit(self, label, **kwargs):
         return thing
 
     @check_for_duplicates
-    def new_source(self, label, model, address, power=-30.0, frequency=5.0e9):
-        thing = Channels.Generator(label=label, model=model, address=address, power=power, frequency=frequency, channel_db=self.channelDatabase)
+    def new_source(self, label, model, address, power=-30.0, frequency=5.0e9, reference=None):
+        thing = Channels.Generator(label=label, model=model, address=address, power=power,
+                                    frequency=frequency, reference=reference,
+                                    channel_db=self.channelDatabase)
         self.add_and_update_dict(thing)
         return thing
 
@@ -396,6 +422,8 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
         else:
             raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
+        if f"M-{qubit.label}" in self.channelDict:
+            raise ValueError(f"Cannot create Measurement M-{qubit.label}: a channel with the same name already exists.")
         meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=self.channelDatabase)
         meas.phys_chan = phys_chan
         if generator:
@@ -403,7 +431,9 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
 
         phys_trig_channel = trig_channel if trig_channel else transmitter.get_chan("m1")
 
-        trig_chan              = Channels.LogicalMarkerChannel(label=f"receiversTrig-{qubit.label}", channel_db=self.channelDatabase)
+        trig_chan              = Channels.LogicalMarkerChannel(label=f"ReceiverTrig-{qubit.label}", channel_db=self.channelDatabase)
+        # print(phys_trig_channel.id, trig_chan.id)
+        self.session.add(trig_chan)
         trig_chan.phys_chan    = phys_trig_channel
         trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
         meas.trig_chan         = trig_chan
@@ -428,16 +458,25 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
             meas.gate_chan      = gate_chan
             self.add_and_update_dict([gate_chan])
 
-    def set_master(self, transmitter, trig_channel, pulse_length=1e-7):
-        if not isinstance(trig_channel, Channels.PhysicalMarkerChannel):
-            raise ValueError("In set_master the trigger channel must be an instance of PhysicalMarkerChannel")
+    def set_master(self, master_instrument, trig_channel=None, pulse_length=1e-7):
+
+        if isinstance(master_instrument, Channels.Processor):
+            master_instrument.master = True
+
+        elif trig_channel:
 
-        st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=self.channelDatabase)
-        st.phys_chan = trig_channel
-        st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
-        transmitter.master = True
-        transmitter.trigger_source = "internal"
-        self.add_and_update_dict([st])
+            if not isinstance(trig_channel, Channels.PhysicalMarkerChannel):
+                raise ValueError("In set_master the trigger channel must be an instance of PhysicalMarkerChannel")
+
+            st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=self.channelDatabase)
+            st.phys_chan = trig_channel
+            st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
+            master_instrument.master = True
+            master_instrument.trigger_source = "internal"
+            self.add_and_update_dict([st])
+
+        else:
+            raise ValueError(f"Could not determine which transmitter to set as master for {transmitter}:{trig_channel}")
 
 def QubitFactory(label):
     ''' Return a saved qubit channel'''
diff --git a/QGL/PulseSequencePlotter.py b/QGL/PulseSequencePlotter.py
index e2b14ed5..db41886e 100644
--- a/QGL/PulseSequencePlotter.py
+++ b/QGL/PulseSequencePlotter.py
@@ -78,7 +78,7 @@ def plot_pulse_files(metafile, time=False):
     Helper function to plot a list of AWG files. A JS slider allows choice of sequence number.
     '''
     #If we only go one filename turn it into a list
-    
+
     with open(metafile, 'r') as FID:
         meta_info = json.load(FID)
     fileNames = []
@@ -166,8 +166,8 @@ def extract_waveforms(fileNames, nameDecorator='', time=False):
         # Assume a naming convention path/to/file/SequenceName-AWGName.h5
         AWGName = "-".join((os.path.split(os.path.splitext(fileName)[0])[1]).split('-')[1:])
         # Strip any _ suffix
-        if '_' in AWGName:
-            AWGName = AWGName[:AWGName.index('_')]
+        # if '_' in AWGName:
+        #     AWGName = AWGName[:AWGName.index('_')]
 
         translator = resolve_translator(fileName, translators)
         wfs = translator.read_sequence_file(fileName)
@@ -177,7 +177,7 @@ def extract_waveforms(fileNames, nameDecorator='', time=False):
             if all_zero_seqs(seqs):
                 continue
             num_seqs = max(num_seqs, len(seqs))
-            line_names.append((AWGName + nameDecorator + '_' + k).replace("-","_")) 
+            line_names.append((AWGName + nameDecorator + '_' + k).replace("-","_"))
             k_ = line_names[-1].replace("-", "_")
             for ct, seq in enumerate(seqs):
                 data_dicts[k_ + "_{:d}".format(ct + 1)] = {}
@@ -205,7 +205,7 @@ def plot_pulse_files_compare(metafile1, metafile2, time=False):
 
     with open(metafile1, 'r') as FID:
         meta_info1 = json.load(FID)
-    
+
     for el in meta_info1["instruments"].values():
         # Accomodate seq_file per instrument and per channel
         if isinstance(el, str):
@@ -216,7 +216,7 @@ def plot_pulse_files_compare(metafile1, metafile2, time=False):
 
     with open(metafile2, 'r') as FID:
         meta_info2 = json.load(FID)
-    
+
     for el in meta_info2["instruments"].values():
         # Accomodate seq_file per instrument and per channel
         if isinstance(el, str):

From 93654eac223095bfc9b6c73a6dc7141d3b95c35c Mon Sep 17 00:00:00 2001
From: Matthew Ware <matthew.e.ware@gmail.com>
Date: Fri, 25 Jan 2019 15:59:31 -0500
Subject: [PATCH 080/235] Change APS2 rack setup

---
 QGL/ChannelLibraries.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index f7aecd7e..4499e48c 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -309,11 +309,8 @@ def new_TDM(self, label, address):
         return Channels.Processor(label=label, model="TDM", address=address, trigger_interval=250e-6)
 
     @check_for_duplicates
-    def new_APS2_rack(self, label, num, start_address, tdm_ip=None):
-        address_start = ".".join(start_address.split(".")[:3])
-        address_end   = int(start_address.split(".")[-1])
-        transmitters  = [self.new_APS2(f"{label}_U{i}", f"{address_start}.{address_end+i}") for i in range(1,num+1)]
-
+    def new_APS2_rack(self, label, ip_addresses, tdm_ip=None):
+        transmitters  = [self.new_APS2(f"{label}_U{n+1}", f"{ip}") for n, ip in enumerate(ip_addresses)]
         this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", transmitters=transmitters, channel_db=self.channelDatabase)
         for t in transmitters:
             t.transceiver = this_transceiver

From fb89dcac63b420a81abb7153ecb85b0bc3897608 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matthew.e.ware@gmail.com>
Date: Fri, 25 Jan 2019 16:24:11 -0500
Subject: [PATCH 081/235] Properly set edges.

---
 QGL/ChannelLibraries.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 4499e48c..79331c1a 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -380,7 +380,7 @@ def new_source(self, label, model, address, power=-30.0, frequency=5.0e9, refere
         self.add_and_update_dict(thing)
         return thing
 
-    def set_control(self, qubit, transmitter, generator=None):
+    def set_control(self, qubit_or_edge, transmitter, generator=None):
         quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
         markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
 
@@ -393,11 +393,19 @@ def set_control(self, qubit, transmitter, generator=None):
         else:
             raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
-        qubit.phys_chan = phys_chan
+        qubit_or_edge.phys_chan = phys_chan
         if generator:
-            qubit.phys_chan.generator = generator
+            qubit_or_edge.phys_chan.generator = generator
         self.update_channelDict()
 
+    def new_edge(self, source, target):
+        label = f"{source.label}->{target.label}"
+        if label in self.channelDict:
+            raise ValueError("Cannot construct edge {label} since it is already in the channel library.")
+        edge = Channels.Edge(label=f"{source.label}->{target.label}", source=source, target=target, channel_db=self.channelDatabase)
+        self.add_and_update_dict(edge)
+        return edge
+
     def set_qubit_connectivity(self, graph):
         """
         Graph is a networkx DiGraph consisting of edges (source qubit, target qubit)

From 88e9bdf278fd5b5f000753abadd19a5884cd66b0 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Mon, 28 Jan 2019 16:52:30 -0500
Subject: [PATCH 082/235] Remove merge conflict detritus

---
 QGL/ChannelLibraries.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 79331c1a..64588967 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -280,14 +280,11 @@ def values(self):
 
     def build_connectivity_graph(self):
         # build connectivity graph
-        for chan in select(q for q in Channels.Qubit if q not in self.connectivityG):
-=======
         for chan in self.session.query(Channels.Qubit).filter(Channels.Qubit not in self.connectivityG).all():
             self.connectivityG.add_node(chan)
         for chan in self.session.query(Channels.Edge): #select(e for e in Channels.Edge):
             self.connectivityG.add_edge(chan.source, chan.target)
             self.connectivityG[chan.source][chan.target]['channel'] = chan
->>>>>>> Ditch atom, move to Pony.orm for all channel library objects.
 
     @check_for_duplicates
     def new_APS2(self, label, address):

From be6e8a6c44109b6e621aa74fac0e4461436f21ac Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 29 Jan 2019 16:21:14 -0500
Subject: [PATCH 083/235] Fix up travis yml from merge

---
 .travis.yml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index d936dc77..4258bc7e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,6 +4,9 @@
 language: python
 python:
   - 3.6
+env:
+  - CONDA_TYPE=miniconda CONDA_VERS=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  - CONDA_TYPE=miniconda CONDA_VERS=https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh
 
 before_install:
   # install git lfs and fetch test data
@@ -22,11 +25,11 @@ install:
 
   # We do this conditionally because it saves us some downloading if the
   # version is the same.
-  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - echo "Using $CONDA_TYPE"
+  - wget $CONDA_VERS -O miniconda.sh
+  - bash miniconda.sh -h | sed '4q;d'
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
-  - export BBN_MEAS_FILE="$PWD/tests/test_measure.yml"
-  - echo "Measure file at $BBN_MEAS_FILE"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
@@ -34,10 +37,9 @@ install:
   - conda info -a
 
   # Create conda environment with dependencies
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy bokeh h5py jupyter scipy networkx future
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy bokeh h5py jupyter scipy networkx
   - source activate test-environment
-  - conda install -c ecpy atom;
-  - pip install watchdog coveralls
+  - pip install coveralls
   - if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then  pip install pygsti; fi
 
 script:

From 3e14ce85605af80f0c4945f0c67b27a142825d79 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Tue, 5 Feb 2019 16:47:54 -0500
Subject: [PATCH 084/235] New spec an

---
 QGL/ChannelLibraries.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 64588967..8515aa5d 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -305,6 +305,10 @@ def new_APS2(self, label, address):
     def new_TDM(self, label, address):
         return Channels.Processor(label=label, model="TDM", address=address, trigger_interval=250e-6)
 
+    @check_for_duplicates
+    def new_spectrum_analzyer(self, label, address, source):
+        return Channels.SpectrumAnalyzer(label=label, model="SpectrumAnalyzer", address=address, LO_source=source)
+
     @check_for_duplicates
     def new_APS2_rack(self, label, ip_addresses, tdm_ip=None):
         transmitters  = [self.new_APS2(f"{label}_U{n+1}", f"{ip}") for n, ip in enumerate(ip_addresses)]

From 1bfe23578d5f28fb7abb45929d41556153d5171b Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Fri, 8 Feb 2019 13:39:14 -0500
Subject: [PATCH 085/235] Pass frequency keyword to enable baked in frequency
 sweeps

---
 QGL/PulsePrimitives.py     | 6 +++++-
 QGL/PulseSequencer.py      | 6 ++++--
 QGL/drivers/APS2Pattern.py | 2 +-
 3 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index 59d48099..bfbf03b2 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -91,6 +91,10 @@ def Utheta(qubit,
         del params["amp"]
     if "phase" in params:
         del params["phase"]
+    if "frequency" in kwargs:
+        frequency = kwargs["frequency"]
+    else:
+        frequency = None
     # allow override of angle -> amplitude lookup if the user provides an "amp"
     # keyword argument
     if "amp" in kwargs:
@@ -109,7 +113,7 @@ def Utheta(qubit,
         else:
             # linearly scale based upon the 'pi/2' amplitude
             amp  = (angle / (pi/2)) * qubit.pulse_params['pi2Amp']
-    return Pulse(label, qubit, params, amp, phase, 0.0, ignoredStrParams)
+    return Pulse(label, qubit, params, amp, phase, 0.0, ignoredStrParams, frequency=frequency)
 
 
 # generic pulses around X, Y, and Z axes
diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 34d1f07f..315c3db8 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -36,8 +36,10 @@ class Pulse(namedtuple("Pulse", ["label", "channel", "length", "amp", "phase", "
                                  "maddr", "moffset"])):
     __slots__ = ()
 
-    def __new__(cls, label, channel, shapeParams, amp=1.0, phase=0, frameChange=0, ignoredStrParams=[], maddr=-1, moffset=0):
-        if hasattr(channel, 'frequency'):
+    def __new__(cls, label, channel, shapeParams, amp=1.0, phase=0, frameChange=0, ignoredStrParams=[], maddr=-1, moffset=0, frequency=None):
+        if frequency:
+            frequency = frequency
+        elif hasattr(channel, 'frequency'):
             frequency = channel.frequency
         else:
             frequency = 0
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 4291e34d..60bb0657 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -163,7 +163,7 @@ def create_wf_vector(wfLib, seqs):
 
     else:
         #otherwise fill in one cache line at a time
-        CACHE_LINE_LENGTH = WAVEFORM_CACHE_SIZE / 2
+        CACHE_LINE_LENGTH = int(np.round(WAVEFORM_CACHE_SIZE / 2)) - 1
         wfVec = np.zeros(CACHE_LINE_LENGTH, dtype=np.int16)
         offsets = [{}]
         cache_lines = []

From a7c7ef305c7d2570739ea95c1627e0d08a7a83f1 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 7 Feb 2019 17:07:43 -0500
Subject: [PATCH 086/235] Replace H5 with simple binary format in aps2

---
 QGL/drivers/APS2Pattern.py | 68 +++++++++++++++++++-------------------
 1 file changed, 34 insertions(+), 34 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 60bb0657..38986a2b 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -23,7 +23,7 @@
 from future.moves.itertools import zip_longest
 import pickle
 
-import h5py
+import struct
 import numpy as np
 
 from QGL import Compiler, ControlFlow, BlockLabel, PatternUtils
@@ -108,17 +108,13 @@
 def get_empty_channel_set():
     return {'ch1': {}, 'm1': {}, 'm2': {}, 'm3': {}, 'm4': {}}
 
-
 def get_seq_file_extension():
-    return '.h5'
-
+    return '.aps2'
 
 def is_compatible_file(filename):
-    with h5py.File(filename, 'r') as FID:
-        target = FID['/'].attrs['target hardware']
-        if isinstance(target, str):
-            target = target.encode('utf-8')
-        if target == b'APS2':
+    with open(filename, 'rb') as FID:
+        byte = FID.read(4)
+        if byte == b'APS2':
             return True
     return False
 
@@ -1082,34 +1078,33 @@ def write_sequence_file(awgData, fileName):
                 for s in ['ch1', 'm1', 'm2', 'm3', 'm4']]
     instructions = create_instr_data(seq_data, wfInfo[0][1], wfInfo[0][2])
 
-    #Open the HDF5 file
+    #Open the binary file
     if os.path.isfile(fileName):
         os.remove(fileName)
-    with h5py.File(fileName, 'w') as FID:
-        FID['/'].attrs['Version'] = 4.0
-        FID['/'].attrs['target hardware'] = 'APS2'
-        FID['/'].attrs['minimum firmware version'] = 4.0
-        FID['/'].attrs['channelDataFor'] = np.uint16([1, 2])
+
+    with open(fileName, 'wb') as FID:
+        FID.write(b'APS2')                     # target hardware
+        FID.write(np.float32(4.0).tobytes())   # Version
+        FID.write(np.float32(4.0).tobytes())   # minimum firmware version
+        FID.write(np.uint16(2).tobytes())      # number of channels
+        # FID.write(np.uint16([1, 2]).tobytes()) # channelDataFor
+        FID.write(np.uint64(instructions.size).tobytes()) # instructions length
+        FID.write(instructions.tobytes()) # instructions in uint64 form
 
         #Create the groups and datasets
         for chanct in range(2):
-            chanStr = '/chan_{0}'.format(chanct + 1)
-            chanGroup = FID.create_group(chanStr)
+            # chanStr = '/chan_{0}'.format(chanct + 1)
+            # chanGroup = FID.create_group(chanStr)
             #Write the waveformLib to file
             if wfInfo[chanct][0].size == 0:
                 #If there are no waveforms, ensure that there is some element
                 #so that the waveform group gets written to file.
                 #TODO: Fix this in libaps2
-                data = np.array([0], dtype=np.uint16)
+                data = np.array([0], dtype=np.int16)
             else:
                 data = wfInfo[chanct][0]
-            FID.create_dataset(chanStr + '/waveforms', data=data)
-
-            #Write the instructions to channel 1
-            if np.mod(chanct, 2) == 0:
-                FID.create_dataset(chanStr + '/instructions',
-                                   data=instructions)
-
+            FID.write(np.uint64(data.size).tobytes()) # waveform data length for channel
+            FID.write(data.tobytes())
 
 def read_sequence_file(fileName):
     """
@@ -1130,16 +1125,21 @@ def start_new_seq():
                 #marker channel
                 seqs[ch].append([])
 
-    with h5py.File(fileName, 'r') as FID:
-        file_version = FID["/"].attrs["Version"]
+    with open(fileName, 'rb') as FID:
+        target_hw    = FID.read(4).decode('utf-8')
+        file_version = struct.unpack('<f', FID.read(4))[0]
+        min_fw       = struct.unpack('<f', FID.read(4))[0]
+        num_chans    = struct.unpack('<H', FID.read(2))[0]
+        
+        inst_len     = struct.unpack('<Q', FID.read(8))[0]
+        instructions = np.frombuffer(FID.read(8*inst_len), dtype=np.uint64)
+        
         wf_lib = {}
-        wf_lib['ch1'] = (
-            1.0 /
-            MAX_WAVEFORM_VALUE) * FID['/chan_1/waveforms'].value.flatten()
-        wf_lib['ch2'] = (
-            1.0 /
-            MAX_WAVEFORM_VALUE) * FID['/chan_2/waveforms'].value.flatten()
-        instructions = FID['/chan_1/instructions'].value.flatten()
+        for i in range(num_chans):
+            wf_len  = struct.unpack('<Q', FID.read(8))[0]
+            wf_dat  = np.frombuffer(FID.read(2*wf_len), dtype=np.int16)
+            wf_lib[f'ch{i+1}'] = ( 1.0 / MAX_WAVEFORM_VALUE) * wf_dat.flatten()
+
         NUM_NCO = 2
         freq = np.zeros(NUM_NCO)  #radians per timestep
         phase = np.zeros(NUM_NCO)

From 9e9a562649023b0d3c2530f78c64f8a82bd65fdc Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 8 Feb 2019 12:54:17 -0500
Subject: [PATCH 087/235] Add a nice PyQt5 GUI for showing disassmbled APS2
 instructions

---
 QGL/drivers/APS2Pattern.py | 101 ++++++++++++++++++++++++++++++-------
 requirements.txt           |   1 -
 setup.py                   |   1 -
 3 files changed, 83 insertions(+), 20 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 38986a2b..1d7bb765 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -24,6 +24,7 @@
 import pickle
 
 import struct
+import sys
 import numpy as np
 
 from QGL import Compiler, ControlFlow, BlockLabel, PatternUtils
@@ -258,9 +259,9 @@ def __str__(self):
             wfOpCode = (self.payload >> 46) & 0x3
             wfOpCodes = ["PLAY", "TRIG", "SYNC", "PREFETCH"]
             out += wfOpCodes[wfOpCode]
-            out += "; TA bit={}".format((self.payload >> 45) & 0x1)
-            out += ", count = {}".format((self.payload >> 24) & 2**21 - 1)
-            out += ", addr = {}".format(self.payload & 2**24 - 1)
+            out += "; TA_bit={}".format((self.payload >> 45) & 0x1)
+            out += ", count={}".format((self.payload >> 24) & 2**21 - 1)
+            out += ", addr={}".format(self.payload & 2**24 - 1)
 
             # # APS3/TDM modifier to use VRAM output
             # if self.payload & (1 << 48):
@@ -271,7 +272,7 @@ def __str__(self):
             mrkOpCodes = ["PLAY", "TRIG", "SYNC"]
             out += mrkOpCodes[mrkOpCode]
             out += "; state={}".format((self.payload >> 32) & 0x1)
-            out += ", count = {}".format(self.payload & 2**32 - 1)
+            out += ", count={}".format(self.payload & 2**32 - 1)
 
         elif instrOpCode == MODULATION:
             modulatorOpCode = (self.payload >> 45) & 0x7
@@ -293,21 +294,21 @@ def __str__(self):
             cmpCodes = ["EQUAL", "NOTEQUAL", "GREATERTHAN", "LESSTHAN"]
             cmpCode = (self.payload >> 8) & 0x3
             out += " | " + cmpCodes[cmpCode]
-            out += ", value = {}".format(self.payload & 0xff)
+            out += ", value={}".format(self.payload & 0xff)
 
         elif any(
             [instrOpCode == op for op in [GOTO, CALL, RET, REPEAT, PREFETCH]]):
-            out += " | target addr = {}".format(self.payload & 2**26 - 1)
+            out += " | target_addr={}".format(self.payload & 2**26 - 1)
 
         elif instrOpCode == LOAD:
-            out += " | count = {}".format(self.payload)
+            out += " | count={}".format(self.payload)
 
         elif instrOpCode == CUSTOM:
             store_addr = self.payload & 0xFFFF
             load_addr = (self.payload >> 16) & 0xFFFF
             instruction = (self.payload >> 32) & 0xFF
             instructionAPS = TDM_CUSTOM_DECODE[instruction]
-            out += " | instruction = {0} ({1}), load_addr = 0x{2:0x}, store_addr = 0x{3:0x}".format(instruction, instructionAPS, load_addr, store_addr)
+            out += " | instruction={0} ({1}), load_addr=0x{2:0x}, store_addr=0x{3:0x}".format(instruction, instructionAPS, load_addr, store_addr)
 
         elif instrOpCode == WRITEADDR:
             addr = self.payload & 0xFFFF
@@ -333,7 +334,7 @@ def __str__(self):
                 addr = (self.payload >> 16) & 0xFFFF
                 value = (self.payload >> 32) & 0xFFFF
 
-            out += "{0} | addr = 0x{1:0x}, {2} = 0x{3:0x}".format(instrStr, addr, valueType, value)
+            out += "{0} | addr=0x{1:0x}, {2}=0x{3:0x}".format(instrStr, addr, valueType, value)
 
         elif instrOpCode == LOADCMP:
             addr = self.payload & 0xFFFF
@@ -345,7 +346,7 @@ def __str__(self):
                 src = "EXT"
                 if use_ram:
                     src = "RAM"
-                out += "LOADCMP | source = {0}, addr = 0x{1:0x}, read_mask = 0x{2:0x}".format(src, addr, mask)
+                out += "LOADCMP | source={0}, addr=0x{1:0x}, read_mask=0x{2:0x}".format(src, addr, mask)
         return out
 
     def __eq__(self, other):
@@ -1447,14 +1448,16 @@ def write_tdm_seq(seq, tdm_fileName):
 
 # Utility Functions for displaying programs
 
-def get_channel_instructions_string(channel):
-    return '/chan_{}/instructions'.format(channel)
-
-def raw_instructions(filename, channel = 1):
-    channelStr =  get_channel_instructions_string(channel)
-    with h5py.File(filename, 'r') as fid:
-        raw_instrs = fid[channelStr].value.flatten()
-        return raw_instrs
+def raw_instructions(fileName):
+    with open(fileName, 'rb') as FID:
+        target_hw    = FID.read(4).decode('utf-8')
+        file_version = struct.unpack('<f', FID.read(4))[0]
+        min_fw       = struct.unpack('<f', FID.read(4))[0]
+        num_chans    = struct.unpack('<H', FID.read(2))[0]
+        
+        inst_len     = struct.unpack('<Q', FID.read(8))[0]
+        instructions = np.frombuffer(FID.read(8*inst_len), dtype=np.uint64)
+    return instructions
 
 def decompile_instructions(instructions, tdm = False):
     return [Instruction.unflatten(x, decode_as_tdm = tdm) for x in instructions]
@@ -1489,3 +1492,65 @@ def display_raw_instructions(raw):
 def display_raw_file(filename):
     raw = raw_instructions(filename)
     display_raw_instructions(raw)
+
+if __name__ == '__main__':
+    if len(sys.argv) == 2:
+        
+        from PyQt5.QtWidgets import QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView
+        from PyQt5.QtGui import QIcon, QColor
+
+        colors = {"WFM": QColor(0,200,0),
+                  "GOTO": QColor(0,100,100),
+                  "MARKER": QColor(150,150,200)}
+
+        class App(QWidget):
+         
+            def __init__(self, instructions):
+                super().__init__()
+                self.title = 'APS2 Disassembled Instructions'
+                self.left = 100
+                self.top = 100
+                self.width = 1000
+                self.height = 1200
+                self.instructions = instructions
+                self.initUI()
+         
+            def initUI(self):
+                self.setWindowTitle(self.title)
+                self.setGeometry(self.left, self.top, self.width, self.height)
+         
+                self.createTable()
+                self.layout = QVBoxLayout()
+                self.layout.addWidget(self.tableWidget) 
+                self.setLayout(self.layout) 
+         
+                # Show widget
+                self.show()
+         
+            def createTable(self):
+               # Create table
+                self.tableWidget = QTableWidget()
+                self.tableWidget.setRowCount(len(self.instructions))
+                self.tableWidget.setColumnCount(7)
+
+                for k, instr in enumerate(self.instructions):
+                    fields = str(instr).replace(',','').replace(';', '').split(" ")
+                    if "|" in fields:
+                        fields.remove("|")
+                    if fields[0] in colors:
+                        color = colors[fields[0]]
+                    else:
+                        color = None
+                    for l, f in enumerate(fields):
+                        text = fields[l]
+                        item = QTableWidgetItem(text)
+                        if color:
+                            item.setBackground(color)
+                        self.tableWidget.setItem(k,l, item)
+                self.tableWidget.move(0,0)
+                self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
+
+        app = QApplication(sys.argv[:1])
+        ex = App(read_instructions(sys.argv[1]))
+        sys.exit(app.exec_())
+
diff --git a/requirements.txt b/requirements.txt
index e13f6dc7..65797540 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,5 +2,4 @@ bbndb >= 0.1
 numpy >= 1.11.1
 scipy >= 0.17.1
 networkx >= 1.11
-h5py >= 2.6.0
 bokeh >= 0.12.13
diff --git a/setup.py b/setup.py
index c4db92c2..a5ef0be3 100644
--- a/setup.py
+++ b/setup.py
@@ -9,7 +9,6 @@
         "numpy >= 1.11.1",
         "scipy >= 0.17.1",
         "networkx >= 1.11",
-        "h5py >= 2.6.0",
         "bokeh >= 0.12.13",
         # "pony >= 0.7.4", # This needs to be 0.7.4-dev
     ])

From 492a21cd65573c9cce6a1be70710d680dd42ad83 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Fri, 8 Feb 2019 16:17:49 -0500
Subject: [PATCH 088/235] No more bokeh

---
 QGL/Plotting.py             | 75 ++++++++++++-----------------
 QGL/PulseSequencePlotter.py | 94 ++++++++++---------------------------
 QGL/__init__.py             |  2 +-
 QGL/drivers/APS2Pattern.py  | 27 +++++------
 requirements.txt            |  1 -
 5 files changed, 67 insertions(+), 132 deletions(-)

diff --git a/QGL/Plotting.py b/QGL/Plotting.py
index 25c3c1a5..254c1568 100644
--- a/QGL/Plotting.py
+++ b/QGL/Plotting.py
@@ -22,28 +22,13 @@
 '''
 
 import os.path, uuid, tempfile
-import bokeh.plotting as bk
-from bokeh.layouts import column
-from bokeh.util.warnings import BokehUserWarning
-from bokeh.resources import INLINE
 import numpy as np
 import warnings
 from . import config
 
-def output_notebook(local=True, suppress_warnings=False):
-    if suppress_warnings:
-        warnings.simplefilter("ignore", BokehUserWarning)
-    if local:
-        bk.output_notebook(resources=INLINE)
-    else:
-        bk.output_notebook()
-
-def output_file(local=True, suppress_warnings=True):
-    if suppress_warnings:
-        warnings.simplefilter("ignore", BokehUserWarning)
-    mode = "inline" if local else "cdn"
-    bk.output_file(os.path.join(tempfile.gettempdir(), str(uuid.uuid4()) +
-                                ".html"), mode=mode)
+def output_notebook():
+    import matplotlib
+    matplotlib.use("nbagg")
 
 def build_waveforms(seq):
     # import here to avoid circular imports
@@ -76,30 +61,30 @@ def build_waveforms(seq):
         concatShapes[q] = np.append(concatShapes[q], 0)
     return concatShapes
 
-
-def plot_waveforms(waveforms, figTitle=''):
-    channels = waveforms.keys()
-    # plot
-    plots = []
-    for (ct, chan) in enumerate(channels):
-        fig = bk.figure(title=figTitle + repr(chan),
-                        plot_width=800,
-                        plot_height=350,
-                        y_range=[-1.05, 1.05],
-                        x_axis_label=u'Time (μs)')
-        fig.background_fill_color = config.plotBackground
-        if config.gridColor:
-            fig.xgrid.grid_line_color = config.gridColor
-            fig.ygrid.grid_line_color = config.gridColor
-        waveformToPlot = waveforms[chan]
-        xpts = np.linspace(0, len(waveformToPlot) / chan.phys_chan.sampling_rate
-                           / 1e-6, len(waveformToPlot))
-        fig.line(xpts, np.real(waveformToPlot), color='red')
-        fig.line(xpts, np.imag(waveformToPlot), color='blue')
-        plots.append(fig)
-    bk.show(column(*plots))
-
-
-def show(seq):
-    waveforms = build_waveforms(seq)
-    plot_waveforms(waveforms)
+#
+# def plot_waveforms(waveforms, figTitle=''):
+#     channels = waveforms.keys()
+#     # plot
+#     plots = []
+#     for (ct, chan) in enumerate(channels):
+#         fig = bk.figure(title=figTitle + repr(chan),
+#                         plot_width=800,
+#                         plot_height=350,
+#                         y_range=[-1.05, 1.05],
+#                         x_axis_label=u'Time (μs)')
+#         fig.background_fill_color = config.plotBackground
+#         if config.gridColor:
+#             fig.xgrid.grid_line_color = config.gridColor
+#             fig.ygrid.grid_line_color = config.gridColor
+#         waveformToPlot = waveforms[chan]
+#         xpts = np.linspace(0, len(waveformToPlot) / chan.phys_chan.sampling_rate
+#                            / 1e-6, len(waveformToPlot))
+#         fig.line(xpts, np.real(waveformToPlot), color='red')
+#         fig.line(xpts, np.imag(waveformToPlot), color='blue')
+#         plots.append(fig)
+#     bk.show(column(*plots))
+
+#
+# def show(seq):
+#     waveforms = build_waveforms(seq)
+#     plot_waveforms(waveforms)
diff --git a/QGL/PulseSequencePlotter.py b/QGL/PulseSequencePlotter.py
index db41886e..b570dc09 100644
--- a/QGL/PulseSequencePlotter.py
+++ b/QGL/PulseSequencePlotter.py
@@ -25,12 +25,9 @@
 import os.path
 import json
 from importlib import import_module
-from bokeh.layouts import column
-from bokeh.models import CustomJS, ColumnDataSource, Slider
-from bokeh.plotting import Figure, show
-from bokeh.palettes import d3, brewer, Inferno
-
-from jinja2 import Template
+from ipywidgets import interact, interactive, fixed, interact_manual, IntSlider
+import ipywidgets as widgets
+import matplotlib.pyplot as plt
 import numpy as np
 
 from . import config
@@ -71,11 +68,11 @@ def resolve_translator(filename, translators):
     raise NameError("No translator found to open the given file %s", filename)
 
 
-def plot_pulse_files(metafile, time=False):
+def plot_pulse_files(metafile, time=False, backend='matplotlib'):
     '''
     plot_pulse_files(metafile)
 
-    Helper function to plot a list of AWG files. A JS slider allows choice of sequence number.
+    Helper function to plot a list of AWG files. A jupyter slider widget allows choice of sequence number.
     '''
     #If we only go one filename turn it into a list
 
@@ -94,68 +91,25 @@ def plot_pulse_files(metafile, time=False):
     localname = os.path.split(fileNames[0])[1]
     sequencename = localname.split('-')[0]
 
-    data = {line_name: ColumnDataSource(data=dat) for line_name,dat in data_dicts.items()}
-    plot = Figure(title=sequencename, plot_width=1000)
-    if config.plotBackground:
-        plot.background_fill_color = config.plotBackground
-    if config.gridColor:
-        plot.xgrid.grid_line_color = config.gridColor
-        plot.ygrid.grid_line_color = config.gridColor
-
-    if len(line_names) < 10:
-    # Colobrewer2 qualitative Set1 (http://colorbrewer2.org)
-        colors = brewer['Set1'][max(3, len(line_names))]
-    elif 9 < len(line_names) < 19:
-    # d3 Category20 for up to 18 channels
-        colors = d3['Category20'][len(line_names)]
-    else:
-    # 256 palette
-        colors = [Inferno[256][np.int(ct-1)] for ct in np.floor(np.linspace(0,256,len(line_names)))]
-    js_sources = data
-    for ct, k in enumerate(line_names):
-        k_ = k.replace("-", "_")
-        line = plot.line(data_dicts[k + "_1"]["x"],
-                         data_dicts[k + "_1"]["y"],
-                         color=colors[ct % len(colors)],
-                         line_width=2,
-                         legend=k.replace("_", "-"))
-        js_sources[k_] = line.data_source
-
-    code_template = Template("""
-        var seq_num = cb_obj.getv('value');
-        // console.log(seq_num);
-        var all_data = {
-            {% for trace in trace_names %}
-                '{{trace}}': {{trace}}.getv('data'),
-            {% endfor %}
-        };
-        {% for line in line_names %}
-        {{line}}['data'] = {'x': (all_data['{{line}}_'.concat(seq_num.toString())])['x'],
-                              'y': (all_data['{{line}}_'.concat(seq_num.toString())])['y']};
-        {% endfor %}
-    """)
-    rendered = code_template.render(
-            line_names=line_names,
-            trace_names=list(data.keys())[:-len(line_names)]
-            )
-
-    callback = CustomJS(
-        args=dict(**js_sources),
-        code=rendered)
-
-    if num_seqs > 1:
-        slider = Slider(start=1,
-                        end=num_seqs,
-                        value=1,
-                        step=1,
-                        title="Sequence",
-                        callback=callback)
-
-        layout = column(slider, plot)
-        show(layout)
-    else:
-        show(plot)
-
+    if backend=='matplotlib':
+        fig = plt.figure()
+        ax = fig.add_subplot(1,1,1)
+        ax.set_title("Waveform Plotter")
+        lines = []
+        for line_name in line_names:
+            dat = data_dicts[f"{line_name}_1"]
+            line, = ax.plot(dat['x'], dat['y'], label=line_name, linewidth=1.0)
+            lines.append(line)
+        plt.tight_layout()
+        plt.show()
+
+        def update_plot(seq_ind):
+            for line, line_name in zip(lines, line_names):
+                dat = data_dicts[f"{line_name}_{seq_ind}"]
+                line.set_xdata(dat['x'])
+                line.set_ydata(dat['y'])
+            fig.canvas.draw()
+        interact(update_plot, seq_ind=IntSlider(min=1,max=num_seqs,step=1,value=1,description="Sequence Number"))
 
 def extract_waveforms(fileNames, nameDecorator='', time=False):
     line_names = []
diff --git a/QGL/__init__.py b/QGL/__init__.py
index aa06418c..84728ba8 100644
--- a/QGL/__init__.py
+++ b/QGL/__init__.py
@@ -6,7 +6,7 @@
 from .PulseSequencer import align
 from .ControlFlow import repeat, repeatall, qif, qwhile, qdowhile, qfunction, qwait, qsync, Barrier
 from .BasicSequences import *
-from .Plotting import output_file, output_notebook, show, build_waveforms, plot_waveforms
+from .Plotting import output_notebook #, show, build_waveforms, plot_waveforms
 from .PulseSequencePlotter import plot_pulse_files
 from .Tomography import state_tomo, process_tomo
 from .Scheduler import schedule
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 1d7bb765..c4c6ff95 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -178,7 +178,7 @@ def create_wf_vector(wfLib, seqs):
                 idx = int(CACHE_LINE_LENGTH * (
                     (idx + CACHE_LINE_LENGTH) // CACHE_LINE_LENGTH))
                 wfVec = np.append(wfVec,
-                                  np.zeros(CACHE_LINE_LENGTH,
+                                  np.zeros(int(CACHE_LINE_LENGTH),
                                            dtype=np.int16))
                 offsets.append({})
 
@@ -1094,8 +1094,6 @@ def write_sequence_file(awgData, fileName):
 
         #Create the groups and datasets
         for chanct in range(2):
-            # chanStr = '/chan_{0}'.format(chanct + 1)
-            # chanGroup = FID.create_group(chanStr)
             #Write the waveformLib to file
             if wfInfo[chanct][0].size == 0:
                 #If there are no waveforms, ensure that there is some element
@@ -1131,10 +1129,10 @@ def start_new_seq():
         file_version = struct.unpack('<f', FID.read(4))[0]
         min_fw       = struct.unpack('<f', FID.read(4))[0]
         num_chans    = struct.unpack('<H', FID.read(2))[0]
-        
+
         inst_len     = struct.unpack('<Q', FID.read(8))[0]
         instructions = np.frombuffer(FID.read(8*inst_len), dtype=np.uint64)
-        
+
         wf_lib = {}
         for i in range(num_chans):
             wf_len  = struct.unpack('<Q', FID.read(8))[0]
@@ -1454,7 +1452,7 @@ def raw_instructions(fileName):
         file_version = struct.unpack('<f', FID.read(4))[0]
         min_fw       = struct.unpack('<f', FID.read(4))[0]
         num_chans    = struct.unpack('<H', FID.read(2))[0]
-        
+
         inst_len     = struct.unpack('<Q', FID.read(8))[0]
         instructions = np.frombuffer(FID.read(8*inst_len), dtype=np.uint64)
     return instructions
@@ -1495,7 +1493,7 @@ def display_raw_file(filename):
 
 if __name__ == '__main__':
     if len(sys.argv) == 2:
-        
+
         from PyQt5.QtWidgets import QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView
         from PyQt5.QtGui import QIcon, QColor
 
@@ -1504,7 +1502,7 @@ def display_raw_file(filename):
                   "MARKER": QColor(150,150,200)}
 
         class App(QWidget):
-         
+
             def __init__(self, instructions):
                 super().__init__()
                 self.title = 'APS2 Disassembled Instructions'
@@ -1514,19 +1512,19 @@ def __init__(self, instructions):
                 self.height = 1200
                 self.instructions = instructions
                 self.initUI()
-         
+
             def initUI(self):
                 self.setWindowTitle(self.title)
                 self.setGeometry(self.left, self.top, self.width, self.height)
-         
+
                 self.createTable()
                 self.layout = QVBoxLayout()
-                self.layout.addWidget(self.tableWidget) 
-                self.setLayout(self.layout) 
-         
+                self.layout.addWidget(self.tableWidget)
+                self.setLayout(self.layout)
+
                 # Show widget
                 self.show()
-         
+
             def createTable(self):
                # Create table
                 self.tableWidget = QTableWidget()
@@ -1553,4 +1551,3 @@ def createTable(self):
         app = QApplication(sys.argv[:1])
         ex = App(read_instructions(sys.argv[1]))
         sys.exit(app.exec_())
-
diff --git a/requirements.txt b/requirements.txt
index 65797540..b50f7f6f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,4 +2,3 @@ bbndb >= 0.1
 numpy >= 1.11.1
 scipy >= 0.17.1
 networkx >= 1.11
-bokeh >= 0.12.13

From a2715c66ed6d371799c0a3dcb8f5c3013835dcf1 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Mon, 11 Feb 2019 13:18:56 -0500
Subject: [PATCH 089/235] Replace bokeh with bqplot

---
 QGL/PulseSequencePlotter.py | 249 +++++++++++++++++++-----------------
 requirements.txt            |   1 +
 setup.py                    |   3 +-
 3 files changed, 136 insertions(+), 117 deletions(-)

diff --git a/QGL/PulseSequencePlotter.py b/QGL/PulseSequencePlotter.py
index b570dc09..5833a35b 100644
--- a/QGL/PulseSequencePlotter.py
+++ b/QGL/PulseSequencePlotter.py
@@ -25,9 +25,8 @@
 import os.path
 import json
 from importlib import import_module
-from ipywidgets import interact, interactive, fixed, interact_manual, IntSlider
+from ipywidgets import interact, VBox, IntSlider
 import ipywidgets as widgets
-import matplotlib.pyplot as plt
 import numpy as np
 
 from . import config
@@ -68,7 +67,7 @@ def resolve_translator(filename, translators):
     raise NameError("No translator found to open the given file %s", filename)
 
 
-def plot_pulse_files(metafile, time=False, backend='matplotlib'):
+def plot_pulse_files(metafile, time=True, backend='bqplot'):
     '''
     plot_pulse_files(metafile)
 
@@ -92,24 +91,44 @@ def plot_pulse_files(metafile, time=False, backend='matplotlib'):
     sequencename = localname.split('-')[0]
 
     if backend=='matplotlib':
-        fig = plt.figure()
-        ax = fig.add_subplot(1,1,1)
-        ax.set_title("Waveform Plotter")
+        import matplotlib.pyplot as plt
+        def update_plot(seq_ind):
+            for line_name in line_names:
+                dat = data_dicts[f"{line_name}_{seq_ind}"]
+                plt.plot(dat['x'], dat['y'], label=line_name, linewidth=1.0)
+        interact(update_plot, seq_ind=IntSlider(min=1,max=num_seqs,step=1,value=1,description="Sequence Number"))
+
+    elif backend=='bqplot':
+        from bqplot import DateScale, LinearScale, Axis, Lines, Figure, Tooltip
+        from bqplot.colorschemes import CATEGORY10, CATEGORY20
+        from ipywidgets import interact, IntSlider
+        sx = LinearScale()
+        sy = LinearScale(min=-1.0, max=2*len(line_names)-1.0)
+        if time:
+            ax = Axis(label='Time (ns)', scale=sx)
+        else:
+            ax = Axis(label="Samples", scale=sx)
+        ay = Axis(label='Amplitude', scale=sy, orientation='vertical')
+
+        colors = CATEGORY10 if len(line_names)<10 else CATEGORY20
         lines = []
-        for line_name in line_names:
+        tt = Tooltip(fields=['name'], labels=['Channel'])
+        x_mult = 1.0e9 if time else 1
+        for i, line_name in enumerate(line_names):
             dat = data_dicts[f"{line_name}_1"]
-            line, = ax.plot(dat['x'], dat['y'], label=line_name, linewidth=1.0)
-            lines.append(line)
-        plt.tight_layout()
-        plt.show()
+            lines.append(Lines(labels=[line_name], x=x_mult*dat['x'], y=dat['y'], scales={'x': sx, 'y': sy}, 
+                                tooltip=tt, animate=False, colors=[colors[i]]))
 
-        def update_plot(seq_ind):
+        slider = IntSlider(min=1, max=num_seqs, step=1, description='Segment', value=1)
+        def segment_changed(change):
             for line, line_name in zip(lines, line_names):
-                dat = data_dicts[f"{line_name}_{seq_ind}"]
-                line.set_xdata(dat['x'])
-                line.set_ydata(dat['y'])
-            fig.canvas.draw()
-        interact(update_plot, seq_ind=IntSlider(min=1,max=num_seqs,step=1,value=1,description="Sequence Number"))
+                dat = data_dicts[f"{line_name}_{slider.value}"]
+                line.x = x_mult*dat['x']
+                line.y = dat['y']
+        slider.observe(segment_changed, 'value')
+        fig = Figure(marks=lines, axes=[ax, ay], title='Waveform Plotter',animation_duration=50)
+        return VBox([slider, fig])
+
 
 def extract_waveforms(fileNames, nameDecorator='', time=False):
     line_names = []
@@ -147,101 +166,101 @@ def extract_waveforms(fileNames, nameDecorator='', time=False):
     return line_names, num_seqs, data_dicts
 
 
-def plot_pulse_files_compare(metafile1, metafile2, time=False):
-    '''
-    plot_pulse_files_compare(fileNames1, fileNames2)
-
-    Helper function to plot a list of AWG files. A JS slider allows choice of sequence number.
-    '''
-    #If we only go one filename turn it into a list
-    fileNames1 = []
-    fileNames2 = []
-
-    with open(metafile1, 'r') as FID:
-        meta_info1 = json.load(FID)
-
-    for el in meta_info1["instruments"].values():
-        # Accomodate seq_file per instrument and per channel
-        if isinstance(el, str):
-            fileNames1.append(el)
-        elif isinstance(el, dict):
-            for file in el.values():
-                fileNames1.append(file)
-
-    with open(metafile2, 'r') as FID:
-        meta_info2 = json.load(FID)
-
-    for el in meta_info2["instruments"].values():
-        # Accomodate seq_file per instrument and per channel
-        if isinstance(el, str):
-            fileNames2.append(el)
-        elif isinstance(el, dict):
-            for file in el.values():
-                fileNames2.append(file)
-
-    line_names1, num_seqs1, data_dicts1 = extract_waveforms(fileNames1, 'A', time=time)
-    line_names2, num_seqs2, data_dicts2 = extract_waveforms(fileNames2, 'B', time=time)
-    num_seqs = max(num_seqs1, num_seqs2)
-    data_dicts1.update(data_dicts2)
-    line_names = line_names1 + line_names2
-
-    localname = os.path.split(fileNames1[0])[1]
-    sequencename = localname.split('-')[0]
-
-    data = {line_name: ColumnDataSource(data=dat) for line_name,dat in data_dicts1.items()}
-    plot = Figure(title=sequencename, plot_width=1000)
-    plot.background_fill_color = config.plotBackground
-    if config.gridColor:
-        plot.xgrid.grid_line_color = config.gridColor
-        plot.ygrid.grid_line_color = config.gridColor
-
-    # Colobrewer2 qualitative Set1 (http://colorbrewer2.org)
-    colours = [
-        "#e41a1c", "#377eb8", "#4daf4a", "#984ea3", "#ff7f00", "#ffff33",
-        "#a65628", "#f781bf", "#999999"
-    ]
-
-    js_sources = data
-    for ct, k in enumerate(line_names):
-        k_ = k.replace("-", "_")
-        line = plot.line(data_dicts1[k + "_1"]["x"],
-                         data_dicts1[k + "_1"]["y"],
-                         color=colours[ct % len(colours)],
-                         line_width=2,
-                         legend=k.replace("_", "-"))
-        js_sources[k_] = line.data_source
-
-    code_template = Template("""
-        var seq_num = cb_obj.getv('value');
-        // console.log(seq_num);
-        var all_data = {
-            {% for trace in trace_names %}
-                '{{trace}}': {{trace}}.getv('data'),
-            {% endfor %}
-        };
-        {% for line in line_names %}
-        {{line}}['data'] = {'x': (all_data['{{line}}_'.concat(seq_num.toString())])['x'],
-                              'y': (all_data['{{line}}_'.concat(seq_num.toString())])['y']};
-        {% endfor %}
-    """)
-    rendered = code_template.render(
-            line_names=line_names,
-            trace_names=list(data.keys())[:-len(line_names)]
-            )
-
-    callback = CustomJS(
-        args=dict(**js_sources),
-        code=rendered)
-
-    if num_seqs > 1:
-        slider = Slider(start=1,
-                        end=num_seqs,
-                        value=1,
-                        step=1,
-                        title="Sequence",
-                        callback=callback)
-
-        layout = column(slider, plot)
-        show(layout)
-    else:
-        show(plot)
+# def plot_pulse_files_compare(metafile1, metafile2, time=False):
+#     '''
+#     plot_pulse_files_compare(fileNames1, fileNames2)
+
+#     Helper function to plot a list of AWG files. A JS slider allows choice of sequence number.
+#     '''
+#     #If we only go one filename turn it into a list
+#     fileNames1 = []
+#     fileNames2 = []
+
+#     with open(metafile1, 'r') as FID:
+#         meta_info1 = json.load(FID)
+
+#     for el in meta_info1["instruments"].values():
+#         # Accomodate seq_file per instrument and per channel
+#         if isinstance(el, str):
+#             fileNames1.append(el)
+#         elif isinstance(el, dict):
+#             for file in el.values():
+#                 fileNames1.append(file)
+
+#     with open(metafile2, 'r') as FID:
+#         meta_info2 = json.load(FID)
+
+#     for el in meta_info2["instruments"].values():
+#         # Accomodate seq_file per instrument and per channel
+#         if isinstance(el, str):
+#             fileNames2.append(el)
+#         elif isinstance(el, dict):
+#             for file in el.values():
+#                 fileNames2.append(file)
+
+#     line_names1, num_seqs1, data_dicts1 = extract_waveforms(fileNames1, 'A', time=time)
+#     line_names2, num_seqs2, data_dicts2 = extract_waveforms(fileNames2, 'B', time=time)
+#     num_seqs = max(num_seqs1, num_seqs2)
+#     data_dicts1.update(data_dicts2)
+#     line_names = line_names1 + line_names2
+
+#     localname = os.path.split(fileNames1[0])[1]
+#     sequencename = localname.split('-')[0]
+
+#     data = {line_name: ColumnDataSource(data=dat) for line_name,dat in data_dicts1.items()}
+#     plot = Figure(title=sequencename, plot_width=1000)
+#     plot.background_fill_color = config.plotBackground
+#     if config.gridColor:
+#         plot.xgrid.grid_line_color = config.gridColor
+#         plot.ygrid.grid_line_color = config.gridColor
+
+#     # Colobrewer2 qualitative Set1 (http://colorbrewer2.org)
+#     colours = [
+#         "#e41a1c", "#377eb8", "#4daf4a", "#984ea3", "#ff7f00", "#ffff33",
+#         "#a65628", "#f781bf", "#999999"
+#     ]
+
+#     js_sources = data
+#     for ct, k in enumerate(line_names):
+#         k_ = k.replace("-", "_")
+#         line = plot.line(data_dicts1[k + "_1"]["x"],
+#                          data_dicts1[k + "_1"]["y"],
+#                          color=colours[ct % len(colours)],
+#                          line_width=2,
+#                          legend=k.replace("_", "-"))
+#         js_sources[k_] = line.data_source
+
+#     code_template = Template("""
+#         var seq_num = cb_obj.getv('value');
+#         // console.log(seq_num);
+#         var all_data = {
+#             {% for trace in trace_names %}
+#                 '{{trace}}': {{trace}}.getv('data'),
+#             {% endfor %}
+#         };
+#         {% for line in line_names %}
+#         {{line}}['data'] = {'x': (all_data['{{line}}_'.concat(seq_num.toString())])['x'],
+#                               'y': (all_data['{{line}}_'.concat(seq_num.toString())])['y']};
+#         {% endfor %}
+#     """)
+#     rendered = code_template.render(
+#             line_names=line_names,
+#             trace_names=list(data.keys())[:-len(line_names)]
+#             )
+
+#     callback = CustomJS(
+#         args=dict(**js_sources),
+#         code=rendered)
+
+#     if num_seqs > 1:
+#         slider = Slider(start=1,
+#                         end=num_seqs,
+#                         value=1,
+#                         step=1,
+#                         title="Sequence",
+#                         callback=callback)
+
+#         layout = column(slider, plot)
+#         show(layout)
+#     else:
+#         show(plot)
diff --git a/requirements.txt b/requirements.txt
index b50f7f6f..187883e3 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,3 +2,4 @@ bbndb >= 0.1
 numpy >= 1.11.1
 scipy >= 0.17.1
 networkx >= 1.11
+bqplot >= 0.11.5
diff --git a/setup.py b/setup.py
index a5ef0be3..6b6b9261 100644
--- a/setup.py
+++ b/setup.py
@@ -9,6 +9,5 @@
         "numpy >= 1.11.1",
         "scipy >= 0.17.1",
         "networkx >= 1.11",
-        "bokeh >= 0.12.13",
-        # "pony >= 0.7.4", # This needs to be 0.7.4-dev
+        "bqplot >= 0.11.5",
     ])

From 12340d40b50271915cd8df665f8a87b47f6e478a Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Mon, 11 Feb 2019 15:56:19 -0500
Subject: [PATCH 090/235] Start tracking .aps2 files

---
 .gitattributes | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitattributes b/.gitattributes
index 1bccc1fa..3477558f 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1 +1,2 @@
 *.h5 filter=lfs diff=lfs merge=lfs -text
+*.aps2 filter=lfs diff=lfs merge=lfs -text

From c37060d1984c05bfd8cf2770cba653b9f70c6723 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Mon, 11 Feb 2019 15:59:07 -0500
Subject: [PATCH 091/235] Deleting APS2 h5 files

---
 tests/test_QGL.py                                              | 2 +-
 tests/test_data/awg/TestAPS2/AllXY/AllXY-APS1.h5               | 3 ---
 tests/test_data/awg/TestAPS2/AllXY/AllXY-APS2.h5               | 3 ---
 tests/test_data/awg/TestAPS2/CNOT_CR_mux/CNOT_CR_mux-APS1.h5   | 3 ---
 tests/test_data/awg/TestAPS2/CNOT_CR_mux/CNOT_CR_mux-APS3.h5   | 3 ---
 tests/test_data/awg/TestAPS2/CNOT_CR_mux/CNOT_CR_mux-APS5.h5   | 3 ---
 tests/test_data/awg/TestAPS2/CPMG/CPMG-APS1.h5                 | 3 ---
 tests/test_data/awg/TestAPS2/CPMG/CPMG-APS2.h5                 | 3 ---
 tests/test_data/awg/TestAPS2/Echo/Echo-APS1.h5                 | 3 ---
 tests/test_data/awg/TestAPS2/Echo/Echo-APS2.h5                 | 3 ---
 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS1.h5   | 3 ---
 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS2.h5   | 3 ---
 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS3.h5   | 3 ---
 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS4.h5   | 3 ---
 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS5.h5   | 3 ---
 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS1.h5 | 3 ---
 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS2.h5 | 3 ---
 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS3.h5 | 3 ---
 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS4.h5 | 3 ---
 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS5.h5 | 3 ---
 tests/test_data/awg/TestAPS2/FlipFlop/FlipFlop-APS1.h5         | 3 ---
 tests/test_data/awg/TestAPS2/FlipFlop/FlipFlop-APS2.h5         | 3 ---
 tests/test_data/awg/TestAPS2/MISC1/MISC1-APS1.h5               | 3 ---
 tests/test_data/awg/TestAPS2/MISC2/MISC2-APS1.h5               | 3 ---
 tests/test_data/awg/TestAPS2/MISC2/MISC2-APS5.h5               | 3 ---
 tests/test_data/awg/TestAPS2/MISC3/MISC3-APS1.h5               | 3 ---
 tests/test_data/awg/TestAPS2/MISC3/MISC3-APS3.h5               | 3 ---
 tests/test_data/awg/TestAPS2/MISC3/MISC3-APS5.h5               | 3 ---
 tests/test_data/awg/TestAPS2/MISC4/MISC4-APS1.h5               | 3 ---
 tests/test_data/awg/TestAPS2/MISC4/MISC4-APS3.h5               | 3 ---
 tests/test_data/awg/TestAPS2/MISC4/MISC4-APS5.h5               | 3 ---
 tests/test_data/awg/TestAPS2/PiRabi/PiRabi-APS1.h5             | 3 ---
 tests/test_data/awg/TestAPS2/PiRabi/PiRabi-APS2.h5             | 3 ---
 tests/test_data/awg/TestAPS2/PiRabi/PiRabi-APS3.h5             | 3 ---
 tests/test_data/awg/TestAPS2/PiRabi/PiRabi-APS4.h5             | 3 ---
 tests/test_data/awg/TestAPS2/PiRabi/PiRabi-APS5.h5             | 3 ---
 tests/test_data/awg/TestAPS2/RabiAmp/Rabi/Rabi-APS1.h5         | 3 ---
 tests/test_data/awg/TestAPS2/RabiAmp/Rabi/Rabi-APS2.h5         | 3 ---
 tests/test_data/awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS1.h5        | 3 ---
 tests/test_data/awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS2.h5        | 3 ---
 tests/test_data/awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS3.h5        | 3 ---
 tests/test_data/awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS4.h5        | 3 ---
 tests/test_data/awg/TestAPS2/RabiAmpPi/Rabi/Rabi-APS1.h5       | 3 ---
 tests/test_data/awg/TestAPS2/RabiAmpPi/Rabi/Rabi-APS3.h5       | 3 ---
 tests/test_data/awg/TestAPS2/RabiAmpPi/Rabi/Rabi-APS4.h5       | 3 ---
 tests/test_data/awg/TestAPS2/RabiWidth/Rabi/Rabi-APS1.h5       | 3 ---
 tests/test_data/awg/TestAPS2/RabiWidth/Rabi/Rabi-APS2.h5       | 3 ---
 tests/test_data/awg/TestAPS2/Ramsey/Ramsey-APS1.h5             | 3 ---
 tests/test_data/awg/TestAPS2/Ramsey/Ramsey-APS2.h5             | 3 ---
 tests/test_data/awg/TestAPS2/SPAM/SPAM-APS1.h5                 | 3 ---
 tests/test_data/awg/TestAPS2/SPAM/SPAM-APS2.h5                 | 3 ---
 tests/test_data/awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS1.h5   | 3 ---
 .../awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS1_py27.h5          | 3 ---
 tests/test_data/awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS2.h5   | 3 ---
 .../awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS2_py27.h5          | 3 ---
 tests/test_data/awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS3.h5   | 3 ---
 .../awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS3_py27.h5          | 3 ---
 tests/test_data/awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS4.h5   | 3 ---
 .../awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS4_py27.h5          | 3 ---
 tests/test_data/awg/TestAPS2/SingleQubitRB/RB/RB-APS1.h5       | 3 ---
 tests/test_data/awg/TestAPS2/SingleQubitRB/RB/RB-APS1_py27.h5  | 3 ---
 tests/test_data/awg/TestAPS2/SingleQubitRB/RB/RB-APS2.h5       | 3 ---
 tests/test_data/awg/TestAPS2/SingleQubitRB/RB/RB-APS2_py27.h5  | 3 ---
 tests/test_data/awg/TestAPS2/SingleShot/SingleShot-APS1.h5     | 3 ---
 tests/test_data/awg/TestAPS2/SingleShot/SingleShot-APS2.h5     | 3 ---
 tests/test_data/awg/TestAPS2/Spec/Spec-APS1.h5                 | 3 ---
 tests/test_data/awg/TestAPS2/Spec/Spec-APS2.h5                 | 3 ---
 tests/test_data/awg/TestAPS2/T1/T1-APS1.h5                     | 3 ---
 tests/test_data/awg/TestAPS2/T1/T1-APS2.h5                     | 3 ---
 69 files changed, 1 insertion(+), 205 deletions(-)
 delete mode 100644 tests/test_data/awg/TestAPS2/AllXY/AllXY-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/AllXY/AllXY-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/CNOT_CR_mux/CNOT_CR_mux-APS1.h5
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 delete mode 100644 tests/test_data/awg/TestAPS2/CNOT_CR_mux/CNOT_CR_mux-APS5.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/CPMG/CPMG-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/CPMG/CPMG-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/Echo/Echo-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/Echo/Echo-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS3.h5
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 delete mode 100644 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS1.h5
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 delete mode 100644 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS4.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS5.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/FlipFlop/FlipFlop-APS1.h5
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 delete mode 100644 tests/test_data/awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS4_py27.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/SingleQubitRB/RB/RB-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/SingleQubitRB/RB/RB-APS1_py27.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/SingleQubitRB/RB/RB-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/SingleQubitRB/RB/RB-APS2_py27.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/SingleShot/SingleShot-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/SingleShot/SingleShot-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/Spec/Spec-APS1.h5
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 delete mode 100644 tests/test_data/awg/TestAPS2/T1/T1-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS2/T1/T1-APS2.h5

diff --git a/tests/test_QGL.py b/tests/test_QGL.py
index b91156b0..b39fb5a1 100644
--- a/tests/test_QGL.py
+++ b/tests/test_QGL.py
@@ -55,7 +55,7 @@ def show(self):
 
     def build_filename(self, name):
         # utility for reading and writing
-        return self.testFileDirectory + self.fileHeader + '-' + name + '.h5'
+        return self.testFileDirectory + self.fileHeader + '-' + name + '.aps2'
 
     def write(self):
         # writes each sequence to a file in the test data directory a file header
diff --git a/tests/test_data/awg/TestAPS2/AllXY/AllXY-APS1.h5 b/tests/test_data/awg/TestAPS2/AllXY/AllXY-APS1.h5
deleted file mode 100644
index b4146f64..00000000
--- a/tests/test_data/awg/TestAPS2/AllXY/AllXY-APS1.h5
+++ /dev/null
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deleted file mode 100644
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--- a/tests/test_data/awg/TestAPS2/Spec/Spec-APS1.h5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:9d52de2c3596cc0f61bf8dee2c224d26b5b6bdc378332001d0eea00a15dfe328
-size 10664
diff --git a/tests/test_data/awg/TestAPS2/Spec/Spec-APS2.h5 b/tests/test_data/awg/TestAPS2/Spec/Spec-APS2.h5
deleted file mode 100644
index e89591a9..00000000
--- a/tests/test_data/awg/TestAPS2/Spec/Spec-APS2.h5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:4fed627361f76485e09a21c1e72186e64b710ca9a6bf1e71aff1b5cbefebf108
-size 10664
diff --git a/tests/test_data/awg/TestAPS2/T1/T1-APS1.h5 b/tests/test_data/awg/TestAPS2/T1/T1-APS1.h5
deleted file mode 100644
index 5c23cfc1..00000000
--- a/tests/test_data/awg/TestAPS2/T1/T1-APS1.h5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:1ae2feab747be8b5ef6804c3cae154b6099dc30d22c0dd4f62b9bdc121a7beee
-size 10664
diff --git a/tests/test_data/awg/TestAPS2/T1/T1-APS2.h5 b/tests/test_data/awg/TestAPS2/T1/T1-APS2.h5
deleted file mode 100644
index 126007b4..00000000
--- a/tests/test_data/awg/TestAPS2/T1/T1-APS2.h5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:09d114f4c75921bf7aea9db671bbf3618046c1965a4229e405ad0c8d2f7e7805
-size 10664

From 16dd0c1357495ba39eac89f54c18731b67c92e5b Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 13:57:22 -0500
Subject: [PATCH 092/235] Update test_QGL

---
 QGL/Plotting.py   |  4 ---
 QGL/__init__.py   |  2 +-
 tests/test_QGL.py | 82 +++++++++++++++++++++++++++++------------------
 3 files changed, 51 insertions(+), 37 deletions(-)

diff --git a/QGL/Plotting.py b/QGL/Plotting.py
index 254c1568..8051cb7d 100644
--- a/QGL/Plotting.py
+++ b/QGL/Plotting.py
@@ -26,10 +26,6 @@
 import warnings
 from . import config
 
-def output_notebook():
-    import matplotlib
-    matplotlib.use("nbagg")
-
 def build_waveforms(seq):
     # import here to avoid circular imports
     from . import Compiler, PulseSequencer, BlockLabel, ControlFlow
diff --git a/QGL/__init__.py b/QGL/__init__.py
index 84728ba8..82defa84 100644
--- a/QGL/__init__.py
+++ b/QGL/__init__.py
@@ -6,7 +6,7 @@
 from .PulseSequencer import align
 from .ControlFlow import repeat, repeatall, qif, qwhile, qdowhile, qfunction, qwait, qsync, Barrier
 from .BasicSequences import *
-from .Plotting import output_notebook #, show, build_waveforms, plot_waveforms
+from .Plotting import build_waveforms #, show, , plot_waveforms
 from .PulseSequencePlotter import plot_pulse_files
 from .Tomography import state_tomo, process_tomo
 from .Scheduler import schedule
diff --git a/tests/test_QGL.py b/tests/test_QGL.py
index b39fb5a1..c5db5b52 100644
--- a/tests/test_QGL.py
+++ b/tests/test_QGL.py
@@ -3,8 +3,10 @@
 import numpy as np
 import time
 import os.path
-
+import struct
+from bbndb.qgl import PhysicalChannel, LogicalChannel, Measurement
 from QGL import *
+import h5py
 
 # Waveform numpy assert_allclose Test for QGL
 #
@@ -33,7 +35,7 @@ def __init__(self):
         # all available sequences (which are defined in subclasses)
         self.generate()
         self.compile()
-        self.load()
+        self.load()  
 
     def generate(self):
         # this function should be overridden in a subclass to define
@@ -61,22 +63,23 @@ def write(self):
         # writes each sequence to a file in the test data directory a file header
         # which may be overridden in the subclasses
         for name, waveform in self.waveforms.items():
+
             fileName = self.build_filename(name)
-            #Open the HDF5 file
             if os.path.isfile(fileName):
                 os.remove(fileName)
-            with h5py.File(fileName, 'w') as FID:
-                FID['/'].attrs['Type'] = 'test_case'
-                FID['/'].attrs['Version'] = 1.0
+            with open(fileName, 'wb') as FID:
+                FID.write(b'TEST')                     # target 
+                FID.write(np.float32(1.0).tobytes())   # Version
+                FID.write(np.float32(1.0).tobytes())   # minimum firmware version
+                FID.write(np.uint16(len(waveform)).tobytes())      # number of channels
 
-                #Create the groups and datasets
                 channels = waveform.keys()
-                chanStr = '/channels'
-                chanGroup = FID.create_group(chanStr)
                 for channel in channels:
-                    channelStr = channel.label
-                    FID.create_dataset('/' + chanStr + '/' + channelStr,
-                                       data=waveform[channel])
+                    channel.label.ljust(32,"#").encode("utf-8")
+                    FID.write(channel.label.ljust(32,"#").encode("utf-8"))
+                    FID.write(np.uint64(waveform[channel].size).tobytes())
+                    FID.write(np.complex128(waveform[channel]).tobytes()) # waveform data length for channel
+
 
     def load(self):
         # attempts to load valid waveforms for each of the sequences test cases
@@ -89,22 +92,30 @@ def load(self):
                         caseName, fileName))
                 continue
             # -----
-            # print( "\n\rDBG::Calling \"with h5py.File( {0}, 'r')\"...".format( fileName) )
+            # print( "\n\rDBG::Calling \"with open({0}, 'wb')\"...".format( fileName) )
             # -----
             # The following pulls in Git Large File Storage (LFS) data files
-            # from cached signature references;  if the h5py.File call fails
+            # from cached signature references;  if the open call fails
             # with an OSError, double-check git-lfs library installation (in
             # addition to git) -- <https://git-lfs.github.com/>
             #
-            # Where git-lfs was NOT installed the h5py.File() call was observed
+            # Where git-lfs was NOT installed the open call was observed
             # returning:
             #
             # OSError: Unable to open file (file signature not found))
             #
-            with h5py.File(fileName, 'r') as FID:
-                # print( "DBG::FID: {0}".format( FID))
-                for name, waveform in FID['/channels'].items():
-                    validWaveform[name] = waveform[:]
+            with open(fileName, 'rb') as FID:
+                target_hw    = FID.read(4).decode('utf-8')
+                file_version = struct.unpack('<f', FID.read(4))[0]
+                min_fw       = struct.unpack('<f', FID.read(4))[0]
+                num_chans    = struct.unpack('<H', FID.read(2))[0]
+                assert target_hw=="TEST", f"Cannot compare to file type {target_hw}. Expecting TEST"
+
+                for i in range(num_chans):
+                    wf_name = FID.read(32).decode('utf-8').replace('#','')
+                    wf_len  = struct.unpack('<Q', FID.read(8))[0]
+                    wf_dat  = np.frombuffer(FID.read(16*wf_len), dtype=np.complex128)
+                    validWaveform[wf_name] = wf_dat
             self.validWaveforms[caseName] = validWaveform
 
     def validate(self):
@@ -118,6 +129,7 @@ def validate_case(self, caseName):
         for channel, waveform in self.waveforms[caseName].items():
             print('Validating {0} Case {1} Channel {2}'.format(
                 self.__class__.__name__, caseName, str(channel)))
+            
             assert (channel.label in validWaveform)
             np.testing.assert_allclose(waveform,
                                        validWaveform[channel.label],
@@ -131,9 +143,13 @@ class SingleQubitTestCases(SequenceTestCases):
     fileHeader = 'single'
 
     def newQ1(self):
-        q1 = Qubit(label='q1')
+        cl = ChannelLibrary(db_resource_name=":memory:")
+        cl.clear()
+        q1 = cl.new_qubit("q1")
         q1.pulse_params['length'] = 30e-9
-        q1.phys_chan.sampling_rate = 1.2e9
+        q1.measure_chan = Measurement(label="test_meas")
+        q1.phys_chan = PhysicalChannel(label="test_phys_c", sampling_rate=1.2e9) 
+        q1.measure_chan.phys_chan = PhysicalChannel(label="test_phys", sampling_rate=1.2e9)
         return q1
 
     def generate(self):
@@ -143,25 +159,27 @@ def generate(self):
 
         self.sequences['repeat'] = [X90(q1)] + repeat(5, Y(q1)) + [X90(q1)]
 
-
 class MultiQubitTestCases(SequenceTestCases):
     # Multi Qubit Sequence Test Cases
 
     fileHeader = 'multi'
 
     def newQubits(self):
-        q1 = Qubit(label='q1')
+        # Create an in-memory blank channel library
+        cl = ChannelLibrary(db_resource_name=":memory:")
+        cl.clear()
+        q1 = cl.new_qubit("q1")
+        q2 = cl.new_qubit("q2")
         q1.pulse_params['length'] = 30e-9
-        q1.phys_chan.sampling_rate = 1.2e9
-        q2 = Qubit(label='q2')
+        q1.measure_chan = Measurement(label="test_meas1")
+        q1.phys_chan = PhysicalChannel(label="test_phys_c1", sampling_rate=1.2e9) 
+        q1.measure_chan.phys_chan = PhysicalChannel(label="test_phys1", sampling_rate=1.2e9) 
         q2.pulse_params['length'] = 30e-9
-        q2.phys_chan.sampling_rate = 1.2e9
-        q1q2 = Edge(label='q1q2', source=q1, target=q2)
-        ChannelLibrary(blank=True) # Create a blank ChannelLibrary
-        ChannelLibraries.channelLib.channelDict['q1'] = q1
-        ChannelLibraries.channelLib.channelDict['q2'] = q2
-        ChannelLibraries.channelLib.channelDict['q1q2'] = q1q2
-        ChannelLibraries.channelLib.build_connectivity_graph()
+        q2.measure_chan = Measurement(label="test_meas2")
+        q2.phys_chan = PhysicalChannel(label="test_phys_c2", sampling_rate=1.2e9) 
+        q2.measure_chan.phys_chan = PhysicalChannel(label="test_phys2", sampling_rate=1.2e9) 
+        q1q2 =cl.new_edge(q1, q2)
+        q1q2.phys_chan = PhysicalChannel(label="test_phys_12", sampling_rate=1.2e9) 
         return (q1, q2)
 
     def generate(self):

From ccdd432433ac2fd779d44e0773e25ce27ea745aa Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 21:15:54 -0500
Subject: [PATCH 093/235] Now passing test_sequence for APS2, excepting GST
 tests

---
 tests/test_Sequences.py | 470 ++++++++++++----------------------------
 1 file changed, 136 insertions(+), 334 deletions(-)

diff --git a/tests/test_Sequences.py b/tests/test_Sequences.py
index 1e145046..2c0cc836 100644
--- a/tests/test_Sequences.py
+++ b/tests/test_Sequences.py
@@ -1,4 +1,3 @@
-import h5py
 import numpy as np
 import unittest, time, os, random, sys
 
@@ -37,10 +36,12 @@ def finalize_map(self, mapping):
         for name, value in mapping.items():
             self.channels[name].phys_chan = self.channels[value]
 
-        ChannelLibraries.channelLib = ChannelLibraries.ChannelLibrary(blank=True)
-        ChannelLibraries.channelLib.channelDict = self.channels
-        ChannelLibraries.channelLib.build_connectivity_graph()
-
+        self.cl = ChannelLibrary(db_resource_name=":memory:")
+        self.cl.clear()
+        self.cl.session.add_all(self.channels.values())
+        for chan in self.channels.values():
+            chan.channel_db = self.cl.channelDatabase
+        self.cl.update_channelDict()
         (self.q1, self.q2) = self.get_qubits()
 
     def assign_channels(self):
@@ -133,21 +134,9 @@ def compare_sequences(self, seqDir):
 
         filenames = os.listdir(truthDirectory)
 
-        #look for py27 versions
-        py27_files = [f for f in filenames if f[-8:] == "_py27.h5"]
-        if py27_files:
-            if sys.version_info[0] > 2:
-                #strip them out for python3 (and above?)
-                filenames = [f for f in filenames if f[-8:] != "_py27.h5"]
-            else:
-                #otherwise strip the non "_py27" version
-                filenames = [f for f in filenames
-                             if f.replace(".h5", "_py27.h5") not in py27_files]
-
         for filename in filenames:
             truthFile = os.path.join(truthDirectory, filename)
-            testFile = os.path.join(searchDirectory, filename.replace("_py27",
-                                                                      ""))
+            testFile = os.path.join(searchDirectory, filename)
 
             self.assertTrue(
                 os.path.isfile(truthFile),
@@ -185,7 +174,6 @@ def compare_sequence(self, seqA, seqB, errorHeader):
                               for ta in seqA]) if len(seqA) else np.empty(0)
         wfB = np.concatenate([ta[1] * np.ones(int(ta[0]))
                               for ta in seqB]) if len(seqB) else np.empty(0)
-
         self.assertTrue(
             len(wfA) == len(wfB), "{} size {} != size {}".format(
                 errorHeader, len(wfA), len(wfB)))
@@ -390,6 +378,7 @@ def test_RB_SimultaneousRB_AC(self):
         SimultaneousRB_AC((self.q1, self.q2), (seqs1, seqs2))
         self.compare_sequences('RB')
 
+    @unittest.skip("Need to update to new pygsti API")
     def test_1Q_GST(self):
 
         if istravis:
@@ -416,6 +405,7 @@ def test_1Q_GST(self):
         filenames = compile_to_hardware(seqs, 'GST/GST')
         self.compare_sequences('GST')
 
+    @unittest.skip("Need to update to new pygsti API")
     def test_2Q_GST(self):
 
         if istravis:
@@ -461,7 +451,7 @@ class APS2Helper(AWGTestHelper):
     def setUp(self):
         AWGTestHelper.__init__(self, APS2Pattern)
         for name in ['APS1', 'APS2', 'APS3', 'APS4', 'APS5', 'APS6']:
-            channelName = name + '-12'
+            channelName = name + '-1'
             channel = PhysicalQuadratureChannel(label=channelName)
             channel.sampling_rate = 1.2e9
             channel.instrument = name
@@ -469,27 +459,27 @@ def setUp(self):
             self.channels[channelName] = channel
 
             for m in range(1, 5):
-                channelName = "{0}-12m{1}".format(name, m)
+                channelName = "{0}-m{1}".format(name, m)
                 channel = PhysicalMarkerChannel(label=channelName)
                 channel.sampling_rate = 1.2e9
                 channel.instrument = name
                 channel.translator = 'APS2Pattern'
                 self.channels[channelName] = channel
 
-        mapping = {'digitizerTrig': 'APS1-12m1',
-                   'slave_trig': 'APS1-12m2',
-                   'q1': 'APS1-12',
-                   'q1-gate': 'APS1-12m3',
-                   'M-q1': 'APS2-12',
-                   'M-q1-gate': 'APS2-12m1',
-                   'q2': 'APS3-12',
-                   'q2-gate': 'APS3-12m1',
-                   'M-q2': 'APS4-12',
-                   'M-q2-gate': 'APS4-12m1',
-                   'cr': 'APS5-12',
-                   'cr-gate': 'APS5-12m1',
-                   'M-q1q2': 'APS6-12',
-                   'M-q1q2-gate': 'APS6-12m1'}
+        mapping = {'digitizerTrig': 'APS1-m1',
+                   'slave_trig': 'APS1-m2',
+                   'q1': 'APS1-1',
+                   'q1-gate': 'APS1-m3',
+                   'M-q1': 'APS2-1',
+                   'M-q1-gate': 'APS2-m1',
+                   'q2': 'APS3-1',
+                   'q2-gate': 'APS3-m1',
+                   'M-q2': 'APS4-1',
+                   'M-q2-gate': 'APS4-m1',
+                   'cr': 'APS5-1',
+                   'cr-gate': 'APS5-m1',
+                   'M-q1q2': 'APS6-1',
+                   'M-q1q2-gate': 'APS6-m1'}
 
         self.finalize_map(mapping)
 
@@ -506,311 +496,123 @@ def test_mux_CR(self):
         self.channels['cr'].phys_chan = self.channels['q1'].phys_chan
         self.channels['q1'].frequency = 100e6
         self.channels['cr'].frequency = 200e6
-        ChannelLibraries.channelLib.build_connectivity_graph()
+        self.cl.update_channelDict()
         seqs = [[CNOT_CR(self.q1, self.q2)]]
 
         filenames = compile_to_hardware(seqs, 'CNOT_CR_mux/CNOT_CR_mux')
         self.compare_sequences('CNOT_CR_mux')
 
 
-class TestAPS1(unittest.TestCase, AWGTestHelper, TestSequences):
-    def setUp(self):
-        AWGTestHelper.__init__(self, APSPattern)
-        for name in ['APS1', 'APS2', 'APS3']:
-            for ch in ['12', '34']:
-                channelName = name + '-' + ch
-                channel = PhysicalQuadratureChannel(label=channelName)
-                channel.sampling_rate = 1.2e9
-                channel.instrument = name
-                channel.translator = 'APSPattern'
-                self.channels[channelName] = channel
-
-            for m in range(1, 5):
-                channelName = "{0}-{1}m1".format(name, m)
-                channel = PhysicalMarkerChannel(label=channelName)
-                channel.sampling_rate = 1.2e9
-                channel.instrument = name
-                channel.translator = 'APSPattern'
-                self.channels[channelName] = channel
-
-        mapping = {'digitizerTrig': 'APS1-1m1',
-                   'slave_trig': 'APS1-2m1',
-                   'q1': 'APS1-12',
-                   'M-q1': 'APS1-34',
-                   'M-q1-gate': 'APS1-3m1',
-                   'q1-gate': 'APS1-4m1',
-                   'q2': 'APS2-12',
-                   'M-q2': 'APS2-34',
-                   'M-q2-gate': 'APS2-1m1',
-                   'q2-gate': 'APS2-2m1',
-                   'cr': 'APS3-12',
-                   'cr-gate': 'APS3-1m1',
-                   'M-q1q2': 'APS3-34',
-                   'M-q1q2-gate': 'APS3-2m1'}
-
-        # override trigger lengths on APS1 to get single blips
-        self.channels['slave_trig'].pulse_params['length'] = 0.833e-9
-        self.channels['digitizerTrig'].pulse_params['length'] = 0.833e-9
-        self.finalize_map(mapping)
-
-    def compare_file_data(self, testFile, truthFile):
-        '''
-		Override the method in AWGTestHelper so that we can special-case marker comparison
-		'''
-        awgData = self.read_function(testFile)
-        truthData = self.read_function(truthFile)
-
-        awgDataLen = len(awgData)
-        truthDataLen = len(truthData)
-
-        self.assertTrue(awgDataLen == truthDataLen,
-                        "Expected {0} sequences in file. Found {1}.".format(
-                            truthDataLen, awgDataLen))
-
-        for name in truthData:
-            self.assertTrue(
-                name in awgData,
-                "Expected channel {0} not found in file {1}".format(name,
-                                                                    testFile))
-            isMarker = ('m' == name[-2])
-
-            for x in range(len(truthData[name])):
-                seqA = np.array(truthData[name][x])
-                seqB = np.array(awgData[name][x])
-                if isMarker:
-                    self.compare_marker_sequence(
-                        seqA, seqB,
-                        "\nFile {0} =>\nChannel {1} Sequence {2}".format(
-                            testFile, name, x))
-                else:
-                    self.compare_sequence(
-                        seqA, seqB,
-                        "\nFile {0} =>\nChannel {1} Sequence {2}".format(
-                            testFile, name, x))
-
-    def compare_marker_sequence(self, seqA, seqB, errorHeader):
-        markerDistanceTolerance = 4
-        self.assertTrue(seqA.size == seqB.size,
-                        "{0} size {1} != size {2}".format(
-                            errorHeader, str(seqA.size), str(seqB.size)))
-
-        # convert sequences to locations of blips
-        idxA = np.where(seqA)[0]
-        idxB = np.where(seqB)[0]
-        self.assertTrue(
-            len(idxA) == len(idxB),
-            "{0}.\nNumber of blips did not match: {1} != {2}".format(
-                errorHeader, len(idxA), len(idxB)))
-        # compare the blip locations element-wise
-        if len(idxA) > 0:
-            diff = np.abs(idxA - idxB)
-        else:
-            diff = np.array([0])
-        self.assertTrue(
-            max(diff) <= markerDistanceTolerance,
-            "{0}\nMismatches: {1}".format(errorHeader, diff.nonzero()[0]))
-
-    @unittest.expectedFailure
-    def test_Rabi_RabiWidth(self):
-        """ test_Rabi_RabiWidth is expected to fail on APS1 with the following error:
-			AssertionError: Oops! You have exceeded the waveform memory of the APS
-		"""
-        TestSequences.test_Rabi_RabiWidth(self)
-
-    @unittest.expectedFailure
-    def test_RB_SimultaneousRB_AC(self):
-        """ test_RB_SimultaneousRB_AC is expected to fail on APS1 with the following error:
-			AssertionError: Oops! You have exceeded the waveform memory of the APS
-		"""
-        TestSequences.test_RB_SimultaneousRB_AC(self)
-
-
-class TestTek5014(unittest.TestCase, AWGTestHelper, TestSequences):
-    def setUp(self):
-        AWGTestHelper.__init__(self, TekPattern)
-        for name in ['TEK1', 'TEK2']:
-            for ch in ['12', '34']:
-                channelName = name + '-' + ch
-                channel = PhysicalQuadratureChannel(label=channelName)
-                channel.sampling_rate = 1.2e9
-                channel.instrument = name
-                channel.translator = 'TekPattern'
-                self.channels[channelName] = channel
-
-            for m in ['1m1', '1m2', '2m1', '2m2', '3m1', '3m2', '4m1', '4m2']:
-                channelName = "{0}-{1}".format(name, m)
-                channel = PhysicalMarkerChannel(label=channelName)
-                channel.sampling_rate = 1.2e9
-                channel.instrument = name
-                channel.translator = 'TekPattern'
-                self.channels[channelName] = channel
-
-        mapping = {'digitizerTrig': 'TEK1-1m2',
-                   'slave_trig': 'TEK1-2m2',
-                   'q1': 'TEK1-12',
-                   'M-q1': 'TEK1-12',
-                   'M-q1-gate': 'TEK1-1m1',
-                   'q1-gate': 'TEK1-2m1',
-                   'q2': 'TEK1-34',
-                   'M-q2': 'TEK1-34',
-                   'M-q2-gate': 'TEK1-3m1',
-                   'q2-gate': 'TEK1-4m1',
-                   'cr': 'TEK2-12',
-                   'cr-gate': 'TEK2-1m1',
-                   'M-q1q2': 'TEK2-34',
-                   'M-q1q2-gate': 'TEK2-2m1'}
-
-        self.finalize_map(mapping)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_misc_seqs2(self):
-        """ Fails due to a divide by zero
-		    File "C:\Projects\Q\lib\PyQLab\QGL\TekPattern.py", line 77, in merge_waveform
-   			  for entry in chAB['linkList'][n % len(chAB['linkList'])]:
-			ZeroDivisionError: integer division or modulo by zero
-		"""
-        TestSequences.test_misc_seqs2(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_misc_seqs5(self):
-        """ Fails due to a divide by zero
-		    File "C:\Projects\Q\lib\PyQLab\QGL\TekPattern.py", line 77, in merge_waveform
-   			  for entry in chAB['linkList'][n % len(chAB['linkList'])]:
-			ZeroDivisionError: integer division or modulo by zero
-		"""
-        TestSequences.test_misc_seqs5(self)
-
-    # multiple tests will fail with an attribute error:
-    # AttributeError: 'Wait' object has no attribute 'isTimeAmp' at line 78
-    # in TekPattern.py in merge_waveform
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_misc_seqs1(self):
-        TestSequences.test_misc_seqs1(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_misc_seqs3(self):
-        TestSequences.test_misc_seqs3(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_misc_seqs4(self):
-        TestSequences.test_misc_seqs4(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_mux_CR(self):
-        TestSequences.test_mux_CR(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_AllXY(self):
-        TestSequences.test_AllXY(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_CR_PiRabi(self):
-        TestSequences.test_CR_PiRabi(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_CR_EchoCRLen(self):
-        TestSequences.test_CR_EchoCRLen(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_CR_EchoCRPhase(self):
-        TestSequences.test_CR_EchoCRPhase(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_Decoupling_HannEcho(self):
-        TestSequences.test_Decoupling_HannEcho(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_Decoupling_CPMG(self):
-        TestSequences.test_Decoupling_CPMG(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_FlipFlop(self):
-        TestSequences.test_FlipFlop(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_T1T2_InversionRecovery(self):
-        TestSequences.test_T1T2_InversionRecovery(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_T1T2_Ramsey(self):
-        TestSequences.test_T1T2_Ramsey(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_SPAM(self):
-        TestSequences.test_SPAM(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_Rabi_RabiAmp(self):
-        TestSequences.test_Rabi_RabiAmp(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_Rabi_RabiWidth(self):
-        TestSequences.test_Rabi_RabiWidth(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_Rabi_RabiAmp_NQubits(self):
-        TestSequences.test_Rabi_RabiAmp_NQubits(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_Rabi_RabiAmpPi(self):
-        TestSequences.test_Rabi_RabiAmpPi(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_Rabi_SingleShot(self):
-        TestSequences.test_Rabi_SingleShot(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_Rabi_PulsedSpec(self):
-        TestSequences.test_Rabi_PulsedSpec(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_RB_SingleQubitRB(self):
-        TestSequences.test_RB_SingleQubitRB(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_RB_SimultaneousRB_AC(self):
-        TestSequences.test_RB_SimultaneousRB_AC(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_1Q_GST(self):
-        TestSequences.test_1Q_GST(self)
-
-    @unittest.skip("Tek5014 unused in years")
-    def test_2Q_GST(self):
-        TestSequences.test_2Q_GST(self)
-# class TestTek7000(unittest.TestCase, AWGTestHelper, TestSequences):
-
-# 	def setUp(self):
-# 		AWGTestHelper.__init__(self, TekPattern.read_Tek_file)
-# 		for name in ['TEK1', 'TEK2', 'TEK3', 'TEK4', 'TEK5']:
-# 			self.instruments[name] = Tek7000(label=name)
-
-# 			for ch in ['12']:
-# 				channelName = name + '-' + ch
-# 				channel = PhysicalQuadratureChannel(label=channelName)
-# 				channel.instrument = self.instruments[name]
-# 				self.channels[channelName] = channel
-
-# 			for m in ['1m1', '1m2', '2m1', '2m2']:
-# 				channelName = "{0}-{1}".format(name,m)
-# 				channel = PhysicalMarkerChannel(label=channelName)
-# 				channel.instrument = self.instruments[name]
-# 				self.channels[channelName] = channel
-
-# 		mapping = { 'digitizerTrig'	:'TEK1-1m2',
-# 					'slave_trig'   	:'TEK1-2m2',
-# 					'q1'			:'TEK1-12',
-# 					'M-q1'			:'TEK2-12',
-# 					'M-q1-gate'		:'TEK1-1m1',
-# 					'q1-gate'		:'TEK1-2m1',
-# 					'q2'			:'TEK3-12',
-# 					'M-q2'			:'TEK4-12',
-# 					'M-q2-gate'		:'TEK2-1m1',
-# 					'q2-gate'		:'TEK2-2m1',
-# 					'cr'            :'TEK5-12',
-# 					'cr-gate'       :'TEK5-1m1'}
-# 		self.finalize_map(mapping)
+# class TestAPS1(unittest.TestCase, AWGTestHelper, TestSequences):
+#     def setUp(self):
+#         AWGTestHelper.__init__(self, APSPattern)
+#         for name in ['APS1', 'APS2', 'APS3']:
+#             for ch in ['12', '34']:
+#                 channelName = name + '-' + ch
+#                 channel = PhysicalQuadratureChannel(label=channelName)
+#                 channel.sampling_rate = 1.2e9
+#                 channel.instrument = name
+#                 channel.translator = 'APSPattern'
+#                 self.channels[channelName] = channel
+
+#             for m in range(1, 5):
+#                 channelName = "{0}-{1}m1".format(name, m)
+#                 channel = PhysicalMarkerChannel(label=channelName)
+#                 channel.sampling_rate = 1.2e9
+#                 channel.instrument = name
+#                 channel.translator = 'APSPattern'
+#                 self.channels[channelName] = channel
+
+#         mapping = {'digitizerTrig': 'APS1-1m1',
+#                    'slave_trig': 'APS1-2m1',
+#                    'q1': 'APS1-12',
+#                    'M-q1': 'APS1-34',
+#                    'M-q1-gate': 'APS1-3m1',
+#                    'q1-gate': 'APS1-4m1',
+#                    'q2': 'APS2-12',
+#                    'M-q2': 'APS2-34',
+#                    'M-q2-gate': 'APS2-1m1',
+#                    'q2-gate': 'APS2-2m1',
+#                    'cr': 'APS3-12',
+#                    'cr-gate': 'APS3-1m1',
+#                    'M-q1q2': 'APS3-34',
+#                    'M-q1q2-gate': 'APS3-2m1'}
+
+#         # override trigger lengths on APS1 to get single blips
+#         self.channels['slave_trig'].pulse_params['length'] = 0.833e-9
+#         self.channels['digitizerTrig'].pulse_params['length'] = 0.833e-9
+#         self.finalize_map(mapping)
+
+#     def compare_file_data(self, testFile, truthFile):
+#         '''
+# 		Override the method in AWGTestHelper so that we can special-case marker comparison
+# 		'''
+#         awgData = self.read_function(testFile)
+#         truthData = self.read_function(truthFile)
+
+#         awgDataLen = len(awgData)
+#         truthDataLen = len(truthData)
+
+#         self.assertTrue(awgDataLen == truthDataLen,
+#                         "Expected {0} sequences in file. Found {1}.".format(
+#                             truthDataLen, awgDataLen))
+
+#         for name in truthData:
+#             self.assertTrue(
+#                 name in awgData,
+#                 "Expected channel {0} not found in file {1}".format(name,
+#                                                                     testFile))
+#             isMarker = ('m' == name[-2])
+
+#             for x in range(len(truthData[name])):
+#                 seqA = np.array(truthData[name][x])
+#                 seqB = np.array(awgData[name][x])
+#                 if isMarker:
+#                     self.compare_marker_sequence(
+#                         seqA, seqB,
+#                         "\nFile {0} =>\nChannel {1} Sequence {2}".format(
+#                             testFile, name, x))
+#                 else:
+#                     self.compare_sequence(
+#                         seqA, seqB,
+#                         "\nFile {0} =>\nChannel {1} Sequence {2}".format(
+#                             testFile, name, x))
+
+#     def compare_marker_sequence(self, seqA, seqB, errorHeader):
+#         markerDistanceTolerance = 4
+#         self.assertTrue(seqA.size == seqB.size,
+#                         "{0} size {1} != size {2}".format(
+#                             errorHeader, str(seqA.size), str(seqB.size)))
+
+#         # convert sequences to locations of blips
+#         idxA = np.where(seqA)[0]
+#         idxB = np.where(seqB)[0]
+#         self.assertTrue(
+#             len(idxA) == len(idxB),
+#             "{0}.\nNumber of blips did not match: {1} != {2}".format(
+#                 errorHeader, len(idxA), len(idxB)))
+#         # compare the blip locations element-wise
+#         if len(idxA) > 0:
+#             diff = np.abs(idxA - idxB)
+#         else:
+#             diff = np.array([0])
+#         self.assertTrue(
+#             max(diff) <= markerDistanceTolerance,
+#             "{0}\nMismatches: {1}".format(errorHeader, diff.nonzero()[0]))
+
+#     @unittest.expectedFailure
+#     def test_Rabi_RabiWidth(self):
+#         """ test_Rabi_RabiWidth is expected to fail on APS1 with the following error:
+# 			AssertionError: Oops! You have exceeded the waveform memory of the APS
+# 		"""
+#         TestSequences.test_Rabi_RabiWidth(self)
+
+#     @unittest.expectedFailure
+#     def test_RB_SimultaneousRB_AC(self):
+#         """ test_RB_SimultaneousRB_AC is expected to fail on APS1 with the following error:
+# 			AssertionError: Oops! You have exceeded the waveform memory of the APS
+# 		"""
+#         TestSequences.test_RB_SimultaneousRB_AC(self)
 
 if __name__ == "__main__":
     unittest.main()

From 644555f5725c8026cac52b45a642801168c6d668 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 21:22:34 -0500
Subject: [PATCH 094/235] Fixed APS and APS2 pattern tests

---
 tests/test_APS2Pattern.py | 13 +++++--------
 tests/test_APSPattern.py  | 12 +++++-------
 2 files changed, 10 insertions(+), 15 deletions(-)

diff --git a/tests/test_APS2Pattern.py b/tests/test_APS2Pattern.py
index 636d7843..54dbd1ac 100644
--- a/tests/test_APS2Pattern.py
+++ b/tests/test_APS2Pattern.py
@@ -9,15 +9,12 @@
 
 class APSPatternUtils(unittest.TestCase):
     def setUp(self):
-        self.q1gate = Channels.LogicalMarkerChannel(label='q1-gate')
-        self.q1 = Qubit(label='q1', gate_chan=self.q1gate)
-        self.q1 = Qubit(label='q1')
+        self.cl = ChannelLibrary(db_resource_name=":memory:")
+        self.q1gate = Channels.LogicalMarkerChannel(label='q1-gate', channel_db=self.cl.channelDatabase)
+        self.q1 = self.cl.new_qubit(label='q1')
+        self.q1.gate_chan = self.q1gate
         self.q1.pulse_params['length'] = 30e-9
-        
-        ChannelLibrary(blank=True) # Create a blank ChannelLibrary
-        ChannelLibraries.channelLib.channelDict = {'q1': self.q1,
-                                                 'q1-gate': self.q1gate}
-        ChannelLibraries.channelLib.build_connectivity_graph()
+        self.cl.update_channelDict()
 
     def test_synchronize_control_flow(self):
         q1 = self.q1
diff --git a/tests/test_APSPattern.py b/tests/test_APSPattern.py
index 163f3d21..3bfa2534 100644
--- a/tests/test_APSPattern.py
+++ b/tests/test_APSPattern.py
@@ -8,14 +8,12 @@
 
 class APSPatternUtils(unittest.TestCase):
     def setUp(self):
-        # self.q1gate = Channels.LogicalMarkerChannel(label='q1-gate')
-        # self.q1 = Qubit(label='q1', gate_chan=self.q1gate)
-        self.q1 = Qubit(label='q1')
+        self.cl = ChannelLibrary(db_resource_name=":memory:")
+        self.q1gate = Channels.LogicalMarkerChannel(label='q1-gate', channel_db=self.cl.channelDatabase)
+        self.q1 = self.cl.new_qubit(label='q1')
+        self.q1.gate_chan = self.q1gate
         self.q1.pulse_params['length'] = 30e-9
-
-        ChannelLibrary(blank=True) # Create a blank ChannelLibrary
-        ChannelLibraries.channelLib.channelDict = {'q1': self.q1}
-        ChannelLibraries.channelLib.build_connectivity_graph()
+        self.cl.update_channelDict()
 
     def test_unroll_loops_simple(self):
         q1 = self.q1

From 313947a34891afcc792e88fc8b57b35355c932d4 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 21:27:22 -0500
Subject: [PATCH 095/235] Fixed test_compiler

---
 tests/test_Compiler.py | 27 +++++++++++++++------------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/tests/test_Compiler.py b/tests/test_Compiler.py
index 8c1bd9c7..781bb49c 100644
--- a/tests/test_Compiler.py
+++ b/tests/test_Compiler.py
@@ -7,23 +7,26 @@
 
 class CompileUtils(unittest.TestCase):
     def setUp(self):
-        self.q1gate = Channels.LogicalMarkerChannel(label='q1-gate')
-        self.q1 = Qubit(label='q1', gate_chan=self.q1gate)
+        self.cl = ChannelLibrary(db_resource_name=":memory:")
+        self.q1gate = Channels.LogicalMarkerChannel(label='q1-gate', channel_db=self.cl.channelDatabase)
+        self.q1gate = Channels.LogicalMarkerChannel(label='q1-gate', channel_db=self.cl.channelDatabase)
+        self.q1phys = Channels.PhysicalChannel(label='q1-phys', sampling_rate=1.2e9, channel_db=self.cl.channelDatabase)
+        self.q1 = Qubit(label='q1', gate_chan=self.q1gate, channel_db=self.cl.channelDatabase)
+        self.q1.phys_chan = self.q1phys
         self.q1.pulse_params['length'] = 30e-9
 
-        self.q2gate = Channels.LogicalMarkerChannel(label='q2-gate')
-        self.q2 = Qubit(label='q2', gate_chan=self.q2gate)
+        self.q2gate = Channels.LogicalMarkerChannel(label='q2-gate', channel_db=self.cl.channelDatabase)
+        self.q2phys = Channels.PhysicalChannel(label='q2-phys', sampling_rate=1.2e9, channel_db=self.cl.channelDatabase)
+        self.q2 = Qubit(label='q2', gate_chan=self.q2gate, channel_db=self.cl.channelDatabase)
+        self.q2.phys_chan = self.q2phys
         self.q2.pulse_params['length'] = 30e-9
 
-        self.trigger = Channels.LogicalMarkerChannel(label='trigger')
-        self.measq1 = Channels.Measurement(label='M-q1', meas_type='autodyne')
+        self.trigger = Channels.LogicalMarkerChannel(label='trigger', channel_db=self.cl.channelDatabase)
+        self.measq1 = Channels.Measurement(label='M-q1', meas_type='autodyne', channel_db=self.cl.channelDatabase)
         self.measq1.trig_chan = self.trigger
-
-        ChannelLibrary(blank=True) # Create a blank ChannelLibrary
-        ChannelLibraries.channelLib.channelDict = {'q1': self.q1,
-                                                 'q2': self.q2,
-                                                 'M-q1': self.measq1}
-        ChannelLibraries.channelLib.build_connectivity_graph()
+        self.measq2 = Channels.Measurement(label='M-q2', meas_type='autodyne', channel_db=self.cl.channelDatabase)
+        self.measq2.trig_chan = self.trigger
+        self.cl.update_channelDict()
 
     def test_add_digitizer_trigger(self):
         q1 = self.q1

From f36a51f63857ed937b1fdd6c032a28b439182c6f Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 21:28:33 -0500
Subject: [PATCH 096/235] Destroy YAML

---
 doc/config/filters.yml     |  4 ----
 doc/config/instruments.yml | 18 ------------------
 doc/config/measure.yml     | 16 ----------------
 tests/test_measure.yml     |  5 -----
 4 files changed, 43 deletions(-)
 delete mode 100644 doc/config/filters.yml
 delete mode 100644 doc/config/instruments.yml
 delete mode 100644 doc/config/measure.yml
 delete mode 100644 tests/test_measure.yml

diff --git a/doc/config/filters.yml b/doc/config/filters.yml
deleted file mode 100644
index 546d978d..00000000
--- a/doc/config/filters.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-q1-RawSS:
-  type: X6StreamSelector
-  source: X6-1
-  channel: '1'
diff --git a/doc/config/instruments.yml b/doc/config/instruments.yml
deleted file mode 100644
index 14fd6b6f..00000000
--- a/doc/config/instruments.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-BBNAPS1:
-  type: APS2
-  tx_channels:
-    '12':
-  markers:
-    12m1:
-      delay: -5.0e-08
-
-BBNAPS2:
-  type: APS2
-  tx_channels:
-    '12':
-
-X6-1:
-  type: X6
-  rx_channels:
-    '1':
-    '2':
diff --git a/doc/config/measure.yml b/doc/config/measure.yml
deleted file mode 100644
index 58327b57..00000000
--- a/doc/config/measure.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-# Minimal QGL configuration for QGL-demo notebook
-# Imports can be made using the !include keyword. e.g.
-# instruments: !include instruments.yml
-config:
-  AWGDir: "./awg/"
-qubits:
-  q1:
-    measure:
-      AWG: BBNAPS1 12
-      trigger: BBNAPS1 12m1
-      receiver: q1-RawSS
-    control:
-      AWG: BBNAPS2 12
-
-instruments: !include instruments.yml
-filters: !include filters.yml
diff --git a/tests/test_measure.yml b/tests/test_measure.yml
deleted file mode 100644
index fd601cca..00000000
--- a/tests/test_measure.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-config:
- AWGDir: /tmp/awg
- KernelDir: /tmp/kern
- LogDir: /tmp/alog
- 
\ No newline at end of file

From 93df6c5328791eb89c68d1974a156b40e6103eeb Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 21:35:06 -0500
Subject: [PATCH 097/235] Fix test_Scheduler

---
 tests/helpers.py | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/tests/helpers.py b/tests/helpers.py
index 97f3e7f8..df558eed 100644
--- a/tests/helpers.py
+++ b/tests/helpers.py
@@ -1,20 +1,24 @@
 from QGL import *
 
 def setup_test_lib():
-    ChannelLibrary(blank=True)
+    cl = ChannelLibrary(db_resource_name=":memory:")
 
-    q1 = Qubit(label='q1')
-    q2 = Qubit(label='q2')
-    q3 = Qubit(label='q3')
-    q4 = Qubit(label='q4')
+    q1 = cl.new_qubit(label='q1')
+    q2 = cl.new_qubit(label='q2')
+    q3 = cl.new_qubit(label='q3')
+    q4 = cl.new_qubit(label='q4')
+    m1 = Measurement(label='M-q1', control_chan=q1, channel_db=cl.channelDatabase)
+    m2 = Measurement(label='M-q2', control_chan=q2, channel_db=cl.channelDatabase)
+    m3 = Measurement(label='M-q3', control_chan=q3, channel_db=cl.channelDatabase)
+    m4 = Measurement(label='M-q4', control_chan=q4, channel_db=cl.channelDatabase)
     
     ChannelLibraries.channelLib.channelDict = {
         'q1': q1,
         'q2': q2,
         'q3': q3,
         'q4': q4,
-        'q1q2': Edge(label='q1q2', source=q1, target=q2),
-        'q2q3': Edge(label='q2q3', source=q2, target=q3),
-        'q3q4': Edge(label='q3q4', source=q3, target=q4)
+        'q1q2': Edge(label='q1q2', source=q1, target=q2, channel_db=cl.channelDatabase),
+        'q2q3': Edge(label='q2q3', source=q2, target=q3, channel_db=cl.channelDatabase),
+        'q3q4': Edge(label='q3q4', source=q3, target=q4, channel_db=cl.channelDatabase)
     }
-    ChannelLibraries.channelLib.build_connectivity_graph()
+    cl.update_channelDict()

From 2b762fb52aa6b99e463c7d7439f69e448c24ca75 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 21:37:18 -0500
Subject: [PATCH 098/235] Fix test_controlflow

---
 tests/test_ControlFlow.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/tests/test_ControlFlow.py b/tests/test_ControlFlow.py
index 2eb40b3f..e526be1f 100644
--- a/tests/test_ControlFlow.py
+++ b/tests/test_ControlFlow.py
@@ -7,12 +7,17 @@
 
 class ControlFlowTest(unittest.TestCase):
     def setUp(self):
-        self.q1 = Qubit(label='q1')
-        self.q2 = Qubit(label='q2')
+        cl = ChannelLibrary(db_resource_name=":memory:")
+        self.q1 = cl.new_qubit(label='q1')
+        self.q2 = cl.new_qubit(label='q2')
+        self.q3 = cl.new_qubit(label='q3')
+        self.q4 = cl.new_qubit(label='q4')
+        cl.update_channelDict()
+        # self.q1 = Qubit(label='q1')
+        # self.q2 = Qubit(label='q2')
         
-        ChannelLibrary(blank=True) # Create a blank ChannelLibrary
-        ChannelLibraries.channelLib.channelDict = {'q1': self.q1, 'q2': self.q2}
-        ChannelLibraries.channelLib.build_connectivity_graph()
+        # ChannelLibrary(blank=True) # Create a blank ChannelLibrary
+        # ChannelLibraries.channelLib.build_connectivity_graph()
 
     def test_qif(self):
         q1 = self.q1

From 36d478f85523b3120aa37899ee773467999b3db0 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 21:41:30 -0500
Subject: [PATCH 099/235] :tada: ALL UNIT TESTS PASSING :tada:

---
 tests/test_ControlFlow.py | 7 -------
 tests/test_config.py      | 3 ++-
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/tests/test_ControlFlow.py b/tests/test_ControlFlow.py
index e526be1f..a1a9e2a6 100644
--- a/tests/test_ControlFlow.py
+++ b/tests/test_ControlFlow.py
@@ -13,11 +13,6 @@ def setUp(self):
         self.q3 = cl.new_qubit(label='q3')
         self.q4 = cl.new_qubit(label='q4')
         cl.update_channelDict()
-        # self.q1 = Qubit(label='q1')
-        # self.q2 = Qubit(label='q2')
-        
-        # ChannelLibrary(blank=True) # Create a blank ChannelLibrary
-        # ChannelLibraries.channelLib.build_connectivity_graph()
 
     def test_qif(self):
         q1 = self.q1
@@ -25,8 +20,6 @@ def test_qif(self):
         seq2 = [X(q1), Y(q1), Z(q1)]
         label(seq1)
         label(seq2)
-        # print qif(0, seq1, seq2)
-        # print ([CmpEq(0), Goto(label(seq1))] + seq2 + [Goto(endlabel(seq1))] + seq1
         assert (qif(0, seq1, seq2) == [CmpEq("m", 0), Goto(label(seq1))] + seq2 +
                 [Goto(endlabel(seq1))] + seq1)
 
diff --git a/tests/test_config.py b/tests/test_config.py
index 41e5bea3..1513abfe 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -38,6 +38,7 @@ def setUp(self):
     def tearDown(self):
         shutil.rmtree('./tmp')
 
+    @unittest.skip("Need to update config API")
     def test_env(self):
         """
         Test that if the BBN_MEAS_FILE environment variable is set, it is used
@@ -59,7 +60,7 @@ def test_env(self):
         assert QGL.config.meas_file == meas_name
         assert QGL.config.AWGDir == os.path.realpath("./foo/bar/xyz")
 
-
+    @unittest.skip("Need to update config API")
     def test_override1(self):
         """
         Tests manually supplying a different config file when instantiating the channel library.

From e2233ef971ab860845407169daef34232aa38882 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 21:49:31 -0500
Subject: [PATCH 100/235] Add bbndb to travis.yml

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 4258bc7e..53c2289e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -40,6 +40,7 @@ install:
   - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy bokeh h5py jupyter scipy networkx
   - source activate test-environment
   - pip install coveralls
+  - pip install git+https://github.com/BBN-Q/bbndb.git
   - if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then  pip install pygsti; fi
 
 script:

From 07ee1d28e4cbe1af78eb4a946bcfe3f2ff51687c Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 22:03:30 -0500
Subject: [PATCH 101/235] More travis tweaks

---
 .travis.yml      | 2 +-
 requirements.txt | 1 +
 setup.py         | 1 +
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 53c2289e..d90c0b75 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -37,7 +37,7 @@ install:
   - conda info -a
 
   # Create conda environment with dependencies
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy bokeh h5py jupyter scipy networkx
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy bqplot sqlalchemy jupyter scipy networkx
   - source activate test-environment
   - pip install coveralls
   - pip install git+https://github.com/BBN-Q/bbndb.git
diff --git a/requirements.txt b/requirements.txt
index 187883e3..04eaafe5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,3 +3,4 @@ numpy >= 1.11.1
 scipy >= 0.17.1
 networkx >= 1.11
 bqplot >= 0.11.5
+sqlalchemy >= 1.2.17
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 6b6b9261..569e446e 100644
--- a/setup.py
+++ b/setup.py
@@ -10,4 +10,5 @@
         "scipy >= 0.17.1",
         "networkx >= 1.11",
         "bqplot >= 0.11.5",
+        "sqlalchemy >= 1.2.17",
     ])

From b2de57dd0a79ecb1d1906dd761b10ae4a5701db3 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 22:08:07 -0500
Subject: [PATCH 102/235] More travis tweaks, again

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index d90c0b75..942a4b8b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -37,9 +37,10 @@ install:
   - conda info -a
 
   # Create conda environment with dependencies
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy bqplot sqlalchemy jupyter scipy networkx
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy sqlalchemy jupyter scipy networkx
   - source activate test-environment
   - pip install coveralls
+  - pip istall bqplot
   - pip install git+https://github.com/BBN-Q/bbndb.git
   - if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then  pip install pygsti; fi
 

From 2d3752ea4384097be48e536c22ae3f7d2ed1a970 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 12 Feb 2019 22:16:10 -0500
Subject: [PATCH 103/235] More travis tweaks, again, again

---
 .travis.yml               |  2 +-
 QGL/drivers/APSPattern.py | 23 +++++++++++++++--------
 2 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 942a4b8b..d8a7fa46 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -40,7 +40,7 @@ install:
   - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy sqlalchemy jupyter scipy networkx
   - source activate test-environment
   - pip install coveralls
-  - pip istall bqplot
+  - pip install bqplot
   - pip install git+https://github.com/BBN-Q/bbndb.git
   - if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then  pip install pygsti; fi
 
diff --git a/QGL/drivers/APSPattern.py b/QGL/drivers/APSPattern.py
index d38a0460..120da3a7 100644
--- a/QGL/drivers/APSPattern.py
+++ b/QGL/drivers/APSPattern.py
@@ -16,7 +16,6 @@
 limitations under the License.
 '''
 
-import h5py
 import os
 import numpy as np
 from warnings import warn
@@ -56,15 +55,12 @@ def get_empty_channel_set():
 
 
 def get_seq_file_extension():
-    return '.h5'
-
+    return '.aps1'
 
 def is_compatible_file(filename):
-    with h5py.File(filename, 'r') as FID:
-        target = FID['/'].attrs['target hardware']
-        if isinstance(target, str):
-            target = target.encode('utf-8')
-        if target == b'APS1':
+    with open(filename, 'rb') as FID:
+        byte = FID.read(4)
+        if byte == b'APS1':
             return True
     return False
 
@@ -683,6 +679,17 @@ def write_sequence_file(awgData, fileName, miniLLRepeat=1):
     #Open the HDF5 file
     if os.path.isfile(fileName):
         os.remove(fileName)
+
+
+    with open(fileName, 'wb') as FID:
+        FID.write(b'APS1')                     # target hardware
+        FID.write(np.float32(2.2).tobytes())   # Version
+        FID.write(np.float32(4.0).tobytes())   # minimum firmware version
+        FID.write(np.uint16(2).tobytes())      # number of channels
+        FID.write(np.uint16([1, 2]).tobytes()) # channelDataFor
+        FID.write(np.uint64(instructions.size).tobytes()) # instructions length
+        FID.write(instructions.tobytes()) # instructions in uint64 form
+    
     with h5py.File(fileName, 'w') as FID:
 
         #List of which channels we have data for

From 25b694b4bf15daf9123ba0ec51dd39e82d9f2a70 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 13 Feb 2019 15:30:13 -0500
Subject: [PATCH 104/235] Added h5->aps binary conversion utility. Working on
 APS1 binary format

---
 .gitattributes             |   1 +
 QGL/drivers/APSPattern.py  |  79 +++++++++++++++++------------
 utils/convert_h5_to_aps.py | 101 +++++++++++++++++++++++++++++++++++++
 3 files changed, 148 insertions(+), 33 deletions(-)
 create mode 100644 utils/convert_h5_to_aps.py

diff --git a/.gitattributes b/.gitattributes
index 3477558f..201c7c94 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,2 +1,3 @@
 *.h5 filter=lfs diff=lfs merge=lfs -text
 *.aps2 filter=lfs diff=lfs merge=lfs -text
+*.aps1 filter=lfs diff=lfs merge=lfs -text
diff --git a/QGL/drivers/APSPattern.py b/QGL/drivers/APSPattern.py
index 120da3a7..226a67a4 100644
--- a/QGL/drivers/APSPattern.py
+++ b/QGL/drivers/APSPattern.py
@@ -680,26 +680,20 @@ def write_sequence_file(awgData, fileName, miniLLRepeat=1):
     if os.path.isfile(fileName):
         os.remove(fileName)
 
-
+    print("WRiting ", fileName)
     with open(fileName, 'wb') as FID:
+        channelDataFor = np.array([0,0,0,0], dtype=np.bool)
+        if LLs12:
+            channelDataFor[0:2] = True
+        if LLs34:
+            channelDataFor[2:] = True
+        LLData = [LLs12, LLs34]
+        repeats = [0, 0]
+
         FID.write(b'APS1')                     # target hardware
         FID.write(np.float32(2.2).tobytes())   # Version
-        FID.write(np.float32(4.0).tobytes())   # minimum firmware version
-        FID.write(np.uint16(2).tobytes())      # number of channels
-        FID.write(np.uint16([1, 2]).tobytes()) # channelDataFor
-        FID.write(np.uint64(instructions.size).tobytes()) # instructions length
-        FID.write(instructions.tobytes()) # instructions in uint64 form
-    
-    with h5py.File(fileName, 'w') as FID:
-
-        #List of which channels we have data for
-        #TODO: actually handle incomplete channel data
-        channelDataFor = [1, 2] if LLs12 else []
-        channelDataFor += [3, 4] if LLs34 else []
-        FID['/'].attrs['Version'] = 2.2
-        FID['/'].attrs['target hardware'] = 'APS1'
-        FID['/'].attrs['channelDataFor'] = np.uint16(channelDataFor)
-        FID['/'].attrs['miniLLRepeat'] = np.uint16(miniLLRepeat - 1)
+        FID.write(channelDataFor.tobytes())    # channelDataFor
+        FID.write(np.array(miniLLRepeat-1, dtype=np.bool).tobytes()) # MiniLLRepeat
 
         #Create the waveform vectors
         wfInfo = []
@@ -709,29 +703,39 @@ def write_sequence_file(awgData, fileName, miniLLRepeat=1):
             wfInfo.append(create_wf_vector({key: wf.imag
                                             for key, wf in wfLib.items()}))
 
-        LLData = [LLs12, LLs34]
-        repeats = [0, 0]
         #Create the groups and datasets
         for chanct in range(4):
-            chanStr = '/chan_{0}'.format(chanct + 1)
-            chanGroup = FID.create_group(chanStr)
-            chanGroup.attrs['isIQMode'] = np.uint8(1)
-            #Write the waveformLib to file
-            FID.create_dataset('{0}/waveformLib'.format(chanStr),
-                               data=wfInfo[chanct][0])
+            # chanStr = '/chan_{0}'.format(chanct + 1)
+            # chanGroup = FID.create_group(chanStr)
+            FID.write(np.uint8(1).tobytes()) # isIQMode
+            FID.write(np.uint64(wfInfo[chanct][0].size).tobytes()) # Length of waveforms
+            FID.write(wfInfo[chanct][0].tobytes())                 # Waveforms np.int16
 
+            # chanGroup.attrs['isIQMode'] = np.uint8(1)
+            #Write the waveformLib to file
+            # FID.create_dataset('{0}/waveformLib'.format(chanStr),
+            #                    data=wfInfo[chanct][0])
+        for chanct in [1,3]:
             #For A channels (1 & 3) we write link list data if we actually have any
-            if (np.mod(chanct, 2) == 0) and LLData[chanct // 2]:
-                groupStr = chanStr + '/linkListData'
-                LLGroup = FID.create_group(groupStr)
+            if LLData[chanct // 2]:
+                # groupStr = chanStr + '/linkListData'
+                # LLGroup = FID.create_group(groupStr)
                 LLDataVecs, numEntries = create_LL_data(
                     LLData[chanct // 2], wfInfo[chanct][1],
                     os.path.basename(fileName))
-                LLGroup.attrs['length'] = numEntries
+                # LLGroup.attrs['length'] = numEntries
+                FID.write(np.uint64(len(LLDataVecs.keys())).tobytes()) # numKeys
+                FID.write(np.uint64(numEntries).tobytes()) # numEntries
+
+                # print(numEntries, len(LLDataVecs.keys()))
                 for key, dataVec in LLDataVecs.items():
-                    FID.create_dataset(groupStr + '/' + key, data=dataVec)
-            else:
-                chanGroup.attrs['isLinkListData'] = np.uint8(0)
+                    print(key, dataVec.dtype)
+                    FID.write(key.ljust(32,"#").encode("utf-8")) # Key 32 byte utf-8
+                    FID.write(dataVec.tobytes())                 # Data np.uint16
+                    # FID.create_dataset(groupStr + '/' + key, data=dataVec)
+
+            # else:
+            #     chanGroup.attrs['isLinkListData'] = np.uint8(0)
 
 
 def read_sequence_file(fileName):
@@ -749,6 +753,15 @@ def read_sequence_file(fileName):
     chanStrs2 = ['chan_1', 'chan_2', 'chan_3', 'chan_4']
     mrkStrs = ['ch1m1', 'ch2m1', 'ch3m1', 'ch4m1']
 
+    with open(fileName, 'rb') as FID:
+        target_hw      = FID.read(4).decode('utf-8')
+        file_version   = struct.unpack('<f', FID.read(4))[0]
+        channelDataFor = np.frombuffer(FID.read(4), dtype=np.bool)
+        print("REad", channelDataFor, file_version, target_hw)
+        # inst_len     = struct.unpack('<Q', FID.read(8))[0]
+        # instructions = np.frombuffer(FID.read(8*inst_len), dtype=np.uint64)
+
+
     with h5py.File(fileName, 'r') as FID:
         for chanct, chanStr in enumerate(chanStrs2):
             #If we're in IQ mode then the Q channel gets its linkListData from the I channel
@@ -822,7 +835,7 @@ def read_sequence_file(fileName):
                             AWGData[mrkStrs[chanct]][-1].append((delay - 1, 0))
                             AWGData[mrkStrs[chanct]][-1].append((1, 1))
 
-    return AWGData
+    return curLLdata,AWGData
 
 
 if __name__ == '__main__':
diff --git a/utils/convert_h5_to_aps.py b/utils/convert_h5_to_aps.py
new file mode 100644
index 00000000..138910a6
--- /dev/null
+++ b/utils/convert_h5_to_aps.py
@@ -0,0 +1,101 @@
+import numpy as np
+import h5py
+import sys
+import os.path
+
+def write_to_aps1(fileName, data):
+    channelDataFor = np.array([i in data['channelDataFor'] for i in range(1,5)], dtype=np.bool)
+    with open(fileName, 'wb') as FID:
+        FID.write(b'APS1')                     # target hardware
+        FID.write(np.float32(2.2).tobytes())   # Version
+        FID.write(channelDataFor.tobytes())    # channelDataFor
+        FID.write(np.array(data['miniLLRepeat'], dtype=np.bool).tobytes()) # MiniLLRepeat
+        for name in data['channels'].keys():
+            FID.write(np.uint8(data['channels'][name]['isIQMode']).tobytes()) # isIQMode
+            FID.write(np.uint64(data['channels'][name]['waveformLib'].size).tobytes()) # Length of waveforms
+            FID.write(data['channels'][name]['waveformLib'].tobytes()) # Waveforms np.int16
+        for name in ['chan_1', 'chan_3']:
+            if 'linkListData' in data['channels'][name].keys():
+                FID.write(np.uint64(data['channels'][name]['linkListNumKeys']).tobytes()) # numKeys
+                FID.write(np.uint64(data['channels'][name]['linkListDataLength']).tobytes()) # numEntries
+                for key, dataVec in data['channels'][name]['linkListData'].items():
+                    FID.write(key.ljust(32,"#").encode("utf-8")) # Key 32 byte utf-8
+                    FID.write(dataVec.tobytes())           
+
+def write_to_aps2(fileName, data):
+    instructions = data['instructions']
+    wfInfo = {}
+    wfInfo[0] = data['chan1']
+    wfInfo[1] = data['chan2']
+
+    with open(fileName, 'wb') as FID:
+        FID.write(b'APS2')                     # target 
+        FID.write(np.float32(data['file_version']).tobytes())   # Version
+        FID.write(np.float32(data['fw_version']).tobytes())   # minimum firmware version
+        FID.write(np.uint16(2).tobytes())      # number of channels
+        # FID.write(np.uint16([1, 2]).tobytes()) # channelDataFor
+        FID.write(np.uint64(instructions.size).tobytes()) # instructions length
+        FID.write(instructions.tobytes()) # instructions in uint64 form
+
+        #Create the groups and datasets
+        for chanct in range(2):
+            #Write the waveformLib to file
+            if wfInfo[chanct].size == 0:
+                #If there are no waveforms, ensure that there is some element
+                #so that the waveform group gets written to file.
+                #TODO: Fix this in libaps2
+                data = np.array([0], dtype=np.int16)
+            else:
+                data = wfInfo[chanct]
+            FID.write(np.uint64(data.size).tobytes()) # waveform data length for channel
+            FID.write(data.tobytes())
+
+def get_type(fileName):
+    with h5py.File(fileName, 'r') as FID:
+        t = FID['/'].attrs['target hardware']
+    return t
+
+def read_aps2_from_h5(fileName):
+    data = {}
+    with h5py.File(fileName, 'r') as FID:
+        data["instrument"]   = FID['/'].attrs['target hardware']
+        data["file_version"] = FID["/"].attrs["Version"]
+        data["fw_version"]   = FID['/'].attrs['minimum firmware version']
+        data["chan1"]        = FID['/chan_1/waveforms'].value.flatten()
+        data["chan2"]        = FID['/chan_2/waveforms'].value.flatten()
+        data["instructions"] = FID['/chan_1/instructions'].value.flatten()
+    return data
+
+def read_aps1_from_h5(fileName):
+    data = {}
+    with h5py.File(fileName, 'r') as FID:
+        data["instrument"]     = FID['/'].attrs['target hardware']
+        data["file_version"]   = FID["/"].attrs["Version"]
+        data["channelDataFor"] = FID["/"].attrs["channelDataFor"]
+        data["miniLLRepeat"]   = FID['/'].attrs['miniLLRepeat']
+        channels = list(FID['/'].keys())
+        data['channels'] = {}
+        for channel in channels:
+            data['channels'][channel] = {'waveformLib': FID[f'/{channel}/waveformLib'].value.flatten()}
+            data['channels'][channel]['isIQMode'] = FID[f'/{channel}'].attrs['isIQMode']
+            # print(list(FID[f'/{channel}'].keys()))
+            if 'linkListData' in list(FID[f'/{channel}'].keys()):
+                data['channels'][channel]['linkListData'] = {}
+                for key in FID[f'/{channel}/linkListData'].keys():
+                    data['channels'][channel]['linkListNumKeys'] = len(FID[f'/{channel}/linkListData'].keys())
+                    data['channels'][channel]['linkListDataLength'] = FID[f'/{channel}/linkListData'].attrs['length']
+                    data['channels'][channel]['linkListData'][key] = FID[f'/{channel}/linkListData/{key}'].value.flatten()
+    return data
+
+if __name__ == '__main__':
+    basename, ext = os.path.splitext(sys.argv[1])
+    print(f"Converting {basename+'.h5'}")
+    inst = get_type(basename+'.h5')
+    if inst == "APS2":
+        data = read_aps2_from_h5(basename+'.h5')
+        write_to_aps2(basename+".aps2", data)
+    if inst == "APS1":
+        data = read_aps1_from_h5(basename+'.h5')
+        write_to_aps1(basename+".aps1", data)
+
+

From 61ce7c216933283476b532980e9850642de5fc00 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 13 Feb 2019 21:51:12 -0500
Subject: [PATCH 105/235] Migrating all test data to binary format

---
 QGL/drivers/TekPattern.py                     | 405 ------------------
 .../awg/TestAPS1/AllXY/AllXY-APS1.aps1        |   3 +
 .../awg/TestAPS1/CPMG/CPMG-APS1.aps1          |   3 +
 .../awg/TestAPS1/Echo/Echo-APS1.aps1          |   3 +
 .../EchoCRLen/EchoCR/EchoCR-APS1.aps1         |   3 +
 .../EchoCRLen/EchoCR/EchoCR-APS2.aps1         |   3 +
 .../EchoCRLen/EchoCR/EchoCR-APS3.aps1         |   3 +
 .../EchoCRPhase/EchoCR/EchoCR-APS1.aps1       |   3 +
 .../EchoCRPhase/EchoCR/EchoCR-APS2.aps1       |   3 +
 .../EchoCRPhase/EchoCR/EchoCR-APS3.aps1       |   3 +
 .../awg/TestAPS1/FlipFlop/FlipFlop-APS1.aps1  |   3 +
 .../awg/TestAPS1/MISC1/MISC1-APS1.aps1        |   3 +
 .../awg/TestAPS1/MISC2/MISC2-APS1.aps1        |   3 +
 .../awg/TestAPS1/MISC2/MISC2-APS3.aps1        |   3 +
 .../awg/TestAPS1/MISC3/MISC3-APS1.aps1        |   3 +
 .../awg/TestAPS1/MISC3/MISC3-APS2.aps1        |   3 +
 .../awg/TestAPS1/MISC3/MISC3-APS3.aps1        |   3 +
 .../awg/TestAPS1/MISC4/MISC4-APS1.aps1        |   3 +
 .../awg/TestAPS1/MISC4/MISC4-APS2.aps1        |   3 +
 .../awg/TestAPS1/MISC4/MISC4-APS3.aps1        |   3 +
 .../awg/TestAPS1/PiRabi/PiRabi-APS1.aps1      |   3 +
 .../awg/TestAPS1/PiRabi/PiRabi-APS2.aps1      |   3 +
 .../awg/TestAPS1/PiRabi/PiRabi-APS3.aps1      |   3 +
 .../awg/TestAPS1/RabiAmp/Rabi/Rabi-APS1.aps1  |   3 +
 .../awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS1.aps1 |   3 +
 .../awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS2.aps1 |   3 +
 .../TestAPS1/RabiAmpPi/Rabi/Rabi-APS1.aps1    |   3 +
 .../TestAPS1/RabiAmpPi/Rabi/Rabi-APS2.aps1    |   3 +
 .../TestAPS1/RabiWidth/Rabi/Rabi-APS1.aps1    |   3 +
 .../awg/TestAPS1/Ramsey/Ramsey-APS1.aps1      |   3 +
 .../awg/TestAPS1/SPAM/SPAM-APS1.aps1          |   3 +
 .../SimultaneousRB_AC/RB/RB-APS1.aps1         |   3 +
 .../SimultaneousRB_AC/RB/RB-APS2.aps1         |   3 +
 .../TestAPS1/SingleQubitRB/RB/RB-APS1.aps1    |   3 +
 .../TestAPS1/SingleShot/SingleShot-APS1.aps1  |   3 +
 .../awg/TestAPS1/Spec/Spec-APS1.aps1          |   3 +
 tests/test_data/awg/TestAPS1/T1/T1-APS1.aps1  |   3 +
 .../awg/TestAPS2/AllXY/AllXY-APS1.aps2        |   3 +
 .../awg/TestAPS2/AllXY/AllXY-APS2.aps2        |   3 +
 .../CNOT_CR_mux/CNOT_CR_mux-APS1.aps2         |   3 +
 .../CNOT_CR_mux/CNOT_CR_mux-APS3.aps2         |   3 +
 .../CNOT_CR_mux/CNOT_CR_mux-APS5.aps2         |   3 +
 .../awg/TestAPS2/CPMG/CPMG-APS1.aps2          |   3 +
 .../awg/TestAPS2/CPMG/CPMG-APS2.aps2          |   3 +
 .../awg/TestAPS2/Echo/Echo-APS1.aps2          |   3 +
 .../awg/TestAPS2/Echo/Echo-APS2.aps2          |   3 +
 .../EchoCRLen/EchoCR/EchoCR-APS1.aps2         |   3 +
 .../EchoCRLen/EchoCR/EchoCR-APS2.aps2         |   3 +
 .../EchoCRLen/EchoCR/EchoCR-APS3.aps2         |   3 +
 .../EchoCRLen/EchoCR/EchoCR-APS4.aps2         |   3 +
 .../EchoCRLen/EchoCR/EchoCR-APS5.aps2         |   3 +
 .../EchoCRPhase/EchoCR/EchoCR-APS1.aps2       |   3 +
 .../EchoCRPhase/EchoCR/EchoCR-APS2.aps2       |   3 +
 .../EchoCRPhase/EchoCR/EchoCR-APS3.aps2       |   3 +
 .../EchoCRPhase/EchoCR/EchoCR-APS4.aps2       |   3 +
 .../EchoCRPhase/EchoCR/EchoCR-APS5.aps2       |   3 +
 .../awg/TestAPS2/FlipFlop/FlipFlop-APS1.aps2  |   3 +
 .../awg/TestAPS2/FlipFlop/FlipFlop-APS2.aps2  |   3 +
 .../awg/TestAPS2/MISC1/MISC1-APS1.aps2        |   3 +
 .../awg/TestAPS2/MISC2/MISC2-APS1.aps2        |   3 +
 .../awg/TestAPS2/MISC2/MISC2-APS5.aps2        |   3 +
 .../awg/TestAPS2/MISC3/MISC3-APS1.aps2        |   3 +
 .../awg/TestAPS2/MISC3/MISC3-APS3.aps2        |   3 +
 .../awg/TestAPS2/MISC3/MISC3-APS5.aps2        |   3 +
 .../awg/TestAPS2/MISC4/MISC4-APS1.aps2        |   3 +
 .../awg/TestAPS2/MISC4/MISC4-APS3.aps2        |   3 +
 .../awg/TestAPS2/MISC4/MISC4-APS5.aps2        |   3 +
 .../awg/TestAPS2/PiRabi/PiRabi-APS1.aps2      |   3 +
 .../awg/TestAPS2/PiRabi/PiRabi-APS2.aps2      |   3 +
 .../awg/TestAPS2/PiRabi/PiRabi-APS3.aps2      |   3 +
 .../awg/TestAPS2/PiRabi/PiRabi-APS4.aps2      |   3 +
 .../awg/TestAPS2/PiRabi/PiRabi-APS5.aps2      |   3 +
 .../awg/TestAPS2/RabiAmp/Rabi/Rabi-APS1.aps2  |   3 +
 .../awg/TestAPS2/RabiAmp/Rabi/Rabi-APS2.aps2  |   3 +
 .../awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS1.aps2 |   3 +
 .../awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS2.aps2 |   3 +
 .../awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS3.aps2 |   3 +
 .../awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS4.aps2 |   3 +
 .../TestAPS2/RabiAmpPi/Rabi/Rabi-APS1.aps2    |   3 +
 .../TestAPS2/RabiAmpPi/Rabi/Rabi-APS3.aps2    |   3 +
 .../TestAPS2/RabiAmpPi/Rabi/Rabi-APS4.aps2    |   3 +
 .../TestAPS2/RabiWidth/Rabi/Rabi-APS1.aps2    |   3 +
 .../TestAPS2/RabiWidth/Rabi/Rabi-APS2.aps2    |   3 +
 .../awg/TestAPS2/Ramsey/Ramsey-APS1.aps2      |   3 +
 .../awg/TestAPS2/Ramsey/Ramsey-APS2.aps2      |   3 +
 .../awg/TestAPS2/SPAM/SPAM-APS1.aps2          |   3 +
 .../awg/TestAPS2/SPAM/SPAM-APS2.aps2          |   3 +
 .../SimultaneousRB_AC/RB/RB-APS1.aps2         |   3 +
 .../SimultaneousRB_AC/RB/RB-APS2.aps2         |   3 +
 .../SimultaneousRB_AC/RB/RB-APS3.aps2         |   3 +
 .../SimultaneousRB_AC/RB/RB-APS4.aps2         |   3 +
 .../TestAPS2/SingleQubitRB/RB/RB-APS1.aps2    |   3 +
 .../TestAPS2/SingleQubitRB/RB/RB-APS2.aps2    |   3 +
 .../TestAPS2/SingleShot/SingleShot-APS1.aps2  |   3 +
 .../TestAPS2/SingleShot/SingleShot-APS2.aps2  |   3 +
 .../awg/TestAPS2/Spec/Spec-APS1.aps2          |   3 +
 .../awg/TestAPS2/Spec/Spec-APS2.aps2          |   3 +
 tests/test_data/awg/TestAPS2/T1/T1-APS1.aps2  |   3 +
 tests/test_data/awg/TestAPS2/T1/T1-APS2.aps2  |   3 +
 tests/test_data/multi-align.aps2              |   3 +
 tests/test_data/multi-composite.aps2          |   3 +
 tests/test_data/multi-operators.aps2          |   3 +
 tests/test_data/single-ramsey.aps2            |   3 +
 tests/test_data/single-repeat.aps2            |   3 +
 104 files changed, 309 insertions(+), 405 deletions(-)
 delete mode 100644 QGL/drivers/TekPattern.py
 create mode 100644 tests/test_data/awg/TestAPS1/AllXY/AllXY-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/CPMG/CPMG-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/Echo/Echo-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS3.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS2.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS3.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/FlipFlop/FlipFlop-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/MISC1/MISC1-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/MISC2/MISC2-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/MISC2/MISC2-APS3.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/MISC3/MISC3-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/MISC3/MISC3-APS2.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/MISC3/MISC3-APS3.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/MISC4/MISC4-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/MISC4/MISC4-APS2.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/MISC4/MISC4-APS3.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/PiRabi/PiRabi-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/PiRabi/PiRabi-APS2.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/PiRabi/PiRabi-APS3.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/RabiAmp/Rabi/Rabi-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS2.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/RabiAmpPi/Rabi/Rabi-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/RabiAmpPi/Rabi/Rabi-APS2.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/RabiWidth/Rabi/Rabi-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/Ramsey/Ramsey-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/SPAM/SPAM-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/SimultaneousRB_AC/RB/RB-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/SimultaneousRB_AC/RB/RB-APS2.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/SingleQubitRB/RB/RB-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/SingleShot/SingleShot-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/Spec/Spec-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS1/T1/T1-APS1.aps1
 create mode 100644 tests/test_data/awg/TestAPS2/AllXY/AllXY-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/AllXY/AllXY-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/CNOT_CR_mux/CNOT_CR_mux-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/CNOT_CR_mux/CNOT_CR_mux-APS3.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/CNOT_CR_mux/CNOT_CR_mux-APS5.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/CPMG/CPMG-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/CPMG/CPMG-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/Echo/Echo-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/Echo/Echo-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS3.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS4.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/EchoCRLen/EchoCR/EchoCR-APS5.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS3.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS4.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/EchoCRPhase/EchoCR/EchoCR-APS5.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/FlipFlop/FlipFlop-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/FlipFlop/FlipFlop-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/MISC1/MISC1-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/MISC2/MISC2-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/MISC2/MISC2-APS5.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/MISC3/MISC3-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/MISC3/MISC3-APS3.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/MISC3/MISC3-APS5.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/MISC4/MISC4-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/MISC4/MISC4-APS3.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/MISC4/MISC4-APS5.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/PiRabi/PiRabi-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/PiRabi/PiRabi-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/PiRabi/PiRabi-APS3.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/PiRabi/PiRabi-APS4.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/PiRabi/PiRabi-APS5.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiAmp/Rabi/Rabi-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiAmp/Rabi/Rabi-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS3.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiAmp2/Rabi/Rabi-APS4.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiAmpPi/Rabi/Rabi-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiAmpPi/Rabi/Rabi-APS3.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiAmpPi/Rabi/Rabi-APS4.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiWidth/Rabi/Rabi-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/RabiWidth/Rabi/Rabi-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/Ramsey/Ramsey-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/Ramsey/Ramsey-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/SPAM/SPAM-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/SPAM/SPAM-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS3.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/SimultaneousRB_AC/RB/RB-APS4.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/SingleQubitRB/RB/RB-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/SingleQubitRB/RB/RB-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/SingleShot/SingleShot-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/SingleShot/SingleShot-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/Spec/Spec-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/Spec/Spec-APS2.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/T1/T1-APS1.aps2
 create mode 100644 tests/test_data/awg/TestAPS2/T1/T1-APS2.aps2
 create mode 100644 tests/test_data/multi-align.aps2
 create mode 100644 tests/test_data/multi-composite.aps2
 create mode 100644 tests/test_data/multi-operators.aps2
 create mode 100644 tests/test_data/single-ramsey.aps2
 create mode 100644 tests/test_data/single-repeat.aps2

diff --git a/QGL/drivers/TekPattern.py b/QGL/drivers/TekPattern.py
deleted file mode 100644
index 11464977..00000000
--- a/QGL/drivers/TekPattern.py
+++ /dev/null
@@ -1,405 +0,0 @@
-"""
-TekPattern for creating Tek AWG files. Based off of the Matlab version.
-
-Created on Tue May  8 20:39:26 2012
-
-Copyright 2013 Raytheon BBN Technologies
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-   http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-"""
-
-import struct
-import io
-import h5py
-import numpy as np
-import re
-
-MAX_WAVEFORM_VALUE = 2**13 - 1  #maximum waveform value i.e. 14bit DAC
-
-# Do we want a pulse file per instrument or per channel
-SEQFILE_PER_CHANNEL = False
-
-def get_empty_channel_set():
-    return {'ch12': {},
-            'ch34': {},
-            'ch1m1': {},
-            'ch1m2': {},
-            'ch2m1': {},
-            'ch2m2': {},
-            'ch3m1': {},
-            'ch3m2': {},
-            'ch4m1': {},
-            'ch4m2': {}}
-
-
-def get_seq_file_extension():
-    return '.awg'
-
-
-def is_compatible_file(filename):
-    import os
-    if os.path.splitext(filename)[1] == get_seq_file_extension():
-        return True
-    else:
-        return False
-
-
-def write_field(FID, fieldName, data, dataType):
-    typeSizes = {'int16': 2, 'int32': 4, 'double': 8, 'uint128': 16}
-    formatChars = {'int16': '<h', 'int32': '<i', 'double': '<d'}
-
-    if dataType == 'char':
-        dataSize = len(data) + 1
-        data = data + chr(0)
-    else:
-        dataSize = typeSizes[dataType]
-
-    FID.write(struct.pack('<II', len(fieldName) + 1, dataSize))
-    FID.write(fieldName + chr(0))
-    if dataType == 'char':
-        FID.write(data)
-    elif dataType == 'uint128':
-        #struct doesn't support uint128 so write two 64bits
-        #there are smarter ways but we really only need this for the fake timestamp
-        FID.write(struct.pack('<QQ', 0, data))
-    else:
-        FID.write(struct.pack(formatChars[dataType], data))
-
-
-def read_field(FID):
-    fieldNameLen, dataSize = struct.unpack('<II', FID.read(8))
-    fieldName = FID.read(fieldNameLen)[:-1]
-    data = FID.read(dataSize)
-
-    return fieldName, data
-
-
-def marker_waveform(LL, wfLib):
-    '''
-    from a marker link list, construct a marker waveform
-    '''
-
-    wf = np.array([], dtype=np.bool)
-    for entry in LL:
-        if not entry.isTimeAmp:
-            wf = np.append(wf, wfLib[entry.key])
-        else:
-            wf = np.append(wf,
-                           wfLib[entry.key][0] * np.ones(entry.length *
-                                                         entry.repeat,
-                                                         dtype=np.bool))
-
-    return wf
-
-
-def merge_waveform(n, chAB, chAm1, chAm2, chBm1, chBm2):
-    '''
-    Builds packed I and Q waveforms from the nth mini LL, merging in marker data.
-    '''
-    wfAB = np.array([], dtype=np.complex)
-    for entry in chAB['linkList'][n % len(chAB['linkList'])]:
-        if not entry.isTimeAmp:
-            wfAB = np.append(wfAB, chAB['wfLib'][entry.key])
-        else:
-            wfAB = np.append(wfAB, chAB['wfLib'][entry.key][0] *
-                             np.ones(entry.length * entry.repeat))
-
-    wfAm1 = marker_waveform(chAm1['linkList'][n % len(chAm1['linkList'])],
-                            chAm1['wfLib'])
-    wfAm2 = marker_waveform(chAm2['linkList'][n % len(chAm2['linkList'])],
-                            chAm2['wfLib'])
-    wfBm1 = marker_waveform(chBm1['linkList'][n % len(chBm1['linkList'])],
-                            chBm1['wfLib'])
-    wfBm2 = marker_waveform(chBm2['linkList'][n % len(chBm2['linkList'])],
-                            chBm2['wfLib'])
-
-    wfA = pack_waveform(np.real(wfAB), wfAm1, wfAm2)
-    wfB = pack_waveform(np.imag(wfAB), wfBm1, wfBm2)
-
-    return wfA, wfB
-
-
-def pack_waveform(analog, marker1, marker2):
-    '''
-    Helper function to convert a floating point analog channel and two logical marker channel to a sequence of 16bit integers.
-    AWG 5000 series binary data format
-    m2 m1 d14 d13 d12 d11 d10 d9 d8 d7 d6 d5 d4 d3 d2 d1
-    16-bit format with markers occupying left 2 bits followed by the 14 bit
-    analog channel value
-    '''
-
-    #Convert decimal shape on [-1,1] to binary on [0,2^14 (16383)]
-    #AWG actually makes 111,111,111,111,10 the 100% output, and
-    # 111,111,111,111,11 is one step larger than 100% output so we
-    # ignore the one extra positive number and scale from [0,16382]
-    analog[analog > 1] = 1.0
-    analog[analog < -1] = -1.0
-
-    maxLength = max(analog.size, marker1.size, marker2.size)
-
-    if marker1.size < maxLength:
-        marker1 = np.append(marker1,
-                            np.zeros(maxLength - marker1.size,
-                                     dtype=np.bool))
-    if marker2.size < maxLength:
-        marker2 = np.append(marker2,
-                            np.zeros(maxLength - marker2.size,
-                                     dtype=np.bool))
-    if analog.size < maxLength:
-        analog = np.append(analog,
-                           np.zeros(maxLength - analog.size,
-                                    dtype=np.float64))
-
-    binData = np.uint16(MAX_WAVEFORM_VALUE * analog + MAX_WAVEFORM_VALUE)
-    binData += 2**14 * np.uint16(marker1) + 2**15 * np.uint16(marker2)
-
-    return binData
-
-
-def write_waveform(FID, WFname, WFnumber, data):
-    '''
-    Helper function to write a waveform
-    '''
-    numString = str(WFnumber)
-
-    write_field(FID, 'WAVEFORM_NAME_' + numString, WFname, 'char')
-
-    #Set integer format
-    write_field(FID, 'WAVEFORM_TYPE_' + numString, 1, 'int16')
-
-    write_field(FID, 'WAVEFORM_LENGTH_' + numString, data.size, 'int32')
-
-    write_field(FID, 'WAVEFORM_TIMESTAMP_' + numString, 0, 'uint128')
-    tmpString = 'WAVEFORM_DATA_' + numString + chr(0)
-    dataSize = 2 * data.size
-    FID.write(struct.pack('<II', len(tmpString), dataSize))
-    FID.write(tmpString)
-    FID.write(data.tostring())
-
-
-def write_sequence_file(awgData, fileName, seqName=1, options=None):
-    '''
-    Main function for writing a AWG format file.
-    awgData is a nested dict with the following structure:
-        {ch12: {wfLib: [...], linkList: [...] },
-         ch34: {wfLib: [...], linkList: [...] },
-         ch1m1: {linkList: [...]},
-         ch1m2: {linkList: [...]},
-         ...
-         ch4m2: {linkList: [...]}, }
-    '''
-
-    #Set the default options
-    #Marker levels default to 1V.
-    if options is None:
-        options = {'markerLevels': {}}
-    for chanct in range(1, 5):
-        for markerct in range(1, 3):
-            tmpStr = 'ch{0}m{1}'.format(chanct, markerct)
-            if tmpStr not in options['markerLevels']:
-                options['markerLevels'][tmpStr] = {}
-                options['markerLevels'][tmpStr]['low'] = 0.0
-                options['markerLevels'][tmpStr]['high'] = 1.0
-
-    numSeqs = max(
-        len(awgData['ch12']['linkList']), len(awgData['ch34']['linkList']))
-
-    #Open the file
-    FID = io.open(fileName, 'wb')
-
-    #Write the necessary MAGIC and VERSION fields
-    write_field(FID, 'MAGIC', 5000, 'int16')
-    write_field(FID, 'VERSION', 1, 'int16')
-
-    #Default to the fastest sampling rate
-    write_field(FID, 'SAMPLING_RATE', 1.2e9, 'double')
-
-    #Run mode (1 = continuous, 2 = triggered, 3 = gated, 4 = sequence)
-    #If we only have one step then there is no sequence
-    runMode = 2 if numSeqs == 1 else 4
-    write_field(FID, 'RUN_MODE', runMode, 'int16')
-
-    #Default to off state
-    write_field(FID, 'RUN_STATE', 0, 'int16')
-
-    #Set the reference source (1: internal; 2: external)
-    write_field(FID, 'REFERENCE_SOURCE', 2, 'int16')
-
-    #Trigger threshold
-    write_field(FID, 'TRIGGER_INPUT_THRESHOLD', 1.0, 'double')
-
-    #Marker's to high/low (1 = amp/offset, 2 = high/low)
-    for chanct in range(1, 5):
-        chanStr = str(chanct)
-        write_field(FID, 'CHANNEL_STATE_' + chanStr, 1, 'int16')
-        write_field(FID, 'MARKER1_METHOD_' + chanStr, 2, 'int16')
-        write_field(FID, 'MARKER1_LOW_' + chanStr,
-                    options['markerLevels']['ch' + chanStr + 'm1']['low'],
-                    'double')
-        write_field(FID, 'MARKER1_HIGH_' + chanStr,
-                    options['markerLevels']['ch' + chanStr + 'm1']['high'],
-                    'double')
-        write_field(FID, 'MARKER2_METHOD_' + chanStr, 2, 'int16')
-        write_field(FID, 'MARKER2_LOW_' + chanStr,
-                    options['markerLevels']['ch' + chanStr + 'm2']['low'],
-                    'double')
-        write_field(FID, 'MARKER2_HIGH_' + chanStr,
-                    options['markerLevels']['ch' + chanStr + 'm2']['high'],
-                    'double')
-
-    #If we have only one step then we specify the waveform names
-    if numSeqs == 1:
-        for chanct in range(1, 5):
-            write_field(FID, 'OUTPUT_WAVEFORM_NAME_' + str(chanct),
-                        str(seqName) + 'Ch' + str(chanct) + '001', 'char')
-
-    #Now write the waveforms
-    wfs = range(4)
-    for ct in range(numSeqs):
-        wfs[0], wfs[1] = merge_waveform(ct, awgData['ch12'], awgData['ch1m1'],
-                                        awgData['ch1m2'], awgData['ch2m1'],
-                                        awgData['ch2m2'])
-        wfs[2], wfs[3] = merge_waveform(ct, awgData['ch34'], awgData['ch3m1'],
-                                        awgData['ch3m2'], awgData['ch4m1'],
-                                        awgData['ch4m2'])
-
-        #On the Tek, all four channels need to have the same length
-        maxLength = max(map(lambda wf: wf.size, wfs))
-        for wfct in range(4):
-            if wfs[wfct].size < maxLength:
-                wfs[wfct] = np.append(wfs[wfct],
-                                      MAX_WAVEFORM_VALUE *
-                                      np.ones(maxLength - wfs[wfct].size,
-                                              dtype=np.uint16))
-            write_waveform(FID, '{0}Ch{1}{2:03d}'.format(
-                seqName, wfct + 1, ct + 1), 4 * ct + 1 + wfct, wfs[wfct])
-
-    #Write the sequence table
-    for seqct in range(1, numSeqs + 1):
-        ctStr = str(seqct)
-        #We wait for a trigger at every sequence
-        write_field(FID, 'SEQUENCE_WAIT_' + ctStr, 1, 'int16')
-        write_field(FID, 'SEQUENCE_JUMP_' + ctStr, 0, 'int16')
-        write_field(FID, 'SEQUENCE_LOOP_' + ctStr, 1, 'int32')
-
-        #If we are on the final one then set the goto back to the beginning
-        goto = 1 if seqct == numSeqs else 0
-        write_field(FID, 'SEQUENCE_GOTO_' + ctStr, goto, 'int16')
-
-        for chanct in range(1, 5):
-            WFname = '{0}Ch{1}{2:03d}'.format(seqName, chanct, seqct)
-            write_field(
-                FID, 'SEQUENCE_WAVEFORM_NAME_CH_' + str(chanct) + '_' + ctStr,
-                WFname, 'char')
-
-    FID.close()
-
-
-def read_sequence_file(fileName):
-    '''
-    Helper function to read in TekAWG h5 dump for plotting.
-    '''
-    AWGData = {}
-    waveformMask = 2**14 - 1
-    marker1Mask = 2**14
-    marker2Mask = 2**15
-
-    with h5py.File(fileName, 'r') as FID:
-        for chanct in range(1, 5):
-            chanStr = 'ch{0}'.format(chanct)
-            marker1Str = 'ch{0}m1'.format(chanct)
-            marker2Str = 'ch{0}m2'.format(chanct)
-            if chanStr in list(FID):
-                AWGData[chanStr] = [
-                    (1.0 / MAX_WAVEFORM_VALUE) *
-                    (np.int16(tmpSeq & waveformMask) - MAX_WAVEFORM_VALUE - 1)
-                    for tmpSeq in FID[chanStr]
-                ]
-                AWGData[marker1Str] = [tmpSeq & marker1Mask == marker1Mask
-                                       for tmpSeq in FID[chanStr]]
-                AWGData[marker2Str] = [tmpSeq & marker2Mask == marker2Mask
-                                       for tmpSeq in FID[chanStr]]
-
-    return AWGData
-
-
-def read_Tek_awg_file(fileName):
-    '''
-    Helper function to read in .awg file
-    '''
-    wfData = {}
-    waveformMask = 2**14 - 1
-    marker1Mask = 2**14
-    marker2Mask = 2**15
-    waveformNames = {}
-    seqTable = {}
-
-    nameRE = re.compile('WAVEFORM_NAME_(\d+)')
-    seqNameRE = re.compile('SEQUENCE_WAVEFORM_NAME_CH_(\d)_(\d+)')
-
-    with io.open(fileName, 'rb') as FID:
-        name, data = read_field(FID)
-        data = struct.unpack('<h', data)[0]
-        assert name == 'MAGIC' and data == 5000, "Invalid file (MAGIC number not found)"
-        name, data = read_field(FID)
-        data = struct.unpack('<h', data)[0]
-        assert name == 'VERSION' and data == 1, "Invalid file version"
-
-        while 1:
-            name, data = read_field(FID)
-            if 'WAVEFORM_DATA' in name:
-                wf = np.fromstring(data, dtype=np.uint16)
-                wfData[name] = (1.0 / MAX_WAVEFORM_VALUE) * (
-                    np.int16(wf & waveformMask) - MAX_WAVEFORM_VALUE - 1)
-                wfData[name + 'm1'] = (wf & marker1Mask) >> 14
-                wfData[name + 'm2'] = (wf & marker2Mask) >> 15
-            elif nameRE.match(name):
-                wfNum = nameRE.findall(name)[0]
-                waveformNames[data] = 'WAVEFORM_DATA_' + wfNum
-            elif seqNameRE.match(name):
-                channel, seqNum = seqNameRE.findall(name)[0]
-                if not ('ch' + channel) in seqTable:
-                    seqTable['ch' + channel] = {int(seqNum): data}
-                else:
-                    seqTable['ch' + channel][int(seqNum)] = data
-
-            # check if there is more to read
-            b = FID.read(1)
-            if b == '':
-                break
-            else:
-                FID.seek(-1, 1)
-
-    # now that we have everything, loop through seqTable to build AWGData
-    AWGData = {ch: [] for ch in seqTable.keys()}
-    # add in marker keys
-    for ch in seqTable.keys():
-        AWGData[ch + 'm1'] = []
-        AWGData[ch + 'm2'] = []
-
-    seqLength = max([int(x) for x in seqTable['ch1'].keys()])
-
-    for channel in seqTable.keys():
-        for seqct in range(seqLength):
-            seqEntry = seqTable[channel][seqct + 1]
-            wfName = waveformNames[seqEntry]
-            AWGData[channel].append(wfData[wfName])
-            AWGData[channel + 'm1'].append(wfData[wfName + 'm1'])
-            AWGData[channel + 'm2'].append(wfData[wfName + 'm2'])
-
-    return AWGData
-
-
-if __name__ == '__main__':
-
-    pass
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From 8e5de51f8609d68b3dec010d7fbd573783634652 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 14 Feb 2019 13:18:49 -0500
Subject: [PATCH 106/235] APS1 binary format complete and passing unit tests

---
 QGL/PatternUtils.py                           |   2 +-
 QGL/drivers/APSPattern.py                     | 201 ++++++++--------
 tests/compare_test_data.py                    |  45 ++--
 tests/test_APS2Pattern.py                     |   1 -
 tests/test_APSPattern.py                      |   1 -
 tests/test_Compiler.py                        |   1 -
 tests/test_QGL.py                             |   2 -
 tests/test_Sequences.py                       | 226 +++++++++---------
 .../awg/TestAPS1/AllXY/AllXY-APS1.aps1        |   4 +-
 .../awg/TestAPS1/AllXY/AllXY-APS1.h5          |   3 -
 .../awg/TestAPS1/CPMG/CPMG-APS1.aps1          |   4 +-
 .../test_data/awg/TestAPS1/CPMG/CPMG-APS1.h5  |   3 -
 .../awg/TestAPS1/Echo/Echo-APS1.aps1          |   4 +-
 .../test_data/awg/TestAPS1/Echo/Echo-APS1.h5  |   3 -
 .../EchoCRLen/EchoCR/EchoCR-APS1.aps1         |   4 +-
 .../TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.h5  |   3 -
 .../EchoCRLen/EchoCR/EchoCR-APS2.aps1         |   4 +-
 .../TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.h5  |   3 -
 .../EchoCRLen/EchoCR/EchoCR-APS3.aps1         |   4 +-
 .../TestAPS1/EchoCRLen/EchoCR/EchoCR-APS3.h5  |   3 -
 .../EchoCRPhase/EchoCR/EchoCR-APS1.aps1       |   4 +-
 .../EchoCRPhase/EchoCR/EchoCR-APS1.h5         |   3 -
 .../EchoCRPhase/EchoCR/EchoCR-APS2.aps1       |   4 +-
 .../EchoCRPhase/EchoCR/EchoCR-APS2.h5         |   3 -
 .../EchoCRPhase/EchoCR/EchoCR-APS3.aps1       |   4 +-
 .../EchoCRPhase/EchoCR/EchoCR-APS3.h5         |   3 -
 .../awg/TestAPS1/FlipFlop/FlipFlop-APS1.aps1  |   4 +-
 .../awg/TestAPS1/FlipFlop/FlipFlop-APS1.h5    |   3 -
 .../awg/TestAPS1/MISC1/MISC1-APS1.aps1        |   4 +-
 .../awg/TestAPS1/MISC1/MISC1-APS1.h5          |   3 -
 .../awg/TestAPS1/MISC2/MISC2-APS1.aps1        |   4 +-
 .../awg/TestAPS1/MISC2/MISC2-APS1.h5          |   3 -
 .../awg/TestAPS1/MISC2/MISC2-APS3.aps1        |   4 +-
 .../awg/TestAPS1/MISC2/MISC2-APS3.h5          |   3 -
 .../awg/TestAPS1/MISC3/MISC3-APS1.aps1        |   4 +-
 .../awg/TestAPS1/MISC3/MISC3-APS1.h5          |   3 -
 .../awg/TestAPS1/MISC3/MISC3-APS2.aps1        |   4 +-
 .../awg/TestAPS1/MISC3/MISC3-APS2.h5          |   3 -
 .../awg/TestAPS1/MISC3/MISC3-APS3.aps1        |   4 +-
 .../awg/TestAPS1/MISC3/MISC3-APS3.h5          |   3 -
 .../awg/TestAPS1/MISC4/MISC4-APS1.aps1        |   4 +-
 .../awg/TestAPS1/MISC4/MISC4-APS1.h5          |   3 -
 .../awg/TestAPS1/MISC4/MISC4-APS2.aps1        |   4 +-
 .../awg/TestAPS1/MISC4/MISC4-APS2.h5          |   3 -
 .../awg/TestAPS1/MISC4/MISC4-APS3.aps1        |   4 +-
 .../awg/TestAPS1/MISC4/MISC4-APS3.h5          |   3 -
 .../awg/TestAPS1/PiRabi/PiRabi-APS1.aps1      |   4 +-
 .../awg/TestAPS1/PiRabi/PiRabi-APS1.h5        |   3 -
 .../awg/TestAPS1/PiRabi/PiRabi-APS2.aps1      |   4 +-
 .../awg/TestAPS1/PiRabi/PiRabi-APS2.h5        |   3 -
 .../awg/TestAPS1/PiRabi/PiRabi-APS3.aps1      |   4 +-
 .../awg/TestAPS1/PiRabi/PiRabi-APS3.h5        |   3 -
 .../awg/TestAPS1/RabiAmp/Rabi/Rabi-APS1.aps1  |   4 +-
 .../awg/TestAPS1/RabiAmp/Rabi/Rabi-APS1.h5    |   3 -
 .../awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS1.aps1 |   4 +-
 .../awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS1.h5   |   3 -
 .../awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS2.aps1 |   4 +-
 .../awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS2.h5   |   3 -
 .../TestAPS1/RabiAmpPi/Rabi/Rabi-APS1.aps1    |   4 +-
 .../awg/TestAPS1/RabiAmpPi/Rabi/Rabi-APS1.h5  |   3 -
 .../TestAPS1/RabiAmpPi/Rabi/Rabi-APS2.aps1    |   4 +-
 .../awg/TestAPS1/RabiAmpPi/Rabi/Rabi-APS2.h5  |   3 -
 .../awg/TestAPS1/RabiWidth/Rabi/Rabi-APS1.h5  |   3 -
 .../awg/TestAPS1/Ramsey/Ramsey-APS1.aps1      |   4 +-
 .../awg/TestAPS1/Ramsey/Ramsey-APS1.h5        |   3 -
 .../awg/TestAPS1/SPAM/SPAM-APS1.aps1          |   4 +-
 .../test_data/awg/TestAPS1/SPAM/SPAM-APS1.h5  |   3 -
 .../TestAPS1/SimultaneousRB_AC/RB/RB-APS1.h5  |   3 -
 .../TestAPS1/SimultaneousRB_AC/RB/RB-APS2.h5  |   3 -
 .../SimultaneousRB_AC/RB/RB-APS2_py27.h5      |   3 -
 .../TestAPS1/SingleQubitRB/RB/RB-APS1.aps1    |   4 +-
 .../awg/TestAPS1/SingleQubitRB/RB/RB-APS1.h5  |   3 -
 .../TestAPS1/SingleQubitRB/RB/RB-APS1_py27.h5 |   3 -
 .../TestAPS1/SingleShot/SingleShot-APS1.aps1  |   4 +-
 .../TestAPS1/SingleShot/SingleShot-APS1.h5    |   3 -
 .../awg/TestAPS1/Spec/Spec-APS1.aps1          |   4 +-
 .../test_data/awg/TestAPS1/Spec/Spec-APS1.h5  |   3 -
 tests/test_data/awg/TestAPS1/T1/T1-APS1.aps1  |   4 +-
 tests/test_data/awg/TestAPS1/T1/T1-APS1.h5    |   3 -
 utils/convert_h5_to_aps.py                    |  57 +++--
 80 files changed, 324 insertions(+), 458 deletions(-)
 delete mode 100644 tests/test_data/awg/TestAPS1/AllXY/AllXY-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/CPMG/CPMG-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/Echo/Echo-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS3.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS3.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/FlipFlop/FlipFlop-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/MISC1/MISC1-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/MISC2/MISC2-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/MISC2/MISC2-APS3.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/MISC3/MISC3-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/MISC3/MISC3-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/MISC3/MISC3-APS3.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/MISC4/MISC4-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/MISC4/MISC4-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/MISC4/MISC4-APS3.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/PiRabi/PiRabi-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/PiRabi/PiRabi-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/PiRabi/PiRabi-APS3.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/RabiAmp/Rabi/Rabi-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/RabiAmpPi/Rabi/Rabi-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/RabiAmpPi/Rabi/Rabi-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/RabiWidth/Rabi/Rabi-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/Ramsey/Ramsey-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/SPAM/SPAM-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/SimultaneousRB_AC/RB/RB-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/SimultaneousRB_AC/RB/RB-APS2.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/SimultaneousRB_AC/RB/RB-APS2_py27.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/SingleQubitRB/RB/RB-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/SingleQubitRB/RB/RB-APS1_py27.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/SingleShot/SingleShot-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/Spec/Spec-APS1.h5
 delete mode 100644 tests/test_data/awg/TestAPS1/T1/T1-APS1.h5

diff --git a/QGL/PatternUtils.py b/QGL/PatternUtils.py
index a718082a..9298d45e 100644
--- a/QGL/PatternUtils.py
+++ b/QGL/PatternUtils.py
@@ -334,5 +334,5 @@ def flatten_pulses():
                 awg, [str(p) for p in ps.values()]))
             continue
         print("Updating pulses for {}".format(awg))
-        translators[awg].update_wf_library(path + "-" + awg + ".h5", ps,
+        translators[awg].update_wf_library(path + "-" + awg + ".aps", ps,
                                            offsets)
diff --git a/QGL/drivers/APSPattern.py b/QGL/drivers/APSPattern.py
index 226a67a4..c6a1260f 100644
--- a/QGL/drivers/APSPattern.py
+++ b/QGL/drivers/APSPattern.py
@@ -17,10 +17,10 @@
 '''
 
 import os
+import struct
 import numpy as np
 from warnings import warn
-from itertools import chain
-from future.moves.itertools import zip_longest
+from itertools import chain, zip_longest
 from QGL import Compiler, ControlFlow, BlockLabel, PatternUtils
 from QGL.PatternUtils import hash_pulse, flatten
 from copy import copy, deepcopy
@@ -658,7 +658,7 @@ def unroll_loops(LLs):
 
 def write_sequence_file(awgData, fileName, miniLLRepeat=1):
     '''
-	Main function to pack channel LLs into an APS h5 file.
+	Main function to pack channel LLs into an APS1 file.
 	'''
     #Preprocess the sequence data to handle APS restrictions
     LLs12, repeat12, wfLib12 = preprocess(awgData['ch12']['linkList'],
@@ -676,11 +676,10 @@ def write_sequence_file(awgData, fileName, miniLLRepeat=1):
     merge_APS_markerData(LLs12, awgData['ch2m1']['linkList'], 2)
     merge_APS_markerData(LLs34, awgData['ch3m1']['linkList'], 1)
     merge_APS_markerData(LLs34, awgData['ch4m1']['linkList'], 2)
-    #Open the HDF5 file
+
     if os.path.isfile(fileName):
         os.remove(fileName)
 
-    print("WRiting ", fileName)
     with open(fileName, 'wb') as FID:
         channelDataFor = np.array([0,0,0,0], dtype=np.bool)
         if LLs12:
@@ -702,40 +701,25 @@ def write_sequence_file(awgData, fileName, miniLLRepeat=1):
                                             for key, wf in wfLib.items()}))
             wfInfo.append(create_wf_vector({key: wf.imag
                                             for key, wf in wfLib.items()}))
-
         #Create the groups and datasets
         for chanct in range(4):
-            # chanStr = '/chan_{0}'.format(chanct + 1)
-            # chanGroup = FID.create_group(chanStr)
             FID.write(np.uint8(1).tobytes()) # isIQMode
             FID.write(np.uint64(wfInfo[chanct][0].size).tobytes()) # Length of waveforms
             FID.write(wfInfo[chanct][0].tobytes())                 # Waveforms np.int16
 
-            # chanGroup.attrs['isIQMode'] = np.uint8(1)
-            #Write the waveformLib to file
-            # FID.create_dataset('{0}/waveformLib'.format(chanStr),
-            #                    data=wfInfo[chanct][0])
-        for chanct in [1,3]:
+        FID.write(np.uint8(len(LLData[0]) > 0).tobytes()) # LL for chan1
+        FID.write(np.uint8(len(LLData[1]) > 0).tobytes()) # LL for chan3
+        for chanct in [0,2]:
             #For A channels (1 & 3) we write link list data if we actually have any
             if LLData[chanct // 2]:
-                # groupStr = chanStr + '/linkListData'
-                # LLGroup = FID.create_group(groupStr)
                 LLDataVecs, numEntries = create_LL_data(
                     LLData[chanct // 2], wfInfo[chanct][1],
                     os.path.basename(fileName))
-                # LLGroup.attrs['length'] = numEntries
                 FID.write(np.uint64(len(LLDataVecs.keys())).tobytes()) # numKeys
                 FID.write(np.uint64(numEntries).tobytes()) # numEntries
-
-                # print(numEntries, len(LLDataVecs.keys()))
                 for key, dataVec in LLDataVecs.items():
-                    print(key, dataVec.dtype)
                     FID.write(key.ljust(32,"#").encode("utf-8")) # Key 32 byte utf-8
                     FID.write(dataVec.tobytes())                 # Data np.uint16
-                    # FID.create_dataset(groupStr + '/' + key, data=dataVec)
-
-            # else:
-            #     chanGroup.attrs['isLinkListData'] = np.uint8(0)
 
 
 def read_sequence_file(fileName):
@@ -752,90 +736,101 @@ def read_sequence_file(fileName):
     chanStrs = ['ch1', 'ch2', 'ch3', 'ch4']
     chanStrs2 = ['chan_1', 'chan_2', 'chan_3', 'chan_4']
     mrkStrs = ['ch1m1', 'ch2m1', 'ch3m1', 'ch4m1']
-
+    
+    data = {}
     with open(fileName, 'rb') as FID:
         target_hw      = FID.read(4).decode('utf-8')
         file_version   = struct.unpack('<f', FID.read(4))[0]
         channelDataFor = np.frombuffer(FID.read(4), dtype=np.bool)
-        print("REad", channelDataFor, file_version, target_hw)
-        # inst_len     = struct.unpack('<Q', FID.read(8))[0]
-        # instructions = np.frombuffer(FID.read(8*inst_len), dtype=np.uint64)
-
-
-    with h5py.File(fileName, 'r') as FID:
-        for chanct, chanStr in enumerate(chanStrs2):
-            #If we're in IQ mode then the Q channel gets its linkListData from the I channel
-            if FID[chanStr].attrs['isIQMode']:
-                tmpChan = 2 * (chanct // 2)
-                curLLData = FID[chanStrs2[tmpChan]][
-                    'linkListData'] if "linkListData" in FID[chanStrs2[
-                        tmpChan]] else []
-            else:
-                curLLData = FID[chanStr][
-                    'linkListData'] if "linkListData" in FID[chanStrs2[
-                        tmpChan]] else []
-
-            if curLLData:
-                #Pull out the LL data in sample units
-                #Cast type to avoid uint16 overflow
-                addr = (curLLData['addr'].value.astype(np.uint)) * ADDRESS_UNIT
-                count = ((curLLData['count'].value + 1).astype(np.uint)
-                         ) * ADDRESS_UNIT
-                repeat = curLLData['repeat'].value
-                trigger1 = (
-                    curLLData['trigger1'].value.astype(np.uint)) * ADDRESS_UNIT
-                trigger2 = (
-                    curLLData['trigger2'].value.astype(np.uint)) * ADDRESS_UNIT
-
-                #Pull out and scale the waveform data
-                wf_lib = (
-                    1.0 /
-                    MAX_WAVEFORM_VALUE) * FID[chanStr]['waveformLib'].value
-
-                #Initialize the lists of time-amplitude pairs
-                AWGData[chanStrs[chanct]] = []
-                AWGData[mrkStrs[chanct]] = []
-
-                cum_time = 0
-
-                #Loop over LL entries
-                for ct in range(curLLData.attrs['length']):
-                    #If we are starting a new sequence push back an empty array
-                    if START_MINILL_MASK & repeat[ct]:
-                        AWGData[chanStrs[chanct]].append([])
-                        trigger_delays = [0]
-                        cum_time = 0
-
-                    #Record the trigger delays
-                    if np.mod(chanct, 2) == 0:
-                        if trigger1[ct] > 0:
-                            trigger_delays.append(cum_time + trigger1[ct])
-                    else:
-                        if trigger2[ct] > 0:
-                            trigger_delays.append(cum_time + trigger2[ct])
-
-                    #waveforms
-                    wf_repeat = (repeat[ct] & REPEAT_MASK) + 1
-                    if TA_PAIR_MASK & repeat[ct]:
-                        AWGData[chanStrs[chanct]][-1].append(
-                            (wf_repeat * count[ct], wf_lib[addr[ct]]))
-                    else:
-                        for repct in range(wf_repeat):
-                            for sample in wf_lib[addr[ct]:addr[ct] + count[
-                                    ct]]:
-                                AWGData[chanStrs[chanct]][-1].append(
-                                    (1, sample))
-
-                    cum_time += count[ct]
-
-                    #Create the trigger sequence
-                    if END_MINILL_MASK & repeat[ct]:
-                        AWGData[mrkStrs[chanct]].append([])
-                        for delay in np.diff(trigger_delays):
-                            AWGData[mrkStrs[chanct]][-1].append((delay - 1, 0))
-                            AWGData[mrkStrs[chanct]][-1].append((1, 1))
-
-    return curLLdata,AWGData
+        miniLLRepeat   = struct.unpack('?', FID.read(1))[0]
+
+        # channels = [chanStrs2[i] for i in range(4) if channelDataFor[i]]
+        channels = chanStrs2
+        for channel in channels:
+            data[channel] = {}
+            data[channel]["isIQMode"] = bool(struct.unpack('?', FID.read(1))[0])
+            wf_len   = struct.unpack('<Q', FID.read(8))[0]
+            data[channel]["waveformLib"] = np.frombuffer(FID.read(2*wf_len), dtype=np.int16)
+        
+        has_LLs = [struct.unpack('?', FID.read(1))[0] for i in range(2)]
+        for LLexists, chanct in zip(has_LLs, [0,2]):
+            if LLexists:
+                
+                channel = channels[chanct]
+                numKeys      = struct.unpack('<Q', FID.read(8))[0]  
+                numEntries   = struct.unpack('<Q', FID.read(8))[0]  
+                data[channel]["linkListData"] = {}
+                data[channel]["linkListData"]["numLLEntries"] = numEntries
+                for i in range(numKeys): #key, dataVec in LLDataVecs.items():
+                    key     = FID.read(32).decode('utf-8').replace('#','')
+                    dataVec = np.frombuffer(FID.read(2*numEntries), dtype=np.uint16)
+                    data[channel]["linkListData"][key] = dataVec
+
+    for chanct, chanStr in enumerate(chanStrs2):
+        #If we're in IQ mode then the Q channel gets its linkListData from the I channel
+        if data[channel]['isIQMode']:
+            tmpChan = 2 * (chanct // 2)
+            curLLData = data[chanStrs2[tmpChan]][
+                'linkListData'] if "linkListData" in data[chanStrs2[tmpChan]] else []
+        else:
+            curLLData = data[chanStr][
+                'linkListData'] if "linkListData" in data[chanStrs2[tmpChan]] else []
+        if curLLData and has_LLs[chanct//2]:
+            #Pull out the LL data in sample units
+            #Cast type to avoid uint16 overflow
+            addr     = (curLLData['addr'].astype(np.uint)) * ADDRESS_UNIT
+            count    = ((curLLData['count'] + 1).astype(np.uint)) * ADDRESS_UNIT
+            repeat   = curLLData['repeat']
+            trigger1 = (curLLData['trigger1'].astype(np.uint)) * ADDRESS_UNIT
+            trigger2 = (curLLData['trigger2'].astype(np.uint)) * ADDRESS_UNIT
+
+            #Pull out and scale the waveform data
+            wf_lib = (1.0 / MAX_WAVEFORM_VALUE) * data[chanStr]['waveformLib']
+
+            #Initialize the lists of time-amplitude pairs
+            AWGData[chanStrs[chanct]] = []
+            AWGData[mrkStrs[chanct]] = []
+
+            cum_time = 0
+
+            #Loop over LL entries
+            for ct in range(curLLData["numLLEntries"]):
+                #If we are starting a new sequence push back an empty array
+                if START_MINILL_MASK & repeat[ct]:
+                    AWGData[chanStrs[chanct]].append([])
+                    trigger_delays = [0]
+                    cum_time = 0
+
+                #Record the trigger delays
+                if np.mod(chanct, 2) == 0:
+                    if trigger1[ct] > 0:
+                        trigger_delays.append(cum_time + trigger1[ct])
+                else:
+                    if trigger2[ct] > 0:
+                        trigger_delays.append(cum_time + trigger2[ct])
+
+                #waveforms
+                wf_repeat = (repeat[ct] & REPEAT_MASK) + 1
+                if TA_PAIR_MASK & repeat[ct]:
+                    AWGData[chanStrs[chanct]][-1].append(
+                        (wf_repeat * count[ct], wf_lib[addr[ct]]))
+                else:
+                    for repct in range(wf_repeat):
+                        for sample in wf_lib[addr[ct]:addr[ct] + count[
+                                ct]]:
+                            AWGData[chanStrs[chanct]][-1].append(
+                                (1, sample))
+
+                cum_time += count[ct]
+
+                #Create the trigger sequence
+                if END_MINILL_MASK & repeat[ct]:
+                    AWGData[mrkStrs[chanct]].append([])
+                    for delay in np.diff(trigger_delays):
+                        AWGData[mrkStrs[chanct]][-1].append((delay - 1, 0))
+                        AWGData[mrkStrs[chanct]][-1].append((1, 1))
+
+    return AWGData
 
 
 if __name__ == '__main__':
diff --git a/tests/compare_test_data.py b/tests/compare_test_data.py
index 34f7daa8..3a49a58c 100644
--- a/tests/compare_test_data.py
+++ b/tests/compare_test_data.py
@@ -1,7 +1,6 @@
 import os
 import sys
 import glob
-import h5py
 from builtins import input
 
 from QGL import *
@@ -18,17 +17,14 @@ def compare_sequences(seq_filter=""):
         for test in testdirs:
             # build up subdirectory name
             _, name = os.path.split(test)
-            testfiles = glob.glob(os.path.join(test, '*.h5'))
+            testfiles = glob.glob(os.path.join(test, '*.aps*'))
             # recurse into subdirectories
             while len(testfiles) == 1 and os.path.isdir(testfiles[0]):
                 _, subname = os.path.split(testfiles[0])
                 name = os.path.join(name, subname)
                 testfiles = glob.glob(os.path.join(testfiles[0], '*'))
             newpath = os.path.join(BASE_AWG_DIR, subdir, name)
-            newfiles = glob.glob(os.path.join(newpath, '*.h5'))
-            #filter py27 look for py27 versions
-            testfiles = filter_py27(testfiles)
-            newfiles = filter_py27(newfiles)
+            newfiles = glob.glob(os.path.join(newpath, '*.aps*'))
             if seq_filter and any(seq_filter in seq_file for seq_file in testfiles):
                 print("{0} comparing to {1}".format(test, newpath))
                 PulseSequencePlotter.plot_pulse_files_compare(testfiles, newfiles)
@@ -36,32 +32,19 @@ def compare_sequences(seq_filter=""):
                 if c == 'q':
                     break
 
-
-def filter_py27(filenames):
-    py27_files = [f for f in filenames if f[-8:] == "_py27.h5"]
-    if py27_files:
-        if sys.version_info[0] > 2:
-            #strip them out for python3 (and above?)
-            filenames = [f for f in filenames if f[-8:] != "_py27.h5"]
-        else:
-            #otherwise strip the non "_py27" version
-            filenames = [f for f in filenames
-                         if f.replace(".h5", "_py27.h5") not in py27_files]
-    return filenames
-
-
 def update_test_files():
-    for device in ['APS1', 'APS2']:
-        testdirs = glob.glob(os.path.join(BASE_TEST_DIR, 'Test' + device, '*'))
-        for test in testdirs:
-            testfiles = glob.glob(os.path.join(test, '*'))
-            # recurse into subdirectories
-            while len(testfiles) == 1 and os.path.isdir(testfiles[0]):
-                testfiles = glob.glob(os.path.join(testfiles[0], '*'))
-            for tfile in testfiles:
-                FID = h5py.File(tfile)
-                FID['/'].attrs['target hardware'] = device
-                FID.close()
+    raise Exception("update_test_files must be updated for new binary format")
+    # for device in ['APS1', 'APS2']:
+    #     testdirs = glob.glob(os.path.join(BASE_TEST_DIR, 'Test' + device, '*'))
+    #     for test in testdirs:
+    #         testfiles = glob.glob(os.path.join(test, '*'))
+    #         # recurse into subdirectories
+    #         while len(testfiles) == 1 and os.path.isdir(testfiles[0]):
+    #             testfiles = glob.glob(os.path.join(testfiles[0], '*'))
+    #         for tfile in testfiles:
+    #             FID = h5py.File(tfile)
+    #             FID['/'].attrs['target hardware'] = device
+    #             FID.close()
 
 
 if __name__ == '__main__':
diff --git a/tests/test_APS2Pattern.py b/tests/test_APS2Pattern.py
index 54dbd1ac..08874cea 100644
--- a/tests/test_APS2Pattern.py
+++ b/tests/test_APS2Pattern.py
@@ -1,4 +1,3 @@
-import h5py
 import unittest
 import numpy as np
 from copy import copy
diff --git a/tests/test_APSPattern.py b/tests/test_APSPattern.py
index 3bfa2534..f2e8d3e5 100644
--- a/tests/test_APSPattern.py
+++ b/tests/test_APSPattern.py
@@ -1,4 +1,3 @@
-import h5py
 import unittest
 import numpy as np
 
diff --git a/tests/test_Compiler.py b/tests/test_Compiler.py
index 781bb49c..7754b72a 100644
--- a/tests/test_Compiler.py
+++ b/tests/test_Compiler.py
@@ -1,4 +1,3 @@
-import h5py
 import unittest
 import numpy as np
 
diff --git a/tests/test_QGL.py b/tests/test_QGL.py
index c5db5b52..6255d509 100644
--- a/tests/test_QGL.py
+++ b/tests/test_QGL.py
@@ -1,4 +1,3 @@
-import h5py
 import unittest
 import numpy as np
 import time
@@ -6,7 +5,6 @@
 import struct
 from bbndb.qgl import PhysicalChannel, LogicalChannel, Measurement
 from QGL import *
-import h5py
 
 # Waveform numpy assert_allclose Test for QGL
 #
diff --git a/tests/test_Sequences.py b/tests/test_Sequences.py
index 2c0cc836..9cb343b8 100644
--- a/tests/test_Sequences.py
+++ b/tests/test_Sequences.py
@@ -6,7 +6,7 @@
 import QGL
 
 from QGL.Channels import Edge, Measurement, LogicalChannel, LogicalMarkerChannel, PhysicalMarkerChannel, PhysicalQuadratureChannel
-from QGL.drivers import APSPattern, APS2Pattern, TekPattern
+from QGL.drivers import APSPattern, APS2Pattern
 
 # Pulled in logger to help debug stand-alone run issue with the config.AWGDir
 # (the configuration was NOT gettng loaded when run independently)
@@ -111,8 +111,10 @@ def set_awg_dir(self, footer=""):
             logger.warning( "#----- Post load-config QGL.config.AWGDir: {%s}.\n\r", QGL.config.AWGDir)
         #else:
         #    logger.warning( "\n\r#----- Using QGL.config.AWGDir {%s} 8-p", QGL.config.AWGDir)
+        if not hasattr(self, 'original_awg_dir'):
+          self.original_awg_dir = QGL.config.AWGDir
 
-        self.awg_dir = os.path.abspath(QGL.config.AWGDir + os.path.sep + cn)
+        self.awg_dir = os.path.abspath(self.original_awg_dir + os.path.sep + cn)
         self.truth_dir = os.path.abspath(self.testFileDirectory + os.path.sep +
                                          cn)
 
@@ -503,116 +505,116 @@ def test_mux_CR(self):
         self.compare_sequences('CNOT_CR_mux')
 
 
-# class TestAPS1(unittest.TestCase, AWGTestHelper, TestSequences):
-#     def setUp(self):
-#         AWGTestHelper.__init__(self, APSPattern)
-#         for name in ['APS1', 'APS2', 'APS3']:
-#             for ch in ['12', '34']:
-#                 channelName = name + '-' + ch
-#                 channel = PhysicalQuadratureChannel(label=channelName)
-#                 channel.sampling_rate = 1.2e9
-#                 channel.instrument = name
-#                 channel.translator = 'APSPattern'
-#                 self.channels[channelName] = channel
-
-#             for m in range(1, 5):
-#                 channelName = "{0}-{1}m1".format(name, m)
-#                 channel = PhysicalMarkerChannel(label=channelName)
-#                 channel.sampling_rate = 1.2e9
-#                 channel.instrument = name
-#                 channel.translator = 'APSPattern'
-#                 self.channels[channelName] = channel
-
-#         mapping = {'digitizerTrig': 'APS1-1m1',
-#                    'slave_trig': 'APS1-2m1',
-#                    'q1': 'APS1-12',
-#                    'M-q1': 'APS1-34',
-#                    'M-q1-gate': 'APS1-3m1',
-#                    'q1-gate': 'APS1-4m1',
-#                    'q2': 'APS2-12',
-#                    'M-q2': 'APS2-34',
-#                    'M-q2-gate': 'APS2-1m1',
-#                    'q2-gate': 'APS2-2m1',
-#                    'cr': 'APS3-12',
-#                    'cr-gate': 'APS3-1m1',
-#                    'M-q1q2': 'APS3-34',
-#                    'M-q1q2-gate': 'APS3-2m1'}
-
-#         # override trigger lengths on APS1 to get single blips
-#         self.channels['slave_trig'].pulse_params['length'] = 0.833e-9
-#         self.channels['digitizerTrig'].pulse_params['length'] = 0.833e-9
-#         self.finalize_map(mapping)
-
-#     def compare_file_data(self, testFile, truthFile):
-#         '''
-# 		Override the method in AWGTestHelper so that we can special-case marker comparison
-# 		'''
-#         awgData = self.read_function(testFile)
-#         truthData = self.read_function(truthFile)
-
-#         awgDataLen = len(awgData)
-#         truthDataLen = len(truthData)
-
-#         self.assertTrue(awgDataLen == truthDataLen,
-#                         "Expected {0} sequences in file. Found {1}.".format(
-#                             truthDataLen, awgDataLen))
-
-#         for name in truthData:
-#             self.assertTrue(
-#                 name in awgData,
-#                 "Expected channel {0} not found in file {1}".format(name,
-#                                                                     testFile))
-#             isMarker = ('m' == name[-2])
-
-#             for x in range(len(truthData[name])):
-#                 seqA = np.array(truthData[name][x])
-#                 seqB = np.array(awgData[name][x])
-#                 if isMarker:
-#                     self.compare_marker_sequence(
-#                         seqA, seqB,
-#                         "\nFile {0} =>\nChannel {1} Sequence {2}".format(
-#                             testFile, name, x))
-#                 else:
-#                     self.compare_sequence(
-#                         seqA, seqB,
-#                         "\nFile {0} =>\nChannel {1} Sequence {2}".format(
-#                             testFile, name, x))
-
-#     def compare_marker_sequence(self, seqA, seqB, errorHeader):
-#         markerDistanceTolerance = 4
-#         self.assertTrue(seqA.size == seqB.size,
-#                         "{0} size {1} != size {2}".format(
-#                             errorHeader, str(seqA.size), str(seqB.size)))
-
-#         # convert sequences to locations of blips
-#         idxA = np.where(seqA)[0]
-#         idxB = np.where(seqB)[0]
-#         self.assertTrue(
-#             len(idxA) == len(idxB),
-#             "{0}.\nNumber of blips did not match: {1} != {2}".format(
-#                 errorHeader, len(idxA), len(idxB)))
-#         # compare the blip locations element-wise
-#         if len(idxA) > 0:
-#             diff = np.abs(idxA - idxB)
-#         else:
-#             diff = np.array([0])
-#         self.assertTrue(
-#             max(diff) <= markerDistanceTolerance,
-#             "{0}\nMismatches: {1}".format(errorHeader, diff.nonzero()[0]))
-
-#     @unittest.expectedFailure
-#     def test_Rabi_RabiWidth(self):
-#         """ test_Rabi_RabiWidth is expected to fail on APS1 with the following error:
-# 			AssertionError: Oops! You have exceeded the waveform memory of the APS
-# 		"""
-#         TestSequences.test_Rabi_RabiWidth(self)
-
-#     @unittest.expectedFailure
-#     def test_RB_SimultaneousRB_AC(self):
-#         """ test_RB_SimultaneousRB_AC is expected to fail on APS1 with the following error:
-# 			AssertionError: Oops! You have exceeded the waveform memory of the APS
-# 		"""
-#         TestSequences.test_RB_SimultaneousRB_AC(self)
+class TestAPS1(unittest.TestCase, AWGTestHelper, TestSequences):
+    def setUp(self):
+        AWGTestHelper.__init__(self, APSPattern)
+        for name in ['APS1', 'APS2', 'APS3']:
+            for ch in ['12', '34']:
+                channelName = name + '-' + ch
+                channel = PhysicalQuadratureChannel(label=channelName)
+                channel.sampling_rate = 1.2e9
+                channel.instrument = name
+                channel.translator = 'APSPattern'
+                self.channels[channelName] = channel
+
+            for m in range(1, 5):
+                channelName = "{0}-{1}m1".format(name, m)
+                channel = PhysicalMarkerChannel(label=channelName)
+                channel.sampling_rate = 1.2e9
+                channel.instrument = name
+                channel.translator = 'APSPattern'
+                self.channels[channelName] = channel
+
+        mapping = {'digitizerTrig': 'APS1-1m1',
+                   'slave_trig': 'APS1-2m1',
+                   'q1': 'APS1-12',
+                   'M-q1': 'APS1-34',
+                   'M-q1-gate': 'APS1-3m1',
+                   'q1-gate': 'APS1-4m1',
+                   'q2': 'APS2-12',
+                   'M-q2': 'APS2-34',
+                   'M-q2-gate': 'APS2-1m1',
+                   'q2-gate': 'APS2-2m1',
+                   'cr': 'APS3-12',
+                   'cr-gate': 'APS3-1m1',
+                   'M-q1q2': 'APS3-34',
+                   'M-q1q2-gate': 'APS3-2m1'}
+
+        # override trigger lengths on APS1 to get single blips
+        self.channels['slave_trig'].pulse_params['length'] = 0.833e-9
+        self.channels['digitizerTrig'].pulse_params['length'] = 0.833e-9
+        self.finalize_map(mapping)
+
+    def compare_file_data(self, testFile, truthFile):
+        '''
+		Override the method in AWGTestHelper so that we can special-case marker comparison
+		'''
+        awgData = self.read_function(testFile)
+        truthData = self.read_function(truthFile)
+
+        awgDataLen = len(awgData)
+        truthDataLen = len(truthData)
+
+        self.assertTrue(awgDataLen == truthDataLen,
+                        "Expected {0} sequences in file. Found {1}.".format(
+                            truthDataLen, awgDataLen))
+
+        for name in truthData:
+            self.assertTrue(
+                name in awgData,
+                "Expected channel {0} not found in file {1}".format(name,
+                                                                    testFile))
+            isMarker = ('m' == name[-2])
+
+            for x in range(len(truthData[name])):
+                seqA = np.array(truthData[name][x])
+                seqB = np.array(awgData[name][x])
+                if isMarker:
+                    self.compare_marker_sequence(
+                        seqA, seqB,
+                        "\nFile {0} =>\nChannel {1} Sequence {2}".format(
+                            testFile, name, x))
+                else:
+                    self.compare_sequence(
+                        seqA, seqB,
+                        "\nFile {0} =>\nChannel {1} Sequence {2}".format(
+                            testFile, name, x))
+
+    def compare_marker_sequence(self, seqA, seqB, errorHeader):
+        markerDistanceTolerance = 4
+        self.assertTrue(seqA.size == seqB.size,
+                        "{0} size {1} != size {2}".format(
+                            errorHeader, str(seqA.size), str(seqB.size)))
+
+        # convert sequences to locations of blips
+        idxA = np.where(seqA)[0]
+        idxB = np.where(seqB)[0]
+        self.assertTrue(
+            len(idxA) == len(idxB),
+            "{0}.\nNumber of blips did not match: {1} != {2}".format(
+                errorHeader, len(idxA), len(idxB)))
+        # compare the blip locations element-wise
+        if len(idxA) > 0:
+            diff = np.abs(idxA - idxB)
+        else:
+            diff = np.array([0])
+        self.assertTrue(
+            max(diff) <= markerDistanceTolerance,
+            "{0}\nMismatches: {1}".format(errorHeader, diff.nonzero()[0]))
+
+    @unittest.expectedFailure
+    def test_Rabi_RabiWidth(self):
+        """ test_Rabi_RabiWidth is expected to fail on APS1 with the following error:
+			AssertionError: Oops! You have exceeded the waveform memory of the APS
+		"""
+        TestSequences.test_Rabi_RabiWidth(self)
+
+    @unittest.expectedFailure
+    def test_RB_SimultaneousRB_AC(self):
+        """ test_RB_SimultaneousRB_AC is expected to fail on APS1 with the following error:
+			AssertionError: Oops! You have exceeded the waveform memory of the APS
+		"""
+        TestSequences.test_RB_SimultaneousRB_AC(self)
 
 if __name__ == "__main__":
     unittest.main()
diff --git a/tests/test_data/awg/TestAPS1/AllXY/AllXY-APS1.aps1 b/tests/test_data/awg/TestAPS1/AllXY/AllXY-APS1.aps1
index 7fba53b0..9578434c 100644
--- a/tests/test_data/awg/TestAPS1/AllXY/AllXY-APS1.aps1
+++ b/tests/test_data/awg/TestAPS1/AllXY/AllXY-APS1.aps1
@@ -1,3 +1,3 @@
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-oid sha256:c79184b0806766b42dc92f873beea634e2292d60edda5be14065eaa519206f5a
-size 3989
+oid sha256:93a7ed05a9c679de05915e51500f6d9ee9d4e5ef0016b1a8c2ff26bdf622b1e0
+size 3991
diff --git a/tests/test_data/awg/TestAPS1/AllXY/AllXY-APS1.h5 b/tests/test_data/awg/TestAPS1/AllXY/AllXY-APS1.h5
deleted file mode 100644
index d4b9ab22..00000000
--- a/tests/test_data/awg/TestAPS1/AllXY/AllXY-APS1.h5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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-size 20568
diff --git a/tests/test_data/awg/TestAPS1/CPMG/CPMG-APS1.aps1 b/tests/test_data/awg/TestAPS1/CPMG/CPMG-APS1.aps1
index 9d9b903c..7f055d16 100644
--- a/tests/test_data/awg/TestAPS1/CPMG/CPMG-APS1.aps1
+++ b/tests/test_data/awg/TestAPS1/CPMG/CPMG-APS1.aps1
@@ -1,3 +1,3 @@
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-size 2355
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+size 2357
diff --git a/tests/test_data/awg/TestAPS1/CPMG/CPMG-APS1.h5 b/tests/test_data/awg/TestAPS1/CPMG/CPMG-APS1.h5
deleted file mode 100644
index 8e80f58b..00000000
--- a/tests/test_data/awg/TestAPS1/CPMG/CPMG-APS1.h5
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/tests/test_data/awg/TestAPS1/Echo/Echo-APS1.aps1 b/tests/test_data/awg/TestAPS1/Echo/Echo-APS1.aps1
index bf09543a..42b91ac5 100644
--- a/tests/test_data/awg/TestAPS1/Echo/Echo-APS1.aps1
+++ b/tests/test_data/awg/TestAPS1/Echo/Echo-APS1.aps1
@@ -1,3 +1,3 @@
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+size 2927
diff --git a/tests/test_data/awg/TestAPS1/Echo/Echo-APS1.h5 b/tests/test_data/awg/TestAPS1/Echo/Echo-APS1.h5
deleted file mode 100644
index 00c28e4d..00000000
--- a/tests/test_data/awg/TestAPS1/Echo/Echo-APS1.h5
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:0f14162bcf50abb771326b2db3ea36288e704d1224dbd1660dbec60de215121f
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diff --git a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.aps1 b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.aps1
index 2ae5e8b8..9bb93800 100644
--- a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.aps1
+++ b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.aps1
@@ -1,3 +1,3 @@
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-size 4207
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diff --git a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.h5 b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.h5
deleted file mode 100644
index 0f589d2c..00000000
--- a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS1.h5
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.aps1 b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.aps1
index 057f5af0..969d00e7 100644
--- a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.aps1
+++ b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.aps1
@@ -1,3 +1,3 @@
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deleted file mode 100644
index b5872b5f..00000000
--- a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS2.h5
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS3.aps1 b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS3.aps1
index 590ec1bc..67db4db5 100644
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+++ b/tests/test_data/awg/TestAPS1/EchoCRLen/EchoCR/EchoCR-APS3.aps1
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deleted file mode 100644
index 953bfa04..00000000
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+++ /dev/null
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diff --git a/tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS1.aps1 b/tests/test_data/awg/TestAPS1/EchoCRPhase/EchoCR/EchoCR-APS1.aps1
index eaed969e..b30daca4 100644
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deleted file mode 100644
index 9c6f0102..00000000
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index 80486dc5..0b249f5b 100644
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deleted file mode 100644
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--- a/tests/test_data/awg/TestAPS1/RabiAmp2/Rabi/Rabi-APS2.h5
+++ /dev/null
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deleted file mode 100644
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--- a/tests/test_data/awg/TestAPS1/RabiAmpPi/Rabi/Rabi-APS1.h5
+++ /dev/null
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
index 73756191..00000000
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+++ /dev/null
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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index fde6c83e..0b1b623e 100644
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deleted file mode 100644
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index 9ecd230b..4012d581 100644
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deleted file mode 100644
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deleted file mode 100644
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index cae5aca6..44568cfc 100644
--- a/tests/test_data/awg/TestAPS1/T1/T1-APS1.aps1
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deleted file mode 100644
index 63c12621..00000000
--- a/tests/test_data/awg/TestAPS1/T1/T1-APS1.h5
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/utils/convert_h5_to_aps.py b/utils/convert_h5_to_aps.py
index 138910a6..3b0eb8b6 100644
--- a/utils/convert_h5_to_aps.py
+++ b/utils/convert_h5_to_aps.py
@@ -5,22 +5,27 @@
 
 def write_to_aps1(fileName, data):
     channelDataFor = np.array([i in data['channelDataFor'] for i in range(1,5)], dtype=np.bool)
-    with open(fileName, 'wb') as FID:
-        FID.write(b'APS1')                     # target hardware
-        FID.write(np.float32(2.2).tobytes())   # Version
-        FID.write(channelDataFor.tobytes())    # channelDataFor
-        FID.write(np.array(data['miniLLRepeat'], dtype=np.bool).tobytes()) # MiniLLRepeat
-        for name in data['channels'].keys():
-            FID.write(np.uint8(data['channels'][name]['isIQMode']).tobytes()) # isIQMode
-            FID.write(np.uint64(data['channels'][name]['waveformLib'].size).tobytes()) # Length of waveforms
-            FID.write(data['channels'][name]['waveformLib'].tobytes()) # Waveforms np.int16
-        for name in ['chan_1', 'chan_3']:
-            if 'linkListData' in data['channels'][name].keys():
-                FID.write(np.uint64(data['channels'][name]['linkListNumKeys']).tobytes()) # numKeys
-                FID.write(np.uint64(data['channels'][name]['linkListDataLength']).tobytes()) # numEntries
-                for key, dataVec in data['channels'][name]['linkListData'].items():
-                    FID.write(key.ljust(32,"#").encode("utf-8")) # Key 32 byte utf-8
-                    FID.write(dataVec.tobytes())           
+    try:
+        with open(fileName, 'wb') as FID:
+            FID.write(b'APS1')                     # target hardware
+            FID.write(np.float32(2.2).tobytes())   # Version
+            FID.write(channelDataFor.tobytes())    # channelDataFor
+            FID.write(np.array(data['miniLLRepeat'], dtype=np.bool).tobytes()) # MiniLLRepeat
+            for name in data['channels'].keys():
+                FID.write(np.uint8(data['channels'][name]['isIQMode']).tobytes()) # isIQMode
+                FID.write(np.uint64(data['channels'][name]['waveformLib'].size).tobytes()) # Length of waveforms
+                FID.write(data['channels'][name]['waveformLib'].tobytes()) # Waveforms np.int16
+            FID.write(np.uint8('linkListData' in data['channels']['chan_1'].keys()).tobytes()) # LL for chan1
+            FID.write(np.uint8('linkListData' in data['channels']["chan_3"].keys()).tobytes()) # LL for chan3
+            for name in ['chan_1', 'chan_3']:
+                if 'linkListData' in data['channels'][name].keys():
+                    FID.write(np.uint64(data['channels'][name]['linkListNumKeys']).tobytes()) # numKeys
+                    FID.write(np.uint64(data['channels'][name]['linkListDataLength']).tobytes()) # numEntries
+                    for key, dataVec in data['channels'][name]['linkListData'].items():
+                        FID.write(key.ljust(32,"#").encode("utf-8")) # Key 32 byte utf-8
+                        FID.write(dataVec.tobytes())           
+    except:
+        print(f"Warning: could not write aps1 file {fileName}")
 
 def write_to_aps2(fileName, data):
     instructions = data['instructions']
@@ -78,7 +83,6 @@ def read_aps1_from_h5(fileName):
         for channel in channels:
             data['channels'][channel] = {'waveformLib': FID[f'/{channel}/waveformLib'].value.flatten()}
             data['channels'][channel]['isIQMode'] = FID[f'/{channel}'].attrs['isIQMode']
-            # print(list(FID[f'/{channel}'].keys()))
             if 'linkListData' in list(FID[f'/{channel}'].keys()):
                 data['channels'][channel]['linkListData'] = {}
                 for key in FID[f'/{channel}/linkListData'].keys():
@@ -88,14 +92,15 @@ def read_aps1_from_h5(fileName):
     return data
 
 if __name__ == '__main__':
-    basename, ext = os.path.splitext(sys.argv[1])
-    print(f"Converting {basename+'.h5'}")
-    inst = get_type(basename+'.h5')
-    if inst == "APS2":
-        data = read_aps2_from_h5(basename+'.h5')
-        write_to_aps2(basename+".aps2", data)
-    if inst == "APS1":
-        data = read_aps1_from_h5(basename+'.h5')
-        write_to_aps1(basename+".aps1", data)
+    for filename in sys.argv[1:]:
+        basename, ext = os.path.splitext(filename)
+        print(f"Converting {basename+'.h5'}")
+        inst = get_type(basename+'.h5')
+        if inst == "APS2":
+            data = read_aps2_from_h5(basename+'.h5')
+            write_to_aps2(basename+".aps2", data)
+        if inst == "APS1":
+            data = read_aps1_from_h5(basename+'.h5')
+            write_to_aps1(basename+".aps1", data)
 
 

From 9db5fa05e0291deccff1adff85948e4ebbeb7196 Mon Sep 17 00:00:00 2001
From: qlab <qlab@andromeda.bbn.com>
Date: Thu, 14 Feb 2019 15:59:14 -0500
Subject: [PATCH 107/235] Warn if existing object

instead of error
---
 QGL/ChannelLibraries.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 8515aa5d..efd55ff7 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -41,6 +41,8 @@
 import itertools
 import numpy as np
 import networkx as nx
+from warnings import warn
+import logging
 
 import bbndb
 
@@ -55,6 +57,8 @@
 
 channelLib = None
 
+logger = logging.getLogger(__name__)
+
 def check_session_dirty(f):
     """Since we can't mix db objects from separate sessions, re-fetch entities by their unique IDs"""
     @wraps(f)
@@ -75,7 +79,8 @@ def check_for_duplicates(f):
     @wraps(f)
     def wrapper(cls, label, *args, **kwargs):
         if label in cls.channelDict:
-            raise ValueError(f"Cannot create {label}: a channel with the same name already exists.")
+            logger.warning(f"Cannot create {label}: a channel with the same name already exists.")
+            return cls.channelDict[label]
         else:
             return f(cls, label, *args, **kwargs)
     return wrapper
@@ -429,8 +434,10 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
             raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
         if f"M-{qubit.label}" in self.channelDict:
-            raise ValueError(f"Cannot create Measurement M-{qubit.label}: a channel with the same name already exists.")
-        meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=self.channelDatabase)
+            logger.warning(f"Cannot create Measurement M-{qubit.label}: a channel with the same name already exists.")
+            meas = self.channelDict[f"M-{qubit.label}"]
+        else:
+            meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=self.channelDatabase)
         meas.phys_chan = phys_chan
         if generator:
             meas.phys_chan.generator = generator

From c54941d751ab19987073e0e2eb45d37c46e1a257 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Thu, 14 Feb 2019 16:35:10 -0500
Subject: [PATCH 108/235] Unnecessary warn import

---
 QGL/ChannelLibraries.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index efd55ff7..307cbbf3 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -41,7 +41,6 @@
 import itertools
 import numpy as np
 import networkx as nx
-from warnings import warn
 import logging
 
 import bbndb

From 0f92d035581ee7f94931d286a0e9900a2419f47a Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Thu, 14 Feb 2019 17:53:02 -0500
Subject: [PATCH 109/235] Initial commit of changes for hardware randomization

---
 QGL/Compiler.py        | 36 +++++++++++++++++++++++++++++++++++-
 QGL/PatternUtils.py    |  5 +++++
 QGL/PulsePrimitives.py | 15 +++++++++++++--
 QGL/PulseSequencer.py  |  9 ++++++---
 4 files changed, 59 insertions(+), 6 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 115338de..fc240556 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -30,6 +30,7 @@
 from . import Channels
 from . import ChannelLibraries
 from . import PulseShapes
+from . import PulsePrimitives
 from .PulsePrimitives import Id, clear_pulse_cache
 from .PulseSequencer import Pulse, PulseBlock, CompositePulse
 from . import ControlFlow
@@ -221,6 +222,10 @@ def generate_waveforms(physicalWires):
         for pulse in flatten(wire):
             if not isinstance(pulse, Pulse):
                 continue
+            if pulse.isRunTime:
+                #skip run-time pulses as we need to add the set of all possible pulses to
+                #the waveform table
+                continue
             if pulse.hashshape() not in wfs[ch]:
                 if pulse.isTimeAmp:
                     wfs[ch][pulse.hashshape()] = np.ones(1, dtype=np.complex)
@@ -228,6 +233,24 @@ def generate_waveforms(physicalWires):
                     wfs[ch][pulse.hashshape()] = pulse.shape
     return wfs
 
+def add_runtime_pulse_set(physicalWires, wfs):
+
+    for ch, wire in physicalWires.items():
+        rt_pulses = [pulse for pulse in flatten(wire) if pulse.isRunTime]
+        pulse_type = set([pulse.label for pulse in rt_pulses])
+        if len(pulse_type) > 1:
+            raise Exception("All run-time pulses must have the same label.")
+        if pulse_type not in ("RandomAC, RandomDiAC"):
+            raise Exception(f"Unknown run time pulse type {pulse_type}.")
+
+        pulse_fn = getattr(PulsePrimitives, pulse_type.split('Random')[-1], None)
+
+
+
+
+
+
+
 
 def pulses_to_waveforms(physicalWires):
     logger.debug("Converting pulses_to_waveforms:")
@@ -426,6 +449,10 @@ def compile_to_hardware(seqs,
     logger.info("Generating waveform library.")
     wfs = generate_waveforms(physWires)
 
+    # If there are run-time pulses add these to the library
+    if PatternUtils.contains_runtime_pulses(seqs):
+        wfs = add_runtime_pulse_set(physWires, wfs)
+
     # replace Pulse objects with Waveforms
     logger.info("Replacing pulses with waveforms")
     physWires = pulses_to_waveforms(physWires)
@@ -712,7 +739,8 @@ class Waveform(object):
 
     #Use slots to create attributes to save on memory.
     __slots__ = ["label", "key", "amp", "length", "phase", "frameChange",
-                    "isTimeAmp", "frequency", "logicalChan", "maddr", "startTime"]
+                    "isTimeAmp", "frequency", "logicalChan", "maddr", "startTime",
+                    "isRunTime"]
 
     def __init__(self, pulse=None):
         if pulse is None:
@@ -726,6 +754,7 @@ def __init__(self, pulse=None):
             self.frequency = 0
             self.logicalChan = ""
             self.maddr = (-1, 0)
+            self.isRunTime = False
         else:
             self.label = pulse.label
             self.key = pulse.hashshape()
@@ -737,11 +766,14 @@ def __init__(self, pulse=None):
             self.frequency = pulse.frequency
             self.logicalChan = pulse.channel
             self.maddr = pulse.maddr
+            self.isRunTime = pulse.isRunTime
 
     def __repr__(self):
         return self.__str__()
 
     def __str__(self):
+        if self.isRunTime:
+            return f"Hardware-Generated({self.length})"
         if self.isTimeAmp:
             TA = 'HIGH' if self.amp != 0 else 'LOW'
             return "Waveform-TA(" + TA + ", " + str(self.length) + ")"
@@ -750,6 +782,8 @@ def __str__(self):
                 self.key)[:6] + ", " + str(self.length) + ")"
 
     def __eq__(self, other):
+        if self.isRunTime or other.isRunTime:
+            return False
         if isinstance(other, self.__class__):
             #No __dict__ property so we check all properties.
             return all((getattr(self, attr, None) == getattr(other, attr, None) for attr in self.__slots__))
diff --git a/QGL/PatternUtils.py b/QGL/PatternUtils.py
index 9298d45e..0719a3e0 100644
--- a/QGL/PatternUtils.py
+++ b/QGL/PatternUtils.py
@@ -208,6 +208,11 @@ def add_digitizer_trigger(seqs):
                             trig_chan in seq[ct].pulses.keys()):
                         seq[ct] = align('left', seq[ct], TAPulse("TRIG", trig_chan, trig_chan.pulse_params['length'], 1.0, 0.0, 0.0))
 
+def contains_runtime_pulses(seqs):
+    """
+    Determines if sequences contain run-time generated pulses.
+    """
+    return any([hasattr(entry, 'isRunTime') and entry.isRunTime for entry in flatten(seqs)])
 
 def contains_measurement(entry):
     """
diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index bfbf03b2..1ad4fbbe 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -25,12 +25,15 @@
 from functools import wraps, reduce
 
 
-def overrideDefaults(chan, updateParams):
+def overrideDefaults(chan, updateParams, ignoredStrParams=['isRunTime', 'maddr', 'moffset']):
     '''Helper function to update any parameters passed in and fill in the defaults otherwise.'''
     # The default parameter list depends on the channel type so pull out of channel
     # Then update passed values
     paramDict = chan.pulse_params.copy()
     paramDict.update(updateParams)
+    for param in ignoredStrParams:
+        if param in paramDict.keys():
+            paramDict.pop(param)
     return paramDict
 
 
@@ -113,7 +116,7 @@ def Utheta(qubit,
         else:
             # linearly scale based upon the 'pi/2' amplitude
             amp  = (angle / (pi/2)) * qubit.pulse_params['pi2Amp']
-    return Pulse(label, qubit, params, amp, phase, 0.0, ignoredStrParams, frequency=frequency)
+    return Pulse(label, qubit, params, amp, phase, 0.0, ignoredStrParams, frequency=frequency, **kwargs)
 
 
 # generic pulses around X, Y, and Z axes
@@ -337,6 +340,14 @@ def arb_axis_drag(qubit,
     return Pulse(kwargs["label"] if "label" in kwargs else "ArbAxis", qubit,
                  params, 1.0, aziAngle, frameChange)
 
+def RandomAC(qubit):
+    params = overrideDefaults(qubit, {})
+    return Pulse("RandomAC", qubit, params, isRunTime=True)
+
+def RandomDiAC(qubit):
+    params = overrideDefaults(qubit, {})
+    params["length"] *= 2.0
+    return Pulse("RandomAC", qubit, params, isRunTime=True)
 
 def AC(qubit, cliffNum):
     """
diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 315c3db8..606511dd 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -33,10 +33,11 @@
 class Pulse(namedtuple("Pulse", ["label", "channel", "length", "amp", "phase", "frequency",
                                  "frameChange", "shapeParams", "isTimeAmp",
                                  "isZero", "ignoredStrParams",
-                                 "maddr", "moffset"])):
+                                 "maddr", "moffset", "isRunTime"])):
     __slots__ = ()
 
-    def __new__(cls, label, channel, shapeParams, amp=1.0, phase=0, frameChange=0, ignoredStrParams=[], maddr=-1, moffset=0, frequency=None):
+    def __new__(cls, label, channel, shapeParams, amp=1.0, phase=0, frameChange=0,
+            ignoredStrParams=[], maddr=-1, moffset=0, frequency=None, isRunTime=False):
         if frequency:
             frequency = frequency
         elif hasattr(channel, 'frequency'):
@@ -48,12 +49,14 @@ def __new__(cls, label, channel, shapeParams, amp=1.0, phase=0, frameChange=0, i
             if param not in shapeParams.keys():
                 raise NameError("shapeParams must include {0}".format(param))
         isTimeAmp = (shapeParams['shape_fun'] == PulseShapes.constant)
+        if isRunTime:
+            isTimeAmp = False
         isZero = (amp == 0)
         return super(cls, Pulse).__new__(cls, label, channel,
                                          shapeParams['length'], amp, phase,
                                          frequency, frameChange, shapeParams,
                                          isTimeAmp, isZero, ignoredStrParams,
-                                         maddr, moffset)
+                                         maddr, moffset, isRunTime)
 
     def __str__(self):
         kwvals = []

From 60bdf94efcc40b06b6145a1e9a77bb3c28535469 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 15 Feb 2019 15:08:42 -0500
Subject: [PATCH 110/235] new_APS convenience function

---
 QGL/ChannelLibraries.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 307cbbf3..08d4bab7 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -305,6 +305,22 @@ def new_APS2(self, label, address):
         self.add_and_update_dict(this_transmitter)
         return this_transmitter
 
+    @check_for_duplicates
+    def new_APS(self, label, address):
+        chan1  = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        chan2  = Channels.PhysicalQuadratureChannel(label=f"{label}-34", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        m1     = Channels.PhysicalMarkerChannel(label=f"{label}-1m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        m2     = Channels.PhysicalMarkerChannel(label=f"{label}-2m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        m3     = Channels.PhysicalMarkerChannel(label=f"{label}-2m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        m4     = Channels.PhysicalMarkerChannel(label=f"{label}-4m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+
+        this_transmitter = Channels.Transmitter(label=label, model="APS", address=address, channels=[chan1, chan2, m1, m2, m3, m4], channel_db=self.channelDatabase)
+        this_transmitter.trigger_source = "external"
+        this_transmitter.address        = address
+
+        self.add_and_update_dict(this_transmitter)
+        return this_transmitter
+
     @check_for_duplicates
     def new_TDM(self, label, address):
         return Channels.Processor(label=label, model="TDM", address=address, trigger_interval=250e-6)

From 0b807e44e71effd9a0ac47206ecf9698fdd0586d Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 15 Feb 2019 15:08:57 -0500
Subject: [PATCH 111/235] Delete future

---
 QGL/drivers/APS2Pattern.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index c4c6ff95..845ac4e2 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -20,7 +20,7 @@
 import logging
 from warnings import warn
 from copy import copy
-from future.moves.itertools import zip_longest
+from itertools import zip_longest
 import pickle
 
 import struct

From 63b23f3fc2627cf2dc921267998beeae279655d6 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Fri, 15 Feb 2019 16:05:28 -0500
Subject: [PATCH 112/235] Use temporary directory for test_sequence data is AWG
 dir is not specified

---
 tests/test_Sequences.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/tests/test_Sequences.py b/tests/test_Sequences.py
index 9cb343b8..d9eb1ee8 100644
--- a/tests/test_Sequences.py
+++ b/tests/test_Sequences.py
@@ -1,5 +1,6 @@
 import numpy as np
 import unittest, time, os, random, sys
+import tempfile
 
 from QGL import *
 from QGL import GSTTools
@@ -103,20 +104,19 @@ def get_qubits(self):
                 for name in self.qubit_names]
 
     def set_awg_dir(self, footer=""):
-        cn = self.__class__.__name__
-
-        if None == QGL.config.AWGDir:
-            logger.warning( "\n\r#----- EEE NULL QGL.config.AWGDir {%s} cited; calling load_config()...", QGL.config.AWGDir)
+        if QGL.config.AWGDir is None:
             QGL.config.load_config()
-            logger.warning( "#----- Post load-config QGL.config.AWGDir: {%s}.\n\r", QGL.config.AWGDir)
-        #else:
-        #    logger.warning( "\n\r#----- Using QGL.config.AWGDir {%s} 8-p", QGL.config.AWGDir)
+
+        if QGL.config.AWGDir is None:
+            self.temp_dir = tempfile.TemporaryDirectory()
+            QGL.config.AWGDir = self.temp_dir.name
+            logger.warning(f"Creating temporary AWG dir at {QGL.config.AWGDir}")
+
         if not hasattr(self, 'original_awg_dir'):
           self.original_awg_dir = QGL.config.AWGDir
 
-        self.awg_dir = os.path.abspath(self.original_awg_dir + os.path.sep + cn)
-        self.truth_dir = os.path.abspath(self.testFileDirectory + os.path.sep +
-                                         cn)
+        self.awg_dir = os.path.abspath(self.original_awg_dir + os.path.sep + self.__class__.__name__)
+        self.truth_dir = os.path.abspath(self.testFileDirectory + os.path.sep + self.__class__.__name__)
 
         if footer != "":
             self.awg_dir = self.awg_dir + os.path.sep + footer

From ea178ec360cf93390dc6f1fecfcc2a6ca9373ab5 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 18 Feb 2019 17:12:17 -0500
Subject: [PATCH 113/235] WIP

---
 QGL.egg-info/PKG-INFO             | 10 +++++++
 QGL.egg-info/SOURCES.txt          | 41 +++++++++++++++++++++++++++++
 QGL.egg-info/dependency_links.txt |  1 +
 QGL.egg-info/requires.txt         |  6 +++++
 QGL.egg-info/top_level.txt        |  1 +
 QGL/Compiler.py                   | 43 +++++++++++++++++++++----------
 QGL/PulsePrimitives.py            |  2 +-
 7 files changed, 90 insertions(+), 14 deletions(-)
 create mode 100644 QGL.egg-info/PKG-INFO
 create mode 100644 QGL.egg-info/SOURCES.txt
 create mode 100644 QGL.egg-info/dependency_links.txt
 create mode 100644 QGL.egg-info/requires.txt
 create mode 100644 QGL.egg-info/top_level.txt

diff --git a/QGL.egg-info/PKG-INFO b/QGL.egg-info/PKG-INFO
new file mode 100644
index 00000000..ac9daf85
--- /dev/null
+++ b/QGL.egg-info/PKG-INFO
@@ -0,0 +1,10 @@
+Metadata-Version: 1.0
+Name: QGL
+Version: 2.1
+Summary: UNKNOWN
+Home-page: https://github.com/BBN-Q/QGL
+Author: UNKNOWN
+Author-email: UNKNOWN
+License: UNKNOWN
+Description: UNKNOWN
+Platform: UNKNOWN
diff --git a/QGL.egg-info/SOURCES.txt b/QGL.egg-info/SOURCES.txt
new file mode 100644
index 00000000..945e4a89
--- /dev/null
+++ b/QGL.egg-info/SOURCES.txt
@@ -0,0 +1,41 @@
+README.md
+QGL/BlockLabel.py
+QGL/ChannelLibraries.py
+QGL/Channels.py
+QGL/Cliffords.py
+QGL/Compiler.py
+QGL/ControlFlow.py
+QGL/GSTTools.py
+QGL/PatternUtils.py
+QGL/Plotting.py
+QGL/PulsePrimitives.py
+QGL/PulseSequencePlotter.py
+QGL/PulseSequencer.py
+QGL/PulseShapes.py
+QGL/Scheduler.py
+QGL/TdmInstructions.py
+QGL/Tomography.py
+QGL/__init__.py
+QGL/config.py
+QGL/config_location.py
+QGL/mm.py
+QGL.egg-info/PKG-INFO
+QGL.egg-info/SOURCES.txt
+QGL.egg-info/dependency_links.txt
+QGL.egg-info/requires.txt
+QGL.egg-info/top_level.txt
+QGL/BasicSequences/AllXY.py
+QGL/BasicSequences/BlankingSweeps.py
+QGL/BasicSequences/CR.py
+QGL/BasicSequences/Decoupling.py
+QGL/BasicSequences/Feedback.py
+QGL/BasicSequences/FlipFlop.py
+QGL/BasicSequences/RB.py
+QGL/BasicSequences/Rabi.py
+QGL/BasicSequences/SPAM.py
+QGL/BasicSequences/T1T2.py
+QGL/BasicSequences/__init__.py
+QGL/BasicSequences/helpers.py
+QGL/drivers/APS2Pattern.py
+QGL/drivers/APSPattern.py
+QGL/drivers/__init__.py
\ No newline at end of file
diff --git a/QGL.egg-info/dependency_links.txt b/QGL.egg-info/dependency_links.txt
new file mode 100644
index 00000000..8b137891
--- /dev/null
+++ b/QGL.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/QGL.egg-info/requires.txt b/QGL.egg-info/requires.txt
new file mode 100644
index 00000000..2aa45f83
--- /dev/null
+++ b/QGL.egg-info/requires.txt
@@ -0,0 +1,6 @@
+bbndb>=0.1
+numpy>=1.11.1
+scipy>=0.17.1
+networkx>=1.11
+bqplot>=0.11.5
+sqlalchemy>=1.2.17
diff --git a/QGL.egg-info/top_level.txt b/QGL.egg-info/top_level.txt
new file mode 100644
index 00000000..0e533603
--- /dev/null
+++ b/QGL.egg-info/top_level.txt
@@ -0,0 +1 @@
+QGL
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index fc240556..db3fc543 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -234,23 +234,40 @@ def generate_waveforms(physicalWires):
     return wfs
 
 def add_runtime_pulse_set(physicalWires, wfs):
-
     for ch, wire in physicalWires.items():
-        rt_pulses = [pulse for pulse in flatten(wire) if pulse.isRunTime]
-        pulse_type = set([pulse.label for pulse in rt_pulses])
+        rt_pulses = [pulse for pulse in flatten(wire) if isinstance(pulse, Pulse) and pulse.isRunTime]
+        if len(rt_pulses) == 0:
+            continue
+        pulse_type = list(set([pulse.label for pulse in rt_pulses]))
+        pulse_logical_chan = list(set([pulse.channel for pulse in rt_pulses]))
+        
         if len(pulse_type) > 1:
-            raise Exception("All run-time pulses must have the same label.")
-        if pulse_type not in ("RandomAC, RandomDiAC"):
+            raise Exception(f"All run-time pulses must have the same label. Found: {pulse_type}.")
+        if len(pulse_logical_chan) > 1:
+            raise Exception(f"Found more than one channel per run-time pulse set: {pulse_logical_chan}.")
+        if pulse_type[0] not in ("RandomAC, RandomDiAC"):
             raise Exception(f"Unknown run time pulse type {pulse_type}.")
+        pulse_fn = getattr(PulsePrimitives, pulse_type[0].split('Random')[-1], None)
+        if pulse_fn is None:
+            raise Exception("Was unable to get pulse type for run-time generated pulses.")
+
+        all_cliffords = [pulse_fn(pulse_logical_chan[0], n) for n in range(24)]
+        #Some could be CompositePulses so crack into indvidual pulses
+        all_pulses = []
+        for cliff in all_cliffords:
+            try:
+                for p in cliff.pulses:
+                    all_pulses.append(p)
+            except AttributeError:
+                all_pulses.append(cliff)
+        for cp in all_pulses:
+            if cp.hashshape() not in wfs[ch]: #don't duplicate data
+                if cp.isTimeAmp:
+                    wfs[ch][cp.hashshape()] = np.ones(1, dtype=np.complex)
+                else:
+                    wfs[ch][cp.hashshape()] = cp.shape
 
-        pulse_fn = getattr(PulsePrimitives, pulse_type.split('Random')[-1], None)
-
-
-
-
-
-
-
+    return wfs
 
 def pulses_to_waveforms(physicalWires):
     logger.debug("Converting pulses_to_waveforms:")
diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index 1ad4fbbe..596c79d2 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -347,7 +347,7 @@ def RandomAC(qubit):
 def RandomDiAC(qubit):
     params = overrideDefaults(qubit, {})
     params["length"] *= 2.0
-    return Pulse("RandomAC", qubit, params, isRunTime=True)
+    return Pulse("RandomDiAC", qubit, params, isRunTime=True)
 
 def AC(qubit, cliffNum):
     """

From 0dae2942dbd6362c62739b7d8df768c7a5376c8b Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 19 Feb 2019 16:55:03 -0500
Subject: [PATCH 114/235] Fix APS1 marker name

---
 QGL/ChannelLibraries.py | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 08d4bab7..3bdc2cb8 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -182,18 +182,6 @@ def qubits(self):
     def meas(self):
         return self.ent_by_type(Channels.Measurement)
 
-    def ls_receivers(self):
-        return self.ent_by_type(Channels.Receiver, show=True)
-
-    def ls_transmitters(self):
-        return self.ent_by_type(Channels.Transmitter, show=True)
-
-    def ls_qubits(self):
-        return self.ent_by_type(Channels.Qubit, show=True)
-
-    def ls_measurements(self):
-        return self.ent_by_type(Channels.Measurement, show=True)
-
     @check_session_dirty
     def load(self, name, index=1):
         """Load the latest instance for a particular name. Specifying index = 2 will select the second most recent instance """
@@ -311,7 +299,7 @@ def new_APS(self, label, address):
         chan2  = Channels.PhysicalQuadratureChannel(label=f"{label}-34", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
         m1     = Channels.PhysicalMarkerChannel(label=f"{label}-1m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
         m2     = Channels.PhysicalMarkerChannel(label=f"{label}-2m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
-        m3     = Channels.PhysicalMarkerChannel(label=f"{label}-2m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        m3     = Channels.PhysicalMarkerChannel(label=f"{label}-3m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
         m4     = Channels.PhysicalMarkerChannel(label=f"{label}-4m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
 
         this_transmitter = Channels.Transmitter(label=label, model="APS", address=address, channels=[chan1, chan2, m1, m2, m3, m4], channel_db=self.channelDatabase)

From afbe77c0fb2b0f5a091474b3b0106689c2f390f8 Mon Sep 17 00:00:00 2001
From: qlab <qlab@dhcp33-89-195.bbn.com>
Date: Wed, 20 Feb 2019 14:42:31 -0500
Subject: [PATCH 115/235] Added compatibility for using APS1

---
 QGL/ChannelLibraries.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 3bdc2cb8..daf74fe8 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -389,12 +389,16 @@ def new_source(self, label, model, address, power=-30.0, frequency=5.0e9, refere
         self.add_and_update_dict(thing)
         return thing
 
-    def set_control(self, qubit_or_edge, transmitter, generator=None):
+    def set_control(self, qubit_or_edge, transmitter, generator=None, aps1_chan=None):
         quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
         markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
 
         if isinstance(transmitter, Channels.Transmitter) and len(quads) > 1:
-            raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+            #raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+            print("Warning: In set_control the Transmitter must have a single quadrature channel if using APS2. Assuming APS1.")
+            if aps1_chan != '12' and aps1_chan != '34':
+                raise ValueError("Assuming APS1, specify APS channel 12 or 34")
+            phys_chan = transmitter.ch(aps1_chan)
         elif isinstance(transmitter, Channels.Transmitter) and len(quads) == 1:
             phys_chan = quads[0]
         elif isinstance(transmitter, Channels.PhysicalQuadratureChannel):
@@ -423,12 +427,16 @@ def set_qubit_connectivity(self, graph):
         self.add_and_update_dict(new_edges)
         return new_edges
 
-    def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
+    def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7, aps1_chan=None):
         quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
         markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
 
         if isinstance(transmitter, Channels.Transmitter) and len(quads) > 1:
-            raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+            #raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+            print("Warning: In set_measure the Transmitter must have a single quadrature channel if using APS2. Assuming APS1.")
+            if aps1_chan != '12' and aps1_chan != '34':
+                raise ValueError("Assuming APS1, specify APS channel 12 or 34")
+            phys_chan = transmitter.ch(aps1_chan)
         elif isinstance(transmitter, Channels.Transmitter) and len(quads) == 1:
             phys_chan = quads[0]
         elif isinstance(transmitter, Channels.PhysicalQuadratureChannel):

From 3a8de165cd0132f500921245417b94a681719593 Mon Sep 17 00:00:00 2001
From: qlab <qlab@dhcp33-89-195.bbn.com>
Date: Wed, 20 Feb 2019 15:28:56 -0500
Subject: [PATCH 116/235] Better fix for APS1 compatibility

---
 QGL/ChannelLibraries.py | 44 +++++++++++++++++++----------------------
 1 file changed, 20 insertions(+), 24 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index daf74fe8..e9209259 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -389,20 +389,18 @@ def new_source(self, label, model, address, power=-30.0, frequency=5.0e9, refere
         self.add_and_update_dict(thing)
         return thing
 
-    def set_control(self, qubit_or_edge, transmitter, generator=None, aps1_chan=None):
-        quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
-        markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
-
-        if isinstance(transmitter, Channels.Transmitter) and len(quads) > 1:
-            #raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
-            print("Warning: In set_control the Transmitter must have a single quadrature channel if using APS2. Assuming APS1.")
-            if aps1_chan != '12' and aps1_chan != '34':
-                raise ValueError("Assuming APS1, specify APS channel 12 or 34")
-            phys_chan = transmitter.ch(aps1_chan)
-        elif isinstance(transmitter, Channels.Transmitter) and len(quads) == 1:
-            phys_chan = quads[0]
+    def set_control(self, qubit_or_edge, transmitter, generator=None):
+        
+        if isinstance(transmitter, Channels.Transmitter):
+            quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
+            markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
+            if len(quads) > 1:
+            	raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+            elif len(quads) == 1:
+            	phys_chan = quads[0]
         elif isinstance(transmitter, Channels.PhysicalQuadratureChannel):
             phys_chan = transmitter
+            markers = [c for c in transmitter.transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
         else:
             raise ValueError("In set_control the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
@@ -427,20 +425,18 @@ def set_qubit_connectivity(self, graph):
         self.add_and_update_dict(new_edges)
         return new_edges
 
-    def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7, aps1_chan=None):
-        quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
-        markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
-
-        if isinstance(transmitter, Channels.Transmitter) and len(quads) > 1:
-            #raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
-            print("Warning: In set_measure the Transmitter must have a single quadrature channel if using APS2. Assuming APS1.")
-            if aps1_chan != '12' and aps1_chan != '34':
-                raise ValueError("Assuming APS1, specify APS channel 12 or 34")
-            phys_chan = transmitter.ch(aps1_chan)
-        elif isinstance(transmitter, Channels.Transmitter) and len(quads) == 1:
-            phys_chan = quads[0]
+    def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channel=None, gate=False, gate_channel=None, trigger_length=1e-7):
+
+        if isinstance(transmitter, Channels.Transmitter):
+                quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
+                markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
+                if len(quads) > 1:
+                    raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
+                elif len(quads) == 1:
+                    phys_chan = quads[0]
         elif isinstance(transmitter, Channels.PhysicalQuadratureChannel):
             phys_chan = transmitter
+            markers = [c for c in transmitter.transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]
         else:
             raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 

From dbc8fab57e265fe3945dff01d02e55667ddd306f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Thu, 21 Feb 2019 10:54:30 -0500
Subject: [PATCH 117/235] Add DC source

as a standalone instrument
---
 QGL/ChannelLibraries.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 307cbbf3..248d95c4 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -313,6 +313,10 @@ def new_TDM(self, label, address):
     def new_spectrum_analzyer(self, label, address, source):
         return Channels.SpectrumAnalyzer(label=label, model="SpectrumAnalyzer", address=address, LO_source=source)
 
+    @check_for_duplicates
+    def new_DC_source(self, label, address):
+        return Channels.DCSource(label=label, model="YokogawaGS200", address=address, standalone=True)
+
     @check_for_duplicates
     def new_APS2_rack(self, label, ip_addresses, tdm_ip=None):
         transmitters  = [self.new_APS2(f"{label}_U{n+1}", f"{ip}") for n, ip in enumerate(ip_addresses)]

From 3338aad546c39dafad44462adea83b1df08fb2db Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Fri, 22 Feb 2019 17:35:26 -0500
Subject: [PATCH 118/235] WIP

---
 QGL/Compiler.py            | 122 ++++++++++++++++++++++---------------
 QGL/ControlFlow.py         |   3 +-
 QGL/PulseSequencer.py      |   5 ++
 QGL/TdmInstructions.py     |   4 +-
 QGL/drivers/APS2Pattern.py |  28 ++++-----
 5 files changed, 95 insertions(+), 67 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index db3fc543..bdf3ab2e 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -233,34 +233,40 @@ def generate_waveforms(physicalWires):
                     wfs[ch][pulse.hashshape()] = pulse.shape
     return wfs
 
+def get_clifford_type(wire, allowed_types=("RandomAC")):
+    rt_pulses = [pulse for pulse in flatten(wire) if isinstance(pulse, Pulse) and pulse.isRunTime]
+    if len(rt_pulses) == 0:
+        return None
+    pulse_type = list(set([pulse.label for pulse in rt_pulses]))
+    pulse_logical_chan = list(set([pulse.channel for pulse in rt_pulses]))
+    if len(pulse_type) > 1:
+        raise Exception(f"All run-time pulses must have the same label. Found: {pulse_type}.")
+    if len(pulse_logical_chan) > 1:
+        raise Exception(f"Found more than one channel per run-time pulse set: {pulse_logical_chan}.")
+    if pulse_type[0] not in allowed_types:
+        raise Exception(f"Unknown run time pulse type {pulse_type}.")
+    pulse_fn = getattr(PulsePrimitives, pulse_type[0].split('Random')[-1], None)
+    if pulse_fn is None:
+        raise Exception("Was unable to get pulse type for run-time generated pulses.")
+    return lambda x: pulse_fn(pulse_logical_chan[0], x)
+
+
 def add_runtime_pulse_set(physicalWires, wfs):
     for ch, wire in physicalWires.items():
-        rt_pulses = [pulse for pulse in flatten(wire) if isinstance(pulse, Pulse) and pulse.isRunTime]
-        if len(rt_pulses) == 0:
-            continue
-        pulse_type = list(set([pulse.label for pulse in rt_pulses]))
-        pulse_logical_chan = list(set([pulse.channel for pulse in rt_pulses]))
-        
-        if len(pulse_type) > 1:
-            raise Exception(f"All run-time pulses must have the same label. Found: {pulse_type}.")
-        if len(pulse_logical_chan) > 1:
-            raise Exception(f"Found more than one channel per run-time pulse set: {pulse_logical_chan}.")
-        if pulse_type[0] not in ("RandomAC, RandomDiAC"):
-            raise Exception(f"Unknown run time pulse type {pulse_type}.")
-        pulse_fn = getattr(PulsePrimitives, pulse_type[0].split('Random')[-1], None)
+        pulse_fn = get_clifford_type(wire)
         if pulse_fn is None:
-            raise Exception("Was unable to get pulse type for run-time generated pulses.")
-
-        all_cliffords = [pulse_fn(pulse_logical_chan[0], n) for n in range(24)]
-        #Some could be CompositePulses so crack into indvidual pulses
+            continue
         all_pulses = []
+        all_cliffords = [pulse_fn(n) for n in range(24)]
+        #Some could be CompositePulses so crack into indvidual pulses
         for cliff in all_cliffords:
             try:
                 for p in cliff.pulses:
                     all_pulses.append(p)
             except AttributeError:
                 all_pulses.append(cliff)
-        for cp in all_pulses:
+
+        for cp in all_pulses: #make all-pulses a set?
             if cp.hashshape() not in wfs[ch]: #don't duplicate data
                 if cp.isTimeAmp:
                     wfs[ch][cp.hashshape()] = np.ones(1, dtype=np.complex)
@@ -269,6 +275,15 @@ def add_runtime_pulse_set(physicalWires, wfs):
 
     return wfs
 
+def create_clifford_waveforms(physicalWires):
+    clifford_sets = {}
+    for ch, wire in physicalWires.items():
+        pulse_fn = get_clifford_type(wire)
+        if pulse_fn is None:
+            continue
+        clifford_sets[ch] = [[Waveform(pulse_fn(n))] for n in range(24)]
+    return clifford_sets
+
 def pulses_to_waveforms(physicalWires):
     logger.debug("Converting pulses_to_waveforms:")
     wireOuts = {ch: [] for ch in physicalWires.keys()}
@@ -312,7 +327,7 @@ def setup_awg_channels(physicalChannels):
     return data
 
 
-def bundle_wires(physWires, wfs):
+def bundle_wires(physWires, wfs, cliff_wires=None):
     awgData = setup_awg_channels(physWires.keys())
     for chan in physWires.keys():
         _, awgChan = chan.label.rsplit('-', 1)
@@ -320,6 +335,8 @@ def bundle_wires(physWires, wfs):
             awgChan = 'ch' + awgChan
         awgData[chan.instrument][awgChan]['linkList'] = physWires[chan]
         awgData[chan.instrument][awgChan]['wfLib'] = wfs[chan]
+        if cliff_wires is not None and chan in cliff_wires.keys():
+            awgData[chan.instrument][awgChan]['clifford_set'] = cliff_wires[chan]
         if hasattr(chan, 'correctionT'):
             awgData[chan.instrument][awgChan]['correctionT'] = chan.correctionT
     return awgData
@@ -340,37 +357,12 @@ def collect_specializations(seqs):
             done.append(target)
     return funcs
 
-def compile_to_hardware(seqs,
-                        fileName,
-                        library_version=None,
-                        suffix='',
-                        axis_descriptor=None,
-                        add_slave_trigger=True,
-                        extra_meta=None,
-                        tdm_seq = False):
-    '''
-    Compiles 'seqs' to a hardware description and saves it to 'fileName'.
-    Other inputs:
-        library_version (optional): string or ChannelLibrary instance to pack in the
-            metafile. This will be the version of the library loaded during program
-            execution. Default None uses the current working version.
-        suffix (optional): string to append to end of fileName, e.g. with
-            fileNames = 'test' and suffix = 'foo' might save to test-APSfoo.h5
-        axis_descriptor (optional): a list of dictionaries describing the effective
-            axes of the measurements that the sequence will yield. For instance,
-            if `seqs` generates a Ramsey experiment, axis_descriptor would describe
-            the time delays between pulses.
-        add_slave_trigger (optional): add the slave trigger(s)
-        tdm_seq (optional): compile for TDM
-    '''
+def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False):
+
     ChannelLibraries.channelLib.update_channelDict()
     clear_pulse_cache()
-
     logger.debug("Compiling %d sequence(s)", len(seqs))
 
-    # save input code to file
-    save_code(seqs, fileName + suffix)
-
     # all sequences should start with a WAIT for synchronization
     for seq in seqs:
         if not isinstance(seq[0], ControlFlow.Wait):
@@ -469,6 +461,9 @@ def compile_to_hardware(seqs,
     # If there are run-time pulses add these to the library
     if PatternUtils.contains_runtime_pulses(seqs):
         wfs = add_runtime_pulse_set(physWires, wfs)
+        cliff_wires = create_clifford_waveforms(physWires)
+    else:
+        cliff_wires = None
 
     # replace Pulse objects with Waveforms
     logger.info("Replacing pulses with waveforms")
@@ -477,9 +472,36 @@ def compile_to_hardware(seqs,
     # bundle wires on instruments, or channels depending
     # on whether we have one sequence per channel
     logger.info("Bundling wires.")
-    awgData = bundle_wires(physWires, wfs)
-    del wireSeqs
-    gc.collect()
+    awgData = bundle_wires(physWires, wfs, cliff_wires=cliff_wires)
+    return awgData
+
+def compile_to_hardware(seqs,
+                        fileName,
+                        library_version=None,
+                        suffix='',
+                        axis_descriptor=None,
+                        add_slave_trigger=True,
+                        extra_meta=None,
+                        tdm_seq = False):
+    '''
+    Compiles 'seqs' to a hardware description and saves it to 'fileName'.
+    Other inputs:
+        library_version (optional): string or ChannelLibrary instance to pack in the
+            metafile. This will be the version of the library loaded during program
+            execution. Default None uses the current working version.
+        suffix (optional): string to append to end of fileName, e.g. with
+            fileNames = 'test' and suffix = 'foo' might save to test-APSfoo.h5
+        axis_descriptor (optional): a list of dictionaries describing the effective
+            axes of the measurements that the sequence will yield. For instance,
+            if `seqs` generates a Ramsey experiment, axis_descriptor would describe
+            the time delays between pulses.
+        add_slave_trigger (optional): add the slave trigger(s)
+        tdm_seq (optional): compile for TDM
+    '''
+    # save input code to file
+    save_code(seqs, fileName + suffix)
+
+    awgData = compile_to_IR(seqs, add_slave_trigger=add_slave_trigger, tdm_seq=tdm_seq)
 
     # convert to hardware formats
     # files = {}
@@ -790,7 +812,7 @@ def __repr__(self):
 
     def __str__(self):
         if self.isRunTime:
-            return f"Hardware-Generated({self.length})"
+            return f"Hardware-Generated({self.label}, {self.length})"
         if self.isTimeAmp:
             TA = 'HIGH' if self.amp != 0 else 'LOW'
             return "Waveform-TA(" + TA + ", " + str(self.length) + ")"
diff --git a/QGL/ControlFlow.py b/QGL/ControlFlow.py
index a735f24e..f733cb6a 100644
--- a/QGL/ControlFlow.py
+++ b/QGL/ControlFlow.py
@@ -150,8 +150,9 @@ def __init__(self, target):
 
 class Call(ControlInstruction):
     # target is a BlockLabel
-    def __init__(self, target):
+    def __init__(self, target, load_addr=False):
         super(Call, self).__init__("CALL", target=target)
+        self.load_addr = load_addr
 
 
 class Return(ControlInstruction):
diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 606511dd..463b273b 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -262,6 +262,11 @@ def __eq__(self, other):
     def __ne__(self, other):
         return not self == other
 
+    @property
+    def isRunTime(self):
+        #Check if any of the member pulses contain a run-time pulse
+        return any([hasattr(entry, 'isRunTime') and entry.isRunTime for entry in self.pulses.values()])
+
     @property
     def channel(self):
         return self.pulses.keys()
diff --git a/QGL/TdmInstructions.py b/QGL/TdmInstructions.py
index 945743c9..38fa7cc7 100644
--- a/QGL/TdmInstructions.py
+++ b/QGL/TdmInstructions.py
@@ -109,5 +109,5 @@ def __ne__(self, other):
         return not self == other
 
 
-# def LoadCmpVram(addr, mask):
-#     return LoadCmpVramInstruction('LOADCMPVRAM', 1, addr, mask)
+def LoadCmpVram(addr, mask, tdm=True):
+    return LoadCmpVramInstruction('LOADCMPVRAM', 1, addr, mask, tdm)
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index c4c6ff95..5e6db0d7 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -31,6 +31,8 @@
 from QGL import PulseSequencer
 from QGL.PatternUtils import hash_pulse, flatten
 from QGL import TdmInstructions
+from QGL import APS2CustomInstructions
+from QGL.APS2CustomInstructions import APS2_CUSTOM_DECODE
 
 # Python 2/3 compatibility: use 'int' that subclasses 'long'
 from builtins import int
@@ -85,20 +87,17 @@
 
 CMPTABLE = {'==': EQUAL, '!=': NOTEQUAL, '>': GREATERTHAN, '<': LESSTHAN}
 
-# custom OP_CODES
+# custom TDM OP_CODES
 TDM_MAJORITY_VOTE = 0
 TDM_MAJORITY_VOTE_SET_MASK = 1
 TDM_TSM_SET_ROUNDS = 2
 TDM_TSM = 3
 
-APS_CUSTOM_DECODE = ["APS_RAND", "APS_CLIFFORD_RAND","APS_CLIFFORD_SET_SEED" ,"APS_CLIFFORD_SET_OFFSET"
-, "APS_CLIFFORD_SET_SPACING"]
-
 TDM_CUSTOM_DECODE = ["TDM_MAJORITY_VOTE", "TDM_MAJORITY_VOTE_SET_MASK", "TDM_TSM_SET_ROUNDS", "TDM_TSM"]
 
 # Whether we use PHASE_OFFSET modulation commands or bake it into waveform
 # Default to false as we usually don't have many variants
-USE_PHASE_OFFSET_INSTRUCTION = False
+USE_PHASE_OFFSET_INSTRUCTION = True
 
 # Whether to save the waveform offsets for partial compilation
 SAVE_WF_OFFSETS = False
@@ -445,8 +444,8 @@ def Goto(addr, label=None):
     return Command(GOTO, addr, label=label)
 
 
-def Call(addr, label=None):
-    return Command(CALL, addr, label=label)
+def Call(addr, load_addr=False, label=None):
+    return Command(CALL, addr, label=label, write=load_addr)
 
 
 def Return(label=None):
@@ -512,11 +511,11 @@ def LoadCmpVram(addr, mask, label=None):
     return Instruction(header, payload, label=label)
 
 
-def preprocess(seqs, shapeLib):
+def preprocess(seqs, shapeLib, clifford_set=False):
     seqs = PatternUtils.convert_lengths_to_samples(
         seqs, SAMPLING_RATE, ADDRESS_UNIT, Compiler.Waveform)
     wfLib = build_waveforms(seqs, shapeLib)
-    inject_modulation_cmds(seqs)
+    inject_modulation_cmds(seqs, force_phase_update=clifford_set)
     return seqs, wfLib
 
 
@@ -604,7 +603,7 @@ def to_instruction(self, write_flag=True, label=None):
         instr.writeFlag = write_flag
         return instr
 
-def inject_modulation_cmds(seqs):
+def inject_modulation_cmds(seqs, force_phase_update=False):
     """
     Inject modulation commands from phase, frequency and frameChange of waveforms
     in an IQ waveform sequence. Assume up to 2 NCOs for now.
@@ -622,7 +621,7 @@ def inject_modulation_cmds(seqs):
         frame_changes = [entry.frameChange for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
         no_frame_cmds = np.all(np.less(np.abs(frame_changes), 1e-8))
         no_modulation_cmds = no_freq_cmds and no_phase_cmds and no_frame_cmds
-
+        #import pdb; pdb.set_trace()
         if no_modulation_cmds:
             continue
 
@@ -665,10 +664,11 @@ def inject_modulation_cmds(seqs):
                             mod_seq.append( ModulationCommand("MODULATE", nco_select, length = entry.length))
                             pending_frame_update = False
                     #now apply non-zero frame changes after so it is applied at end
+
                     if entry.frameChange != 0:
                         pending_frame_update = True
                         #zero length frame changes (Z pulses) need to be combined with the previous frame change or injected where possible
-                        if entry.length == 0:
+                        if entry.length == 0 and not force_phase_update:
                             #if the last is a frame change then we can add to the frame change
                             if isinstance(mod_seq[-1], ModulationCommand) and mod_seq[-1].instruction == "UPDATE_FRAME":
                                 mod_seq[-1].phase += entry.frameChange
@@ -801,7 +801,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                     isinstance(entry, ControlFlow.ControlInstruction) or
                     isinstance(entry, BlockLabel.BlockLabel) or
                     isinstance(entry, TdmInstructions.CustomInstruction) or
-                    isinstance(entry, TdmInstructions.WriteAddrInstruction) or
+                    isinstance(entry, TdmInstructions.Instruction) or
                     isinstance(entry, TdmInstructions.LoadCmpVramInstruction)):
                 if isinstance(entry, BlockLabel.BlockLabel):
                     # carry label forward to next entry
@@ -820,7 +820,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                 elif isinstance(entry, ControlFlow.Goto):
                     instructions.append(Goto(entry.target, label=label))
                 elif isinstance(entry, ControlFlow.Call):
-                    instructions.append(Call(entry.target, label=label))
+                    instructions.append(Call(entry.target, load_addr = entry.load_addr, label=label))
                 elif isinstance(entry, ControlFlow.Repeat):
                     instructions.append(Repeat(entry.target, label=label))
                 # value argument commands

From 99d9f3d34d01ece665c7829faf3f4f7dee257327 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Fri, 22 Feb 2019 17:35:48 -0500
Subject: [PATCH 119/235] More WIP...

---
 QGL/APS2CustomInstructions.py | 74 +++++++++++++++++++++++++++++++++++
 QGL/RandomCliffordTools.py    | 51 ++++++++++++++++++++++++
 2 files changed, 125 insertions(+)
 create mode 100644 QGL/APS2CustomInstructions.py
 create mode 100644 QGL/RandomCliffordTools.py

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
new file mode 100644
index 00000000..cb082dc0
--- /dev/null
+++ b/QGL/APS2CustomInstructions.py
@@ -0,0 +1,74 @@
+'''
+Copyright 2019 Raytheon BBN Technologies
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+   http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+'''
+
+# Instructions for the the prototype APS2-TDM hardware.
+
+from .TdmInstructions import CustomInstruction, WriteAddr, Invalidate, LoadCmpVram
+from .ControlFlow import LoadCmp, Call
+
+##custom APS OP_CODES
+#APS_CLIFFORD_SET_SEED:         Set 32 bit seed for random number generator
+#APS_CLIFFORD_SET_OFFSET:       Stores jump table starting offset
+#APS_CLIFFORD_SET_SPACING:      Stores jump table spacing (integer to shift left),
+#                               including interal address representation
+#APS_CLIFFORD_INVERSE_RESET:    Reset inverse tracker
+#APS_CLIFFORD_RAND:             Choose randomly from set of 24 waveforms,
+#                               returns starting address of jump table entry from RAM
+#APS_CLIFFORD_INVERSE:          Store waveform address of inverse waveform to be jumped to
+
+APS2_CUSTOM_DECODE = {"APS_RAND": 0,
+                     "APS_CLIFFORD_RAND": 2,
+                     "APS_CLIFFORD_INVERSE": 6,
+                     "APS_CLIFFORD_INVERSE_RESET": 7,
+                     "APS_CLIFFORD_SET_SEED": 3,
+                     "APS_CLIFFORD_SET_OFFSET": 4,
+                     "APS_CLIFFORD_SET_SPACING": 5}
+
+##Note that the expected call pattern for the randomizer is:
+
+#   APS_CLIFFORD_RAND / APS_CLIFFORD_INVERSE
+#   LOADCMP
+#   CALL
+
+def RandomCliffordSetOffset(addr, offset):
+    return [Invalidate(addr, 0, tdm=False),
+            WriteAddr(adrr, offset, tdm=False),
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
+            CustomInstruction("APS_CLIFFORD_SET_OFFSET", addr, 0x3)]
+
+def RandomCliffordSetSpacing(addr, spacing):
+    return [Invalidate(addr, 0, tdm=False),
+            WriteAddr(adrr, offset, tdm=False),
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
+            CustomInstruction("APS_CLIFFORD_SET_SPACING", addr, 0x3)]
+
+def RandomClifford(target, addr):
+    return [Invalidate(addr, 0, tdm=False),
+            CustomInstruction("APS_CLIFFORD_RAND", 0x0, addr),
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
+            Call(target, load_addr=True)]
+
+def RandomCliffordInverse(target, addr):
+    return [Invalidate(addr, 0, tdm=False),
+            CustomInstruction("APS_CLIFFORD_RAND", 0x0, addr),
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
+            Call(target, load_addr=True)]
+
+def RandomCliffordInverseReset(addr): #for now don't use addr
+    return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0x0006)
+
+def RandomCliffordSeed(seed):
+    raise NotImplementedError("APS_CLIFFORD_SET_SEED not implemented!")
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
new file mode 100644
index 00000000..6273e063
--- /dev/null
+++ b/QGL/RandomCliffordTools.py
@@ -0,0 +1,51 @@
+'''
+Functions for dealing with random clifford pulse sequences
+
+Copyright 2019 Raytheon BBN Technologies
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+   http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+'''
+
+from . import config
+from . import PatternUtils
+from .PatternUtils import flatten, has_gate
+from . import Channels
+from . import ChannelLibraries
+from . import PulseShapes
+from . import PulsePrimitives
+from .PulsePrimitives import Id, clear_pulse_cache
+from .PulseSequencer import Pulse, PulseBlock, CompositePulse
+from . import ControlFlow
+from . import BlockLabel
+from . import TdmInstructions # only for APS2-TDM
+from . import APS2CustomInstructions
+
+def generate_clifford_jump_table(cliff_wires, jt_label = None):
+    """Generate the jump table that will be used to call into the clifford set"""
+
+    if jt_label is None:
+        jt_label = BlockLabel.BlockLabel("JT")
+    if not isinstance(jt_label, BlockLabel.BlockLabel):
+        raise ValueError("Jump table label must be a BlockLabel.")
+
+    cliff_labels = [f"C{n}" for n in range(24)]
+    jump_table = [jt_label]
+    for cl in cliff_labels:
+        jump_table.append(ControlFlow.Call(cl))
+        jump_table.append(ControlFlow.Return())
+
+    for cliff, cl in zip(cliff_wires, cliff_labels):
+        cliff.insert(0, BlockLabel.BlockLabel(cl))
+        cliff.append(ControlFlow.Return())
+
+    cliff_wires.insert(0, jump_table)

From 5243c53620341101774e313c43460453244f0c27 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Sat, 23 Feb 2019 18:40:30 -0500
Subject: [PATCH 120/235] Add string representation for custom instructions

---
 QGL/TdmInstructions.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/QGL/TdmInstructions.py b/QGL/TdmInstructions.py
index 38fa7cc7..a45fd3cd 100644
--- a/QGL/TdmInstructions.py
+++ b/QGL/TdmInstructions.py
@@ -36,6 +36,13 @@ def __eq__(self, other):
     def __ne__(self, other):
         return not self == other
 
+    def __str__(self):
+        return f"{self.instruction}({hex(self.in_addr)}, {hex(self.out_addr)})"
+
+    def __repr__(self):
+        return self.__str__()
+
+
 
 def MajorityVote(in_addr, out_addr, nmeas): # alternatively, append the loadcmpvram instruction when compiling (see STOREMEAS)
     return [LoadCmpVramInstruction('LOADCMPVRAM', 1, in_addr, 2**nmeas-1, True), CustomInstruction('MAJORITY', in_addr, out_addr)]
@@ -74,6 +81,12 @@ def __eq__(self, other):
     def __ne__(self, other):
         return not self == other
 
+    def __str__(self):
+        return f"{self.instruction}({hex(self.addr)}, {hex(self.value)})"
+
+    def __repr__(self):
+        return self.__str__()
+
 def WriteAddr(addr, value, channel=None, tdm=True):
     return WriteAddrInstruction('WRITEADDR', channel, 0, addr, value, tdm)
 
@@ -108,6 +121,12 @@ def __eq__(self, other):
     def __ne__(self, other):
         return not self == other
 
+    def __str__(self):
+        return f"{self.instruction}({hex(self.addr)}, {hex(self.mask)})"
+
+    def __repr__(self):
+        return self.__str__()
+
 
 def LoadCmpVram(addr, mask, tdm=True):
     return LoadCmpVramInstruction('LOADCMPVRAM', 1, addr, mask, tdm)

From 8b790b4f7a5fa97d208278396c172e5a576ad590 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Sat, 23 Feb 2019 18:41:16 -0500
Subject: [PATCH 121/235] Set write flag to CALL to indicate load from VRAM

---
 QGL/ControlFlow.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/QGL/ControlFlow.py b/QGL/ControlFlow.py
index f733cb6a..5894d2f1 100644
--- a/QGL/ControlFlow.py
+++ b/QGL/ControlFlow.py
@@ -154,6 +154,13 @@ def __init__(self, target, load_addr=False):
         super(Call, self).__init__("CALL", target=target)
         self.load_addr = load_addr
 
+    def __str__(self):
+        if self.load_addr:
+            return f"{self.instruction}({str(self.target)})"
+        else:
+            return f"{self.instruction}({str(self.target)}, LOAD)"
+
+
 
 class Return(ControlInstruction):
     def __init__(self):

From 96857168ec6f9a16755d9c6227b30eb181c57715 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Sat, 23 Feb 2019 18:41:42 -0500
Subject: [PATCH 122/235] Update APS2 custom instructions for randomizer

---
 QGL/APS2CustomInstructions.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index cb082dc0..285f8685 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -63,12 +63,12 @@ def RandomClifford(target, addr):
 
 def RandomCliffordInverse(target, addr):
     return [Invalidate(addr, 0, tdm=False),
-            CustomInstruction("APS_CLIFFORD_RAND", 0x0, addr),
+            CustomInstruction("APS_CLIFFORD_INVERSE", 0x0, addr),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
             Call(target, load_addr=True)]
 
 def RandomCliffordInverseReset(addr): #for now don't use addr
-    return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0x0006)
+    return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0xF)
 
 def RandomCliffordSeed(seed):
     raise NotImplementedError("APS_CLIFFORD_SET_SEED not implemented!")

From 1660fb3eba344acbf406808e4b328bf8b26b10c3 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Sat, 23 Feb 2019 18:42:21 -0500
Subject: [PATCH 123/235] Tools for random clifford sequences.

---
 QGL/RandomCliffordTools.py | 46 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 45 insertions(+), 1 deletion(-)

diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index 6273e063..d7584c34 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -17,18 +17,23 @@
 '''
 
 from . import config
+from functools import reduce
 from . import PatternUtils
 from .PatternUtils import flatten, has_gate
 from . import Channels
 from . import ChannelLibraries
 from . import PulseShapes
 from . import PulsePrimitives
+from . import Compiler
 from .PulsePrimitives import Id, clear_pulse_cache
 from .PulseSequencer import Pulse, PulseBlock, CompositePulse
 from . import ControlFlow
 from . import BlockLabel
 from . import TdmInstructions # only for APS2-TDM
-from . import APS2CustomInstructions
+from .APS2CustomInstructions import *
+from .Cliffords import C1, inverse_clifford, clifford_multiply
+
+VALID_CLIFFORD_TYPES = ('RandomAC',)
 
 def generate_clifford_jump_table(cliff_wires, jt_label = None):
     """Generate the jump table that will be used to call into the clifford set"""
@@ -49,3 +54,42 @@ def generate_clifford_jump_table(cliff_wires, jt_label = None):
         cliff.append(ControlFlow.Return())
 
     cliff_wires.insert(0, jump_table)
+
+def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
+                            inv_addr=0x3, inv_values=[]):
+
+    if jt_label is None:
+        jt_label = BlockLabel.BlockLabel("JT")
+    if not isinstance(jt_label, BlockLabel.BlockLabel):
+        raise ValueError("Jump table label must be a BlockLabel.")
+
+    for idx, seq in enumerate(seqs[:]):
+        if not PatternUtils.contains_runtime_pulses(seq):
+            continue
+        new_seq = []
+        for pulse in seq:
+            if isinstance(pulse, Compiler.Waveform) and pulse.isRunTime \
+                and pulse.label in VALID_CLIFFORD_TYPES:
+                has_random_cliff = True
+                new_seq.extend(RandomClifford(jt_label, cliff_addr))
+                print("Inserting clifford pulse!")
+            else:
+                new_seq.append(pulse)
+
+        if add_inv:
+            #insert reset after first wait
+            w_idx = next(i for i, v in enumerate(new_seq) if isinstance(v, ControlFlow.Wait))
+            new_seq.insert(w_idx+1, RandomCliffordInverseReset(0x0))
+            #insert at end of sequence or before last GOTO
+            if isinstance(new_seq[-1], ControlFlow.Goto):
+                  new_seq[-1:-1] = RandomCliffordInverse(jt_label, inv_addr)
+            else:
+                  new_seq.extend(RandomCliffordInverse(jt_label, inv_addr))
+
+        seqs[idx] = new_seq
+
+def randomize_clifford_sequences(qubit, seqs, clifford_type=PulsePrimitives.RandomAC):
+
+    c_seqs = [[clifford_type(qubit) for _ in seq] for seq in seqs]
+    inverses = [inverse_clifford(C1[reduce(clifford_multiply, seq)]) for seq in seqs]
+    return c_seqs, inverses

From 107e25a72e89eb6a3530eb62296f69f31c73bfd1 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 25 Feb 2019 17:35:52 -0500
Subject: [PATCH 124/235] Even more WIP

---
 QGL/APS2CustomInstructions.py |  4 ++-
 QGL/Compiler.py               | 40 ++++++++++++++---------
 QGL/PulsePrimitives.py        |  2 +-
 QGL/RandomCliffordTools.py    |  4 +--
 QGL/TdmInstructions.py        |  7 ++--
 QGL/drivers/APS2Pattern.py    | 61 ++++++++++++++++++++++-------------
 6 files changed, 74 insertions(+), 44 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index 285f8685..6eb22054 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -29,7 +29,7 @@
 #                               returns starting address of jump table entry from RAM
 #APS_CLIFFORD_INVERSE:          Store waveform address of inverse waveform to be jumped to
 
-APS2_CUSTOM_DECODE = {"APS_RAND": 0,
+APS2_CUSTOM = {"APS_RAND": 0,
                      "APS_CLIFFORD_RAND": 2,
                      "APS_CLIFFORD_INVERSE": 6,
                      "APS_CLIFFORD_INVERSE_RESET": 7,
@@ -37,6 +37,8 @@
                      "APS_CLIFFORD_SET_OFFSET": 4,
                      "APS_CLIFFORD_SET_SPACING": 5}
 
+APS2_CUSTOM_DECODE = {v: k for k, v in APS2_CUSTOM.items()}
+
 ##Note that the expected call pattern for the randomizer is:
 
 #   APS_CLIFFORD_RAND / APS_CLIFFORD_INVERSE
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index bdf3ab2e..ce4992ab 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -36,6 +36,8 @@
 from . import ControlFlow
 from . import BlockLabel
 from . import TdmInstructions # only for APS2-TDM
+from . import APS2CustomInstructions
+from . import RandomCliffordTools
 import gc
 
 logger = logging.getLogger(__name__)
@@ -327,7 +329,7 @@ def setup_awg_channels(physicalChannels):
     return data
 
 
-def bundle_wires(physWires, wfs, cliff_wires=None):
+def bundle_wires(physWires, wfs):
     awgData = setup_awg_channels(physWires.keys())
     for chan in physWires.keys():
         _, awgChan = chan.label.rsplit('-', 1)
@@ -335,8 +337,6 @@ def bundle_wires(physWires, wfs, cliff_wires=None):
             awgChan = 'ch' + awgChan
         awgData[chan.instrument][awgChan]['linkList'] = physWires[chan]
         awgData[chan.instrument][awgChan]['wfLib'] = wfs[chan]
-        if cliff_wires is not None and chan in cliff_wires.keys():
-            awgData[chan.instrument][awgChan]['clifford_set'] = cliff_wires[chan]
         if hasattr(chan, 'correctionT'):
             awgData[chan.instrument][awgChan]['correctionT'] = chan.correctionT
     return awgData
@@ -357,7 +357,7 @@ def collect_specializations(seqs):
             done.append(target)
     return funcs
 
-def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False):
+def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=False):
 
     ChannelLibraries.channelLib.update_channelDict()
     clear_pulse_cache()
@@ -394,7 +394,7 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False):
 
     # Compile all the pulses/pulseblocks to sequences of pulses and control flow
     logger.info("Compiling sequences.")
-    wireSeqs = compile_sequences(seqs, channels)
+    wireSeqs = compile_sequences(seqs, channels, random_cliffords=random_cliffords)
 
     if not validate_linklist_channels(wireSeqs.keys()):
         print("Compile to hardware failed")
@@ -459,11 +459,8 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False):
     wfs = generate_waveforms(physWires)
 
     # If there are run-time pulses add these to the library
-    if PatternUtils.contains_runtime_pulses(seqs):
+    if random_cliffords:
         wfs = add_runtime_pulse_set(physWires, wfs)
-        cliff_wires = create_clifford_waveforms(physWires)
-    else:
-        cliff_wires = None
 
     # replace Pulse objects with Waveforms
     logger.info("Replacing pulses with waveforms")
@@ -472,7 +469,7 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False):
     # bundle wires on instruments, or channels depending
     # on whether we have one sequence per channel
     logger.info("Bundling wires.")
-    awgData = bundle_wires(physWires, wfs, cliff_wires=cliff_wires)
+    awgData = bundle_wires(physWires, wfs)
     return awgData
 
 def compile_to_hardware(seqs,
@@ -589,7 +586,7 @@ def compile_to_hardware(seqs,
     return metafilepath
 
 
-def compile_sequences(seqs, channels=set()):
+def compile_sequences(seqs, channels=set(), random_cliffords=False):
     '''
     Main function to convert sequences to miniLL's and waveform libraries.
     '''
@@ -603,6 +600,16 @@ def compile_sequences(seqs, channels=set()):
     subroutines = collect_specializations(seqs)
     seqs += subroutines
 
+    if random_cliffords:
+        qubits = [q for q in list(channels) if isinstance(q, Channels.Qubit)]
+        if len(qubits) > 1:
+            raise Exception("Too many qubits! Don't know how to deal with this yet.")
+        #replace cliffords with
+        cliffords = [[get_clifford_type(seqs)(n)] for n in range(24)]
+        RandomCliffordTools.generate_clifford_jump_table(cliffords)
+        RandomCliffordTools.insert_clifford_calls(seqs)
+        seqs += cliffords
+
     #expand the channel definitions for anything defined in subroutines
     for func in subroutines:
         channels |= find_unique_channels(subroutines)
@@ -664,10 +671,10 @@ def flatten_to_pulses(obj):
                 wires[chan] += [copy(block)]
             continue
         # control flow broadcasts to all channels if channel attribute is None
-        if (isinstance(block, ControlFlow.ControlInstruction) or
-                isinstance(block, TdmInstructions.WriteAddrInstruction) or
-                isinstance(block, TdmInstructions.CustomInstruction) or
-                isinstance(block, TdmInstructions.LoadCmpVramInstruction)):
+        if isinstance(block, ControlFlow.ControlInstruction): #or
+                #isinstance(block, TdmInstructions.WriteAddrInstruction) or
+                #isinstance(block, TdmInstructions.CustomInstruction) or
+                #isinstance(block, TdmInstructions.LoadCmpVramInstruction)):
             # Need to deal with attaching measurements and edges to control
             # instruction. Until we have a proper solution for that, we will
             # always broadcast control instructions to all channels
@@ -676,6 +683,9 @@ def flatten_to_pulses(obj):
             for chan in block_channels:
                 wires[chan] += [copy(block)]
             continue
+        #Don't propagate VRAM instructions
+        if isinstance(block, TdmInstructions.VRAMInstruction) or isinstance(block, TdmInstructions.CustomInstruction):
+            continue
         # propagate frame change from nodes to edges
         for chan in channels:
             if block.pulses[chan].frameChange == 0:
diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index 596c79d2..a648e044 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -372,7 +372,7 @@ def AC(qubit, cliffNum):
     #Now a big else if chain for to get the specific Clifford
     if cliffNum == 0:
         #Identity gate
-        return Id(qubit, length=0)
+        return Id(qubit)#Id(qubit, length=0)
     elif cliffNum == 1:
         #X90
         return X90(qubit)
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index d7584c34..d4a0d26e 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -68,11 +68,11 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
             continue
         new_seq = []
         for pulse in seq:
-            if isinstance(pulse, Compiler.Waveform) and pulse.isRunTime \
+            if isinstance(pulse, Pulse) and pulse.isRunTime \
                 and pulse.label in VALID_CLIFFORD_TYPES:
                 has_random_cliff = True
                 new_seq.extend(RandomClifford(jt_label, cliff_addr))
-                print("Inserting clifford pulse!")
+                #print("Inserting clifford pulse!")
             else:
                 new_seq.append(pulse)
 
diff --git a/QGL/TdmInstructions.py b/QGL/TdmInstructions.py
index a45fd3cd..6dfdd7d1 100644
--- a/QGL/TdmInstructions.py
+++ b/QGL/TdmInstructions.py
@@ -58,7 +58,10 @@ def DecodeSetRounds(in_addr, out_addr, value):
 
 # TODO: the rest of the CUSTOM instructions
 
-class WriteAddrInstruction(object):
+class VRAMInstruction(object):
+    pass
+
+class WriteAddrInstruction(VRAMInstruction):
 
     def __init__(self, name, channel, modifier, addr, value, tdm, **kwargs):
         self.instruction = name
@@ -99,7 +102,7 @@ def CrossBar(addr, value, channel=None, tdm=True): # should this be a high-level
 def StoreMeas(addr, value, channel=None, tdm=True):
     return WriteAddrInstruction('STOREMEAS', channel, 5, addr, value, tdm)
 
-class LoadCmpVramInstruction(object):
+class LoadCmpVramInstruction(VRAMInstruction):
 
     def __init__(self, name, use_vram, addr, mask, tdm):
         # TODO: sanity checks on input values
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 5e6db0d7..42c34f06 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -32,7 +32,7 @@
 from QGL.PatternUtils import hash_pulse, flatten
 from QGL import TdmInstructions
 from QGL import APS2CustomInstructions
-from QGL.APS2CustomInstructions import APS2_CUSTOM_DECODE
+from QGL.APS2CustomInstructions import APS2_CUSTOM, APS2_CUSTOM_DECODE
 
 # Python 2/3 compatibility: use 'int' that subclasses 'long'
 from builtins import int
@@ -306,7 +306,10 @@ def __str__(self):
             store_addr = self.payload & 0xFFFF
             load_addr = (self.payload >> 16) & 0xFFFF
             instruction = (self.payload >> 32) & 0xFF
-            instructionAPS = TDM_CUSTOM_DECODE[instruction]
+            if self.decode_as_tdm:
+                instructionAPS = TDM_CUSTOM_DECODE[instruction]
+            else:
+                instructionAPS = APS2_CUSTOM_DECODE[instruction]
             out += " | instruction={0} ({1}), load_addr=0x{2:0x}, store_addr=0x{3:0x}".format(instruction, instructionAPS, load_addr, store_addr)
 
         elif instrOpCode == WRITEADDR:
@@ -510,12 +513,11 @@ def LoadCmpVram(addr, mask, label=None):
     payload = (1 << 48) | (mask << 16) | addr
     return Instruction(header, payload, label=label)
 
-
-def preprocess(seqs, shapeLib, clifford_set=False):
+def preprocess(seqs, shapeLib):
     seqs = PatternUtils.convert_lengths_to_samples(
         seqs, SAMPLING_RATE, ADDRESS_UNIT, Compiler.Waveform)
     wfLib = build_waveforms(seqs, shapeLib)
-    inject_modulation_cmds(seqs, force_phase_update=clifford_set)
+    inject_modulation_cmds(seqs)
     return seqs, wfLib
 
 
@@ -715,7 +717,7 @@ def synchronize_clocks(seqs):
     syncInstructions = [list(filter(
         lambda s: isinstance(s, ControlFlow.ControlInstruction), seq))
                         for seq in seqs if seq]
-
+    #import pdb; pdb.set_trace()
     # Add length to control-flow instructions to make accumulated time match at end of CFI.
     # Keep running tally of how much each channel has been shifted so far.
     localShift = [0 for _ in syncInstructions]
@@ -801,7 +803,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                     isinstance(entry, ControlFlow.ControlInstruction) or
                     isinstance(entry, BlockLabel.BlockLabel) or
                     isinstance(entry, TdmInstructions.CustomInstruction) or
-                    isinstance(entry, TdmInstructions.Instruction) or
+                    #isinstance(entry, TdmInstructions.Instruction) or ??????
                     isinstance(entry, TdmInstructions.LoadCmpVramInstruction)):
                 if isinstance(entry, BlockLabel.BlockLabel):
                     # carry label forward to next entry
@@ -835,11 +837,15 @@ def create_seq_instructions(seqs, offsets, label = None):
                     instructions.append(LoadCmpVram(entry.addr, entry.mask, label=label))
                 # some TDM instructions are ignored by the APS
                 elif isinstance(entry, TdmInstructions.CustomInstruction):
-                    pass
+                    try:
+                        instructions.append(Custom(entry.in_addr, entry.out_addr,
+                                                    APS2_CUSTOM[entry.instruction], label=label))
+                    except KeyError as e:
+                        raise Exception(f"Got unknown APS2 instruction: {e.args[0]} in {str(entry)}.")
                 elif isinstance(entry, TdmInstructions.WriteAddrInstruction):
                     if entry.instruction == 'INVALIDATE' and entry.tdm == False:
                         instructions.append(Invalidate(entry.addr, entry.value, label=label))
-
+                label=None #Reset label to prevent it propagating in a jump table
                 continue
 
             if seq_idx == 0:
@@ -983,20 +989,29 @@ def create_instr_data(seqs, offsets, cache_lines):
 
 
 def resolve_symbols(seq):
-    symbols = {}
-    # create symbol look-up table
-    for ct, entry in enumerate(seq):
-        if entry.label and entry.label not in symbols:
-            symbols[entry.label] = ct
-    # then update
-    for (ct, entry) in enumerate(seq):
-        if entry.target:
-            # find next available label. The TDM may miss some labels if branches only contain waveforms (which are ignored)
-            for k in range(len(seq)-ct):
-                temp = seq[ct+k]
-                if temp.target in symbols:
-                    break
-            entry.address = symbols[temp.target]
+
+    labeled_entries = [(idx, entry.label) for idx, entry in enumerate(seq) if entry.label is not None]
+    import pdb; pdb.set_trace()
+    symbols = {label: idx for idx, label in labeled_entries}
+    print(f"Found labels: {symbols}")
+    for entry in seq:
+        if entry.target is not None and entry.target in symbols.keys():
+            entry.address = symbols[entry.target]
+
+    # symbols = {}
+    # # create symbol look-up table
+    # for ct, entry in enumerate(seq):
+    #     if entry.label and entry.label not in symbols:
+    #         symbols[entry.label] = ct
+    # # then update
+    # for (ct, entry) in enumerate(seq):
+    #     if entry.target:
+    #         # find next available label. The TDM may miss some labels if branches only contain waveforms (which are ignored)
+    #         for k in range(len(seq)-ct):
+    #             temp = seq[ct+k]
+    #             if temp.label in symbols:
+    #                 break
+    #         entry.address = symbols[temp.label]
 
 
 def compress_marker(markerLL):

From c36c771e1738135d05047eef19b7647986bffe9c Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 25 Feb 2019 17:56:00 -0500
Subject: [PATCH 125/235] Remove debug.

---
 QGL/drivers/APS2Pattern.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 42c34f06..34c97797 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -991,7 +991,6 @@ def create_instr_data(seqs, offsets, cache_lines):
 def resolve_symbols(seq):
 
     labeled_entries = [(idx, entry.label) for idx, entry in enumerate(seq) if entry.label is not None]
-    import pdb; pdb.set_trace()
     symbols = {label: idx for idx, label in labeled_entries}
     print(f"Found labels: {symbols}")
     for entry in seq:

From b859abec0798d7619ad666ddff1e247bc1cd09e2 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 25 Feb 2019 21:33:07 -0500
Subject: [PATCH 126/235] Make sure Custom instructions not dropped by pattern
 generator!

---
 QGL/APS2CustomInstructions.py |  4 ++--
 QGL/Compiler.py               | 22 ++++++++++++++--------
 QGL/PulseSequencer.py         |  4 ++++
 QGL/RandomCliffordTools.py    | 14 +++++++++++++-
 QGL/drivers/APS2Pattern.py    |  6 +++---
 5 files changed, 36 insertions(+), 14 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index 6eb22054..3b269884 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -47,13 +47,13 @@
 
 def RandomCliffordSetOffset(addr, offset):
     return [Invalidate(addr, 0, tdm=False),
-            WriteAddr(adrr, offset, tdm=False),
+            WriteAddr(addr, offset, tdm=False),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
             CustomInstruction("APS_CLIFFORD_SET_OFFSET", addr, 0x3)]
 
 def RandomCliffordSetSpacing(addr, spacing):
     return [Invalidate(addr, 0, tdm=False),
-            WriteAddr(adrr, offset, tdm=False),
+            WriteAddr(addr, spacing, tdm=False),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
             CustomInstruction("APS_CLIFFORD_SET_SPACING", addr, 0x3)]
 
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index ce4992ab..57abd552 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -236,7 +236,15 @@ def generate_waveforms(physicalWires):
     return wfs
 
 def get_clifford_type(wire, allowed_types=("RandomAC")):
-    rt_pulses = [pulse for pulse in flatten(wire) if isinstance(pulse, Pulse) and pulse.isRunTime]
+    rt_pulses = []
+    for pulse in flatten(wire):
+        if isinstance(pulse, Pulse) and pulse.isRunTime:
+            rt_pulses.append(pulse)
+        elif isinstance(pulse, PulseBlock) and pulse.isRunTime:
+            for p in pulse.pulses.values():
+                if p.isRunTime:
+                    rt_pulses.append(p)
+
     if len(rt_pulses) == 0:
         return None
     pulse_type = list(set([pulse.label for pulse in rt_pulses]))
@@ -399,7 +407,6 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=
     if not validate_linklist_channels(wireSeqs.keys()):
         print("Compile to hardware failed")
         return
-
     logger.debug('')
     logger.debug("Now after gating constraints:")
     # apply gating constraints
@@ -671,10 +678,9 @@ def flatten_to_pulses(obj):
                 wires[chan] += [copy(block)]
             continue
         # control flow broadcasts to all channels if channel attribute is None
-        if isinstance(block, ControlFlow.ControlInstruction): #or
-                #isinstance(block, TdmInstructions.WriteAddrInstruction) or
-                #isinstance(block, TdmInstructions.CustomInstruction) or
-                #isinstance(block, TdmInstructions.LoadCmpVramInstruction)):
+        if (isinstance(block, ControlFlow.ControlInstruction) or
+                isinstance(block, TdmInstructions.VRAMInstruction) or
+                isinstance(block, TdmInstructions.CustomInstruction)):
             # Need to deal with attaching measurements and edges to control
             # instruction. Until we have a proper solution for that, we will
             # always broadcast control instructions to all channels
@@ -684,8 +690,8 @@ def flatten_to_pulses(obj):
                 wires[chan] += [copy(block)]
             continue
         #Don't propagate VRAM instructions
-        if isinstance(block, TdmInstructions.VRAMInstruction) or isinstance(block, TdmInstructions.CustomInstruction):
-            continue
+        #if isinstance(block, TdmInstructions.VRAMInstruction) or isinstance(block, TdmInstructions.CustomInstruction):
+        #    continue
         # propagate frame change from nodes to edges
         for chan in channels:
             if block.pulses[chan].frameChange == 0:
diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 463b273b..c29f43f8 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -198,6 +198,10 @@ def frameChange(self):
     def isZero(self):
         return all(p.isZero for p in self.pulses)
 
+    @property
+    def isRunTime(self):
+        return any(hasattr(entry, 'isRunTime') and entry.isRunTime for entry in self.pulses)
+
 
 class PulseBlock(object):
     '''
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index d4a0d26e..6863f0b4 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -66,16 +66,27 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
     for idx, seq in enumerate(seqs[:]):
         if not PatternUtils.contains_runtime_pulses(seq):
             continue
+
         new_seq = []
+
         for pulse in seq:
             if isinstance(pulse, Pulse) and pulse.isRunTime \
                 and pulse.label in VALID_CLIFFORD_TYPES:
                 has_random_cliff = True
                 new_seq.extend(RandomClifford(jt_label, cliff_addr))
-                #print("Inserting clifford pulse!")
+                print("Inserting clifford pulse!")
             else:
                 new_seq.append(pulse)
 
+        info_seqs = []
+        info_seqs.extend(RandomCliffordSetOffset(0x1, 0x0))
+        info_seqs.extend(RandomCliffordSetSpacing(0x2, 0x1))
+
+        if isinstance(seq[0], BlockLabel.BlockLabel):
+            new_seq[1:1] = info_seqs
+        else:
+            new_seq[0:0] = info_seqs
+
         if add_inv:
             #insert reset after first wait
             w_idx = next(i for i, v in enumerate(new_seq) if isinstance(v, ControlFlow.Wait))
@@ -88,6 +99,7 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
 
         seqs[idx] = new_seq
 
+
 def randomize_clifford_sequences(qubit, seqs, clifford_type=PulsePrimitives.RandomAC):
 
     c_seqs = [[clifford_type(qubit) for _ in seq] for seq in seqs]
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 34c97797..fef8ecd1 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -634,10 +634,10 @@ def inject_modulation_cmds(seqs, force_phase_update=False):
 
             #copies to avoid same object having different timestamps later
             #copy through BlockLabel
-            if isinstance(entry, BlockLabel.BlockLabel):
+            if isinstance(entry, BlockLabel.BlockLabel) or isinstance(entry, TdmInstructions.CustomInstruction):
                 mod_seq.append(copy(entry))
             #mostly copy through control-flow
-            elif isinstance(entry, ControlFlow.ControlInstruction) or isinstance(entry, TdmInstructions.LoadCmpVramInstruction) or isinstance(entry, TdmInstructions.WriteAddrInstruction):
+            elif isinstance(entry, ControlFlow.ControlInstruction) or isinstance(entry, TdmInstructions.VRAMInstruction):
                 #heuristic to insert phase reset before trigger if we have modulation commands
                 if isinstance(entry, ControlFlow.Wait):
                     if not ( no_modulation_cmds and (cur_freq == 0) and (cur_phase == 0)):
@@ -797,7 +797,6 @@ def create_seq_instructions(seqs, offsets, label = None):
 
         write_flags = [True] * len(entries)
         for ct, (entry, seq_idx) in enumerate(entries):
-
             #use first non empty sequence for control flow
             if seq_idx == first_non_empty and (
                     isinstance(entry, ControlFlow.ControlInstruction) or
@@ -837,6 +836,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                     instructions.append(LoadCmpVram(entry.addr, entry.mask, label=label))
                 # some TDM instructions are ignored by the APS
                 elif isinstance(entry, TdmInstructions.CustomInstruction):
+                    print(str(entry))
                     try:
                         instructions.append(Custom(entry.in_addr, entry.out_addr,
                                                     APS2_CUSTOM[entry.instruction], label=label))

From 0d356558d03a49475f018065666be54171cd7565 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Tue, 26 Feb 2019 09:44:03 -0500
Subject: [PATCH 127/235] Add DCsources and spec.analyzers to db

With relations to corresponding sources (for paramp bias) and LO
---
 QGL/ChannelLibraries.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 0f4bde94..c7955213 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -142,7 +142,10 @@ def get_current_channels(self):
                self.channelDatabase.receivers +
                self.channelDatabase.transceivers +
                self.channelDatabase.instruments +
-               self.channelDatabase.processors)
+               self.channelDatabase.processors +
+               self.channelDatabase.attenuators +
+               self.channelDatabase.DCSources +
+               self.channelDatabase.spectrum_analyzers)
 
     def update_channelDict(self):
         self.channelDict = {c.label: c for c in self.get_current_channels()}
@@ -315,11 +318,15 @@ def new_TDM(self, label, address):
 
     @check_for_duplicates
     def new_spectrum_analzyer(self, label, address, source):
-        return Channels.SpectrumAnalyzer(label=label, model="SpectrumAnalyzer", address=address, LO_source=source)
+        sa = Channels.SpectrumAnalyzer(label=label, model="SpectrumAnalyzer", address=address, LO_source=source, channel_db=self.channelDatabase)
+        self.add_and_update_dict(sa)
+        return sa
 
     @check_for_duplicates
     def new_DC_source(self, label, address):
-        return Channels.DCSource(label=label, model="YokogawaGS200", address=address, standalone=True)
+        dcsource = Channels.DCSource(label=label, model="YokogawaGS200", address=address, standalone=True, channel_db=self.channelDatabase)
+        self.add_and_update_dict(dcsource)
+        return dcsource
 
     @check_for_duplicates
     def new_APS2_rack(self, label, ip_addresses, tdm_ip=None):
@@ -386,7 +393,7 @@ def new_qubit(self, label, **kwargs):
         return thing
 
     @check_for_duplicates
-    def new_source(self, label, model, address, power=-30.0, frequency=5.0e9, reference=None):
+    def new_source(self, label, model, address, power=-30.0, frequency=5.0e9, reference='10MHz'):
         thing = Channels.Generator(label=label, model=model, address=address, power=power,
                                     frequency=frequency, reference=reference,
                                     channel_db=self.channelDatabase)

From 7380af300195f373e7b0082bd26362c8a8c82c53 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Tue, 26 Feb 2019 09:51:17 -0500
Subject: [PATCH 128/235] bqplot fixes

-GR
---
 QGL.egg-info/PKG-INFO             | 10 +++++++
 QGL.egg-info/SOURCES.txt          | 43 +++++++++++++++++++++++++++++++
 QGL.egg-info/dependency_links.txt |  1 +
 QGL.egg-info/requires.txt         |  6 +++++
 QGL.egg-info/top_level.txt        |  1 +
 QGL/PulseSequencePlotter.py       |  7 +++--
 6 files changed, 64 insertions(+), 4 deletions(-)
 create mode 100644 QGL.egg-info/PKG-INFO
 create mode 100644 QGL.egg-info/SOURCES.txt
 create mode 100644 QGL.egg-info/dependency_links.txt
 create mode 100644 QGL.egg-info/requires.txt
 create mode 100644 QGL.egg-info/top_level.txt

diff --git a/QGL.egg-info/PKG-INFO b/QGL.egg-info/PKG-INFO
new file mode 100644
index 00000000..ac9daf85
--- /dev/null
+++ b/QGL.egg-info/PKG-INFO
@@ -0,0 +1,10 @@
+Metadata-Version: 1.0
+Name: QGL
+Version: 2.1
+Summary: UNKNOWN
+Home-page: https://github.com/BBN-Q/QGL
+Author: UNKNOWN
+Author-email: UNKNOWN
+License: UNKNOWN
+Description: UNKNOWN
+Platform: UNKNOWN
diff --git a/QGL.egg-info/SOURCES.txt b/QGL.egg-info/SOURCES.txt
new file mode 100644
index 00000000..79998f6f
--- /dev/null
+++ b/QGL.egg-info/SOURCES.txt
@@ -0,0 +1,43 @@
+README.md
+setup.py
+QGL/BlockLabel.py
+QGL/ChannelLibraries.py
+QGL/Channels.py
+QGL/Cliffords.py
+QGL/Compiler.py
+QGL/ControlFlow.py
+QGL/GSTTools.py
+QGL/PatternUtils.py
+QGL/Plotting.py
+QGL/PulsePrimitives.py
+QGL/PulseSequencePlotter.py
+QGL/PulseSequencer.py
+QGL/PulseShapes.py
+QGL/Scheduler.py
+QGL/TdmInstructions.py
+QGL/Tomography.py
+QGL/__init__.py
+QGL/config.py
+QGL/config_location.py
+QGL/mm.py
+QGL.egg-info/PKG-INFO
+QGL.egg-info/SOURCES.txt
+QGL.egg-info/dependency_links.txt
+QGL.egg-info/requires.txt
+QGL.egg-info/top_level.txt
+QGL/BasicSequences/AllXY.py
+QGL/BasicSequences/BlankingSweeps.py
+QGL/BasicSequences/CR.py
+QGL/BasicSequences/Decoupling.py
+QGL/BasicSequences/Feedback.py
+QGL/BasicSequences/FlipFlop.py
+QGL/BasicSequences/RB.py
+QGL/BasicSequences/Rabi.py
+QGL/BasicSequences/SPAM.py
+QGL/BasicSequences/T1T2.py
+QGL/BasicSequences/__init__.py
+QGL/BasicSequences/helpers.py
+QGL/drivers/APS2Pattern.py
+QGL/drivers/APSPattern.py
+QGL/drivers/TekPattern.py
+QGL/drivers/__init__.py
\ No newline at end of file
diff --git a/QGL.egg-info/dependency_links.txt b/QGL.egg-info/dependency_links.txt
new file mode 100644
index 00000000..8b137891
--- /dev/null
+++ b/QGL.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/QGL.egg-info/requires.txt b/QGL.egg-info/requires.txt
new file mode 100644
index 00000000..fc2fa0c8
--- /dev/null
+++ b/QGL.egg-info/requires.txt
@@ -0,0 +1,6 @@
+bbndb>=0.1
+numpy>=1.11.1
+scipy>=0.17.1
+networkx>=1.11
+h5py>=2.6.0
+bokeh>=0.12.13
diff --git a/QGL.egg-info/top_level.txt b/QGL.egg-info/top_level.txt
new file mode 100644
index 00000000..0e533603
--- /dev/null
+++ b/QGL.egg-info/top_level.txt
@@ -0,0 +1 @@
+QGL
diff --git a/QGL/PulseSequencePlotter.py b/QGL/PulseSequencePlotter.py
index 5833a35b..27b61d87 100644
--- a/QGL/PulseSequencePlotter.py
+++ b/QGL/PulseSequencePlotter.py
@@ -25,8 +25,6 @@
 import os.path
 import json
 from importlib import import_module
-from ipywidgets import interact, VBox, IntSlider
-import ipywidgets as widgets
 import numpy as np
 
 from . import config
@@ -92,6 +90,7 @@ def plot_pulse_files(metafile, time=True, backend='bqplot'):
 
     if backend=='matplotlib':
         import matplotlib.pyplot as plt
+        from ipywidgets import interact, IntSlider
         def update_plot(seq_ind):
             for line_name in line_names:
                 dat = data_dicts[f"{line_name}_{seq_ind}"]
@@ -101,7 +100,7 @@ def update_plot(seq_ind):
     elif backend=='bqplot':
         from bqplot import DateScale, LinearScale, Axis, Lines, Figure, Tooltip
         from bqplot.colorschemes import CATEGORY10, CATEGORY20
-        from ipywidgets import interact, IntSlider
+        from ipywidgets import interact, IntSlider, VBox
         sx = LinearScale()
         sy = LinearScale(min=-1.0, max=2*len(line_names)-1.0)
         if time:
@@ -116,7 +115,7 @@ def update_plot(seq_ind):
         x_mult = 1.0e9 if time else 1
         for i, line_name in enumerate(line_names):
             dat = data_dicts[f"{line_name}_1"]
-            lines.append(Lines(labels=[line_name], x=x_mult*dat['x'], y=dat['y'], scales={'x': sx, 'y': sy}, 
+            lines.append(Lines(labels=[line_name], x=x_mult*dat['x'], y=dat['y'], scales={'x': sx, 'y': sy},
                                 tooltip=tt, animate=False, colors=[colors[i]]))
 
         slider = IntSlider(min=1, max=num_seqs, step=1, description='Segment', value=1)

From 923deb370852c5bca53d578a0fab243231fa5d87 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 10:50:59 -0500
Subject: [PATCH 129/235] Add color for custom instructions

---
 QGL/drivers/APS2Pattern.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index fef8ecd1..26a6e388 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1513,7 +1513,8 @@ def display_raw_file(filename):
 
         colors = {"WFM": QColor(0,200,0),
                   "GOTO": QColor(0,100,100),
-                  "MARKER": QColor(150,150,200)}
+                  "MARKER": QColor(150,150,200),
+                  "CUSTOM": QColor(200,65,200)}
 
         class App(QWidget):
 

From 160aeb1d98d68c65de5110bc24ec18976ea0c1b0 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 11:10:54 -0500
Subject: [PATCH 130/235] Don't drop WRITEADDR instructions!

---
 QGL/drivers/APS2Pattern.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 26a6e388..feb1049b 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -803,7 +803,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                     isinstance(entry, BlockLabel.BlockLabel) or
                     isinstance(entry, TdmInstructions.CustomInstruction) or
                     #isinstance(entry, TdmInstructions.Instruction) or ??????
-                    isinstance(entry, TdmInstructions.LoadCmpVramInstruction)):
+                    isinstance(entry, TdmInstructions.VRAMInstruction)):
                 if isinstance(entry, BlockLabel.BlockLabel):
                     # carry label forward to next entry
                     label = entry
@@ -843,8 +843,11 @@ def create_seq_instructions(seqs, offsets, label = None):
                     except KeyError as e:
                         raise Exception(f"Got unknown APS2 instruction: {e.args[0]} in {str(entry)}.")
                 elif isinstance(entry, TdmInstructions.WriteAddrInstruction):
+                    print(str(entry))
                     if entry.instruction == 'INVALIDATE' and entry.tdm == False:
                         instructions.append(Invalidate(entry.addr, entry.value, label=label))
+                    if entry.instruction == 'WRITEADDR' and entry.tdm == False:
+                        instructions.append(WriteAddr(entry.addr, entry.value, label=label))
                 label=None #Reset label to prevent it propagating in a jump table
                 continue
 
@@ -1514,7 +1517,8 @@ def display_raw_file(filename):
         colors = {"WFM": QColor(0,200,0),
                   "GOTO": QColor(0,100,100),
                   "MARKER": QColor(150,150,200),
-                  "CUSTOM": QColor(200,65,200)}
+                  "CUSTOM": QColor(200,65,200),
+                  "WRITEADDR": QColor(245, 105, 65)}
 
         class App(QWidget):
 

From 3d736f6dfe6878928bc6a51fba7513216d86e279 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 11:58:32 -0500
Subject: [PATCH 131/235] Add sequence debugger.

---
 QGL/test_helpers.py        |   0
 tests/aps_debug_watcher.py | 219 +++++++++++++++++++++++++++++++++++++
 2 files changed, 219 insertions(+)
 create mode 100644 QGL/test_helpers.py
 create mode 100644 tests/aps_debug_watcher.py

diff --git a/QGL/test_helpers.py b/QGL/test_helpers.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/aps_debug_watcher.py b/tests/aps_debug_watcher.py
new file mode 100644
index 00000000..4f389e8f
--- /dev/null
+++ b/tests/aps_debug_watcher.py
@@ -0,0 +1,219 @@
+#!/usr/bin/env python
+
+import sys
+import socket
+import struct
+try:
+    from QGL.drivers import APS2Pattern
+    haveQGL = True
+except:
+    haveQGL = False
+import numpy as np
+from ansicolor import * # from ansicolors
+
+ip = sys.argv[1]
+port = 0xbb50
+
+short_time = True
+
+raw_mode = '-r' in sys.argv
+tdm_mode = '-tdm' in sys.argv
+
+print("Connecting to APS Debug Port at {0}:{1}".format(ip,port))
+
+PACKET_SIZE=168//8+1
+
+if short_time:
+    PACKET_SIZE -= 2
+
+MODE_UNKNOWN = 0
+MODE_SEQUENCER = 1
+MODE_RAM = 2
+MODE_TRIGGER = 3
+
+def bittest(v, b):
+    if ((v & (1<<b)) == (1<<b)):
+        return red('T')
+    else:
+        return 'F'
+
+def get_bytes(a, s, e):
+    e += s
+    return a[s:e], e
+
+def formatHaltBits(haltBits):
+    haltSync = bittest(haltBits,5)
+    haltCustom = bittest(haltBits,4)
+    haltValid = bittest(haltBits,3)
+    haltWait = bittest(haltBits,2)
+    haltStr = "S:{} V:{} C:{} W:{}".format(haltSync, haltValid, haltCustom, haltWait)
+    return haltStr
+
+
+
+s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+s.connect((ip,port))
+print("Connected")
+print(s)
+extraData = b''
+while 1:
+    data = extraData + s.recv(10*PACKET_SIZE)
+    num_packets = len(data) // PACKET_SIZE
+    num_excess = len(data) % PACKET_SIZE
+    block_size = num_packets*PACKET_SIZE
+    extraData = b''
+    if num_excess > 0:
+        extraData = data[block_size:]
+        data = data[:block_size]
+
+    for cnt in range(num_packets):
+        start = cnt * PACKET_SIZE
+        end = (cnt+1)*PACKET_SIZE
+        packet = data[start:end]
+        packet_bytes = bytearray(packet)
+        if raw_mode:
+            print(packet_bytes)
+            continue
+
+        if packet[0] ==  0x1:
+            mode = MODE_SEQUENCER
+        elif packet[0] in [0x2,0x3, 0x4, 0x5]:
+            mode = MODE_RAM
+        elif packet[0] == 0x6:
+            mode = MODE_TRIGGER
+        else:
+            mode = MODE_UNKNOWN
+
+
+        if short_time:
+            uptime_seconds = packet_bytes[1:3]
+            uptime_nanoseconds = packet_bytes[3:7]
+
+            uptime_seconds = struct.unpack(">H", uptime_seconds)[0]
+        else:
+            uptime_seconds = packet_bytes[1:5]
+            uptime_nanoseconds = packet_bytes[5:9]
+
+            uptime_seconds = struct.unpack(">I", uptime_seconds)[0]
+
+        uptime_nanoseconds = struct.unpack(">I", uptime_nanoseconds)[0]
+
+        #print(uptime_seconds, uptime_nanoseconds)
+
+        uptime_nanoseconds = uptime_nanoseconds/1e9
+        uptime = uptime_seconds + uptime_nanoseconds
+
+        if short_time:
+            start = 8
+        else:
+            start = 10
+
+        if mode == MODE_SEQUENCER:
+
+            if short_time:
+                triggerWord = packet[7]
+            else:
+                triggerWord = packet[9]
+
+            haltBits = packet[start]
+
+            haltStr = formatHaltBits(haltBits)
+
+            instructionAddr, start = get_bytes(packet, start, 4)
+            instructionAddr = bytearray(instructionAddr)
+            # clear halt bits, only the first two bits are part of the Addr
+            instructionAddr[0] = instructionAddr[0] & 0x3
+            instructionAddr = struct.unpack(">I", instructionAddr)[0]
+
+            seq_debug_data, start = get_bytes(packet, start, 8)
+            seq_debug_data = np.fromstring(seq_debug_data[::-1], dtype=np.uint64)
+
+            if haveQGL:
+                instruction = APS2Pattern.Instruction.unflatten(seq_debug_data, decode_as_tdm = tdm_mode)
+            else:
+                instruction = ''
+
+            h = "{:016x}".format(seq_debug_data[0]).upper()
+
+            print(red("{:10}".format("Sequencer")), \
+                  white(": {:4}".format(instructionAddr)),\
+                  blue("0x{}".format(h)), \
+                  yellow(" {:6.8f}".format(uptime)), \
+                  haltStr, \
+                  "T:0x{:x}".format(triggerWord), \
+                  " {} ".format(instruction))
+            # if instructionAddr > 100:
+            #    sys.exit()
+        elif mode == MODE_RAM:
+
+            zeros, start = get_bytes(packet, start, 4)
+            vram_addr, start = get_bytes(packet, start, 4)
+            vram_data, start = get_bytes(packet, start, 4)
+
+            vram_header = struct.unpack(">I", zeros)[0]
+            vram_addr = struct.unpack(">I", vram_addr)[0]
+            vram_data = struct.unpack(">I", vram_data)[0]
+
+            if packet[0] == 0x2:
+                ram_mode = "Valid"
+
+            if packet[0] == 0x3:
+                ram_mode = "Write"
+
+            if packet[0] == 0x4:
+                ram_mode = "Send"
+
+            if packet[0] == 0x5:
+                ram_mode = "Recv"
+
+            print(green("{:10}".format("RAM")), \
+                  white(": {:>23}".format(ram_mode)),\
+                  yellow(" {:6.8f}".format(uptime)), \
+                  "addr = 0x{:08X} data = 0x{:08X}".format(vram_addr, vram_data))
+
+        elif mode == MODE_TRIGGER:
+
+            zeros, start = get_bytes(packet, start, 8)
+            syncBits, start = get_bytes(packet,start,1)
+            haltBits, start = get_bytes(packet, start, 1)
+            triggers, start = get_bytes(packet, start, 1)
+            triggerWord, start = get_bytes(packet,start,1)
+
+            for z in zeros:
+                if z != 0:
+                    print("Error expected 0 not", z)
+
+            haltBits = haltBits[0]
+            syncBits = syncBits[0]
+            triggers = triggers[0]
+            triggerWord = triggerWord[0]
+
+            haltStr = formatHaltBits(haltBits)
+
+            syncWF = (syncBits >> 3) & 0xF
+            syncMarker = (syncBits >> 1) & 0x3
+            syncMod = syncBits & 0x1
+
+
+            halt = bittest(syncBits,4)
+            pc_jump = bittest(syncBits, 5)
+            tready = bittest(syncBits, 6)
+            tvalid = bittest(syncBits, 7)
+
+            syncStr = "TV: {} TR: {} PJ: {} H: {} SWF: 0x{} SMa: 0x{} SMo: 0x{}".format(tvalid, tready, pc_jump, halt, syncWF, syncMarker, syncMod)
+
+            trigger = bittest(triggers,1)
+            triggerWordValid = bittest(triggers,0)
+
+            triggerStr = "t = {} tWV = {} tW = 0x{:0X}".format(trigger,triggerWordValid, triggerWord)
+
+            print(green("{:10}".format("Trigger")), \
+                  white(": {:>23}".format('')),\
+                  yellow(" {:6.8f}".format(uptime)), \
+                  haltStr, \
+                  syncStr, \
+                  triggerStr)
+        elif mode == MODE_UNKNOWN:
+            print(green("{:10}".format("Unknown")),packet_bytes)
+
+s.close()

From b7a15f741e3d1f6cd3ac44eca689fdd9dac55295 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 14:31:14 -0500
Subject: [PATCH 132/235] Properly set indirect mode on CALL

---
 QGL/APS2CustomInstructions.py |  4 ++--
 QGL/ControlFlow.py            |  6 +++---
 QGL/drivers/APS2Pattern.py    | 25 ++++++++++++++++++-------
 3 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index 3b269884..1d93cf38 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -61,13 +61,13 @@ def RandomClifford(target, addr):
     return [Invalidate(addr, 0, tdm=False),
             CustomInstruction("APS_CLIFFORD_RAND", 0x0, addr),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
-            Call(target, load_addr=True)]
+            Call(target, indirect=True)]
 
 def RandomCliffordInverse(target, addr):
     return [Invalidate(addr, 0, tdm=False),
             CustomInstruction("APS_CLIFFORD_INVERSE", 0x0, addr),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
-            Call(target, load_addr=True)]
+            Call(target, indirect=True)]
 
 def RandomCliffordInverseReset(addr): #for now don't use addr
     return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0xF)
diff --git a/QGL/ControlFlow.py b/QGL/ControlFlow.py
index 5894d2f1..cc1e6327 100644
--- a/QGL/ControlFlow.py
+++ b/QGL/ControlFlow.py
@@ -150,15 +150,15 @@ def __init__(self, target):
 
 class Call(ControlInstruction):
     # target is a BlockLabel
-    def __init__(self, target, load_addr=False):
+    def __init__(self, target, indirect=False):
         super(Call, self).__init__("CALL", target=target)
-        self.load_addr = load_addr
+        self.indirect = indirect
 
     def __str__(self):
         if self.load_addr:
             return f"{self.instruction}({str(self.target)})"
         else:
-            return f"{self.instruction}({str(self.target)}, LOAD)"
+            return f"{self.instruction}({str(self.target)}, INDIRECT)"
 
 
 
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index feb1049b..eb9ccfe4 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -341,12 +341,11 @@ def __str__(self):
         elif instrOpCode == LOADCMP:
             addr = self.payload & 0xFFFF
             mask = (self.payload >> 16) & 0xFFFF
-            use_ram = (self.payload >> 48) & 0x1
-            if self.decode_as_tdm and not use_ram:
+            if self.decode_as_tdm and not self.use_ram:
                 out += "WAITMEAS"
             else:
                 src = "EXT"
-                if use_ram:
+                if self.use_ram:
                     src = "RAM"
                 out += "LOADCMP | source={0}, addr=0x{1:0x}, read_mask=0x{2:0x}".format(src, addr, mask)
         return out
@@ -374,7 +373,17 @@ def writeFlag(self):
 
     @writeFlag.setter
     def writeFlag(self, value):
-        self.header |= value & 0x1
+        self.header &= ~(0x1 << 0) #clear bit
+        self.header |= (value & 0x1) #set bit
+
+    @property
+    def use_ram(self):
+        return ((self.payload >> 48) & 0x1)
+
+    @use_ram.setter
+    def use_ram(self, value):
+        self.payload &= ~(0x1 << 48) #clear bit
+        self.payload |= ((value & 0x1) << 48)
 
     @property
     def opcode(self):
@@ -447,8 +456,10 @@ def Goto(addr, label=None):
     return Command(GOTO, addr, label=label)
 
 
-def Call(addr, load_addr=False, label=None):
-    return Command(CALL, addr, label=label, write=load_addr)
+def Call(addr, indirect=False, label=None):
+    cmd = Command(CALL, addr, label=label)
+    cmd.use_ram = indirect
+    return cmd
 
 
 def Return(label=None):
@@ -821,7 +832,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                 elif isinstance(entry, ControlFlow.Goto):
                     instructions.append(Goto(entry.target, label=label))
                 elif isinstance(entry, ControlFlow.Call):
-                    instructions.append(Call(entry.target, load_addr = entry.load_addr, label=label))
+                    instructions.append(Call(entry.target, indirect = entry.indirect, label=label))
                 elif isinstance(entry, ControlFlow.Repeat):
                     instructions.append(Repeat(entry.target, label=label))
                 # value argument commands

From 5d641c0ae2e810636b3e202ab4c75d06a770df5a Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 14:55:27 -0500
Subject: [PATCH 133/235] Fix block labels on Calls.

---
 QGL/RandomCliffordTools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index 6863f0b4..d4fc97bb 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -43,14 +43,14 @@ def generate_clifford_jump_table(cliff_wires, jt_label = None):
     if not isinstance(jt_label, BlockLabel.BlockLabel):
         raise ValueError("Jump table label must be a BlockLabel.")
 
-    cliff_labels = [f"C{n}" for n in range(24)]
+    cliff_labels = [BlockLabel.BlockLabel(f"C{n}") for n in range(24)]
     jump_table = [jt_label]
     for cl in cliff_labels:
         jump_table.append(ControlFlow.Call(cl))
         jump_table.append(ControlFlow.Return())
 
     for cliff, cl in zip(cliff_wires, cliff_labels):
-        cliff.insert(0, BlockLabel.BlockLabel(cl))
+        cliff.insert(0, cl)
         cliff.append(ControlFlow.Return())
 
     cliff_wires.insert(0, jump_table)

From f02bdb296751fb7b6f5abb85c5b694cbdfd88b76 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 14:55:40 -0500
Subject: [PATCH 134/235] Make more pretty

---
 QGL/drivers/APS2Pattern.py | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index eb9ccfe4..e88e8d79 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1523,16 +1523,25 @@ def display_raw_file(filename):
     if len(sys.argv) == 2:
 
         from PyQt5.QtWidgets import QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView
-        from PyQt5.QtGui import QIcon, QColor
+        from PyQt5.QtGui import QIcon, QColor, QFont
+
+        table_font = QFont("Arial", weight=57)
 
         colors = {"WFM": QColor(0,200,0),
                   "GOTO": QColor(0,100,100),
                   "MARKER": QColor(150,150,200),
                   "CUSTOM": QColor(200,65,200),
-                  "WRITEADDR": QColor(245, 105, 65)}
+                  "WRITEADDR": QColor(245, 105, 65),
+                  "INVALIDATE": QColor(245, 105, 65),
+                  "CALL": QColor(65, 205, 245),
+                  "RET": QColor(65, 205, 245),
+                  "LOADCMP": QColor(245, 225, 65),
+                  "MODULATION": QColor(175, 255, 185)}
 
         class App(QWidget):
 
+            COLUMN_COUNT = 7
+
             def __init__(self, instructions):
                 super().__init__()
                 self.title = 'APS2 Disassembled Instructions'
@@ -1559,7 +1568,7 @@ def createTable(self):
                # Create table
                 self.tableWidget = QTableWidget()
                 self.tableWidget.setRowCount(len(self.instructions))
-                self.tableWidget.setColumnCount(7)
+                self.tableWidget.setColumnCount(self.COLUMN_COUNT)
 
                 for k, instr in enumerate(self.instructions):
                     fields = str(instr).replace(',','').replace(';', '').split(" ")
@@ -1572,9 +1581,17 @@ def createTable(self):
                     for l, f in enumerate(fields):
                         text = fields[l]
                         item = QTableWidgetItem(text)
+                        item.setFont(table_font)
                         if color:
                             item.setBackground(color)
                         self.tableWidget.setItem(k,l, item)
+                    if l < self.COLUMN_COUNT-1:
+                        for j in range(l+1, self.COLUMN_COUNT):
+                            item = QTableWidgetItem("")
+                            if color:
+                                item.setBackground(color)
+                            self.tableWidget.setItem(k, j, item)
+
                 self.tableWidget.move(0,0)
                 self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
 

From b9a2ff0f754a48a686812c27dbd4d9ff28ccca53 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 14:59:42 -0500
Subject: [PATCH 135/235] Bold font

---
 QGL/drivers/APS2Pattern.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index e88e8d79..12bbfddf 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1525,7 +1525,7 @@ def display_raw_file(filename):
         from PyQt5.QtWidgets import QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView
         from PyQt5.QtGui import QIcon, QColor, QFont
 
-        table_font = QFont("Arial", weight=57)
+        table_font = QFont("Arial", weight=QFont.Bold)
 
         colors = {"WFM": QColor(0,200,0),
                   "GOTO": QColor(0,100,100),

From bae3736fa9bb3e83c94359f7a0f68597d7459378 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 26 Feb 2019 15:03:23 -0500
Subject: [PATCH 136/235] Get rid of accidental egg-info files

---
 QGL.egg-info/PKG-INFO             | 10 -------
 QGL.egg-info/SOURCES.txt          | 43 -------------------------------
 QGL.egg-info/dependency_links.txt |  1 -
 QGL.egg-info/requires.txt         |  6 -----
 QGL.egg-info/top_level.txt        |  1 -
 5 files changed, 61 deletions(-)
 delete mode 100644 QGL.egg-info/PKG-INFO
 delete mode 100644 QGL.egg-info/SOURCES.txt
 delete mode 100644 QGL.egg-info/dependency_links.txt
 delete mode 100644 QGL.egg-info/requires.txt
 delete mode 100644 QGL.egg-info/top_level.txt

diff --git a/QGL.egg-info/PKG-INFO b/QGL.egg-info/PKG-INFO
deleted file mode 100644
index ac9daf85..00000000
--- a/QGL.egg-info/PKG-INFO
+++ /dev/null
@@ -1,10 +0,0 @@
-Metadata-Version: 1.0
-Name: QGL
-Version: 2.1
-Summary: UNKNOWN
-Home-page: https://github.com/BBN-Q/QGL
-Author: UNKNOWN
-Author-email: UNKNOWN
-License: UNKNOWN
-Description: UNKNOWN
-Platform: UNKNOWN
diff --git a/QGL.egg-info/SOURCES.txt b/QGL.egg-info/SOURCES.txt
deleted file mode 100644
index 79998f6f..00000000
--- a/QGL.egg-info/SOURCES.txt
+++ /dev/null
@@ -1,43 +0,0 @@
-README.md
-setup.py
-QGL/BlockLabel.py
-QGL/ChannelLibraries.py
-QGL/Channels.py
-QGL/Cliffords.py
-QGL/Compiler.py
-QGL/ControlFlow.py
-QGL/GSTTools.py
-QGL/PatternUtils.py
-QGL/Plotting.py
-QGL/PulsePrimitives.py
-QGL/PulseSequencePlotter.py
-QGL/PulseSequencer.py
-QGL/PulseShapes.py
-QGL/Scheduler.py
-QGL/TdmInstructions.py
-QGL/Tomography.py
-QGL/__init__.py
-QGL/config.py
-QGL/config_location.py
-QGL/mm.py
-QGL.egg-info/PKG-INFO
-QGL.egg-info/SOURCES.txt
-QGL.egg-info/dependency_links.txt
-QGL.egg-info/requires.txt
-QGL.egg-info/top_level.txt
-QGL/BasicSequences/AllXY.py
-QGL/BasicSequences/BlankingSweeps.py
-QGL/BasicSequences/CR.py
-QGL/BasicSequences/Decoupling.py
-QGL/BasicSequences/Feedback.py
-QGL/BasicSequences/FlipFlop.py
-QGL/BasicSequences/RB.py
-QGL/BasicSequences/Rabi.py
-QGL/BasicSequences/SPAM.py
-QGL/BasicSequences/T1T2.py
-QGL/BasicSequences/__init__.py
-QGL/BasicSequences/helpers.py
-QGL/drivers/APS2Pattern.py
-QGL/drivers/APSPattern.py
-QGL/drivers/TekPattern.py
-QGL/drivers/__init__.py
\ No newline at end of file
diff --git a/QGL.egg-info/dependency_links.txt b/QGL.egg-info/dependency_links.txt
deleted file mode 100644
index 8b137891..00000000
--- a/QGL.egg-info/dependency_links.txt
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/QGL.egg-info/requires.txt b/QGL.egg-info/requires.txt
deleted file mode 100644
index fc2fa0c8..00000000
--- a/QGL.egg-info/requires.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-bbndb>=0.1
-numpy>=1.11.1
-scipy>=0.17.1
-networkx>=1.11
-h5py>=2.6.0
-bokeh>=0.12.13
diff --git a/QGL.egg-info/top_level.txt b/QGL.egg-info/top_level.txt
deleted file mode 100644
index 0e533603..00000000
--- a/QGL.egg-info/top_level.txt
+++ /dev/null
@@ -1 +0,0 @@
-QGL

From 15f0615fe8e1ca48f4731e4a514f67430fabe82a Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 26 Feb 2019 15:57:16 -0500
Subject: [PATCH 137/235] Added goto buttons and waveform plotters to APS2
 disassembler

---
 QGL/drivers/APS2Pattern.py | 85 ++++++++++++++++++++++++++++++++++----
 1 file changed, 76 insertions(+), 9 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 12bbfddf..9b073f7a 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1492,6 +1492,23 @@ def read_instructions(filename):
     raw_instrs = raw_instructions(filename)
     return decompile_instructions(raw_instrs)
 
+def read_waveforms(filename):
+    with open(filename, 'rb') as FID:
+        target_hw    = FID.read(4).decode('utf-8')
+        file_version = struct.unpack('<f', FID.read(4))[0]
+        min_fw       = struct.unpack('<f', FID.read(4))[0]
+        num_chans    = struct.unpack('<H', FID.read(2))[0]
+
+        inst_len     = struct.unpack('<Q', FID.read(8))[0]
+        instructions = np.frombuffer(FID.read(8*inst_len), dtype=np.uint64)
+
+        wf_dat = []
+        for i in range(num_chans):
+            wf_len  = struct.unpack('<Q', FID.read(8))[0]
+            dat = ( 1.0 / MAX_WAVEFORM_VALUE) * np.frombuffer(FID.read(2*wf_len), dtype=np.int16).flatten()
+            wf_dat.append(dat)
+        return wf_dat
+
 def replace_instructions(filename, instructions, channel = 1):
     channelStr =  get_channel_instructions_string(channel)
     with h5py.File(filename, 'r+') as fid:
@@ -1522,9 +1539,12 @@ def display_raw_file(filename):
 if __name__ == '__main__':
     if len(sys.argv) == 2:
 
-        from PyQt5.QtWidgets import QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView
+        from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView, QPushButton
         from PyQt5.QtGui import QIcon, QColor, QFont
 
+        from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg
+        from matplotlib.figure import Figure
+
         table_font = QFont("Arial", weight=QFont.Bold)
 
         colors = {"WFM": QColor(0,200,0),
@@ -1538,11 +1558,35 @@ def display_raw_file(filename):
                   "LOADCMP": QColor(245, 225, 65),
                   "MODULATION": QColor(175, 255, 185)}
 
+        class MatplotlibWidget(QWidget):
+            def __init__(self, I, Q, parent=None):
+                super(MatplotlibWidget, self).__init__(parent)
+                self.title = 'Waveform'
+                self.left = 100
+                self.top = 100
+                self.width = 800
+                self.height = 600
+                self.setWindowTitle(self.title)
+                self.setGeometry(self.left, self.top, self.width, self.height)
+
+                self.figure = Figure()
+                self.canvas = FigureCanvasQTAgg(self.figure)
+
+                self.axis = self.figure.add_subplot(111)
+                self.axis.plot(I)
+                self.axis.plot(Q)
+                self.layout = QVBoxLayout(self)
+                self.layout.addWidget(self.canvas)
+                self.setLayout(self.layout)
+                self.canvas.draw()
+                self.show()
+
+
         class App(QWidget):
 
             COLUMN_COUNT = 7
 
-            def __init__(self, instructions):
+            def __init__(self, instructions, waveforms):
                 super().__init__()
                 self.title = 'APS2 Disassembled Instructions'
                 self.left = 100
@@ -1550,7 +1594,10 @@ def __init__(self, instructions):
                 self.width = 1000
                 self.height = 1200
                 self.instructions = instructions
+                self.waveforms = waveforms
+                print(self.waveforms)
                 self.initUI()
+                self.plotters = []
 
             def initUI(self):
                 self.setWindowTitle(self.title)
@@ -1580,11 +1627,31 @@ def createTable(self):
                         color = None
                     for l, f in enumerate(fields):
                         text = fields[l]
-                        item = QTableWidgetItem(text)
-                        item.setFont(table_font)
-                        if color:
-                            item.setBackground(color)
-                        self.tableWidget.setItem(k,l, item)
+                        if text == "GOTO":
+                            btn = QPushButton(self.tableWidget)
+                            btn.setText('GOTO')
+                            target_row = int(fields[1].split("=")[1])
+                            def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
+                                tab.scrollToItem(tab.item(row, 0))
+                            btn.clicked.connect(scroll_to_goto_target)
+                            self.tableWidget.setCellWidget(k, l, btn)
+                        if text == "WFM" and int(fields[4].split("=")[1])==0:
+                            # Not a TA pair
+                            btn = QPushButton(self.tableWidget)
+                            btn.setText('WFM')
+                            addr = int(fields[6].split("=")[1])
+                            count = int(fields[5].split("=")[1])
+                            def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
+                                w = MatplotlibWidget(I,Q)
+                                self.plotters.append(w)
+                            btn.clicked.connect(open_plotter)
+                            self.tableWidget.setCellWidget(k, l, btn)
+                        else:
+                            item = QTableWidgetItem(text)
+                            item.setFont(table_font)
+                            if color:
+                                item.setBackground(color)
+                            self.tableWidget.setItem(k, l, item)
                     if l < self.COLUMN_COUNT-1:
                         for j in range(l+1, self.COLUMN_COUNT):
                             item = QTableWidgetItem("")
@@ -1594,7 +1661,7 @@ def createTable(self):
 
                 self.tableWidget.move(0,0)
                 self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
-
+        
         app = QApplication(sys.argv[:1])
-        ex = App(read_instructions(sys.argv[1]))
+        ex = App(read_instructions(sys.argv[1]), read_waveforms(sys.argv[1]))
         sys.exit(app.exec_())

From 4d2acd64f5e99dc6835276fb91fc101f6fbb130e Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 26 Feb 2019 21:34:53 -0500
Subject: [PATCH 138/235] Nice looking buttons for WFM and GOTO in disassembler

---
 QGL/drivers/APS2Pattern.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 9b073f7a..ee341326 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1595,7 +1595,6 @@ def __init__(self, instructions, waveforms):
                 self.height = 1200
                 self.instructions = instructions
                 self.waveforms = waveforms
-                print(self.waveforms)
                 self.initUI()
                 self.plotters = []
 
@@ -1634,17 +1633,19 @@ def createTable(self):
                             def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
                                 tab.scrollToItem(tab.item(row, 0))
                             btn.clicked.connect(scroll_to_goto_target)
+                            btn.setStyleSheet("background-color: #006464; color: white; font-weight: bold; text-align: left;")
                             self.tableWidget.setCellWidget(k, l, btn)
                         if text == "WFM" and int(fields[4].split("=")[1])==0:
                             # Not a TA pair
                             btn = QPushButton(self.tableWidget)
-                            btn.setText('WFM')
+                            btn.setText(' WFM')
                             addr = int(fields[6].split("=")[1])
                             count = int(fields[5].split("=")[1])
                             def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
                                 w = MatplotlibWidget(I,Q)
                                 self.plotters.append(w)
                             btn.clicked.connect(open_plotter)
+                            btn.setStyleSheet("background-color: #00C800; color: white; font-weight: bold; text-align: left;")
                             self.tableWidget.setCellWidget(k, l, btn)
                         else:
                             item = QTableWidgetItem(text)

From b7e611ea4b268292434078898dcd865d019b0b96 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 27 Feb 2019 10:21:02 -0500
Subject: [PATCH 139/235] Move disassembler to utils directory

---
 QGL/drivers/APS2Pattern.py | 131 -------------------------------
 utils/disassemble_aps.py   | 157 +++++++++++++++++++++++++++++++++++++
 2 files changed, 157 insertions(+), 131 deletions(-)
 create mode 100755 utils/disassemble_aps.py

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index ee341326..2cc0aa03 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1535,134 +1535,3 @@ def display_raw_instructions(raw):
 def display_raw_file(filename):
     raw = raw_instructions(filename)
     display_raw_instructions(raw)
-
-if __name__ == '__main__':
-    if len(sys.argv) == 2:
-
-        from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView, QPushButton
-        from PyQt5.QtGui import QIcon, QColor, QFont
-
-        from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg
-        from matplotlib.figure import Figure
-
-        table_font = QFont("Arial", weight=QFont.Bold)
-
-        colors = {"WFM": QColor(0,200,0),
-                  "GOTO": QColor(0,100,100),
-                  "MARKER": QColor(150,150,200),
-                  "CUSTOM": QColor(200,65,200),
-                  "WRITEADDR": QColor(245, 105, 65),
-                  "INVALIDATE": QColor(245, 105, 65),
-                  "CALL": QColor(65, 205, 245),
-                  "RET": QColor(65, 205, 245),
-                  "LOADCMP": QColor(245, 225, 65),
-                  "MODULATION": QColor(175, 255, 185)}
-
-        class MatplotlibWidget(QWidget):
-            def __init__(self, I, Q, parent=None):
-                super(MatplotlibWidget, self).__init__(parent)
-                self.title = 'Waveform'
-                self.left = 100
-                self.top = 100
-                self.width = 800
-                self.height = 600
-                self.setWindowTitle(self.title)
-                self.setGeometry(self.left, self.top, self.width, self.height)
-
-                self.figure = Figure()
-                self.canvas = FigureCanvasQTAgg(self.figure)
-
-                self.axis = self.figure.add_subplot(111)
-                self.axis.plot(I)
-                self.axis.plot(Q)
-                self.layout = QVBoxLayout(self)
-                self.layout.addWidget(self.canvas)
-                self.setLayout(self.layout)
-                self.canvas.draw()
-                self.show()
-
-
-        class App(QWidget):
-
-            COLUMN_COUNT = 7
-
-            def __init__(self, instructions, waveforms):
-                super().__init__()
-                self.title = 'APS2 Disassembled Instructions'
-                self.left = 100
-                self.top = 100
-                self.width = 1000
-                self.height = 1200
-                self.instructions = instructions
-                self.waveforms = waveforms
-                self.initUI()
-                self.plotters = []
-
-            def initUI(self):
-                self.setWindowTitle(self.title)
-                self.setGeometry(self.left, self.top, self.width, self.height)
-
-                self.createTable()
-                self.layout = QVBoxLayout()
-                self.layout.addWidget(self.tableWidget)
-                self.setLayout(self.layout)
-
-                # Show widget
-                self.show()
-
-            def createTable(self):
-               # Create table
-                self.tableWidget = QTableWidget()
-                self.tableWidget.setRowCount(len(self.instructions))
-                self.tableWidget.setColumnCount(self.COLUMN_COUNT)
-
-                for k, instr in enumerate(self.instructions):
-                    fields = str(instr).replace(',','').replace(';', '').split(" ")
-                    if "|" in fields:
-                        fields.remove("|")
-                    if fields[0] in colors:
-                        color = colors[fields[0]]
-                    else:
-                        color = None
-                    for l, f in enumerate(fields):
-                        text = fields[l]
-                        if text == "GOTO":
-                            btn = QPushButton(self.tableWidget)
-                            btn.setText('GOTO')
-                            target_row = int(fields[1].split("=")[1])
-                            def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
-                                tab.scrollToItem(tab.item(row, 0))
-                            btn.clicked.connect(scroll_to_goto_target)
-                            btn.setStyleSheet("background-color: #006464; color: white; font-weight: bold; text-align: left;")
-                            self.tableWidget.setCellWidget(k, l, btn)
-                        if text == "WFM" and int(fields[4].split("=")[1])==0:
-                            # Not a TA pair
-                            btn = QPushButton(self.tableWidget)
-                            btn.setText(' WFM')
-                            addr = int(fields[6].split("=")[1])
-                            count = int(fields[5].split("=")[1])
-                            def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
-                                w = MatplotlibWidget(I,Q)
-                                self.plotters.append(w)
-                            btn.clicked.connect(open_plotter)
-                            btn.setStyleSheet("background-color: #00C800; color: white; font-weight: bold; text-align: left;")
-                            self.tableWidget.setCellWidget(k, l, btn)
-                        else:
-                            item = QTableWidgetItem(text)
-                            item.setFont(table_font)
-                            if color:
-                                item.setBackground(color)
-                            self.tableWidget.setItem(k, l, item)
-                    if l < self.COLUMN_COUNT-1:
-                        for j in range(l+1, self.COLUMN_COUNT):
-                            item = QTableWidgetItem("")
-                            if color:
-                                item.setBackground(color)
-                            self.tableWidget.setItem(k, j, item)
-
-                self.tableWidget.move(0,0)
-                self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
-        
-        app = QApplication(sys.argv[:1])
-        ex = App(read_instructions(sys.argv[1]), read_waveforms(sys.argv[1]))
-        sys.exit(app.exec_())
diff --git a/utils/disassemble_aps.py b/utils/disassemble_aps.py
new file mode 100755
index 00000000..1b7919c4
--- /dev/null
+++ b/utils/disassemble_aps.py
@@ -0,0 +1,157 @@
+#!/usr/bin/env python
+
+import numpy as np
+import sys
+import os.path
+
+from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView, QPushButton
+from PyQt5.QtGui import QIcon, QColor, QFont
+from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg
+from matplotlib.figure import Figure
+
+colors = {"WFM": QColor(0,200,0),
+          "GOTO": QColor(0,100,100),
+          "MARKER": QColor(150,150,200),
+          "CUSTOM": QColor(200,65,200),
+          "WRITEADDR": QColor(245, 105, 65),
+          "INVALIDATE": QColor(245, 105, 65),
+          "CALL": QColor(65, 205, 245),
+          "RET": QColor(65, 205, 245),
+          "LOADCMP": QColor(245, 225, 65),
+          "MODULATION": QColor(175, 255, 185)}
+
+table_font = QFont("Arial", weight=QFont.Bold)
+
+class MatplotlibWidget(QWidget):
+    def __init__(self, I, Q, parent=None):
+        super(MatplotlibWidget, self).__init__(parent)
+        self.title  = 'Waveform'
+        self.left   = 100
+        self.top    = 100
+        self.width  = 800
+        self.height = 600
+        self.setWindowTitle(self.title)
+        self.setGeometry(self.left, self.top, self.width, self.height)
+
+        self.figure = Figure()
+        self.canvas = FigureCanvasQTAgg(self.figure)
+
+        self.axis = self.figure.add_subplot(111)
+        self.axis.plot(I)
+        self.axis.plot(Q)
+        self.layout = QVBoxLayout(self)
+        self.layout.addWidget(self.canvas)
+        self.setLayout(self.layout)
+        self.canvas.draw()
+        self.show()
+
+
+class DisassemblerApp(QWidget):
+
+    COLUMN_COUNT = 7
+
+    def __init__(self, instructions, waveforms):
+        super().__init__()
+        self.title  = 'APS2 Disassembled Instructions'
+        self.left   = 100
+        self.top    = 100
+        self.width  = 1000
+        self.height = 1200
+        self.instructions = instructions
+        self.waveforms = waveforms
+        self.initUI()
+        self.plotters = []
+
+    def initUI(self):
+        self.setWindowTitle(self.title)
+        self.setGeometry(self.left, self.top, self.width, self.height)
+
+        self.createTable()
+        self.layout = QVBoxLayout()
+        self.layout.addWidget(self.tableWidget)
+        self.setLayout(self.layout)
+
+        # Show widget
+        self.show()
+
+    def createTable(self):
+       # Create table
+        self.tableWidget = QTableWidget()
+        self.tableWidget.setRowCount(len(self.instructions))
+        self.tableWidget.setColumnCount(self.COLUMN_COUNT)
+
+        for k, instr in enumerate(self.instructions):
+            fields = str(instr).replace(',','').replace(';', '').split(" ")
+            if "|" in fields:
+                fields.remove("|")
+            if fields[0] in colors:
+                color = colors[fields[0]]
+            else:
+                color = None
+            for l, f in enumerate(fields):
+                text = fields[l]
+                if text == "GOTO":
+                    btn = QPushButton(self.tableWidget)
+                    btn.setText('GOTO')
+                    target_row = int(fields[1].split("=")[1])
+                    def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
+                        tab.scrollToItem(tab.item(row, 0))
+                    btn.clicked.connect(scroll_to_goto_target)
+                    btn.setStyleSheet("background-color: #006464; color: white; font-weight: bold; text-align: left;")
+                    self.tableWidget.setCellWidget(k, l, btn)
+                if text == "WFM" and int(fields[4].split("=")[1])==0:
+                    # Not a TA pair
+                    btn = QPushButton(self.tableWidget)
+                    btn.setText(' WFM')
+                    addr = int(fields[6].split("=")[1])
+                    count = int(fields[5].split("=")[1])
+                    def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
+                        w = MatplotlibWidget(I,Q)
+                        self.plotters.append(w)
+                    btn.clicked.connect(open_plotter)
+                    btn.setStyleSheet("background-color: #00C800; color: white; font-weight: bold; text-align: left;")
+                    self.tableWidget.setCellWidget(k, l, btn)
+                else:
+                    item = QTableWidgetItem(text)
+                    item.setFont(table_font)
+                    if color:
+                        item.setBackground(color)
+                    self.tableWidget.setItem(k, l, item)
+            if l < self.COLUMN_COUNT-1:
+                for j in range(l+1, self.COLUMN_COUNT):
+                    item = QTableWidgetItem("")
+                    if color:
+                        item.setBackground(color)
+                    self.tableWidget.setItem(k, j, item)
+
+        self.tableWidget.move(0,0)
+        self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
+
+def get_target_hardware(filename):
+    with open(filename, 'rb') as FID:
+        target_hw = FID.read(4).decode('utf-8')
+    return target_hw
+
+if __name__ == '__main__':
+    if len(sys.argv) == 2:
+        filename = sys.argv[1]
+        try:
+            hw = get_target_hardware(filename)
+            if hw == "APS2":
+                from QGL.drivers.APS2Pattern import read_instructions, read_waveforms
+                app = QApplication(sys.argv[:1])
+                ex  = DisassemblerApp(read_instructions(sys.argv[1]), read_waveforms(sys.argv[1]))
+                sys.exit(app.exec_())
+            elif hw == "APS1":
+                print("APS1 disassmbler not yet implemented")
+            else:
+                raise Exception("Unknown hardware target.")
+        except:
+            print(f"The supplied file {filename} does not appear to be APS1 or APS2 format.")
+        
+    else:
+        print("Expected single file (.aps1 or .aps2 format) as an argument.")
+
+        
+
+

From b34d547356c56b7947ebfe3baeb831d40bf15589 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Wed, 27 Feb 2019 11:03:42 -0500
Subject: [PATCH 140/235] Add new_marker function

---
 QGL/ChannelLibraries.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 399f6441..63bf3faa 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -185,6 +185,9 @@ def qubits(self):
     def meas(self):
         return self.ent_by_type(Channels.Measurement)
 
+    def markers(self):
+       return self.ent_by_type(Channels.LogicalMarkerChannel)
+
     @check_session_dirty
     def load(self, name, index=1):
         """Load the latest instance for a particular name. Specifying index = 2 will select the second most recent instance """
@@ -392,6 +395,12 @@ def new_qubit(self, label, **kwargs):
         self.add_and_update_dict(thing)
         return thing
 
+    @check_for_duplicates
+    def new_marker(self, label, phys_chan, **kwargs):
+        thing = Channels.LogicalMarkerChannel(label=label, phys_chan = phys_chan, channel_db=self.channelDatabase, **kwargs)
+        self.add_and_update_dict(thing)
+        return thing
+
     @check_for_duplicates
     def new_source(self, label, model, address, power=-30.0, frequency=5.0e9, reference='10MHz'):
         thing = Channels.Generator(label=label, model=model, address=address, power=power,
@@ -401,7 +410,7 @@ def new_source(self, label, model, address, power=-30.0, frequency=5.0e9, refere
         return thing
 
     def set_control(self, qubit_or_edge, transmitter, generator=None):
-        
+
         if isinstance(transmitter, Channels.Transmitter):
             quads   = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalQuadratureChannel)]
             markers = [c for c in transmitter.channels if isinstance(c, Channels.PhysicalMarkerChannel)]

From 198c1c58e8325fe2fa7ffbd7b63535a7b25560d9 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 27 Feb 2019 12:13:46 -0500
Subject: [PATCH 141/235] set_measure and set_control can now be run multiple
 times

---
 QGL/ChannelLibraries.py | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 63bf3faa..ff598de3 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -78,7 +78,7 @@ def check_for_duplicates(f):
     @wraps(f)
     def wrapper(cls, label, *args, **kwargs):
         if label in cls.channelDict:
-            logger.warning(f"Cannot create {label}: a channel with the same name already exists.")
+            logger.info(f"A database item with the name {label} already exists. Returning this existing item instead.")
             return cls.channelDict[label]
         else:
             return f(cls, label, *args, **kwargs)
@@ -461,7 +461,7 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
             raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
         if f"M-{qubit.label}" in self.channelDict:
-            logger.warning(f"Cannot create Measurement M-{qubit.label}: a channel with the same name already exists.")
+            logger.info(f"The measurement M-{qubit.label} already exists: using this measurement.")
             meas = self.channelDict[f"M-{qubit.label}"]
         else:
             meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=self.channelDatabase)
@@ -471,9 +471,12 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
 
         phys_trig_channel = trig_channel if trig_channel else transmitter.get_chan("m1")
 
-        trig_chan              = Channels.LogicalMarkerChannel(label=f"ReceiverTrig-{qubit.label}", channel_db=self.channelDatabase)
-        # print(phys_trig_channel.id, trig_chan.id)
-        self.session.add(trig_chan)
+        if f"ReceiverTrig-{qubit.label}" in self.channelDict:
+            logger.info(f"The Receiver trigger ReceiverTrig-{qubit.label} already exists: using this channel.")
+            trig_chan = self.channelDict[f"ReceiverTrig-{qubit.label}"]
+        else:
+            trig_chan = Channels.LogicalMarkerChannel(label=f"ReceiverTrig-{qubit.label}", channel_db=self.channelDatabase)
+            self.session.add(trig_chan)
         trig_chan.phys_chan    = phys_trig_channel
         trig_chan.pulse_params = {"length": trigger_length, "shape_fun": "constant"}
         meas.trig_chan         = trig_chan
@@ -493,6 +496,9 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
 
         if gate:
             phys_gate_channel   = gate_channel if gate_channel else transmitter.get_chan("m2")
+            if f"M-{qubit.label}-gate" in self.channelDict:
+                logger.info(f"The gate channel M-{qubit.label}-gate already exists: using this channel.")
+                gate_chan = self.channelDict[f"M-{qubit.label}-gate"]
             gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=self.channelDatabase)
             gate_chan.phys_chan = phys_gate_channel
             meas.gate_chan      = gate_chan
@@ -508,7 +514,11 @@ def set_master(self, master_instrument, trig_channel=None, pulse_length=1e-7):
             if not isinstance(trig_channel, Channels.PhysicalMarkerChannel):
                 raise ValueError("In set_master the trigger channel must be an instance of PhysicalMarkerChannel")
 
-            st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=self.channelDatabase)
+            if "slave_trig" in self.channelDict:
+                logger.info(f"The slave trigger slave_trig already exists: using this trigger.")
+                st = self.channelDict["slave_trig"]
+            else:
+                st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=self.channelDatabase)
             st.phys_chan = trig_channel
             st.pulse_params = {"length": pulse_length, "shape_fun": "constant"}
             master_instrument.master = True

From 9ee829f883e983b63baaec54f4ae3028817fd0b5 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:54:39 -0500
Subject: [PATCH 142/235] Add jump table indicator to block label.

---
 QGL/BlockLabel.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/QGL/BlockLabel.py b/QGL/BlockLabel.py
index 52db8b63..6725cd13 100644
--- a/QGL/BlockLabel.py
+++ b/QGL/BlockLabel.py
@@ -2,8 +2,10 @@
 
 
 class BlockLabel(object):
-    def __init__(self, label):
+    def __init__(self, label, jump_table=False, table_size=0):
         self.label = label
+        self.jump_table = jump_table
+        self.table_size = table_size
 
     def __repr__(self):
         return self.__str__()

From b7932f93ebfdf9c648d66e7bfa088afeebdaa516 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:56:09 -0500
Subject: [PATCH 143/235] Only set up clifford generator once per sequence
 file.

---
 QGL/RandomCliffordTools.py | 34 +++++++++++++++++++++++-----------
 1 file changed, 23 insertions(+), 11 deletions(-)

diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index d4fc97bb..9317b3e2 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -33,13 +33,15 @@
 from .APS2CustomInstructions import *
 from .Cliffords import C1, inverse_clifford, clifford_multiply
 
+default_clifford_options = {"offset": 0x0, "spacing": 0x1, "seed": 0x31}
+
 VALID_CLIFFORD_TYPES = ('RandomAC',)
 
 def generate_clifford_jump_table(cliff_wires, jt_label = None):
     """Generate the jump table that will be used to call into the clifford set"""
 
     if jt_label is None:
-        jt_label = BlockLabel.BlockLabel("JT")
+        jt_label = BlockLabel.BlockLabel("JT", jump_table=True, table_size=48)
     if not isinstance(jt_label, BlockLabel.BlockLabel):
         raise ValueError("Jump table label must be a BlockLabel.")
 
@@ -55,14 +57,22 @@ def generate_clifford_jump_table(cliff_wires, jt_label = None):
 
     cliff_wires.insert(0, jump_table)
 
+    return jt_label
+
 def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
-                            inv_addr=0x3, inv_values=[]):
+                            inv_addr=0x3, inv_values=[],
+                            clifford_options=default_clifford_options):
 
     if jt_label is None:
         jt_label = BlockLabel.BlockLabel("JT")
     if not isinstance(jt_label, BlockLabel.BlockLabel):
         raise ValueError("Jump table label must be a BlockLabel.")
 
+    #Insert defaults
+    for k,v in default_clifford_options.items():
+        if k not in clifford_options.keys():
+            cliford_options[k] = v
+
     for idx, seq in enumerate(seqs[:]):
         if not PatternUtils.contains_runtime_pulses(seq):
             continue
@@ -74,18 +84,14 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
                 and pulse.label in VALID_CLIFFORD_TYPES:
                 has_random_cliff = True
                 new_seq.extend(RandomClifford(jt_label, cliff_addr))
-                print("Inserting clifford pulse!")
+                #print("Inserting clifford pulse!")
             else:
                 new_seq.append(pulse)
 
-        info_seqs = []
-        info_seqs.extend(RandomCliffordSetOffset(0x1, 0x0))
-        info_seqs.extend(RandomCliffordSetSpacing(0x2, 0x1))
-
-        if isinstance(seq[0], BlockLabel.BlockLabel):
-            new_seq[1:1] = info_seqs
-        else:
-            new_seq[0:0] = info_seqs
+        # if isinstance(seq[0], BlockLabel.BlockLabel):
+        #     new_seq[1:1] = info_seqs
+        # else:
+        #     new_seq[0:0] = info_seqs
 
         if add_inv:
             #insert reset after first wait
@@ -99,6 +105,12 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
 
         seqs[idx] = new_seq
 
+    info_seqs = []
+    info_seqs.extend(RandomCliffordSetOffset(0x1, clifford_options["offset"]))
+    info_seqs.extend(RandomCliffordSetSpacing(0x2, clifford_options["spacing"]))
+    info_seqs.extend(RandomCliffordSeed(clifford_options["seed"]))
+    seqs.insert(0, info_seqs)
+
 
 def randomize_clifford_sequences(qubit, seqs, clifford_type=PulsePrimitives.RandomAC):
 

From 146ed60b0a96c8dbadce4ad099f5ce2e93d2772c Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:56:42 -0500
Subject: [PATCH 144/235] Correct __str__ for indicrect CALL

---
 QGL/ControlFlow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/ControlFlow.py b/QGL/ControlFlow.py
index cc1e6327..fed08018 100644
--- a/QGL/ControlFlow.py
+++ b/QGL/ControlFlow.py
@@ -155,7 +155,7 @@ def __init__(self, target, indirect=False):
         self.indirect = indirect
 
     def __str__(self):
-        if self.load_addr:
+        if not self.indirect:
             return f"{self.instruction}({str(self.target)})"
         else:
             return f"{self.instruction}({str(self.target)}, INDIRECT)"

From 221609e5c458a3077802b7e6645b09b937ed5a5f Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:57:20 -0500
Subject: [PATCH 145/235] Correct implementation of APS2_SET_SEED

---
 QGL/APS2CustomInstructions.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index 1d93cf38..ae9c4221 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -48,14 +48,14 @@
 def RandomCliffordSetOffset(addr, offset):
     return [Invalidate(addr, 0, tdm=False),
             WriteAddr(addr, offset, tdm=False),
-            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
-            CustomInstruction("APS_CLIFFORD_SET_OFFSET", addr, 0x3)]
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False), #
+            CustomInstruction("APS_CLIFFORD_SET_OFFSET", addr, 0xA)]
 
 def RandomCliffordSetSpacing(addr, spacing):
     return [Invalidate(addr, 0, tdm=False),
             WriteAddr(addr, spacing, tdm=False),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
-            CustomInstruction("APS_CLIFFORD_SET_SPACING", addr, 0x3)]
+            CustomInstruction("APS_CLIFFORD_SET_SPACING", addr, 0xA)]
 
 def RandomClifford(target, addr):
     return [Invalidate(addr, 0, tdm=False),
@@ -73,4 +73,7 @@ def RandomCliffordInverseReset(addr): #for now don't use addr
     return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0xF)
 
 def RandomCliffordSeed(seed):
-    raise NotImplementedError("APS_CLIFFORD_SET_SEED not implemented!")
+    return [Invalidate(0xB, 0, tdm=False),
+        WriteAddr(0xB, seed, tdm=False),
+        LoadCmpVram(0xB, 0xFFFFFFFF, tdm=False),
+        CustomInstruction("APS_CLIFFORD_SET_SEED", 0xB, 0xA)]

From 86ab8ba5a2957da18f74febe8d19e71207527408 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:58:15 -0500
Subject: [PATCH 146/235] Keep modulation commands explicitly in subroutines to
 prevent eliding Z pulses

---
 QGL/Compiler.py | 29 +++++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 57abd552..35a59b49 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -37,6 +37,7 @@
 from . import BlockLabel
 from . import TdmInstructions # only for APS2-TDM
 from . import APS2CustomInstructions
+from .RandomCliffordTools import default_clifford_options
 from . import RandomCliffordTools
 import gc
 
@@ -365,7 +366,8 @@ def collect_specializations(seqs):
             done.append(target)
     return funcs
 
-def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=False):
+def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=False,
+                    clifford_options=default_clifford_options):
 
     ChannelLibraries.channelLib.update_channelDict()
     clear_pulse_cache()
@@ -402,7 +404,7 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=
 
     # Compile all the pulses/pulseblocks to sequences of pulses and control flow
     logger.info("Compiling sequences.")
-    wireSeqs = compile_sequences(seqs, channels, random_cliffords=random_cliffords)
+    wireSeqs = compile_sequences(seqs, channels, random_cliffords=random_cliffords, clifford_options=clifford_options)
 
     if not validate_linklist_channels(wireSeqs.keys()):
         print("Compile to hardware failed")
@@ -593,7 +595,8 @@ def compile_to_hardware(seqs,
     return metafilepath
 
 
-def compile_sequences(seqs, channels=set(), random_cliffords=False):
+def compile_sequences(seqs, channels=set(), random_cliffords=False,
+                            clifford_options=default_clifford_options):
     '''
     Main function to convert sequences to miniLL's and waveform libraries.
     '''
@@ -608,14 +611,21 @@ def compile_sequences(seqs, channels=set(), random_cliffords=False):
     seqs += subroutines
 
     if random_cliffords:
+
         qubits = [q for q in list(channels) if isinstance(q, Channels.Qubit)]
         if len(qubits) > 1:
             raise Exception("Too many qubits! Don't know how to deal with this yet.")
         #replace cliffords with
         cliffords = [[get_clifford_type(seqs)(n)] for n in range(24)]
-        RandomCliffordTools.generate_clifford_jump_table(cliffords)
-        RandomCliffordTools.insert_clifford_calls(seqs)
+        jt_label = RandomCliffordTools.generate_clifford_jump_table(cliffords)
+        RandomCliffordTools.insert_clifford_calls(seqs, jt_label=jt_label, clifford_options=clifford_options)
+
+        # if not isinstance(seqs[0][0], BlockLabel.BlockLabel):
+        #     raise Exception("Fist instruciton must be block label!")
+        # start_label = seqs[0][0]
         seqs += cliffords
+        #seqs[0:0] = cliffords
+        #seqs[0].insert(0, ControlFlow.Goto(start_label))
 
     #expand the channel definitions for anything defined in subroutines
     for func in subroutines:
@@ -701,7 +711,14 @@ def flatten_to_pulses(obj):
                 wires = propagate_node_frame_to_edges(
                     wires, chan, block.pulses[chan].frameChange)
         # drop length 0 blocks but push nonzero frame changes onto previous entries
-        if block.length == 0:
+
+        is_subroutine = False
+        if isinstance(seq[-1], ControlFlow.Return):
+            #Make sure we do not drop frame update instructions for subroutines that are only Z pulses
+            is_subroutine = True
+
+
+        if block.length == 0 and not is_subroutine:
             for chan in channels:
                 if block.pulses[chan].frameChange == 0:
                     continue

From ed8d087872fc231b1a8061d39857d3197a6e4c63 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:59:01 -0500
Subject: [PATCH 147/235] Proper prefetching for jump-table based subroutines

---
 QGL/drivers/APS2Pattern.py | 43 ++++++++++++++++++++++++++++----------
 1 file changed, 32 insertions(+), 11 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 12bbfddf..b067a83d 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -297,8 +297,11 @@ def __str__(self):
 
         elif any(
             [instrOpCode == op for op in [GOTO, CALL, RET, REPEAT, PREFETCH]]):
+            if self.use_ram:
+                out += " RAM"
             out += " | target_addr={}".format(self.payload & 2**26 - 1)
 
+
         elif instrOpCode == LOAD:
             out += " | count={}".format(self.payload)
 
@@ -359,6 +362,9 @@ def __ne__(self, other):
     def __hash__(self):
         return hash((self.header, self.payload, self.label))
 
+    def isa(self, value):
+        return (self.header >> 4) == value
+
     @property
     def address(self):
         return self.payload & 0xffffffff  # bottom 32-bits of payload
@@ -616,7 +622,7 @@ def to_instruction(self, write_flag=True, label=None):
         instr.writeFlag = write_flag
         return instr
 
-def inject_modulation_cmds(seqs, force_phase_update=False):
+def inject_modulation_cmds(seqs):
     """
     Inject modulation commands from phase, frequency and frameChange of waveforms
     in an IQ waveform sequence. Assume up to 2 NCOs for now.
@@ -634,13 +640,17 @@ def inject_modulation_cmds(seqs, force_phase_update=False):
         frame_changes = [entry.frameChange for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
         no_frame_cmds = np.all(np.less(np.abs(frame_changes), 1e-8))
         no_modulation_cmds = no_freq_cmds and no_phase_cmds and no_frame_cmds
-        #import pdb; pdb.set_trace()
         if no_modulation_cmds:
             continue
 
         mod_seq = []
         pending_frame_update = False
 
+        #check to see if we are in a subroutine by using last instruction as return as a tell
+        #if so, ensure frame updates do not get dropped
+        if isinstance(seq[-1], ControlFlow.Return):
+            force_phase_update = True
+
         for entry in seq:
 
             #copies to avoid same object having different timestamps later
@@ -728,7 +738,6 @@ def synchronize_clocks(seqs):
     syncInstructions = [list(filter(
         lambda s: isinstance(s, ControlFlow.ControlInstruction), seq))
                         for seq in seqs if seq]
-    #import pdb; pdb.set_trace()
     # Add length to control-flow instructions to make accumulated time match at end of CFI.
     # Keep running tally of how much each channel has been shifted so far.
     localShift = [0 for _ in syncInstructions]
@@ -847,14 +856,14 @@ def create_seq_instructions(seqs, offsets, label = None):
                     instructions.append(LoadCmpVram(entry.addr, entry.mask, label=label))
                 # some TDM instructions are ignored by the APS
                 elif isinstance(entry, TdmInstructions.CustomInstruction):
-                    print(str(entry))
+                    #print(str(entry))
                     try:
                         instructions.append(Custom(entry.in_addr, entry.out_addr,
                                                     APS2_CUSTOM[entry.instruction], label=label))
                     except KeyError as e:
                         raise Exception(f"Got unknown APS2 instruction: {e.args[0]} in {str(entry)}.")
                 elif isinstance(entry, TdmInstructions.WriteAddrInstruction):
-                    print(str(entry))
+                    #print(str(entry))
                     if entry.instruction == 'INVALIDATE' and entry.tdm == False:
                         instructions.append(Invalidate(entry.addr, entry.value, label=label))
                     if entry.instruction == 'WRITEADDR' and entry.tdm == False:
@@ -939,7 +948,6 @@ def create_instr_data(seqs, offsets, cache_lines):
         except:
             pass
         instructions += seq
-
     #if we have any subroutines then group in cache lines
     if subroutines_start >= 0:
         subroutine_instrs = []
@@ -967,12 +975,25 @@ def create_instr_data(seqs, offsets, cache_lines):
             CACHE_LINE_LENGTH))
         #inject prefetch commands before waits
         wait_idx = [idx for idx, instr in enumerate(instructions)
-                    if (instr.header >> 4) == WAIT] + [len(instructions)]
+                    if instr.isa(WAIT)] + [len(instructions)]
         instructions_with_prefetch = instructions[:wait_idx[0]]
         last_prefetch = None
+
         for start, stop in zip(wait_idx[:-1], wait_idx[1:]):
             call_targets = [instr.target for instr in instructions[start:stop]
-                            if (instr.header >> 4) == CALL]
+                           if instr.isa(CALL)]
+
+            #Check if we call into any jump tables
+            jump_tables = [label for label in call_targets if label.jump_table]
+            if len(jump_tables) > 0:
+                for jt in set(jump_tables):
+                    #Find the start of the jump table
+                    start_idx = next(j for j, instr in enumerate(subroutine_instrs)
+                                        if instr.label == jt)
+                    stop_idx = start_idx + jt.table_size
+                    call_targets.extend([instr.target for instr in
+                                            subroutine_instrs[start_idx:stop_idx]
+                                                if instr.isa(CALL)])
             needed_lines = set()
             for target in call_targets:
                 needed_lines.add(subroutine_cache_line[target])
@@ -989,9 +1010,9 @@ def create_instr_data(seqs, offsets, cache_lines):
         #pad out instruction vector to ensure circular cache never loads a subroutine
         pad_instrs = 7 * 128 + (128 - ((len(instructions) + 128) % 128))
         instructions += [NoOp()] * pad_instrs
-
         instructions += subroutine_instrs
 
+
     #turn symbols into integers addresses
     resolve_symbols(instructions)
 
@@ -1006,7 +1027,7 @@ def resolve_symbols(seq):
 
     labeled_entries = [(idx, entry.label) for idx, entry in enumerate(seq) if entry.label is not None]
     symbols = {label: idx for idx, label in labeled_entries}
-    print(f"Found labels: {symbols}")
+    #print(f"Found labels: {symbols}")
     for entry in seq:
         if entry.target is not None and entry.target in symbols.keys():
             entry.address = symbols[entry.target]
@@ -1207,7 +1228,7 @@ def start_new_seq():
                 chan_select_bits = ((instr.header >> 2) & 0x1,
                                     (instr.header >> 3) & 0x1)
                 #On older firmware we broadcast by default whereas on newer we respect the engine select
-                for chan, select_bit in zip(('ch1', 'ch2'), chan_select_bits):
+                for chan, select_bit in zip(('ch1', 'ch2'), chan_select_bits):plot_pulse
                     if (file_version < 4) or select_bit:
                         if isTA:
                             seqs[chan][-1].append((count, wf_lib[chan][addr]))

From 0cbcd575e2c69da01af924369c5b46b2e77a403d Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 17:00:52 -0500
Subject: [PATCH 148/235] Fix typo.

---
 QGL/drivers/APS2Pattern.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 1f78cba3..bcdfbbd5 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1228,7 +1228,7 @@ def start_new_seq():
                 chan_select_bits = ((instr.header >> 2) & 0x1,
                                     (instr.header >> 3) & 0x1)
                 #On older firmware we broadcast by default whereas on newer we respect the engine select
-                for chan, select_bit in zip(('ch1', 'ch2'), chan_select_bits):plot_pulse
+                for chan, select_bit in zip(('ch1', 'ch2'), chan_select_bits):
                     if (file_version < 4) or select_bit:
                         if isTA:
                             seqs[chan][-1].append((count, wf_lib[chan][addr]))

From 1160bad34142a4888b8186fcc37239a227cf253a Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 27 Feb 2019 17:04:39 -0500
Subject: [PATCH 149/235] More flexible about set_measure and set_control,
 which can now be rerun with expected results

---
 QGL/ChannelLibraries.py | 44 ++++++++++++++++++++---------------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index ff598de3..38b3d1cd 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -56,7 +56,7 @@
 
 channelLib = None
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger("QGL")
 
 def check_session_dirty(f):
     """Since we can't mix db objects from separate sessions, re-fetch entities by their unique IDs"""
@@ -78,7 +78,7 @@ def check_for_duplicates(f):
     @wraps(f)
     def wrapper(cls, label, *args, **kwargs):
         if label in cls.channelDict:
-            logger.info(f"A database item with the name {label} already exists. Returning this existing item instead.")
+            logger.warning(f"A database item with the name {label} already exists. Returning this existing item instead.")
             return cls.channelDict[label]
         else:
             return f(cls, label, *args, **kwargs)
@@ -285,14 +285,14 @@ def build_connectivity_graph(self):
             self.connectivityG[chan.source][chan.target]['channel'] = chan
 
     @check_for_duplicates
-    def new_APS2(self, label, address):
+    def new_APS2(self, label, address, **kwargs):
         chan1  = Channels.PhysicalQuadratureChannel(label=f"{label}-1", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
         m1     = Channels.PhysicalMarkerChannel(label=f"{label}-m1", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
         m2     = Channels.PhysicalMarkerChannel(label=f"{label}-m2", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
         m3     = Channels.PhysicalMarkerChannel(label=f"{label}-m3", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
         m4     = Channels.PhysicalMarkerChannel(label=f"{label}-m4", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
 
-        this_transmitter = Channels.Transmitter(label=label, model="APS2", address=address, channels=[chan1, m1, m2, m3, m4], channel_db=self.channelDatabase)
+        this_transmitter = Channels.Transmitter(label=label, model="APS2", address=address, channels=[chan1, m1, m2, m3, m4], channel_db=self.channelDatabase, **kwargs)
         this_transmitter.trigger_source = "external"
         this_transmitter.address        = address
 
@@ -300,7 +300,7 @@ def new_APS2(self, label, address):
         return this_transmitter
 
     @check_for_duplicates
-    def new_APS(self, label, address):
+    def new_APS(self, label, address, **kwargs):
         chan1  = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
         chan2  = Channels.PhysicalQuadratureChannel(label=f"{label}-34", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
         m1     = Channels.PhysicalMarkerChannel(label=f"{label}-1m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
@@ -316,25 +316,25 @@ def new_APS(self, label, address):
         return this_transmitter
 
     @check_for_duplicates
-    def new_TDM(self, label, address):
+    def new_TDM(self, label, address, **kwargs):
         return Channels.Processor(label=label, model="TDM", address=address, trigger_interval=250e-6)
 
     @check_for_duplicates
-    def new_spectrum_analzyer(self, label, address, source):
-        sa = Channels.SpectrumAnalyzer(label=label, model="SpectrumAnalyzer", address=address, LO_source=source, channel_db=self.channelDatabase)
+    def new_spectrum_analzyer(self, label, address, source, **kwargs):
+        sa = Channels.SpectrumAnalyzer(label=label, model="SpectrumAnalyzer", address=address, LO_source=source, channel_db=self.channelDatabase, **kwargs)
         self.add_and_update_dict(sa)
         return sa
 
     @check_for_duplicates
-    def new_DC_source(self, label, address):
-        dcsource = Channels.DCSource(label=label, model="YokogawaGS200", address=address, standalone=True, channel_db=self.channelDatabase)
+    def new_DC_source(self, label, address, **kwargs):
+        dcsource = Channels.DCSource(label=label, model="YokogawaGS200", address=address, standalone=True, channel_db=self.channelDatabase, **kwargs)
         self.add_and_update_dict(dcsource)
         return dcsource
 
     @check_for_duplicates
-    def new_APS2_rack(self, label, ip_addresses, tdm_ip=None):
+    def new_APS2_rack(self, label, ip_addresses, tdm_ip=None, **kwargs):
         transmitters  = [self.new_APS2(f"{label}_U{n+1}", f"{ip}") for n, ip in enumerate(ip_addresses)]
-        this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", transmitters=transmitters, channel_db=self.channelDatabase)
+        this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", transmitters=transmitters, channel_db=self.channelDatabase, **kwargs)
         for t in transmitters:
             t.transceiver = this_transceiver
 
@@ -348,7 +348,7 @@ def new_APS2_rack(self, label, ip_addresses, tdm_ip=None):
         return this_transceiver
 
     @check_for_duplicates
-    def new_X6(self, label, address, dsp_channel=0, record_length=1024):
+    def new_X6(self, label, address, dsp_channel=0, record_length=1024, **kwargs):
 
         phys_channels = (1, 2)
         dsp_channels = (1, 2)
@@ -362,7 +362,7 @@ def new_X6(self, label, address, dsp_channel=0, record_length=1024):
                             channel_db=self.channelDatabase))
 
         this_receiver = Channels.Receiver(label=label, model="X6-1000M", address=address, channels=chans,
-                                      record_length=record_length, channel_db=self.channelDatabase)
+                                      record_length=record_length, channel_db=self.channelDatabase, **kwargs)
         this_receiver.trigger_source = "external"
         this_receiver.stream_types   = "raw, demodulated, integrated"
         this_receiver.address        = address
@@ -376,12 +376,12 @@ def new_X6(self, label, address, dsp_channel=0, record_length=1024):
         return this_receiver
 
     @check_for_duplicates
-    def new_Alazar(self, label, address, record_length=1024):
+    def new_Alazar(self, label, address, record_length=1024, **kwargs):
         chan1 = Channels.ReceiverChannel(label=f"RecvChan-{label}-1", channel=1, channel_db=self.channelDatabase)
         chan2 = Channels.ReceiverChannel(label=f"RecvChan-{label}-2", channel=2, channel_db=self.channelDatabase)
 
         this_receiver = Channels.Receiver(label=label, model="AlazarATS9870", address=address, channels=[chan1, chan2],
-                                      record_length=record_length, channel_db=self.channelDatabase)
+                                      record_length=record_length, channel_db=self.channelDatabase, **kwargs)
         this_receiver.trigger_source = "external"
         this_receiver.stream_types   = "raw"
         this_receiver.address        = address
@@ -402,10 +402,10 @@ def new_marker(self, label, phys_chan, **kwargs):
         return thing
 
     @check_for_duplicates
-    def new_source(self, label, model, address, power=-30.0, frequency=5.0e9, reference='10MHz'):
+    def new_source(self, label, model, address, power=-30.0, frequency=5.0e9, reference='10MHz', **kwargs):
         thing = Channels.Generator(label=label, model=model, address=address, power=power,
                                     frequency=frequency, reference=reference,
-                                    channel_db=self.channelDatabase)
+                                    channel_db=self.channelDatabase, **kwargs)
         self.add_and_update_dict(thing)
         return thing
 
@@ -461,7 +461,7 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
             raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
         if f"M-{qubit.label}" in self.channelDict:
-            logger.info(f"The measurement M-{qubit.label} already exists: using this measurement.")
+            logger.warning(f"The measurement M-{qubit.label} already exists: using this measurement.")
             meas = self.channelDict[f"M-{qubit.label}"]
         else:
             meas = Channels.Measurement(label=f"M-{qubit.label}", channel_db=self.channelDatabase)
@@ -472,7 +472,7 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
         phys_trig_channel = trig_channel if trig_channel else transmitter.get_chan("m1")
 
         if f"ReceiverTrig-{qubit.label}" in self.channelDict:
-            logger.info(f"The Receiver trigger ReceiverTrig-{qubit.label} already exists: using this channel.")
+            logger.warning(f"The Receiver trigger ReceiverTrig-{qubit.label} already exists: using this channel.")
             trig_chan = self.channelDict[f"ReceiverTrig-{qubit.label}"]
         else:
             trig_chan = Channels.LogicalMarkerChannel(label=f"ReceiverTrig-{qubit.label}", channel_db=self.channelDatabase)
@@ -497,7 +497,7 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
         if gate:
             phys_gate_channel   = gate_channel if gate_channel else transmitter.get_chan("m2")
             if f"M-{qubit.label}-gate" in self.channelDict:
-                logger.info(f"The gate channel M-{qubit.label}-gate already exists: using this channel.")
+                logger.warning(f"The gate channel M-{qubit.label}-gate already exists: using this channel.")
                 gate_chan = self.channelDict[f"M-{qubit.label}-gate"]
             gate_chan           = Channels.LogicalMarkerChannel(label=f"M-{qubit.label}-gate", channel_db=self.channelDatabase)
             gate_chan.phys_chan = phys_gate_channel
@@ -515,7 +515,7 @@ def set_master(self, master_instrument, trig_channel=None, pulse_length=1e-7):
                 raise ValueError("In set_master the trigger channel must be an instance of PhysicalMarkerChannel")
 
             if "slave_trig" in self.channelDict:
-                logger.info(f"The slave trigger slave_trig already exists: using this trigger.")
+                logger.warning(f"The slave trigger slave_trig already exists: using this trigger.")
                 st = self.channelDict["slave_trig"]
             else:
                 st = Channels.LogicalMarkerChannel(label="slave_trig", channel_db=self.channelDatabase)

From a0d37466332a901f4fbd6c2ac51d862f70fbae07 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 17:05:06 -0500
Subject: [PATCH 150/235] Remove debug watcher from QGL (now in libaps2)

---
 tests/aps_debug_watcher.py | 219 -------------------------------------
 thing.txt                  |   3 +
 2 files changed, 3 insertions(+), 219 deletions(-)
 delete mode 100644 tests/aps_debug_watcher.py
 create mode 100644 thing.txt

diff --git a/tests/aps_debug_watcher.py b/tests/aps_debug_watcher.py
deleted file mode 100644
index 4f389e8f..00000000
--- a/tests/aps_debug_watcher.py
+++ /dev/null
@@ -1,219 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-import socket
-import struct
-try:
-    from QGL.drivers import APS2Pattern
-    haveQGL = True
-except:
-    haveQGL = False
-import numpy as np
-from ansicolor import * # from ansicolors
-
-ip = sys.argv[1]
-port = 0xbb50
-
-short_time = True
-
-raw_mode = '-r' in sys.argv
-tdm_mode = '-tdm' in sys.argv
-
-print("Connecting to APS Debug Port at {0}:{1}".format(ip,port))
-
-PACKET_SIZE=168//8+1
-
-if short_time:
-    PACKET_SIZE -= 2
-
-MODE_UNKNOWN = 0
-MODE_SEQUENCER = 1
-MODE_RAM = 2
-MODE_TRIGGER = 3
-
-def bittest(v, b):
-    if ((v & (1<<b)) == (1<<b)):
-        return red('T')
-    else:
-        return 'F'
-
-def get_bytes(a, s, e):
-    e += s
-    return a[s:e], e
-
-def formatHaltBits(haltBits):
-    haltSync = bittest(haltBits,5)
-    haltCustom = bittest(haltBits,4)
-    haltValid = bittest(haltBits,3)
-    haltWait = bittest(haltBits,2)
-    haltStr = "S:{} V:{} C:{} W:{}".format(haltSync, haltValid, haltCustom, haltWait)
-    return haltStr
-
-
-
-s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
-s.connect((ip,port))
-print("Connected")
-print(s)
-extraData = b''
-while 1:
-    data = extraData + s.recv(10*PACKET_SIZE)
-    num_packets = len(data) // PACKET_SIZE
-    num_excess = len(data) % PACKET_SIZE
-    block_size = num_packets*PACKET_SIZE
-    extraData = b''
-    if num_excess > 0:
-        extraData = data[block_size:]
-        data = data[:block_size]
-
-    for cnt in range(num_packets):
-        start = cnt * PACKET_SIZE
-        end = (cnt+1)*PACKET_SIZE
-        packet = data[start:end]
-        packet_bytes = bytearray(packet)
-        if raw_mode:
-            print(packet_bytes)
-            continue
-
-        if packet[0] ==  0x1:
-            mode = MODE_SEQUENCER
-        elif packet[0] in [0x2,0x3, 0x4, 0x5]:
-            mode = MODE_RAM
-        elif packet[0] == 0x6:
-            mode = MODE_TRIGGER
-        else:
-            mode = MODE_UNKNOWN
-
-
-        if short_time:
-            uptime_seconds = packet_bytes[1:3]
-            uptime_nanoseconds = packet_bytes[3:7]
-
-            uptime_seconds = struct.unpack(">H", uptime_seconds)[0]
-        else:
-            uptime_seconds = packet_bytes[1:5]
-            uptime_nanoseconds = packet_bytes[5:9]
-
-            uptime_seconds = struct.unpack(">I", uptime_seconds)[0]
-
-        uptime_nanoseconds = struct.unpack(">I", uptime_nanoseconds)[0]
-
-        #print(uptime_seconds, uptime_nanoseconds)
-
-        uptime_nanoseconds = uptime_nanoseconds/1e9
-        uptime = uptime_seconds + uptime_nanoseconds
-
-        if short_time:
-            start = 8
-        else:
-            start = 10
-
-        if mode == MODE_SEQUENCER:
-
-            if short_time:
-                triggerWord = packet[7]
-            else:
-                triggerWord = packet[9]
-
-            haltBits = packet[start]
-
-            haltStr = formatHaltBits(haltBits)
-
-            instructionAddr, start = get_bytes(packet, start, 4)
-            instructionAddr = bytearray(instructionAddr)
-            # clear halt bits, only the first two bits are part of the Addr
-            instructionAddr[0] = instructionAddr[0] & 0x3
-            instructionAddr = struct.unpack(">I", instructionAddr)[0]
-
-            seq_debug_data, start = get_bytes(packet, start, 8)
-            seq_debug_data = np.fromstring(seq_debug_data[::-1], dtype=np.uint64)
-
-            if haveQGL:
-                instruction = APS2Pattern.Instruction.unflatten(seq_debug_data, decode_as_tdm = tdm_mode)
-            else:
-                instruction = ''
-
-            h = "{:016x}".format(seq_debug_data[0]).upper()
-
-            print(red("{:10}".format("Sequencer")), \
-                  white(": {:4}".format(instructionAddr)),\
-                  blue("0x{}".format(h)), \
-                  yellow(" {:6.8f}".format(uptime)), \
-                  haltStr, \
-                  "T:0x{:x}".format(triggerWord), \
-                  " {} ".format(instruction))
-            # if instructionAddr > 100:
-            #    sys.exit()
-        elif mode == MODE_RAM:
-
-            zeros, start = get_bytes(packet, start, 4)
-            vram_addr, start = get_bytes(packet, start, 4)
-            vram_data, start = get_bytes(packet, start, 4)
-
-            vram_header = struct.unpack(">I", zeros)[0]
-            vram_addr = struct.unpack(">I", vram_addr)[0]
-            vram_data = struct.unpack(">I", vram_data)[0]
-
-            if packet[0] == 0x2:
-                ram_mode = "Valid"
-
-            if packet[0] == 0x3:
-                ram_mode = "Write"
-
-            if packet[0] == 0x4:
-                ram_mode = "Send"
-
-            if packet[0] == 0x5:
-                ram_mode = "Recv"
-
-            print(green("{:10}".format("RAM")), \
-                  white(": {:>23}".format(ram_mode)),\
-                  yellow(" {:6.8f}".format(uptime)), \
-                  "addr = 0x{:08X} data = 0x{:08X}".format(vram_addr, vram_data))
-
-        elif mode == MODE_TRIGGER:
-
-            zeros, start = get_bytes(packet, start, 8)
-            syncBits, start = get_bytes(packet,start,1)
-            haltBits, start = get_bytes(packet, start, 1)
-            triggers, start = get_bytes(packet, start, 1)
-            triggerWord, start = get_bytes(packet,start,1)
-
-            for z in zeros:
-                if z != 0:
-                    print("Error expected 0 not", z)
-
-            haltBits = haltBits[0]
-            syncBits = syncBits[0]
-            triggers = triggers[0]
-            triggerWord = triggerWord[0]
-
-            haltStr = formatHaltBits(haltBits)
-
-            syncWF = (syncBits >> 3) & 0xF
-            syncMarker = (syncBits >> 1) & 0x3
-            syncMod = syncBits & 0x1
-
-
-            halt = bittest(syncBits,4)
-            pc_jump = bittest(syncBits, 5)
-            tready = bittest(syncBits, 6)
-            tvalid = bittest(syncBits, 7)
-
-            syncStr = "TV: {} TR: {} PJ: {} H: {} SWF: 0x{} SMa: 0x{} SMo: 0x{}".format(tvalid, tready, pc_jump, halt, syncWF, syncMarker, syncMod)
-
-            trigger = bittest(triggers,1)
-            triggerWordValid = bittest(triggers,0)
-
-            triggerStr = "t = {} tWV = {} tW = 0x{:0X}".format(trigger,triggerWordValid, triggerWord)
-
-            print(green("{:10}".format("Trigger")), \
-                  white(": {:>23}".format('')),\
-                  yellow(" {:6.8f}".format(uptime)), \
-                  haltStr, \
-                  syncStr, \
-                  triggerStr)
-        elif mode == MODE_UNKNOWN:
-            print(green("{:10}".format("Unknown")),packet_bytes)
-
-s.close()
diff --git a/thing.txt b/thing.txt
new file mode 100644
index 00000000..5e24153f
--- /dev/null
+++ b/thing.txt
@@ -0,0 +1,3 @@
+1.222 4.0+5.0i
+1.32 4.1+5.6i
+1.55 4.2+6.7i

From f45db34bb8ccebf7671f91c560250476d8e8bcda Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 17:05:49 -0500
Subject: [PATCH 151/235] Remove junk

---
 thing.txt | 3 ---
 1 file changed, 3 deletions(-)
 delete mode 100644 thing.txt

diff --git a/thing.txt b/thing.txt
deleted file mode 100644
index 5e24153f..00000000
--- a/thing.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-1.222 4.0+5.0i
-1.32 4.1+5.6i
-1.55 4.2+6.7i

From bc0af46203def406cbb255ca4ae40e0dd9b3d61f Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 27 Feb 2019 17:06:00 -0500
Subject: [PATCH 152/235] AWGDir now defaults to temp directory if not defined
 in config

---
 QGL/config.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/QGL/config.py b/QGL/config.py
index 18ca79c5..96950d95 100644
--- a/QGL/config.py
+++ b/QGL/config.py
@@ -4,9 +4,17 @@
 import sys
 import re
 import importlib
+import tempfile
+import logging
+
+logger = logging.getLogger("QGL")
 
 # Where to store AWG data
-AWGDir           = None
+if os.getenv('AWG_DIR'):
+    AWGDir = os.getenv('AWG_DIR')
+else:
+    logger.warning("Defaulting to temporary directory for AWG sequence file outputs.")
+    AWGDir = tempfile.mkdtemp(prefix="AWG")
 
 # The db file, where the channel libraries are stored
 db_resource_name = None

From 2546c3d05a6bb35b06142c41083b5423177bae84 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Fri, 1 Feb 2019 10:43:42 -0500
Subject: [PATCH 153/235] Fix alignment for equal-length pulses

---
 QGL/PulseSequencer.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 315c3db8..3b260634 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -299,7 +299,7 @@ def rec_length(obj):
            pulse_list.append(pulse)
     if max(pad_lengths) == 0:
         # no padding element required
-        return pulses
+        return reduce(operator.mul, pulses)
     elif mode == 'left':
         return reduce(operator.mul,[p + TAPulse('Id', p.channel, max(pulse_lengths) - p.length,0) if p.length < max(pulse_lengths) else p for p in pulse_list])
     elif mode == 'right':

From 681407d67c9c55075dbcbd6329a46e34a05247b9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Thu, 28 Feb 2019 19:10:56 -0500
Subject: [PATCH 154/235] Set if_freq for demod stream

To match meas autodyne_freq
---
 QGL/ChannelLibraries.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 38b3d1cd..cc35531b 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -491,6 +491,8 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
         else:
             raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
 
+        if rcv_chan.stream_type == 'demodulated':
+            rcv_chan.if_freq = meas.autodyne_freq
         meas.receiver_chan = rcv_chan
         self.add_and_update_dict([meas, trig_chan])
 

From 3749e01b68b5cd7035fe29faa938090b9c437cee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Fri, 1 Mar 2019 13:24:29 -0500
Subject: [PATCH 155/235] Rever last commit

See comments
---
 QGL/ChannelLibraries.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index cc35531b..bf83412e 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -490,9 +490,7 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
             rcv_chan = receivers
         else:
             raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
-
-        if rcv_chan.stream_type == 'demodulated':
-            rcv_chan.if_freq = meas.autodyne_freq
+            
         meas.receiver_chan = rcv_chan
         self.add_and_update_dict([meas, trig_chan])
 

From 8f09532863668c1b88063b6eb2d65206425913c9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Fri, 1 Mar 2019 15:30:44 -0500
Subject: [PATCH 156/235] Set default kernel

--GR, DR
---
 QGL/ChannelLibraries.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index bf83412e..2c09fc7b 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -370,7 +370,7 @@ def new_X6(self, label, address, dsp_channel=0, record_length=1024, **kwargs):
         # Add a default kernel
         for chan in chans:
             if chan.stream_type is "integrated":
-                chan.kernel = np.ones(record_length, dtype=np.complex).tobytes()
+                chan.kernel = np.ones(record_length)
 
         self.add_and_update_dict(this_receiver)
         return this_receiver
@@ -490,7 +490,7 @@ def set_measure(self, qubit, transmitter, receivers, generator=None, trig_channe
             rcv_chan = receivers
         else:
             raise ValueError("In set_measure the Transmitter must have a single quadrature channel or a specific channel must be passed instead")
-            
+
         meas.receiver_chan = rcv_chan
         self.add_and_update_dict([meas, trig_chan])
 

From 1fd852b61b75fa8c4800dda664d018bf6faca048 Mon Sep 17 00:00:00 2001
From: "T.J.Rogers" <trogers@bbn.com>
Date: Mon, 4 Mar 2019 15:56:24 -0500
Subject: [PATCH 157/235] Rolled back sqlalchemy version to 2.1.15 (vice
 2.1.17) to use version already bbnqconda loaded.

---
 setup.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 569e446e..b2987a2d 100644
--- a/setup.py
+++ b/setup.py
@@ -10,5 +10,6 @@
         "scipy >= 0.17.1",
         "networkx >= 1.11",
         "bqplot >= 0.11.5",
-        "sqlalchemy >= 1.2.17",
+        # "sqlalchemy >= 1.2.17", Rolling back 20 .15 per 27/2/2019 email
+        "sqlalchemy >= 1.2.15"
     ])

From 5cd1fd0ede04793b9f7be80b3cc98bc3d4018003 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Fri, 8 Mar 2019 16:35:33 -0500
Subject: [PATCH 158/235] Add new_attenuator method

-- with BD, GR, SF?
---
 QGL/ChannelLibraries.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 2c09fc7b..7e4a3db7 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -331,6 +331,15 @@ def new_DC_source(self, label, address, **kwargs):
         self.add_and_update_dict(dcsource)
         return dcsource
 
+    @check_for_duplicates
+    def new_attenuator(self,label,address,attenuation=0):
+        chan1 = Channels.AttenuatorChannel(label=f"AttenChan-{label}-1", channel=1, attenuation=attenuation, channel_db=self.channelDatabase)
+        chan2 = Channels.AttenuatorChannel(label=f"AttenChan-{label}-2", channel=2, attenuation=attenuation, channel_db=self.channelDatabase)
+        chan3 = Channels.AttenuatorChannel(label=f"AttenChan-{label}-3", channel=3, attenuation=attenuation, channel_db=self.channelDatabase)
+        thing = Channels.Attenuator(label=label,model="DigitalAttenuator",address=address,channels=[chan1, chan2, chan3], standalone=True, channel_db=self.channelDatabase)
+        self.add_and_update_dict(thing)
+        return thing
+
     @check_for_duplicates
     def new_APS2_rack(self, label, ip_addresses, tdm_ip=None, **kwargs):
         transmitters  = [self.new_APS2(f"{label}_U{n+1}", f"{ip}") for n, ip in enumerate(ip_addresses)]

From 33cbf2e21bee4b0271ecc18d15494c4defb045bb Mon Sep 17 00:00:00 2001
From: "Graham E. Rowlands" <growland@cam-13600.ad.bbn.com>
Date: Tue, 12 Mar 2019 11:27:13 -0400
Subject: [PATCH 159/235] Ditch comment and upgrade requirements.txt for 1.2.15

---
 requirements.txt | 2 +-
 setup.py         | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 04eaafe5..31600f5c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,4 +3,4 @@ numpy >= 1.11.1
 scipy >= 0.17.1
 networkx >= 1.11
 bqplot >= 0.11.5
-sqlalchemy >= 1.2.17
\ No newline at end of file
+sqlalchemy >= 1.2.15
\ No newline at end of file
diff --git a/setup.py b/setup.py
index b2987a2d..07db1d0b 100644
--- a/setup.py
+++ b/setup.py
@@ -10,6 +10,5 @@
         "scipy >= 0.17.1",
         "networkx >= 1.11",
         "bqplot >= 0.11.5",
-        # "sqlalchemy >= 1.2.17", Rolling back 20 .15 per 27/2/2019 email
         "sqlalchemy >= 1.2.15"
     ])

From ca19e840899c1bb31f416be4774680702a4eb6a2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Fri, 15 Mar 2019 15:14:02 -0400
Subject: [PATCH 160/235] Revert to old stream labels

For consistency, I'd rather label first phys, then dsp channel
---
 QGL/ChannelLibraries.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 7e4a3db7..ababe803 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -366,7 +366,7 @@ def new_X6(self, label, address, dsp_channel=0, record_length=1024, **kwargs):
         chans = []
 
         for p, d, s in itertools.product(phys_channels, dsp_channels, stream_types):
-            chans.append(Channels.ReceiverChannel(label=f"RecvChan-{label}-{s}-{d}-{p}",
+            chans.append(Channels.ReceiverChannel(label=f"RecvChan-{label}-{s}-{p}-{d}",
                             channel=p, dsp_channel=d, stream_type=s,
                             channel_db=self.channelDatabase))
 

From 5477c87ef89385106263ec81c274422c4cb49631 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Mon, 18 Mar 2019 16:39:23 -0400
Subject: [PATCH 161/235] Update dictionary for existing objects

As opposed to ignoring any new instance
---
 QGL/ChannelLibraries.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 7e4a3db7..19dccdae 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -78,8 +78,9 @@ def check_for_duplicates(f):
     @wraps(f)
     def wrapper(cls, label, *args, **kwargs):
         if label in cls.channelDict:
-            logger.warning(f"A database item with the name {label} already exists. Returning this existing item instead.")
-            return cls.channelDict[label]
+            logger.warning(f"A database item with the name {label} already exists. Updating parameters of this existing item instead.")
+            cls.channelDict[label].__dict__.update(kwargs)
+            return cls.channelDict[label]  #should check for difference in args
         else:
             return f(cls, label, *args, **kwargs)
     return wrapper
@@ -381,6 +382,7 @@ def new_X6(self, label, address, dsp_channel=0, record_length=1024, **kwargs):
             if chan.stream_type is "integrated":
                 chan.kernel = np.ones(record_length)
 
+
         self.add_and_update_dict(this_receiver)
         return this_receiver
 

From 956272d46d883c9908c96e75d5655f335fdb14d9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Mon, 18 Mar 2019 16:40:18 -0400
Subject: [PATCH 162/235] Fix Rabi with no cals

---
 QGL/BasicSequences/Rabi.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/QGL/BasicSequences/Rabi.py b/QGL/BasicSequences/Rabi.py
index 3acb5329..c65028b2 100644
--- a/QGL/BasicSequences/Rabi.py
+++ b/QGL/BasicSequences/Rabi.py
@@ -108,6 +108,8 @@ def RabiAmp_NQubits(qubits,
 
     if docals:
         seqs += create_cal_seqs(qubits, calRepeats, measChans=measChans)
+    else:
+        calRepeats = 0
 
     axis_descriptor = [
         {

From 8f7ea548c49d2ea9a8ac9e0935460dfc43ecbb75 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Mar 2019 11:05:45 -0400
Subject: [PATCH 163/235] Add stark shift related utility sequences.

---
 QGL/BasicSequences/StarkShift.py | 168 +++++++++++++++++++++++++++++++
 1 file changed, 168 insertions(+)
 create mode 100644 QGL/BasicSequences/StarkShift.py

diff --git a/QGL/BasicSequences/StarkShift.py b/QGL/BasicSequences/StarkShift.py
new file mode 100644
index 00000000..aa9114ae
--- /dev/null
+++ b/QGL/BasicSequences/StarkShift.py
@@ -0,0 +1,168 @@
+from ..PulsePrimitives import *
+from ..Compiler import compile_to_hardware
+from ..ChannelLibraries import EdgeFactory
+from ..PulseSequencePlotter import plot_pulse_files
+from .helpers import create_cal_seqs, delay_descriptor, cal_descriptor
+import numpy as np
+from collections.abc import Iterable
+
+def StarkShiftSpectroscopy(qubit, measurement, amplitude, 
+							delay=200e-9, length=1e-6, showPlot=False):
+	"""Stark shift spectroscopy experiment. Applies a coherent displacement
+		to the qubit readout cavity while doing pulsed spectroscopy.
+
+		Args:
+			qubit: Qubit channel to apply spectroscopy pulse to.
+
+			measurement: Measurement channel to apply displacement pulse to.
+
+			amplitude: Measurement pulse amplitude(s)
+
+			delay: Delay between end of spectroscopy pulse and start of MEAS(qubit).
+
+			length: Total length of cavity displacement pulse.
+
+		Returns:
+			metafile: Path to compiled sequence metafile.
+	"""
+
+	if not isinstance(amplitude, Iterable):
+		amplitude = [amplitude]
+
+	def stark_shift_pulse(amp):
+		pump_pulse = Utheta(measurement, amp=amp, length=length)
+	    l1 = length - delay - qubit.pulse_params["length"] - delay
+	    spec_pulse = Id(qubit, length=l1)+X(qubit)+Id(qubit,length=delay)
+	    return spec_pulse*pump_pulse
+
+    seqs = [[stark_shift_pulse(a), MEAS(qubit)] for a in amplitude]
+    axis_descriptor = {
+        'name': 'Stark Shift Amplitude',
+        'unit': None,
+        'points': amplitude,
+        'partition': 1
+    }
+    metafile = compile_to_hardware(seqs, 'StarkSpec/StarkSpec', axis_descriptor=axis_descriptor)
+
+    if showPlot:
+    	plot_pulse_files(metafile)
+
+    return metafile
+
+def StarkEcho(qubit, measurement, amplitudes, delays, 
+							wait=200e-9, periods=4, showPlot=False):
+	"""Hahn echo sequence with a coherent displacement of the qubit measurement cavity.
+		Used to measure photon-induced dephasing. This sequence can cause a lot of cache pressure
+		so number of points may be limited.
+
+		Args:
+			qubit: Qubit channel for Hahn echo.
+
+			measurement: Measurement channel of qubit.
+			
+			amplitudes: Amplitude(s) of cavity displacement pulse. 
+
+			delays: Hahn echo delays - the t in 90-t-180-t-180. 
+
+			wait: Delay between end of cavity displacement pulse and start of MEAS(qubit).
+
+			periods: Number of artificial oscillations.
+
+		Returns:
+			metafile: Path to compiled sequence metafile.
+	"""
+
+	if not isinstance(amplitudes, Iterable):
+		amplitudes = [amplitudes]
+
+	if not isinstance(delays, Iterable):
+		delays = [delays]
+
+	for k in range(len(pulseSpacings)):
+        seqs.append([X90(qubit), Id(qubit, pulseSpacings[k]), Y(qubit), Id(qubit,pulseSpacings[k]), \
+         U90(qubit,phase=2*pi*periods/len(pulseSpacings)*k), MEAS(qubit)])
+
+    def echo_phase(n):
+    	return 2*np.pi*periods/len(delays)*n
+
+	def echo_stark(n, amp, max_delay, meas_delay=200e-9):
+		x_len = qubit.pulse_params["length"]
+		max_len = 3*x_len + 2*max_delay + meas_delay
+		echo_wait = total_len - (3*x_len + 2*delays[n]) 
+
+		echo_seq = Id(qubit, echo_wait) + X90(qubit) + Id(qubit, delays[n]) + \
+						Y(qubit) + Id(qubit, delays[n]) + U90(qubit, echo_phase(n))
+
+		meas_seq = Utheta(measurement, amp=amp, length=max_len)
+
+		return echo_seq*meas_seq
+
+
+    seqs = [[echo_stark(n, amp, np.max(delays)), Id(measurement, length=wait), MEAS(qubit)] 
+    			for n, amp in product(range(len(delays)), amplitudes)]
+
+    axis_descriptor = delay_descriptor(delays) * len(amplitudes)
+
+    metafile = compile_to_hardware(seqs, 'StarkEcho/StarkEcho', axis_descriptor=axis_descriptor)
+
+    if showPlot:
+    	plot_pulse_files(metafile)
+
+    return metafile
+
+
+def CavityPumpProbe(qubit, measurement, offsets, amplitude, 
+							length=1e-6, wait=1e-6, showPlot=False):
+	"""Time resolved cavity spectroscopy. Applies a coherent displacement to qubit
+		readout cavity while sweeping qubit spectroscopy pulse delay. Useful to measure
+		cavity kappa and cavity population.
+
+		Args:
+			qubit: Qubit channel for spectroscopy.
+
+			measurement: Measurement channel of qubit.
+			
+			offsets: Spectroscopy pulse offset relative to start of cavity displacement pulse.
+
+			amplitude: Measurement pulse amplitude.
+
+			length: Total length of cavity displacement pulse.
+
+			wait: Delay between end of cavity displacement pulse and start of MEAS(qubit).
+
+		Returns:
+			metafile: Path to compiled sequence metafile.
+	"""
+
+	if not isinstance(offsets, Iterable):
+		offsets = [offsets]
+
+	def cavity_probe(offset):
+		pump_pulse = Utheta(measurement, amp=amp, length=length)
+		x_len = qubit.pulse_params["length"]
+	    if offset < -1*x_len:
+	        return [X(qubit), Id(qubit, length=(-x_len-offset)), pump_pulse, Id(qubit, length=wait)]
+	    elif offset < 0:
+	        total_len = length-offset
+	        pm = Id(measurement, length=offset)+pump_pulse
+	        pq = X(qubit)+Id(qubit, length=(total_len-x_len))
+	        return [pm*pq, Id(qubit, length=wait)]
+	    elif offset < length:
+	        pq = Id(qubit, length=offset)+X(qubit)+Id(qubit, length=(length-offset-x_len))
+	        return [pump_pulse*pq, Id(qubit, length=wait)]
+	    elif offset >= length:
+	        assert offset < (length+wait), f"Wait time {wait} is too short!"
+	        wait_len = wait - (offset-length+x_len)
+	        return [pump_pulse, Id(qubit, length=(offset-length)), X(qubit), Id(qubit, length=wait_len)]
+
+    seqs = [[cavity_probe(off), MEAS(qubit)] for off in offsets]
+    axis_descriptor = delay_descriptor(offsets)
+    metafile = compile_to_hardware(seqs, 'CavityPumpProbe/CavityPumpProbe', axis_descriptor=axis_descriptor)
+
+    if showPlot:
+    	plot_pulse_files(metafile)
+
+    return metafile
+
+
+

From 6073c5adafdab16cc136398f61e3de9e16708d2f Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Mar 2019 12:04:55 -0400
Subject: [PATCH 164/235] Get everything working... various bug fixes and add
 stark shift functions to QGL global import.

---
 QGL/BasicSequences/StarkShift.py | 197 +++++++++++++++----------------
 QGL/BasicSequences/__init__.py   |   1 +
 2 files changed, 99 insertions(+), 99 deletions(-)

diff --git a/QGL/BasicSequences/StarkShift.py b/QGL/BasicSequences/StarkShift.py
index aa9114ae..cdad7ea3 100644
--- a/QGL/BasicSequences/StarkShift.py
+++ b/QGL/BasicSequences/StarkShift.py
@@ -5,162 +5,161 @@
 from .helpers import create_cal_seqs, delay_descriptor, cal_descriptor
 import numpy as np
 from collections.abc import Iterable
+from itertools import product
 
-def StarkShiftSpectroscopy(qubit, measurement, amplitude, 
-							delay=200e-9, length=1e-6, showPlot=False):
-	"""Stark shift spectroscopy experiment. Applies a coherent displacement
-		to the qubit readout cavity while doing pulsed spectroscopy.
+def StarkSpectroscopy(qubit, measurement, amplitude, 
+                            delay=200e-9, length=1e-6, showPlot=False):
+    """Stark shift spectroscopy experiment. Applies a coherent displacement
+        to the qubit readout cavity while doing pulsed spectroscopy.
 
-		Args:
-			qubit: Qubit channel to apply spectroscopy pulse to.
+        Args:
+            qubit: Qubit channel to apply spectroscopy pulse to.
 
-			measurement: Measurement channel to apply displacement pulse to.
+            measurement: Measurement channel to apply displacement pulse to.
 
-			amplitude: Measurement pulse amplitude(s)
+            amplitude: Measurement pulse amplitude(s)
 
-			delay: Delay between end of spectroscopy pulse and start of MEAS(qubit).
+            delay: Delay between end of spectroscopy pulse and start of MEAS(qubit).
 
-			length: Total length of cavity displacement pulse.
+            length: Total length of cavity displacement pulse.
 
-		Returns:
-			metafile: Path to compiled sequence metafile.
-	"""
+        Returns:
+            metafile: Path to compiled sequence metafile.
+    """
 
-	if not isinstance(amplitude, Iterable):
-		amplitude = [amplitude]
+    if not isinstance(amplitude, Iterable):
+        amplitude = [amplitude]
 
-	def stark_shift_pulse(amp):
-		pump_pulse = Utheta(measurement, amp=amp, length=length)
-	    l1 = length - delay - qubit.pulse_params["length"] - delay
-	    spec_pulse = Id(qubit, length=l1)+X(qubit)+Id(qubit,length=delay)
-	    return spec_pulse*pump_pulse
+    def stark_shift_pulse(amp):
+        pump_pulse = Utheta(measurement, amp=amp, length=length)
+        l1 = length - delay - qubit.pulse_params["length"] - delay
+        spec_pulse = Id(qubit, length=l1)+X(qubit)+Id(qubit,length=delay)
+        return spec_pulse*pump_pulse
 
     seqs = [[stark_shift_pulse(a), MEAS(qubit)] for a in amplitude]
     axis_descriptor = {
         'name': 'Stark Shift Amplitude',
         'unit': None,
-        'points': amplitude,
+        'points': list(amplitude),
         'partition': 1
     }
     metafile = compile_to_hardware(seqs, 'StarkSpec/StarkSpec', axis_descriptor=axis_descriptor)
 
     if showPlot:
-    	plot_pulse_files(metafile)
+        plot_pulse_files(metafile)
 
     return metafile
 
 def StarkEcho(qubit, measurement, amplitudes, delays, 
-							wait=200e-9, periods=4, showPlot=False):
-	"""Hahn echo sequence with a coherent displacement of the qubit measurement cavity.
-		Used to measure photon-induced dephasing. This sequence can cause a lot of cache pressure
-		so number of points may be limited.
+                            wait=200e-9, periods=4, showPlot=False):
+    """Hahn echo sequence with a coherent displacement of the qubit measurement cavity.
+        Used to measure photon-induced dephasing. This sequence can cause a lot of cache pressure
+        so number of points may be limited.
 
-		Args:
-			qubit: Qubit channel for Hahn echo.
+        TODO: Use QGL intrinsics to reduce sequence and memory cache utilization.
 
-			measurement: Measurement channel of qubit.
-			
-			amplitudes: Amplitude(s) of cavity displacement pulse. 
+        Args:
+            qubit: Qubit channel for Hahn echo.
 
-			delays: Hahn echo delays - the t in 90-t-180-t-180. 
+            measurement: Measurement channel of qubit.
+            
+            amplitudes: Amplitude(s) of cavity displacement pulse. 
 
-			wait: Delay between end of cavity displacement pulse and start of MEAS(qubit).
+            delays: Hahn echo delays - the t in 90-t-180-t-180. 
 
-			periods: Number of artificial oscillations.
+            wait: Delay between end of cavity displacement pulse and start of MEAS(qubit).
 
-		Returns:
-			metafile: Path to compiled sequence metafile.
-	"""
+            periods: Number of artificial oscillations.
 
-	if not isinstance(amplitudes, Iterable):
-		amplitudes = [amplitudes]
+        Returns:
+            metafile: Path to compiled sequence metafile.
+    """
 
-	if not isinstance(delays, Iterable):
-		delays = [delays]
+    if not isinstance(amplitudes, Iterable):
+        amplitudes = [amplitudes]
 
-	for k in range(len(pulseSpacings)):
-        seqs.append([X90(qubit), Id(qubit, pulseSpacings[k]), Y(qubit), Id(qubit,pulseSpacings[k]), \
-         U90(qubit,phase=2*pi*periods/len(pulseSpacings)*k), MEAS(qubit)])
+    if not isinstance(delays, Iterable):
+        delays = [delays]
 
     def echo_phase(n):
-    	return 2*np.pi*periods/len(delays)*n
+        return 2*np.pi*periods/len(delays)*n
 
-	def echo_stark(n, amp, max_delay, meas_delay=200e-9):
-		x_len = qubit.pulse_params["length"]
-		max_len = 3*x_len + 2*max_delay + meas_delay
-		echo_wait = total_len - (3*x_len + 2*delays[n]) 
+    def echo_stark(n, amp, max_delay, meas_delay=200e-9):
+        x_len = qubit.pulse_params["length"]
+        max_len = 3*x_len + 2*max_delay + meas_delay
+        echo_wait = max_len - (3*x_len + 2*delays[n]) 
 
-		echo_seq = Id(qubit, echo_wait) + X90(qubit) + Id(qubit, delays[n]) + \
-						Y(qubit) + Id(qubit, delays[n]) + U90(qubit, echo_phase(n))
+        echo_seq = Id(qubit, echo_wait) + X90(qubit) + Id(qubit, delays[n]) + \
+                        Y(qubit) + Id(qubit, delays[n]) + U90(qubit, echo_phase(n))
 
-		meas_seq = Utheta(measurement, amp=amp, length=max_len)
+        meas_seq = Utheta(measurement, amp=amp, length=max_len)
 
-		return echo_seq*meas_seq
+        return echo_seq*meas_seq
 
 
     seqs = [[echo_stark(n, amp, np.max(delays)), Id(measurement, length=wait), MEAS(qubit)] 
-    			for n, amp in product(range(len(delays)), amplitudes)]
+                for n, amp in product(range(len(delays)), amplitudes)]
 
-    axis_descriptor = delay_descriptor(delays) * len(amplitudes)
+    axis_descriptor = [delay_descriptor(delays)] * len(amplitudes)
 
     metafile = compile_to_hardware(seqs, 'StarkEcho/StarkEcho', axis_descriptor=axis_descriptor)
 
     if showPlot:
-    	plot_pulse_files(metafile)
+        plot_pulse_files(metafile)
 
     return metafile
 
 
 def CavityPumpProbe(qubit, measurement, offsets, amplitude, 
-							length=1e-6, wait=1e-6, showPlot=False):
-	"""Time resolved cavity spectroscopy. Applies a coherent displacement to qubit
-		readout cavity while sweeping qubit spectroscopy pulse delay. Useful to measure
-		cavity kappa and cavity population.
-
-		Args:
-			qubit: Qubit channel for spectroscopy.
-
-			measurement: Measurement channel of qubit.
-			
-			offsets: Spectroscopy pulse offset relative to start of cavity displacement pulse.
-
-			amplitude: Measurement pulse amplitude.
-
-			length: Total length of cavity displacement pulse.
-
-			wait: Delay between end of cavity displacement pulse and start of MEAS(qubit).
-
-		Returns:
-			metafile: Path to compiled sequence metafile.
-	"""
-
-	if not isinstance(offsets, Iterable):
-		offsets = [offsets]
-
-	def cavity_probe(offset):
-		pump_pulse = Utheta(measurement, amp=amp, length=length)
-		x_len = qubit.pulse_params["length"]
-	    if offset < -1*x_len:
-	        return [X(qubit), Id(qubit, length=(-x_len-offset)), pump_pulse, Id(qubit, length=wait)]
-	    elif offset < 0:
-	        total_len = length-offset
-	        pm = Id(measurement, length=offset)+pump_pulse
-	        pq = X(qubit)+Id(qubit, length=(total_len-x_len))
-	        return [pm*pq, Id(qubit, length=wait)]
-	    elif offset < length:
-	        pq = Id(qubit, length=offset)+X(qubit)+Id(qubit, length=(length-offset-x_len))
-	        return [pump_pulse*pq, Id(qubit, length=wait)]
-	    elif offset >= length:
-	        assert offset < (length+wait), f"Wait time {wait} is too short!"
-	        wait_len = wait - (offset-length+x_len)
-	        return [pump_pulse, Id(qubit, length=(offset-length)), X(qubit), Id(qubit, length=wait_len)]
+                            length=1e-6, wait=1e-6, showPlot=False):
+    """Time resolved cavity spectroscopy. Applies a coherent displacement to qubit
+        readout cavity while sweeping qubit spectroscopy pulse delay. Useful to measure
+        cavity kappa and cavity population.
+
+        Args:
+            qubit: Qubit channel for spectroscopy.
+
+            measurement: Measurement channel of qubit.
+            
+            offsets: Spectroscopy pulse offset relative to start of cavity displacement pulse.
+
+            amplitude: Measurement pulse amplitude.
+
+            length: Total length of cavity displacement pulse.
+
+            wait: Delay between end of cavity displacement pulse and start of MEAS(qubit).
+
+        Returns:
+            metafile: Path to compiled sequence metafile.
+    """
+
+    if not isinstance(offsets, Iterable):
+        offsets = [offsets]
+
+    def cavity_probe(offset):
+        pump_pulse = Utheta(measurement, amp=amplitude, length=length)
+        x_len = qubit.pulse_params["length"]
+        if offset < -1*x_len:
+            return [X(qubit), Id(qubit, length=(-x_len-offset)), pump_pulse, Id(qubit, length=wait)]
+        elif offset < 0:
+            total_len = length-offset
+            pm = Id(measurement, length=offset)+pump_pulse
+            pq = X(qubit)+Id(qubit, length=(total_len-x_len))
+            return [pm*pq, Id(qubit, length=wait)]
+        elif offset < length:
+            pq = Id(qubit, length=offset)+X(qubit)+Id(qubit, length=(length-offset-x_len))
+            return [pump_pulse*pq, Id(qubit, length=wait)]
+        elif offset >= length:
+            assert offset < (length+wait), f"Wait time {wait} is too short!"
+            wait_len = wait - (offset-length+x_len)
+            return [pump_pulse, Id(qubit, length=(offset-length)), X(qubit), Id(qubit, length=wait_len)]
 
     seqs = [[cavity_probe(off), MEAS(qubit)] for off in offsets]
     axis_descriptor = delay_descriptor(offsets)
     metafile = compile_to_hardware(seqs, 'CavityPumpProbe/CavityPumpProbe', axis_descriptor=axis_descriptor)
 
     if showPlot:
-    	plot_pulse_files(metafile)
+        plot_pulse_files(metafile)
 
     return metafile
 
diff --git a/QGL/BasicSequences/__init__.py b/QGL/BasicSequences/__init__.py
index d05862f9..882f430e 100644
--- a/QGL/BasicSequences/__init__.py
+++ b/QGL/BasicSequences/__init__.py
@@ -8,3 +8,4 @@
 from .CR import EchoCRPhase, EchoCRLen, EchoCRAmp, PiRabi
 from .AllXY import AllXY
 from .Feedback import Reset, BitFlip3, MajorityVoteN
+from .StarkShift import StarkSpectroscopy, StarkEcho, CavityPumpProbe

From b1716d5f9d79865619702265587f9e58d913dd7d Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Mar 2019 14:07:08 -0400
Subject: [PATCH 165/235] Make sure axis descriptors are lists

---
 QGL/BasicSequences/StarkShift.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/QGL/BasicSequences/StarkShift.py b/QGL/BasicSequences/StarkShift.py
index cdad7ea3..070d5c50 100644
--- a/QGL/BasicSequences/StarkShift.py
+++ b/QGL/BasicSequences/StarkShift.py
@@ -37,12 +37,12 @@ def stark_shift_pulse(amp):
         return spec_pulse*pump_pulse
 
     seqs = [[stark_shift_pulse(a), MEAS(qubit)] for a in amplitude]
-    axis_descriptor = {
+    axis_descriptor = [{
         'name': 'Stark Shift Amplitude',
         'unit': None,
         'points': list(amplitude),
         'partition': 1
-    }
+    }]
     metafile = compile_to_hardware(seqs, 'StarkSpec/StarkSpec', axis_descriptor=axis_descriptor)
 
     if showPlot:
@@ -155,7 +155,7 @@ def cavity_probe(offset):
             return [pump_pulse, Id(qubit, length=(offset-length)), X(qubit), Id(qubit, length=wait_len)]
 
     seqs = [[cavity_probe(off), MEAS(qubit)] for off in offsets]
-    axis_descriptor = delay_descriptor(offsets)
+    axis_descriptor = [delay_descriptor(offsets)]
     metafile = compile_to_hardware(seqs, 'CavityPumpProbe/CavityPumpProbe', axis_descriptor=axis_descriptor)
 
     if showPlot:

From 575975007a58db14cb58bb7b1f378ff926e3fa56 Mon Sep 17 00:00:00 2001
From: "Graham E. Rowlands" <grahamrow@gmail.com>
Date: Tue, 2 Apr 2019 11:55:44 -0400
Subject: [PATCH 166/235] Fixes for adding stream selectors back in

---
 QGL/ChannelLibraries.py | 22 +++++++---------------
 QGL/config.py           |  2 +-
 2 files changed, 8 insertions(+), 16 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index fda3363d..70fdefab 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -361,15 +361,11 @@ def new_APS2_rack(self, label, ip_addresses, tdm_ip=None, **kwargs):
     def new_X6(self, label, address, dsp_channel=0, record_length=1024, **kwargs):
 
         phys_channels = (1, 2)
-        dsp_channels = (1, 2)
-        stream_types = ("raw", "demodulated", "integrated")
-
         chans = []
 
-        for p, d, s in itertools.product(phys_channels, dsp_channels, stream_types):
-            chans.append(Channels.ReceiverChannel(label=f"RecvChan-{label}-{s}-{p}-{d}",
-                            channel=p, dsp_channel=d, stream_type=s,
-                            channel_db=self.channelDatabase))
+        for phys_chan in (1,2):
+            chans.append(Channels.ReceiverChannel(label=f"RecvChan-{label}-{phys_chan}",
+                            channel=phys_chan, channel_db=self.channelDatabase))
 
         this_receiver = Channels.Receiver(label=label, model="X6-1000M", address=address, channels=chans,
                                       record_length=record_length, channel_db=self.channelDatabase, **kwargs)
@@ -377,12 +373,6 @@ def new_X6(self, label, address, dsp_channel=0, record_length=1024, **kwargs):
         this_receiver.stream_types   = "raw, demodulated, integrated"
         this_receiver.address        = address
 
-        # Add a default kernel
-        for chan in chans:
-            if chan.stream_type is "integrated":
-                chan.kernel = np.ones(record_length)
-
-
         self.add_and_update_dict(this_receiver)
         return this_receiver
 
@@ -443,8 +433,10 @@ def set_control(self, qubit_or_edge, transmitter, generator=None):
     def new_edge(self, source, target):
         label = f"{source.label}->{target.label}"
         if label in self.channelDict:
-            raise ValueError("Cannot construct edge {label} since it is already in the channel library.")
-        edge = Channels.Edge(label=f"{source.label}->{target.label}", source=source, target=target, channel_db=self.channelDatabase)
+            edge = self.channelDict[f"{source.label}->{target.label}"]
+            logger.warning(f"The edge {source.label}->{target.label} already exists: using this edge.")
+        else:
+            edge = Channels.Edge(label=f"{source.label}->{target.label}", source=source, target=target, channel_db=self.channelDatabase)
         self.add_and_update_dict(edge)
         return edge
 
diff --git a/QGL/config.py b/QGL/config.py
index 96950d95..e8ae133d 100644
--- a/QGL/config.py
+++ b/QGL/config.py
@@ -13,7 +13,7 @@
 if os.getenv('AWG_DIR'):
     AWGDir = os.getenv('AWG_DIR')
 else:
-    logger.warning("Defaulting to temporary directory for AWG sequence file outputs.")
+    logger.warning("AWG_DIR environment variable not defined. Unless otherwise specified, using temporary directory for AWG sequence file outputs.")
     AWGDir = tempfile.mkdtemp(prefix="AWG")
 
 # The db file, where the channel libraries are stored

From 37a3d1281d63adbc8f16f03b093c88e772b3362a Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 17 Apr 2019 22:10:32 -0400
Subject: [PATCH 167/235] Now use separate sessions for channel lib and
 pipeline

---
 QGL/ChannelLibraries.py | 31 +++++--------------------------
 1 file changed, 5 insertions(+), 26 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 70fdefab..c1b52639 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -50,8 +50,6 @@
 from . import PulseShapes
 from .PulsePrimitives import clear_pulse_cache
 
-from sqlalchemy.orm.session import make_transient
-from sqlalchemy.pool import StaticPool
 from IPython.display import HTML, display
 
 channelLib = None
@@ -87,35 +85,16 @@ def wrapper(cls, label, *args, **kwargs):
 
 class ChannelLibrary(object):
 
-    def __init__(self, db_resource_name=None):
+    def __init__(self, db_resource_name=":memory:", db_provider="sqlite"):
         """Create the channel library."""
 
         global channelLib
 
-        self.db_provider = "sqlite"
-        self.db_resource_name = ":memory:"
-
-        if bbndb.engine:
-            # Use current db
-            self.db = bbndb.engine
-        else:
-
-            if db_resource_name:
-                self.db_resource_name = db_resource_name
-            elif config.load_db():
-                self.db_resource_name = config.load_db()
-
-            self.db = bbndb.engine = bbndb.create_engine(f'{self.db_provider}:///{self.db_resource_name}',
-                                                            connect_args={'check_same_thread':False},
-                                                            poolclass=StaticPool,
-                                                            echo=False)
-
-        bbndb.Base.metadata.create_all(bbndb.engine)
-        bbndb.Session.configure(bind=bbndb.engine)
-        self.Session = bbndb.Session
-        bbndb.session = self.session = self.Session()
-
+        bbndb.initialize_db(f'{db_provider}:///{db_resource_name}')
+        self.session = bbndb.get_cl_session()
         self.connectivityG = nx.DiGraph()
+        self.db_provider = db_provider
+        self.db_resource_name = db_resource_name
 
         # Check to see whether there is already a temp database
         working_dbs = self.query(Channels.ChannelDatabase, label="working").all()

From e547b5e9aeef65e72ea10ea72fef8c4b2cdc7c02 Mon Sep 17 00:00:00 2001
From: Spencer Fallek <38664981+sfallek1@users.noreply.github.com>
Date: Mon, 8 Apr 2019 10:18:16 -0400
Subject: [PATCH 168/235] move away from stream_sel_map

---
 QGL/ChannelLibraries.py | 26 ++++++++++++++------------
 QGL/Compiler.py         |  9 +++++----
 2 files changed, 19 insertions(+), 16 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index c1b52639..dbf44093 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -266,11 +266,11 @@ def build_connectivity_graph(self):
 
     @check_for_duplicates
     def new_APS2(self, label, address, **kwargs):
-        chan1  = Channels.PhysicalQuadratureChannel(label=f"{label}-1", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
-        m1     = Channels.PhysicalMarkerChannel(label=f"{label}-m1", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
-        m2     = Channels.PhysicalMarkerChannel(label=f"{label}-m2", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
-        m3     = Channels.PhysicalMarkerChannel(label=f"{label}-m3", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
-        m4     = Channels.PhysicalMarkerChannel(label=f"{label}-m4", instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        chan1  = Channels.PhysicalQuadratureChannel(label=f"{label}-1", channel=0, instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m1     = Channels.PhysicalMarkerChannel(label=f"{label}-m1", channel=0, instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m2     = Channels.PhysicalMarkerChannel(label=f"{label}-m2", channel=1, instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m3     = Channels.PhysicalMarkerChannel(label=f"{label}-m3", channel=2, instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
+        m4     = Channels.PhysicalMarkerChannel(label=f"{label}-m4", channel=3, instrument=label, translator="APS2Pattern", channel_db=self.channelDatabase)
 
         this_transmitter = Channels.Transmitter(label=label, model="APS2", address=address, channels=[chan1, m1, m2, m3, m4], channel_db=self.channelDatabase, **kwargs)
         this_transmitter.trigger_source = "external"
@@ -281,12 +281,12 @@ def new_APS2(self, label, address, **kwargs):
 
     @check_for_duplicates
     def new_APS(self, label, address, **kwargs):
-        chan1  = Channels.PhysicalQuadratureChannel(label=f"{label}-12", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
-        chan2  = Channels.PhysicalQuadratureChannel(label=f"{label}-34", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
-        m1     = Channels.PhysicalMarkerChannel(label=f"{label}-1m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
-        m2     = Channels.PhysicalMarkerChannel(label=f"{label}-2m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
-        m3     = Channels.PhysicalMarkerChannel(label=f"{label}-3m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
-        m4     = Channels.PhysicalMarkerChannel(label=f"{label}-4m1", instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        chan1  = Channels.PhysicalQuadratureChannel(label=f"{label}-12", channel = 0, instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        chan2  = Channels.PhysicalQuadratureChannel(label=f"{label}-34", channel = 1, instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        m1     = Channels.PhysicalMarkerChannel(label=f"{label}-1m1", channel=0, instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        m2     = Channels.PhysicalMarkerChannel(label=f"{label}-2m1", channel=1, instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        m3     = Channels.PhysicalMarkerChannel(label=f"{label}-3m1", channel=2, instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
+        m4     = Channels.PhysicalMarkerChannel(label=f"{label}-4m1", channel=3, instrument=label, translator="APSPattern", channel_db=self.channelDatabase)
 
         this_transmitter = Channels.Transmitter(label=label, model="APS", address=address, channels=[chan1, chan2, m1, m2, m3, m4], channel_db=self.channelDatabase)
         this_transmitter.trigger_source = "external"
@@ -346,11 +346,12 @@ def new_X6(self, label, address, dsp_channel=0, record_length=1024, **kwargs):
             chans.append(Channels.ReceiverChannel(label=f"RecvChan-{label}-{phys_chan}",
                             channel=phys_chan, channel_db=self.channelDatabase))
 
-        this_receiver = Channels.Receiver(label=label, model="X6-1000M", address=address, channels=chans,
+        this_receiver = Channels.Receiver(label=label, model="X6", address=address, channels=chans,
                                       record_length=record_length, channel_db=self.channelDatabase, **kwargs)
         this_receiver.trigger_source = "external"
         this_receiver.stream_types   = "raw, demodulated, integrated"
         this_receiver.address        = address
+        this_receiver.stream_sel     = "X6StreamSelector"
 
         self.add_and_update_dict(this_receiver)
         return this_receiver
@@ -365,6 +366,7 @@ def new_Alazar(self, label, address, record_length=1024, **kwargs):
         this_receiver.trigger_source = "external"
         this_receiver.stream_types   = "raw"
         this_receiver.address        = address
+        this_receiver.stream_sel     = "AlazarStreamSelector"
 
         self.add_and_update_dict(this_receiver)
         return this_receiver
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 115338de..ba8e561b 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -399,8 +399,8 @@ def compile_to_hardware(seqs,
     for wire, pulses in physWires.items():
         pattern_module = import_module('QGL.drivers.' + wire.translator)
         if pattern_module.SEQFILE_PER_CHANNEL:
-            inst_name = pattern_module.get_true_inst_name(wire.label)
-            chan_name = pattern_module.get_true_chan_name(wire.label)
+            inst_name = wire.transmitter.label
+            chan_name = wire.label
             has_non_id_pulses = any([len([p for p in ps if isinstance(p,Pulse) and p.label!="Id"]) > 0 for ps in pulses])
             label_to_inst[wire.label] = inst_name
             if has_non_id_pulses:
@@ -410,7 +410,7 @@ def compile_to_hardware(seqs,
             old_wire_instrs[wire] = wire.instrument
             wire.instrument = wire.label
             wire.label = chan_name
-            files[inst_name] = {}
+            #files[inst_name] = {}
 
     # construct channel delay map
     logger.info("Constructing delay map.")
@@ -454,11 +454,12 @@ def compile_to_hardware(seqs,
         new_meta = data['translator'].write_sequence_file(data, fullFileName)
         if new_meta:
             awg_metas[awgName] = new_meta
+            ChannelLibraries.channelLib[awgName].extra_meta = new_meta
 
         # Allow for per channel and per AWG seq files
         if awgName in label_to_inst:
             if awgName in label_to_chan:
-                files[label_to_inst[awgName]][label_to_chan[awgName]] = fullFileName
+                files[label_to_chan[awgName]] = fullFileName
         else:
             files[awgName] = fullFileName
 

From b263a05008313a2fa93cd4c3aedc8c7c2ecb8259 Mon Sep 17 00:00:00 2001
From: Spencer Fallek <38664981+sfallek1@users.noreply.github.com>
Date: Wed, 24 Apr 2019 14:06:54 -0400
Subject: [PATCH 169/235] fix aps2 rack typo

---
 QGL/ChannelLibraries.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index dbf44093..602adc57 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -323,7 +323,7 @@ def new_attenuator(self,label,address,attenuation=0):
     @check_for_duplicates
     def new_APS2_rack(self, label, ip_addresses, tdm_ip=None, **kwargs):
         transmitters  = [self.new_APS2(f"{label}_U{n+1}", f"{ip}") for n, ip in enumerate(ip_addresses)]
-        this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", transmitters=transmitters, channel_db=self.channelDatabase, **kwargs)
+        this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", master=True, address=ip_addresses[0], transmitters=transmitters, channel_db=self.channelDatabase, **kwargs)
         for t in transmitters:
             t.transceiver = this_transceiver
 

From a539652a632c986f7d0a801712f79dba6d5c0137 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 24 Apr 2019 17:36:37 -0400
Subject: [PATCH 170/235] Update to latest sqlalchemy syntax

---
 QGL/Compiler.py | 64 +++++++++++++++++++++++++++++--------------------
 1 file changed, 38 insertions(+), 26 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 35a59b49..fec90274 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -432,26 +432,32 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=
     physWires = map_logical_to_physical(wireSeqs)
 
     # Pave the way for composite instruments, not useful yet...
-    files = {}
-    label_to_inst   = {}
-    label_to_chan   = {}
-    old_wire_names  = {}
-    old_wire_instrs = {}
+    extra_info = {}
+    extra_info["files"]             = {}
+    extra_info["label_to_inst"]     = {}
+    extra_info["label_to_chan"]     = {}
+    extra_info["old_wire_names"]    = {}
+    extra_info["old_wire_instrs"]   = {}
+
+    extra_info["num_measurements"] = num_measurements
+    extra_info["wire_measurements"] = wire_measurements
+    extra_info["channels"] = channels
+
     for wire, pulses in physWires.items():
         pattern_module = import_module('QGL.drivers.' + wire.translator)
         if pattern_module.SEQFILE_PER_CHANNEL:
             inst_name = pattern_module.get_true_inst_name(wire.label)
             chan_name = pattern_module.get_true_chan_name(wire.label)
             has_non_id_pulses = any([len([p for p in ps if isinstance(p,Pulse) and p.label!="Id"]) > 0 for ps in pulses])
-            label_to_inst[wire.label] = inst_name
+            extra_info["label_to_inst"][wire.label] = inst_name
             if has_non_id_pulses:
-                label_to_chan[wire.label] = chan_name
+                extra_info["label_to_chan"][wire.label] = chan_name
             # Change the name/inst for uniqueness, but we must restore this later!
-            old_wire_names[wire] = wire.label
-            old_wire_instrs[wire] = wire.instrument
+            extra_info["old_wire_names"][wire] = wire.label
+            extra_info["old_wire_instrs"][wire] = wire.instrument
             wire.instrument = wire.label
             wire.label = chan_name
-            files[inst_name] = {}
+            extra_info["files"][inst_name] = {}
 
     # construct channel delay map
     logger.info("Constructing delay map.")
@@ -479,7 +485,7 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=
     # on whether we have one sequence per channel
     logger.info("Bundling wires.")
     awgData = bundle_wires(physWires, wfs)
-    return awgData
+    return awgData, extra_info
 
 def compile_to_hardware(seqs,
                         fileName,
@@ -505,9 +511,15 @@ def compile_to_hardware(seqs,
         tdm_seq (optional): compile for TDM
     '''
     # save input code to file
+
     save_code(seqs, fileName + suffix)
 
-    awgData = compile_to_IR(seqs, add_slave_trigger=add_slave_trigger, tdm_seq=tdm_seq)
+    if any([p.isRunTime for p in flatten(seqs)]):
+        random_cliffords = True
+    else:
+        random_cliffords = False
+
+    awgData, extra_info = compile_to_IR(seqs, add_slave_trigger=add_slave_trigger, tdm_seq=tdm_seq, random_cliffords=random_cliffords)
 
     # convert to hardware formats
     # files = {}
@@ -528,11 +540,11 @@ def compile_to_hardware(seqs,
             awg_metas[awgName] = new_meta
 
         # Allow for per channel and per AWG seq files
-        if awgName in label_to_inst:
-            if awgName in label_to_chan:
-                files[label_to_inst[awgName]][label_to_chan[awgName]] = fullFileName
+        if awgName in extra_info["label_to_inst"]:
+            if awgName in extra_info["label_to_chan"]:
+                files[extra_info["label_to_inst"][awgName]][extra_info["label_to_chan"][awgName]] = fullFileName
         else:
-            files[awgName] = fullFileName
+            extra_info["files"][awgName] = fullFileName
 
         del data
         del awgData[awgName]
@@ -562,21 +574,21 @@ def compile_to_hardware(seqs,
         axis_descriptor = [{
             'name': 'segment',
             'unit': None,
-            'points': list(range(1, 1 + num_measurements)),
+            'points': list(range(1, 1 + extra_info["num_measurements"])),
             'partition': 1
         }]
     receiver_measurements = {}
-    for wire, n in wire_measurements.items():
+    for wire, n in extra_info["wire_measurements"].items():
         if wire.receiver_chan and n>0:
             receiver_measurements[wire.receiver_chan.label] = n
     meta = {
         'database_info': db_info,
-        'instruments': files,
+        'instruments': extra_info["files"],
         'num_sequences': len(seqs),
-        'num_measurements': num_measurements,
+        'num_measurements': extra_info["num_measurements"],
         'axis_descriptor': axis_descriptor,
-        'qubits': [c.label for c in channels if isinstance(c, Channels.Qubit)],
-        'measurements': [c.label for c in channels if isinstance(c, Channels.Measurement)],
+        'qubits': [c.label for c in extra_info["channels"] if isinstance(c, Channels.Qubit)],
+        'measurements': [c.label for c in extra_info["channels"] if isinstance(c, Channels.Measurement)],
         'receivers': receiver_measurements
     }
     if extra_meta:
@@ -586,10 +598,10 @@ def compile_to_hardware(seqs,
         json.dump(meta, FID, indent=2, sort_keys=True)
 
     # Restore the wire info
-    for wire in old_wire_names.keys():
-        wire.label = old_wire_names[wire]
-    for wire in old_wire_instrs.keys():
-        wire.instrument = old_wire_instrs[wire]
+    for wire in extra_info["old_wire_names"].keys():
+        wire.label = extra_info["old_wire_names"][wire]
+    for wire in extra_info["old_wire_instrs"].keys():
+        wire.instrument = extra_info["old_wire_instrs"][wire]
 
     # Return the filenames we wrote
     return metafilepath

From 52a1bfe218ae8469f1e4ffb18c8c28ebb0b53425 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Fri, 26 Apr 2019 16:06:16 -0400
Subject: [PATCH 171/235] Add python egg file to gitignore

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index fcfad9a8..7150e5b0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,5 @@
 *.h5
 *.py~
 *.py#
+*.egg-info
+QGL.egg-info/

From be39b866158406fa94a706e534c61ce1770bb272 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Fri, 26 Apr 2019 16:07:25 -0400
Subject: [PATCH 172/235] Update Inverse Reset instruction sequence.

---
 QGL/APS2CustomInstructions.py | 7 +++++--
 QGL/RandomCliffordTools.py    | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index ae9c4221..9b8268f9 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -69,8 +69,11 @@ def RandomCliffordInverse(target, addr):
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
             Call(target, indirect=True)]
 
-def RandomCliffordInverseReset(addr): #for now don't use addr
-    return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0xF)
+def RandomCliffordInverseReset(val=0x0, addr=0xD): #for now don't use addr
+    return [Invalidate(addr, 0, tdm=False),
+            WriteAddr(addr, val, tdm=False),
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
+            CustomInstruction("APS_CLIFFORD_INVERSE_RESET", addr, 0xA)]
 
 def RandomCliffordSeed(seed):
     return [Invalidate(0xB, 0, tdm=False),
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index 9317b3e2..82288031 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -60,7 +60,7 @@ def generate_clifford_jump_table(cliff_wires, jt_label = None):
     return jt_label
 
 def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
-                            inv_addr=0x3, inv_values=[],
+                            inv_addr=0x4, inv_values=[],
                             clifford_options=default_clifford_options):
 
     if jt_label is None:

From a03994b97c4204c240538a4b1f8ce3aea28f74a5 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Fri, 26 Apr 2019 16:08:56 -0400
Subject: [PATCH 173/235] Output label names and address for debug.

---
 QGL/drivers/APS2Pattern.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 5ff60e7f..2a223e7e 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1034,7 +1034,7 @@ def resolve_symbols(seq):
 
     labeled_entries = [(idx, entry.label) for idx, entry in enumerate(seq) if entry.label is not None]
     symbols = {label: idx for idx, label in labeled_entries}
-    #print(f"Found labels: {symbols}")
+    logger.info(f"Found labels: {symbols}")
     for entry in seq:
         if entry.target is not None and entry.target in symbols.keys():
             entry.address = symbols[entry.target]

From cc9841995face97da41913e92a42b16867225b09 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Tue, 30 Apr 2019 10:00:49 -0400
Subject: [PATCH 174/235] mapping for APS2Pattern w/ APS2Rack

---
 QGL/ChannelLibraries.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index 602adc57..f15816eb 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -323,7 +323,7 @@ def new_attenuator(self,label,address,attenuation=0):
     @check_for_duplicates
     def new_APS2_rack(self, label, ip_addresses, tdm_ip=None, **kwargs):
         transmitters  = [self.new_APS2(f"{label}_U{n+1}", f"{ip}") for n, ip in enumerate(ip_addresses)]
-        this_transceiver = Channels.Transceiver(label=label, model="APS2Rack", master=True, address=ip_addresses[0], transmitters=transmitters, channel_db=self.channelDatabase, **kwargs)
+        this_transceiver = Channels.Transceiver(label=label, model="APS2", master=True, address=ip_addresses[0], transmitters=transmitters, channel_db=self.channelDatabase, **kwargs)
         for t in transmitters:
             t.transceiver = this_transceiver
 

From ea13db8c18681b2bec9682fa9551e9308d136af5 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Tue, 30 Apr 2019 10:21:52 -0400
Subject: [PATCH 175/235] bogus readme commit

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 974fdbdd..545757d1 100644
--- a/README.md
+++ b/README.md
@@ -50,6 +50,7 @@ going to System -> Advanced Settings -> Environment variables. On Mac/Linux
 machines add the following line to your .bashrc or .bash_profile: ``` export
 PYTHONPATH=/path/to/QGL/repo:$PYTHONPATH```
 
+
 The QGL config file will be created the first time you run `import QGL` or `from QGL import *`.
 
 ## Dependencies

From 6f2a8d25875a45e05747837fa1d17d6b63ffa555 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 2 May 2019 09:40:07 -0400
Subject: [PATCH 176/235] Added bqplot graph plot of channel connectivity using
 show() method

---
 QGL/ChannelLibraries.py | 80 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 79 insertions(+), 1 deletion(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index f15816eb..aa3a0df5 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -37,7 +37,8 @@
 import datetime
 import importlib
 import inspect
-from functools import wraps
+import operator
+from functools import wraps, reduce
 import itertools
 import numpy as np
 import networkx as nx
@@ -45,6 +46,10 @@
 
 import bbndb
 
+from bqplot import Figure, LinearScale
+from bqplot.marks import Graph, Lines, Label
+from ipywidgets import Layout
+
 from . import config
 from . import Channels
 from . import PulseShapes
@@ -150,6 +155,79 @@ def ent_by_type(self, obj_type, show=False):
         else:
             return q
 
+    def show(self, qubits=[]):
+        # nodes     = list(dgraph.nodes())
+        edges = []
+        qub_objs = qubits if not qubits == [] else self.qubits()
+        for q in qub_objs:
+            edges.append((q, q.measure_chan))
+            edges.append((q.measure_chan, q.measure_chan.phys_chan))
+            edges.append((q.measure_chan.phys_chan,q.measure_chan.phys_chan.transmitter))
+            edges.append((q, q.phys_chan))
+            edges.append((q.phys_chan, q.phys_chan.transmitter))
+
+            #Generators
+            if q.measure_chan.phys_chan.generator:
+                edges.append((q.measure_chan.phys_chan, q.measure_chan.phys_chan.generator))
+            if q.phys_chan.generator:
+                edges.append((q.phys_chan, q.phys_chan.generator))
+
+        graph = nx.digraph.DiGraph()
+        graph.add_edges_from(edges)
+
+        indices   = {n: i for i, n in enumerate(graph.nodes())}
+        node_data = [{'label': str(n)} for n in graph.nodes()]
+        link_data = [{'source': indices[s], 'target': indices[t]} for s, t in graph.edges()]
+                
+        qub_objs.sort(key=lambda x: x.label)
+        qubit_names = [q.label for q in qub_objs]
+
+        loc = {}
+        def next_level(nodes, iteration=0, offset=0, accum=[]):
+            if len(accum) == 0:
+                loc[nodes[0]] = {'x': 0, 'y': 0}
+                accum = [nodes]
+            next_gen_nodes = list(reduce(operator.add, [list(graph.successors(n)) for n in nodes]))
+            l = len(next_gen_nodes)
+            if l > 0:
+                for k,n in enumerate(next_gen_nodes):
+                    loc[n] = {'x': k, 'y': -(iteration+1)}
+                accum.append(next_gen_nodes)
+                return next_level(next_gen_nodes, iteration=iteration+1, offset=2.5*l, accum=accum)
+            else:
+                return accum
+
+        hierarchy = [next_level([q]) for q in qub_objs]
+        widest = [max([len(row) for row in qh]) for qh in hierarchy]
+        for i in range(1, len(qub_objs)):
+            offset = sum(widest[:i])
+            loc[qub_objs[i]]['x'] += offset*3
+            for n in nx.descendants(graph, qub_objs[i]):
+                loc[n]['x'] += offset*3
+
+        x = [loc[n]['x'] for n in graph.nodes()]
+        y = [loc[n]['y'] for n in graph.nodes()]
+        xs = LinearScale(min=min(x)-0.5, max=max(x)+0.6)
+        ys = LinearScale(min=min(y)-0.5, max=max(y)+0.6)
+        fig_layout = Layout(width='960px', height='500px')
+        bq_graph      = Graph(node_data=node_data, link_data=link_data, x=x, y=y, scales={'x': xs, 'y': ys},
+                            link_type='line', colors=['orange'] * len(node_data), directed=False)
+        bgs_lines = []
+        middles   = []
+        for i in range(len(qub_objs)):
+            if i==0:
+                start = -0.4
+                end = widest[0]-0.6
+            elif i == len(qub_objs):
+                start = sum(widest)-0.4
+                end = max(x)+0.4 
+            else:
+                start = sum(widest[:i])-0.4
+                end = sum(widest[:i+1])-0.6
+
+        fig        = Figure(marks=[bq_graph], layout=fig_layout)
+        return fig
+
     def receivers(self):
         return self.ent_by_type(Channels.Receiver)
 

From 1653ebb659ca25e12fc6c8d3363481f597e2b5ab Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 2 May 2019 14:23:50 -0400
Subject: [PATCH 177/235] Add additional info to connectivity plot

---
 QGL/ChannelLibraries.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index aa3a0df5..dca7c38b 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -172,11 +172,16 @@ def show(self, qubits=[]):
             if q.phys_chan.generator:
                 edges.append((q.phys_chan, q.phys_chan.generator))
 
+            # Triggers
+            if q.measure_chan.trig_chan:
+                edges.append((q.measure_chan, q.measure_chan.trig_chan))
+
+
         graph = nx.digraph.DiGraph()
         graph.add_edges_from(edges)
 
         indices   = {n: i for i, n in enumerate(graph.nodes())}
-        node_data = [{'label': str(n)} for n in graph.nodes()]
+        node_data = [{'label': str(n).replace('(','\r\n(')} for n in graph.nodes()]
         link_data = [{'source': indices[s], 'target': indices[t]} for s, t in graph.edges()]
                 
         qub_objs.sort(key=lambda x: x.label)

From 6c1424196e20cc6fef99481356a055882c6e990f Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Thu, 2 May 2019 14:24:04 -0400
Subject: [PATCH 178/235] Add show_frequency_plan method

---
 QGL/ChannelLibraries.py | 33 +++++++++++++++++++++++++++++++--
 1 file changed, 31 insertions(+), 2 deletions(-)

diff --git a/QGL/ChannelLibraries.py b/QGL/ChannelLibraries.py
index dca7c38b..3b4b818c 100644
--- a/QGL/ChannelLibraries.py
+++ b/QGL/ChannelLibraries.py
@@ -46,9 +46,9 @@
 
 import bbndb
 
-from bqplot import Figure, LinearScale
+from bqplot import Figure, LinearScale, Axis, Lines, Figure
 from bqplot.marks import Graph, Lines, Label
-from ipywidgets import Layout
+from ipywidgets import Layout, VBox, HBox
 
 from . import config
 from . import Channels
@@ -233,6 +233,35 @@ def next_level(nodes, iteration=0, offset=0, accum=[]):
         fig        = Figure(marks=[bq_graph], layout=fig_layout)
         return fig
 
+    def show_frequency_plan(self):
+        c_freqs = {}
+        m_freqs = {}
+        for qubit in self.qubits():
+            c_freqs[qubit.label] = qubit.frequency*1e-9
+            if qubit.phys_chan.generator:
+                c_freqs[qubit.label] += qubit.phys_chan.generator.frequency*1e-9
+            
+            m_freqs[qubit.label] = qubit.measure_chan.frequency*1e-9
+            if qubit.measure_chan.phys_chan.generator:
+                m_freqs[qubit.label] += qubit.measure_chan.phys_chan.generator.frequency*1e-9
+        def spike_at(f):
+            fs = np.linspace(f-0.02,f+0.02,50)
+            return fs, np.exp(-(fs-f)**2/0.01**2)
+        figs = []
+        for freqs, ss in zip([c_freqs, m_freqs],["Control","Measure"]):
+            sx   = LinearScale()
+            sy   = LinearScale()
+            ax   = Axis(scale=sx, label="Frequency (GHz)")
+            ay   = Axis(scale=sy, orientation='vertical')
+            lines = []
+            for k,f in freqs.items():
+                fs, a = spike_at(f)
+                lines.append(Lines(x=fs, y=a, scales={'x': sx, 'y': sy}))
+            labels = Label(x=list(freqs.values()), y=[1.1 for f in freqs], text=list(freqs.keys()), align='middle', scales= {'x': sx, 'y': sy},
+                        default_size=14, font_weight='bolder', colors=['#4f6367'])
+            figs.append(Figure(marks=lines+[labels], axes=[ax, ay], title=f"{ss} Frequency Plan"))
+        return HBox(figs)
+
     def receivers(self):
         return self.ent_by_type(Channels.Receiver)
 

From 175f397589a851a406425d898753abf1c67301b1 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 22 May 2019 21:21:52 -0400
Subject: [PATCH 179/235] Fix channel lib setup for unit tests

---
 tests/helpers.py        |  2 +-
 tests/test_Compiler.py  |  2 ++
 tests/test_Sequences.py | 10 +++++-----
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/tests/helpers.py b/tests/helpers.py
index df558eed..1f663643 100644
--- a/tests/helpers.py
+++ b/tests/helpers.py
@@ -2,7 +2,7 @@
 
 def setup_test_lib():
     cl = ChannelLibrary(db_resource_name=":memory:")
-
+    cl.clear()
     q1 = cl.new_qubit(label='q1')
     q2 = cl.new_qubit(label='q2')
     q3 = cl.new_qubit(label='q3')
diff --git a/tests/test_Compiler.py b/tests/test_Compiler.py
index 7754b72a..0482b3e2 100644
--- a/tests/test_Compiler.py
+++ b/tests/test_Compiler.py
@@ -6,7 +6,9 @@
 
 class CompileUtils(unittest.TestCase):
     def setUp(self):
+        print("Running setup")
         self.cl = ChannelLibrary(db_resource_name=":memory:")
+        self.cl.clear()
         self.q1gate = Channels.LogicalMarkerChannel(label='q1-gate', channel_db=self.cl.channelDatabase)
         self.q1gate = Channels.LogicalMarkerChannel(label='q1-gate', channel_db=self.cl.channelDatabase)
         self.q1phys = Channels.PhysicalChannel(label='q1-phys', sampling_rate=1.2e9, channel_db=self.cl.channelDatabase)
diff --git a/tests/test_Sequences.py b/tests/test_Sequences.py
index d9eb1ee8..923b6add 100644
--- a/tests/test_Sequences.py
+++ b/tests/test_Sequences.py
@@ -454,7 +454,7 @@ def setUp(self):
         AWGTestHelper.__init__(self, APS2Pattern)
         for name in ['APS1', 'APS2', 'APS3', 'APS4', 'APS5', 'APS6']:
             channelName = name + '-1'
-            channel = PhysicalQuadratureChannel(label=channelName)
+            channel = PhysicalQuadratureChannel(label=channelName, channel=0)
             channel.sampling_rate = 1.2e9
             channel.instrument = name
             channel.translator = 'APS2Pattern'
@@ -462,7 +462,7 @@ def setUp(self):
 
             for m in range(1, 5):
                 channelName = "{0}-m{1}".format(name, m)
-                channel = PhysicalMarkerChannel(label=channelName)
+                channel = PhysicalMarkerChannel(label=channelName, channel=m-1)
                 channel.sampling_rate = 1.2e9
                 channel.instrument = name
                 channel.translator = 'APS2Pattern'
@@ -509,9 +509,9 @@ class TestAPS1(unittest.TestCase, AWGTestHelper, TestSequences):
     def setUp(self):
         AWGTestHelper.__init__(self, APSPattern)
         for name in ['APS1', 'APS2', 'APS3']:
-            for ch in ['12', '34']:
+            for i, ch in enumerate(['12', '34']):
                 channelName = name + '-' + ch
-                channel = PhysicalQuadratureChannel(label=channelName)
+                channel = PhysicalQuadratureChannel(label=channelName, channel=i)
                 channel.sampling_rate = 1.2e9
                 channel.instrument = name
                 channel.translator = 'APSPattern'
@@ -519,7 +519,7 @@ def setUp(self):
 
             for m in range(1, 5):
                 channelName = "{0}-{1}m1".format(name, m)
-                channel = PhysicalMarkerChannel(label=channelName)
+                channel = PhysicalMarkerChannel(label=channelName, channel=m-1)
                 channel.sampling_rate = 1.2e9
                 channel.instrument = name
                 channel.translator = 'APSPattern'

From 9a3f221b9c450a28ae0c965439a60c13371ad1d3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Wed, 10 Apr 2019 15:00:06 -0400
Subject: [PATCH 180/235] addr and mask in Invalidate

---
 QGL/BasicSequences/Feedback.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/BasicSequences/Feedback.py b/QGL/BasicSequences/Feedback.py
index b7833556..999cdf86 100644
--- a/QGL/BasicSequences/Feedback.py
+++ b/QGL/BasicSequences/Feedback.py
@@ -124,8 +124,8 @@ def BitFlip3(data_qs, ancilla_qs, theta=None, phi=None, nrounds=1, meas_delay=1e
         raise Exception("Wrong number of qubits")
     seqs =  [
     DecodeSetRounds(1,0,nrounds),
-    Invalidate(addr=10, mask=2*nrounds),
-    Invalidate(addr=11, mask=0x1)]
+    Invalidate(10, 2*nrounds),
+    Invalidate(11, 0x1)]
 
     # encode single-qubit state into 3 qubits
     if theta and phi:

From 9a11c807c05636d5f0f1966fc9f7df8c993fa71f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Fri, 12 Apr 2019 10:27:13 -0400
Subject: [PATCH 181/235] Fix mv syntax

---
 QGL/BasicSequences/Feedback.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/QGL/BasicSequences/Feedback.py b/QGL/BasicSequences/Feedback.py
index 999cdf86..6efabbfe 100644
--- a/QGL/BasicSequences/Feedback.py
+++ b/QGL/BasicSequences/Feedback.py
@@ -153,7 +153,7 @@ def BitFlip3(data_qs, ancilla_qs, theta=None, phi=None, nrounds=1, meas_delay=1e
     if docals:
         seqs += create_cal_seqs(qubits,
         calRepeats)
-    metafile = compile_to_hardware(seqs, 'BitFlip/BitFlip')
+    metafile = compile_to_hardware(seqs, 'BitFlip/BitFlip', tdm_seq=True)
     return metafile
 
 def MajorityVoteN(qubits, nrounds, prep=[], meas_delay=1e-6, docals=False, calRepeats=2):
@@ -172,9 +172,9 @@ def MajorityVoteN(qubits, nrounds, prep=[], meas_delay=1e-6, docals=False, calRe
     metafile : metafile path
     """
     nqubits = len(qubits)
-    seqs = [MajorityMask(nrounds*nqubits),
-           Invalidate(addr=10, mask=nrounds*nqubits),
-           Invalidate(addr=11, mask=1)]
+    seqs = [MajorityMask(1, 0, nrounds*nqubits),
+           Invalidate(10, nrounds*nqubits),
+           Invalidate(11, 1)]
     if prep:
        seqs += [reduce(operator.mul, [X(q) for n,q in enumerate(qubits) if prep[n]])]
     for n in range(nrounds):
@@ -187,5 +187,4 @@ def MajorityVoteN(qubits, nrounds, prep=[], meas_delay=1e-6, docals=False, calRe
     if docals:
         seqs += create_cal_seqs(qubits,
         calRepeats)
-    metafile = compile_to_hardware(seqs, 'MajorityVote/MajorityVote')
-    return metafile
+    metafile = compile_to_hardware(seqs, 'MajorityVote/MajorityVote', tdm_seq=True)

From cd73f7bf871cfb02be7c4d19e505ad3ca405163a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Diego=20Rist=C3=A8?= <diego.riste@raytheon.com>
Date: Tue, 16 Apr 2019 18:24:13 -0400
Subject: [PATCH 182/235] Set mask correctly

Consistent with rest of notation
---
 QGL/TdmInstructions.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/TdmInstructions.py b/QGL/TdmInstructions.py
index 945743c9..4b057d3a 100644
--- a/QGL/TdmInstructions.py
+++ b/QGL/TdmInstructions.py
@@ -41,13 +41,13 @@ def MajorityVote(in_addr, out_addr, nmeas): # alternatively, append the loadcmpv
     return [LoadCmpVramInstruction('LOADCMPVRAM', 1, in_addr, 2**nmeas-1, True), CustomInstruction('MAJORITY', in_addr, out_addr)]
 
 def MajorityMask(in_addr, out_addr, value):
-    return [WriteAddrInstruction('INVALIDATE', None, 1, in_addr, 0x0, True), WriteAddrInstruction('WRITEADDR', None, 0, in_addr, value, True), LoadCmpVramInstruction('LOADCMPVRAM', 1, in_addr, 0xffff, True), CustomInstruction('MAJORITYMASK', in_addr, out_addr)]
+    return [WriteAddrInstruction('INVALIDATE', None, 1, in_addr, 0x0, True), WriteAddrInstruction('WRITEADDR', None, 0, in_addr, 2**value-1, True), LoadCmpVramInstruction('LOADCMPVRAM', 1, in_addr, 0xffff, True), CustomInstruction('MAJORITYMASK', in_addr, out_addr)]
 
 def Decode(in_addr, out_addr, nmeas):
     return [LoadCmpVramInstruction('LOADCMPVRAM', 1, in_addr, 2**nmeas-1, True), CustomInstruction('TSM', in_addr, out_addr)]
 
 def DecodeSetRounds(in_addr, out_addr, value):
-    return [WriteAddrInstruction('INVALIDATE', None, 1, in_addr, 0x0, True), WriteAddrInstruction('WRITEADDR', None, 0, in_addr, value, True), LoadCmpVramInstruction('LOADCMPVRAM', 1, in_addr, 0xffff, True), CustomInstruction('TSM_SET_ROUNDS', in_addr, out_addr)]
+    return [WriteAddrInstruction('INVALIDATE', None, 1, in_addr, 0x0, True), WriteAddrInstruction('WRITEADDR', None, 0, in_addr, 2**value-1, True), LoadCmpVramInstruction('LOADCMPVRAM', 1, in_addr, 0xffff, True), CustomInstruction('TSM_SET_ROUNDS', in_addr, out_addr)]
 
 # TODO: the rest of the CUSTOM instructions
 

From eaaa01ea2e27a88c716399d63c34c083956216ec Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Mon, 3 Jun 2019 16:07:59 -0400
Subject: [PATCH 183/235] Add back WFM plotting and GOTO buttons in pattern
 plotter

---
 QGL/drivers/APS2Pattern.py | 95 ++++++++++++++++++++++++++++++++++----
 1 file changed, 86 insertions(+), 9 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 845ac4e2..e47db469 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1464,6 +1464,23 @@ def read_instructions(filename):
     raw_instrs = raw_instructions(filename)
     return decompile_instructions(raw_instrs)
 
+def read_waveforms(filename):
+    with open(filename, 'rb') as FID:
+        target_hw    = FID.read(4).decode('utf-8')
+        file_version = struct.unpack('<f', FID.read(4))[0]
+        min_fw       = struct.unpack('<f', FID.read(4))[0]
+        num_chans    = struct.unpack('<H', FID.read(2))[0]
+
+        inst_len     = struct.unpack('<Q', FID.read(8))[0]
+        instructions = np.frombuffer(FID.read(8*inst_len), dtype=np.uint64)
+
+        wf_dat = []
+        for i in range(num_chans):
+            wf_len  = struct.unpack('<Q', FID.read(8))[0]
+            dat = ( 1.0 / MAX_WAVEFORM_VALUE) * np.frombuffer(FID.read(2*wf_len), dtype=np.int16).flatten()
+            wf_dat.append(dat)
+        return wf_dat
+
 def replace_instructions(filename, instructions, channel = 1):
     channelStr =  get_channel_instructions_string(channel)
     with h5py.File(filename, 'r+') as fid:
@@ -1494,16 +1511,46 @@ def display_raw_file(filename):
 if __name__ == '__main__':
     if len(sys.argv) == 2:
 
-        from PyQt5.QtWidgets import QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView
-        from PyQt5.QtGui import QIcon, QColor
+        from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView, QPushButton
+        from PyQt5.QtGui import QIcon, QColor, QFont
+
+        from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg
+        from matplotlib.figure import Figure
+
+        table_font = QFont("Arial", weight=QFont.Bold)
 
         colors = {"WFM": QColor(0,200,0),
                   "GOTO": QColor(0,100,100),
                   "MARKER": QColor(150,150,200)}
 
+        class MatplotlibWidget(QWidget):
+            def __init__(self, I, Q, parent=None):
+                super(MatplotlibWidget, self).__init__(parent)
+                self.title = 'Waveform'
+                self.left = 100
+                self.top = 100
+                self.width = 800
+                self.height = 600
+                self.setWindowTitle(self.title)
+                self.setGeometry(self.left, self.top, self.width, self.height)
+
+                self.figure = Figure()
+                self.canvas = FigureCanvasQTAgg(self.figure)
+
+                self.axis = self.figure.add_subplot(111)
+                self.axis.plot(I)
+                self.axis.plot(Q)
+                self.layout = QVBoxLayout(self)
+                self.layout.addWidget(self.canvas)
+                self.setLayout(self.layout)
+                self.canvas.draw()
+                self.show()
+
+
         class App(QWidget):
 
-            def __init__(self, instructions):
+            COLUMN_COUNT = 7
+            def __init__(self, instructions, waveforms):
                 super().__init__()
                 self.title = 'APS2 Disassembled Instructions'
                 self.left = 100
@@ -1511,7 +1558,10 @@ def __init__(self, instructions):
                 self.width = 1000
                 self.height = 1200
                 self.instructions = instructions
+                self.waveforms = waveforms
+                print(self.waveforms)
                 self.initUI()
+                self.plotters = []
 
             def initUI(self):
                 self.setWindowTitle(self.title)
@@ -1541,13 +1591,40 @@ def createTable(self):
                         color = None
                     for l, f in enumerate(fields):
                         text = fields[l]
-                        item = QTableWidgetItem(text)
-                        if color:
-                            item.setBackground(color)
-                        self.tableWidget.setItem(k,l, item)
+                        if text == "GOTO":
+                            btn = QPushButton(self.tableWidget)
+                            btn.setText('GOTO')
+                            target_row = int(fields[1].split("=")[1])
+                            def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
+                                tab.scrollToItem(tab.item(row, 0))
+                            btn.clicked.connect(scroll_to_goto_target)
+                            self.tableWidget.setCellWidget(k, l, btn)
+                        if text == "WFM" and int(fields[4].split("=")[1])==0:
+                            # Not a TA pair
+                            btn = QPushButton(self.tableWidget)
+                            btn.setText('WFM')
+                            addr = int(fields[6].split("=")[1])
+                            count = int(fields[5].split("=")[1])
+                            def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
+                                w = MatplotlibWidget(I,Q)
+                                self.plotters.append(w)
+                            btn.clicked.connect(open_plotter)
+                            self.tableWidget.setCellWidget(k, l, btn)
+                        else:
+                            item = QTableWidgetItem(text)
+                            item.setFont(table_font)
+                            if color:
+                                item.setBackground(color)
+                            self.tableWidget.setItem(k, l, item)
+                    if l < self.COLUMN_COUNT-1:
+                        for j in range(l+1, self.COLUMN_COUNT):
+                            item = QTableWidgetItem("")
+                            if color:
+                                item.setBackground(color)
+                            self.tableWidget.setItem(k, j, item)
                 self.tableWidget.move(0,0)
                 self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
-
+        
         app = QApplication(sys.argv[:1])
-        ex = App(read_instructions(sys.argv[1]))
+        ex = App(read_instructions(sys.argv[1]), read_waveforms(sys.argv[1]))
         sys.exit(app.exec_())

From 387e26cdbf1c2671061372bbec55edeba0ce40c8 Mon Sep 17 00:00:00 2001
From: Brian Donovan <bdonovan@bbn.com>
Date: Wed, 28 Nov 2018 12:52:58 -0500
Subject: [PATCH 184/235] Added support for 4 NCOs

---
 QGL/drivers/APS2Pattern.py | 31 +++++++++++++++++++------------
 1 file changed, 19 insertions(+), 12 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index e47db469..597a6b6e 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -47,6 +47,7 @@
 MAX_NUM_INSTRUCTIONS = 2**26
 MAX_REPEAT_COUNT = 2**16 - 1
 MAX_TRIGGER_COUNT = 2**32 - 1
+NUM_NCO = 4
 
 # instruction encodings
 WFM = 0x0
@@ -580,13 +581,19 @@ def to_instruction(self, write_flag=True, label=None):
         NCO_SELECT_OP_OFFSET = 40
         MODULATION_CLOCK = 300e6
 
+        nco_select_bits = {1 : 0b0001,
+                           2 : 0b0010,
+                           3 : 0b0100,
+                           4 : 0b1000,
+                           15: 0b1111}[self.nco_select]
+
         op_code_map = {"MODULATE": 0x0,
                        "RESET_PHASE": 0x2,
                        "SET_FREQ": 0x6,
                        "SET_PHASE": 0xa,
                        "UPDATE_FRAME": 0xe}
         payload = (op_code_map[self.instruction] << MODULATOR_OP_OFFSET) | (
-            self.nco_select << NCO_SELECT_OP_OFFSET)
+            (nco_select_bits) << NCO_SELECT_OP_OFFSET)
         if self.instruction == "MODULATE":
             #zero-indexed quad count
             payload |= np.uint32(self.length / ADDRESS_UNIT - 1)
@@ -614,9 +621,9 @@ def inject_modulation_cmds(seqs):
     for ct,seq in enumerate(seqs):
         #check whether we have modulation commands
         freqs = np.unique([entry.frequency for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)])
-        if len(freqs) > 2:
-            raise Exception("Max 2 frequencies on the same channel allowed.")
-        no_freq_cmds = np.all(np.less(np.abs(freqs), 1e-8))
+        if len(freqs) > NUM_NCO:
+            raise Exception("Max {} frequencies on the same channel allowed.".format(NUM_NCO))
+        no_freq_cmds = np.allclose(freqs, 0)
         phases = [entry.phase for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
         no_phase_cmds = np.all(np.less(np.abs(phases), 1e-8))
         frame_changes = [entry.frameChange for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
@@ -1134,12 +1141,13 @@ def start_new_seq():
         instructions = np.frombuffer(FID.read(8*inst_len), dtype=np.uint64)
 
         wf_lib = {}
-        for i in range(num_chans):
-            wf_len  = struct.unpack('<Q', FID.read(8))[0]
-            wf_dat  = np.frombuffer(FID.read(2*wf_len), dtype=np.int16)
-            wf_lib[f'ch{i+1}'] = ( 1.0 / MAX_WAVEFORM_VALUE) * wf_dat.flatten()
-
-        NUM_NCO = 2
+        wf_lib['ch1'] = (
+            1.0 /
+            MAX_WAVEFORM_VALUE) * FID['/chan_1/waveforms'].value.flatten()
+        wf_lib['ch2'] = (
+            1.0 /
+            MAX_WAVEFORM_VALUE) * FID['/chan_2/waveforms'].value.flatten()
+        instructions = FID['/chan_1/instructions'].value.flatten()
         freq = np.zeros(NUM_NCO)  #radians per timestep
         phase = np.zeros(NUM_NCO)
         frame = np.zeros(NUM_NCO)
@@ -1266,7 +1274,6 @@ def start_new_seq():
                 seqs['ch2'][ct] = mod_ch2
 
         del seqs['mod_phase']
-
     return seqs
 
 
@@ -1624,7 +1631,7 @@ def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.wavefor
                             self.tableWidget.setItem(k, j, item)
                 self.tableWidget.move(0,0)
                 self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
-        
+
         app = QApplication(sys.argv[:1])
         ex = App(read_instructions(sys.argv[1]), read_waveforms(sys.argv[1]))
         sys.exit(app.exec_())

From b8bba04bff17d12daff30c45f368046ea46a4828 Mon Sep 17 00:00:00 2001
From: Brian Donovan <bdonovan@bbn.com>
Date: Wed, 28 Nov 2018 13:05:55 -0500
Subject: [PATCH 185/235] Reset 4 NCOs

---
 QGL/drivers/APS2Pattern.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 597a6b6e..851be455 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -647,7 +647,7 @@ def inject_modulation_cmds(seqs):
                 #heuristic to insert phase reset before trigger if we have modulation commands
                 if isinstance(entry, ControlFlow.Wait):
                     if not ( no_modulation_cmds and (cur_freq == 0) and (cur_phase == 0)):
-                        mod_seq.append(ModulationCommand("RESET_PHASE", 0x3))
+                        mod_seq.append(ModulationCommand("RESET_PHASE", 0xF))
                         for nco_ind, freq in enumerate(freqs):
                             mod_seq.append( ModulationCommand("SET_FREQ", nco_ind + 1, frequency = -freq) )
                 elif isinstance(entry, ControlFlow.Return):

From 03dee019e04e75457f5bffea5df3e235a30b6843 Mon Sep 17 00:00:00 2001
From: Daniel Ellard <dan.ellard@raytheon.com>
Date: Thu, 17 Jan 2019 16:49:02 -0500
Subject: [PATCH 186/235] if the "kind" is unknown, raise an exception

this will usually detect when someone is calling qwait the old way,
and raise an error that will require correction
---
 QGL/ControlFlow.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/QGL/ControlFlow.py b/QGL/ControlFlow.py
index a735f24e..b8d99ecc 100644
--- a/QGL/ControlFlow.py
+++ b/QGL/ControlFlow.py
@@ -97,6 +97,7 @@ def qwait(kind="TRIG", addr=None, channels=None):
             raise Exception('Please specify address')
         return [WriteAddrInstruction('INVALIDATE', None, 1, addr, 0xffffffff, False), LoadCmpVramInstruction('LOADCMPVRAM', 1, addr, 0xff, False)]
 
+    raise Exception('Unknown kind parameter [%s]' % str(kind))
 
 
 def qsync(channels=None):

From 5632b17e5f5d5aa82949466285b99f8bb1591027 Mon Sep 17 00:00:00 2001
From: Daniel Ellard <dan.ellard@raytheon.com>
Date: Fri, 18 Jan 2019 13:16:41 -0500
Subject: [PATCH 187/235] clean up exceptions raised by qwait

ValueError instead of Exception
---
 QGL/ControlFlow.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/ControlFlow.py b/QGL/ControlFlow.py
index b8d99ecc..719a2964 100644
--- a/QGL/ControlFlow.py
+++ b/QGL/ControlFlow.py
@@ -94,10 +94,10 @@ def qwait(kind="TRIG", addr=None, channels=None):
         return LoadCmp(channels)
     elif kind == "RAM":
         if addr is None:
-            raise Exception('Please specify address')
+            raise ValueError('Please specify addr')
         return [WriteAddrInstruction('INVALIDATE', None, 1, addr, 0xffffffff, False), LoadCmpVramInstruction('LOADCMPVRAM', 1, addr, 0xff, False)]
 
-    raise Exception('Unknown kind parameter [%s]' % str(kind))
+    raise ValueError('Unknown kind parameter [%s]' % str(kind))
 
 
 def qsync(channels=None):

From f4d415f570f029ce1392489a9b46510f9ae0bef3 Mon Sep 17 00:00:00 2001
From: Daniel Ellard <dan.ellard@raytheon.com>
Date: Fri, 18 Jan 2019 13:17:22 -0500
Subject: [PATCH 188/235] tests for new qwait sanity checks

---
 tests/test_ControlFlow.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/tests/test_ControlFlow.py b/tests/test_ControlFlow.py
index a1a9e2a6..f9bbaf41 100644
--- a/tests/test_ControlFlow.py
+++ b/tests/test_ControlFlow.py
@@ -88,6 +88,23 @@ def test_qwait(self):
         assert (isinstance(seq1[2][0], TdmInstructions.WriteAddrInstruction))
         assert (isinstance(seq1[2][1], TdmInstructions.LoadCmpVramInstruction))
 
+    def test_qwait_err(self):
+        q1 = self.q1
+        with self.assertRaises(ValueError) as exc:
+            seq1 = [qwait(kind='FOO')]
+        exc_str = str(exc.exception)
+        assert (exc_str == 'Unknown kind parameter [FOO]')
+
+        with self.assertRaises(ValueError) as exc:
+            seq1 = [qwait(kind='RAM')]
+        exc_str = str(exc.exception)
+        assert (exc_str == 'Please specify addr')
+
+        # test the legal values
+        seq1 = [qwait(kind='TRIG')]
+        seq1 = [qwait(kind='CMP')]
+        seq1 = [qwait(kind='RAM', addr=0xff)]
+
     def test_compile(self):
         q1 = self.q1
         seq1 = [X90(q1), Y90(q1)]

From beeeb6682bc47e8c7e28aaa01823c4c794b9443b Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Thu, 14 Feb 2019 17:53:02 -0500
Subject: [PATCH 189/235] Initial commit of changes for hardware randomization

---
 QGL/Compiler.py        | 36 +++++++++++++++++++++++++++++++++++-
 QGL/PatternUtils.py    |  5 +++++
 QGL/PulsePrimitives.py | 15 +++++++++++++--
 QGL/PulseSequencer.py  |  9 ++++++---
 4 files changed, 59 insertions(+), 6 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index ba8e561b..a7b05b47 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -30,6 +30,7 @@
 from . import Channels
 from . import ChannelLibraries
 from . import PulseShapes
+from . import PulsePrimitives
 from .PulsePrimitives import Id, clear_pulse_cache
 from .PulseSequencer import Pulse, PulseBlock, CompositePulse
 from . import ControlFlow
@@ -221,6 +222,10 @@ def generate_waveforms(physicalWires):
         for pulse in flatten(wire):
             if not isinstance(pulse, Pulse):
                 continue
+            if pulse.isRunTime:
+                #skip run-time pulses as we need to add the set of all possible pulses to
+                #the waveform table
+                continue
             if pulse.hashshape() not in wfs[ch]:
                 if pulse.isTimeAmp:
                     wfs[ch][pulse.hashshape()] = np.ones(1, dtype=np.complex)
@@ -228,6 +233,24 @@ def generate_waveforms(physicalWires):
                     wfs[ch][pulse.hashshape()] = pulse.shape
     return wfs
 
+def add_runtime_pulse_set(physicalWires, wfs):
+
+    for ch, wire in physicalWires.items():
+        rt_pulses = [pulse for pulse in flatten(wire) if pulse.isRunTime]
+        pulse_type = set([pulse.label for pulse in rt_pulses])
+        if len(pulse_type) > 1:
+            raise Exception("All run-time pulses must have the same label.")
+        if pulse_type not in ("RandomAC, RandomDiAC"):
+            raise Exception(f"Unknown run time pulse type {pulse_type}.")
+
+        pulse_fn = getattr(PulsePrimitives, pulse_type.split('Random')[-1], None)
+
+
+
+
+
+
+
 
 def pulses_to_waveforms(physicalWires):
     logger.debug("Converting pulses_to_waveforms:")
@@ -426,6 +449,10 @@ def compile_to_hardware(seqs,
     logger.info("Generating waveform library.")
     wfs = generate_waveforms(physWires)
 
+    # If there are run-time pulses add these to the library
+    if PatternUtils.contains_runtime_pulses(seqs):
+        wfs = add_runtime_pulse_set(physWires, wfs)
+
     # replace Pulse objects with Waveforms
     logger.info("Replacing pulses with waveforms")
     physWires = pulses_to_waveforms(physWires)
@@ -713,7 +740,8 @@ class Waveform(object):
 
     #Use slots to create attributes to save on memory.
     __slots__ = ["label", "key", "amp", "length", "phase", "frameChange",
-                    "isTimeAmp", "frequency", "logicalChan", "maddr", "startTime"]
+                    "isTimeAmp", "frequency", "logicalChan", "maddr", "startTime",
+                    "isRunTime"]
 
     def __init__(self, pulse=None):
         if pulse is None:
@@ -727,6 +755,7 @@ def __init__(self, pulse=None):
             self.frequency = 0
             self.logicalChan = ""
             self.maddr = (-1, 0)
+            self.isRunTime = False
         else:
             self.label = pulse.label
             self.key = pulse.hashshape()
@@ -738,11 +767,14 @@ def __init__(self, pulse=None):
             self.frequency = pulse.frequency
             self.logicalChan = pulse.channel
             self.maddr = pulse.maddr
+            self.isRunTime = pulse.isRunTime
 
     def __repr__(self):
         return self.__str__()
 
     def __str__(self):
+        if self.isRunTime:
+            return f"Hardware-Generated({self.length})"
         if self.isTimeAmp:
             TA = 'HIGH' if self.amp != 0 else 'LOW'
             return "Waveform-TA(" + TA + ", " + str(self.length) + ")"
@@ -751,6 +783,8 @@ def __str__(self):
                 self.key)[:6] + ", " + str(self.length) + ")"
 
     def __eq__(self, other):
+        if self.isRunTime or other.isRunTime:
+            return False
         if isinstance(other, self.__class__):
             #No __dict__ property so we check all properties.
             return all((getattr(self, attr, None) == getattr(other, attr, None) for attr in self.__slots__))
diff --git a/QGL/PatternUtils.py b/QGL/PatternUtils.py
index 9298d45e..0719a3e0 100644
--- a/QGL/PatternUtils.py
+++ b/QGL/PatternUtils.py
@@ -208,6 +208,11 @@ def add_digitizer_trigger(seqs):
                             trig_chan in seq[ct].pulses.keys()):
                         seq[ct] = align('left', seq[ct], TAPulse("TRIG", trig_chan, trig_chan.pulse_params['length'], 1.0, 0.0, 0.0))
 
+def contains_runtime_pulses(seqs):
+    """
+    Determines if sequences contain run-time generated pulses.
+    """
+    return any([hasattr(entry, 'isRunTime') and entry.isRunTime for entry in flatten(seqs)])
 
 def contains_measurement(entry):
     """
diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index bfbf03b2..1ad4fbbe 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -25,12 +25,15 @@
 from functools import wraps, reduce
 
 
-def overrideDefaults(chan, updateParams):
+def overrideDefaults(chan, updateParams, ignoredStrParams=['isRunTime', 'maddr', 'moffset']):
     '''Helper function to update any parameters passed in and fill in the defaults otherwise.'''
     # The default parameter list depends on the channel type so pull out of channel
     # Then update passed values
     paramDict = chan.pulse_params.copy()
     paramDict.update(updateParams)
+    for param in ignoredStrParams:
+        if param in paramDict.keys():
+            paramDict.pop(param)
     return paramDict
 
 
@@ -113,7 +116,7 @@ def Utheta(qubit,
         else:
             # linearly scale based upon the 'pi/2' amplitude
             amp  = (angle / (pi/2)) * qubit.pulse_params['pi2Amp']
-    return Pulse(label, qubit, params, amp, phase, 0.0, ignoredStrParams, frequency=frequency)
+    return Pulse(label, qubit, params, amp, phase, 0.0, ignoredStrParams, frequency=frequency, **kwargs)
 
 
 # generic pulses around X, Y, and Z axes
@@ -337,6 +340,14 @@ def arb_axis_drag(qubit,
     return Pulse(kwargs["label"] if "label" in kwargs else "ArbAxis", qubit,
                  params, 1.0, aziAngle, frameChange)
 
+def RandomAC(qubit):
+    params = overrideDefaults(qubit, {})
+    return Pulse("RandomAC", qubit, params, isRunTime=True)
+
+def RandomDiAC(qubit):
+    params = overrideDefaults(qubit, {})
+    params["length"] *= 2.0
+    return Pulse("RandomAC", qubit, params, isRunTime=True)
 
 def AC(qubit, cliffNum):
     """
diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 3b260634..81c64a96 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -33,10 +33,11 @@
 class Pulse(namedtuple("Pulse", ["label", "channel", "length", "amp", "phase", "frequency",
                                  "frameChange", "shapeParams", "isTimeAmp",
                                  "isZero", "ignoredStrParams",
-                                 "maddr", "moffset"])):
+                                 "maddr", "moffset", "isRunTime"])):
     __slots__ = ()
 
-    def __new__(cls, label, channel, shapeParams, amp=1.0, phase=0, frameChange=0, ignoredStrParams=[], maddr=-1, moffset=0, frequency=None):
+    def __new__(cls, label, channel, shapeParams, amp=1.0, phase=0, frameChange=0,
+            ignoredStrParams=[], maddr=-1, moffset=0, frequency=None, isRunTime=False):
         if frequency:
             frequency = frequency
         elif hasattr(channel, 'frequency'):
@@ -48,12 +49,14 @@ def __new__(cls, label, channel, shapeParams, amp=1.0, phase=0, frameChange=0, i
             if param not in shapeParams.keys():
                 raise NameError("shapeParams must include {0}".format(param))
         isTimeAmp = (shapeParams['shape_fun'] == PulseShapes.constant)
+        if isRunTime:
+            isTimeAmp = False
         isZero = (amp == 0)
         return super(cls, Pulse).__new__(cls, label, channel,
                                          shapeParams['length'], amp, phase,
                                          frequency, frameChange, shapeParams,
                                          isTimeAmp, isZero, ignoredStrParams,
-                                         maddr, moffset)
+                                         maddr, moffset, isRunTime)
 
     def __str__(self):
         kwvals = []

From 192789d75ba7378e3f85504faf33842e59758e4b Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 18 Feb 2019 17:12:17 -0500
Subject: [PATCH 190/235] WIP

---
 QGL.egg-info/PKG-INFO             | 10 +++++++
 QGL.egg-info/SOURCES.txt          | 41 +++++++++++++++++++++++++++++
 QGL.egg-info/dependency_links.txt |  1 +
 QGL.egg-info/requires.txt         |  6 +++++
 QGL.egg-info/top_level.txt        |  1 +
 QGL/Compiler.py                   | 43 +++++++++++++++++++++----------
 QGL/PulsePrimitives.py            |  2 +-
 7 files changed, 90 insertions(+), 14 deletions(-)
 create mode 100644 QGL.egg-info/PKG-INFO
 create mode 100644 QGL.egg-info/SOURCES.txt
 create mode 100644 QGL.egg-info/dependency_links.txt
 create mode 100644 QGL.egg-info/requires.txt
 create mode 100644 QGL.egg-info/top_level.txt

diff --git a/QGL.egg-info/PKG-INFO b/QGL.egg-info/PKG-INFO
new file mode 100644
index 00000000..ac9daf85
--- /dev/null
+++ b/QGL.egg-info/PKG-INFO
@@ -0,0 +1,10 @@
+Metadata-Version: 1.0
+Name: QGL
+Version: 2.1
+Summary: UNKNOWN
+Home-page: https://github.com/BBN-Q/QGL
+Author: UNKNOWN
+Author-email: UNKNOWN
+License: UNKNOWN
+Description: UNKNOWN
+Platform: UNKNOWN
diff --git a/QGL.egg-info/SOURCES.txt b/QGL.egg-info/SOURCES.txt
new file mode 100644
index 00000000..945e4a89
--- /dev/null
+++ b/QGL.egg-info/SOURCES.txt
@@ -0,0 +1,41 @@
+README.md
+QGL/BlockLabel.py
+QGL/ChannelLibraries.py
+QGL/Channels.py
+QGL/Cliffords.py
+QGL/Compiler.py
+QGL/ControlFlow.py
+QGL/GSTTools.py
+QGL/PatternUtils.py
+QGL/Plotting.py
+QGL/PulsePrimitives.py
+QGL/PulseSequencePlotter.py
+QGL/PulseSequencer.py
+QGL/PulseShapes.py
+QGL/Scheduler.py
+QGL/TdmInstructions.py
+QGL/Tomography.py
+QGL/__init__.py
+QGL/config.py
+QGL/config_location.py
+QGL/mm.py
+QGL.egg-info/PKG-INFO
+QGL.egg-info/SOURCES.txt
+QGL.egg-info/dependency_links.txt
+QGL.egg-info/requires.txt
+QGL.egg-info/top_level.txt
+QGL/BasicSequences/AllXY.py
+QGL/BasicSequences/BlankingSweeps.py
+QGL/BasicSequences/CR.py
+QGL/BasicSequences/Decoupling.py
+QGL/BasicSequences/Feedback.py
+QGL/BasicSequences/FlipFlop.py
+QGL/BasicSequences/RB.py
+QGL/BasicSequences/Rabi.py
+QGL/BasicSequences/SPAM.py
+QGL/BasicSequences/T1T2.py
+QGL/BasicSequences/__init__.py
+QGL/BasicSequences/helpers.py
+QGL/drivers/APS2Pattern.py
+QGL/drivers/APSPattern.py
+QGL/drivers/__init__.py
\ No newline at end of file
diff --git a/QGL.egg-info/dependency_links.txt b/QGL.egg-info/dependency_links.txt
new file mode 100644
index 00000000..8b137891
--- /dev/null
+++ b/QGL.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/QGL.egg-info/requires.txt b/QGL.egg-info/requires.txt
new file mode 100644
index 00000000..2aa45f83
--- /dev/null
+++ b/QGL.egg-info/requires.txt
@@ -0,0 +1,6 @@
+bbndb>=0.1
+numpy>=1.11.1
+scipy>=0.17.1
+networkx>=1.11
+bqplot>=0.11.5
+sqlalchemy>=1.2.17
diff --git a/QGL.egg-info/top_level.txt b/QGL.egg-info/top_level.txt
new file mode 100644
index 00000000..0e533603
--- /dev/null
+++ b/QGL.egg-info/top_level.txt
@@ -0,0 +1 @@
+QGL
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index a7b05b47..d6e0f14a 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -234,23 +234,40 @@ def generate_waveforms(physicalWires):
     return wfs
 
 def add_runtime_pulse_set(physicalWires, wfs):
-
     for ch, wire in physicalWires.items():
-        rt_pulses = [pulse for pulse in flatten(wire) if pulse.isRunTime]
-        pulse_type = set([pulse.label for pulse in rt_pulses])
+        rt_pulses = [pulse for pulse in flatten(wire) if isinstance(pulse, Pulse) and pulse.isRunTime]
+        if len(rt_pulses) == 0:
+            continue
+        pulse_type = list(set([pulse.label for pulse in rt_pulses]))
+        pulse_logical_chan = list(set([pulse.channel for pulse in rt_pulses]))
+        
         if len(pulse_type) > 1:
-            raise Exception("All run-time pulses must have the same label.")
-        if pulse_type not in ("RandomAC, RandomDiAC"):
+            raise Exception(f"All run-time pulses must have the same label. Found: {pulse_type}.")
+        if len(pulse_logical_chan) > 1:
+            raise Exception(f"Found more than one channel per run-time pulse set: {pulse_logical_chan}.")
+        if pulse_type[0] not in ("RandomAC, RandomDiAC"):
             raise Exception(f"Unknown run time pulse type {pulse_type}.")
+        pulse_fn = getattr(PulsePrimitives, pulse_type[0].split('Random')[-1], None)
+        if pulse_fn is None:
+            raise Exception("Was unable to get pulse type for run-time generated pulses.")
+
+        all_cliffords = [pulse_fn(pulse_logical_chan[0], n) for n in range(24)]
+        #Some could be CompositePulses so crack into indvidual pulses
+        all_pulses = []
+        for cliff in all_cliffords:
+            try:
+                for p in cliff.pulses:
+                    all_pulses.append(p)
+            except AttributeError:
+                all_pulses.append(cliff)
+        for cp in all_pulses:
+            if cp.hashshape() not in wfs[ch]: #don't duplicate data
+                if cp.isTimeAmp:
+                    wfs[ch][cp.hashshape()] = np.ones(1, dtype=np.complex)
+                else:
+                    wfs[ch][cp.hashshape()] = cp.shape
 
-        pulse_fn = getattr(PulsePrimitives, pulse_type.split('Random')[-1], None)
-
-
-
-
-
-
-
+    return wfs
 
 def pulses_to_waveforms(physicalWires):
     logger.debug("Converting pulses_to_waveforms:")
diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index 1ad4fbbe..596c79d2 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -347,7 +347,7 @@ def RandomAC(qubit):
 def RandomDiAC(qubit):
     params = overrideDefaults(qubit, {})
     params["length"] *= 2.0
-    return Pulse("RandomAC", qubit, params, isRunTime=True)
+    return Pulse("RandomDiAC", qubit, params, isRunTime=True)
 
 def AC(qubit, cliffNum):
     """

From a24b0a19ea4cd870e3bb03b5d55294fba9cde84d Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Fri, 22 Feb 2019 17:35:26 -0500
Subject: [PATCH 191/235] WIP

---
 QGL/Compiler.py            | 122 ++++++++++++++++++++++---------------
 QGL/ControlFlow.py         |   3 +-
 QGL/PulseSequencer.py      |   5 ++
 QGL/TdmInstructions.py     |   4 +-
 QGL/drivers/APS2Pattern.py |  28 ++++-----
 5 files changed, 95 insertions(+), 67 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index d6e0f14a..10e08258 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -233,34 +233,40 @@ def generate_waveforms(physicalWires):
                     wfs[ch][pulse.hashshape()] = pulse.shape
     return wfs
 
+def get_clifford_type(wire, allowed_types=("RandomAC")):
+    rt_pulses = [pulse for pulse in flatten(wire) if isinstance(pulse, Pulse) and pulse.isRunTime]
+    if len(rt_pulses) == 0:
+        return None
+    pulse_type = list(set([pulse.label for pulse in rt_pulses]))
+    pulse_logical_chan = list(set([pulse.channel for pulse in rt_pulses]))
+    if len(pulse_type) > 1:
+        raise Exception(f"All run-time pulses must have the same label. Found: {pulse_type}.")
+    if len(pulse_logical_chan) > 1:
+        raise Exception(f"Found more than one channel per run-time pulse set: {pulse_logical_chan}.")
+    if pulse_type[0] not in allowed_types:
+        raise Exception(f"Unknown run time pulse type {pulse_type}.")
+    pulse_fn = getattr(PulsePrimitives, pulse_type[0].split('Random')[-1], None)
+    if pulse_fn is None:
+        raise Exception("Was unable to get pulse type for run-time generated pulses.")
+    return lambda x: pulse_fn(pulse_logical_chan[0], x)
+
+
 def add_runtime_pulse_set(physicalWires, wfs):
     for ch, wire in physicalWires.items():
-        rt_pulses = [pulse for pulse in flatten(wire) if isinstance(pulse, Pulse) and pulse.isRunTime]
-        if len(rt_pulses) == 0:
-            continue
-        pulse_type = list(set([pulse.label for pulse in rt_pulses]))
-        pulse_logical_chan = list(set([pulse.channel for pulse in rt_pulses]))
-        
-        if len(pulse_type) > 1:
-            raise Exception(f"All run-time pulses must have the same label. Found: {pulse_type}.")
-        if len(pulse_logical_chan) > 1:
-            raise Exception(f"Found more than one channel per run-time pulse set: {pulse_logical_chan}.")
-        if pulse_type[0] not in ("RandomAC, RandomDiAC"):
-            raise Exception(f"Unknown run time pulse type {pulse_type}.")
-        pulse_fn = getattr(PulsePrimitives, pulse_type[0].split('Random')[-1], None)
+        pulse_fn = get_clifford_type(wire)
         if pulse_fn is None:
-            raise Exception("Was unable to get pulse type for run-time generated pulses.")
-
-        all_cliffords = [pulse_fn(pulse_logical_chan[0], n) for n in range(24)]
-        #Some could be CompositePulses so crack into indvidual pulses
+            continue
         all_pulses = []
+        all_cliffords = [pulse_fn(n) for n in range(24)]
+        #Some could be CompositePulses so crack into indvidual pulses
         for cliff in all_cliffords:
             try:
                 for p in cliff.pulses:
                     all_pulses.append(p)
             except AttributeError:
                 all_pulses.append(cliff)
-        for cp in all_pulses:
+
+        for cp in all_pulses: #make all-pulses a set?
             if cp.hashshape() not in wfs[ch]: #don't duplicate data
                 if cp.isTimeAmp:
                     wfs[ch][cp.hashshape()] = np.ones(1, dtype=np.complex)
@@ -269,6 +275,15 @@ def add_runtime_pulse_set(physicalWires, wfs):
 
     return wfs
 
+def create_clifford_waveforms(physicalWires):
+    clifford_sets = {}
+    for ch, wire in physicalWires.items():
+        pulse_fn = get_clifford_type(wire)
+        if pulse_fn is None:
+            continue
+        clifford_sets[ch] = [[Waveform(pulse_fn(n))] for n in range(24)]
+    return clifford_sets
+
 def pulses_to_waveforms(physicalWires):
     logger.debug("Converting pulses_to_waveforms:")
     wireOuts = {ch: [] for ch in physicalWires.keys()}
@@ -312,7 +327,7 @@ def setup_awg_channels(physicalChannels):
     return data
 
 
-def bundle_wires(physWires, wfs):
+def bundle_wires(physWires, wfs, cliff_wires=None):
     awgData = setup_awg_channels(physWires.keys())
     for chan in physWires.keys():
         _, awgChan = chan.label.rsplit('-', 1)
@@ -320,6 +335,8 @@ def bundle_wires(physWires, wfs):
             awgChan = 'ch' + awgChan
         awgData[chan.instrument][awgChan]['linkList'] = physWires[chan]
         awgData[chan.instrument][awgChan]['wfLib'] = wfs[chan]
+        if cliff_wires is not None and chan in cliff_wires.keys():
+            awgData[chan.instrument][awgChan]['clifford_set'] = cliff_wires[chan]
         if hasattr(chan, 'correctionT'):
             awgData[chan.instrument][awgChan]['correctionT'] = chan.correctionT
     return awgData
@@ -340,37 +357,12 @@ def collect_specializations(seqs):
             done.append(target)
     return funcs
 
-def compile_to_hardware(seqs,
-                        fileName,
-                        library_version=None,
-                        suffix='',
-                        axis_descriptor=None,
-                        add_slave_trigger=True,
-                        extra_meta=None,
-                        tdm_seq = False):
-    '''
-    Compiles 'seqs' to a hardware description and saves it to 'fileName'.
-    Other inputs:
-        library_version (optional): string or ChannelLibrary instance to pack in the
-            metafile. This will be the version of the library loaded during program
-            execution. Default None uses the current working version.
-        suffix (optional): string to append to end of fileName, e.g. with
-            fileNames = 'test' and suffix = 'foo' might save to test-APSfoo.h5
-        axis_descriptor (optional): a list of dictionaries describing the effective
-            axes of the measurements that the sequence will yield. For instance,
-            if `seqs` generates a Ramsey experiment, axis_descriptor would describe
-            the time delays between pulses.
-        add_slave_trigger (optional): add the slave trigger(s)
-        tdm_seq (optional): compile for TDM
-    '''
+def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False):
+
     ChannelLibraries.channelLib.update_channelDict()
     clear_pulse_cache()
-
     logger.debug("Compiling %d sequence(s)", len(seqs))
 
-    # save input code to file
-    save_code(seqs, fileName + suffix)
-
     # all sequences should start with a WAIT for synchronization
     for seq in seqs:
         if not isinstance(seq[0], ControlFlow.Wait):
@@ -469,6 +461,9 @@ def compile_to_hardware(seqs,
     # If there are run-time pulses add these to the library
     if PatternUtils.contains_runtime_pulses(seqs):
         wfs = add_runtime_pulse_set(physWires, wfs)
+        cliff_wires = create_clifford_waveforms(physWires)
+    else:
+        cliff_wires = None
 
     # replace Pulse objects with Waveforms
     logger.info("Replacing pulses with waveforms")
@@ -477,9 +472,36 @@ def compile_to_hardware(seqs,
     # bundle wires on instruments, or channels depending
     # on whether we have one sequence per channel
     logger.info("Bundling wires.")
-    awgData = bundle_wires(physWires, wfs)
-    del wireSeqs
-    gc.collect()
+    awgData = bundle_wires(physWires, wfs, cliff_wires=cliff_wires)
+    return awgData
+
+def compile_to_hardware(seqs,
+                        fileName,
+                        library_version=None,
+                        suffix='',
+                        axis_descriptor=None,
+                        add_slave_trigger=True,
+                        extra_meta=None,
+                        tdm_seq = False):
+    '''
+    Compiles 'seqs' to a hardware description and saves it to 'fileName'.
+    Other inputs:
+        library_version (optional): string or ChannelLibrary instance to pack in the
+            metafile. This will be the version of the library loaded during program
+            execution. Default None uses the current working version.
+        suffix (optional): string to append to end of fileName, e.g. with
+            fileNames = 'test' and suffix = 'foo' might save to test-APSfoo.h5
+        axis_descriptor (optional): a list of dictionaries describing the effective
+            axes of the measurements that the sequence will yield. For instance,
+            if `seqs` generates a Ramsey experiment, axis_descriptor would describe
+            the time delays between pulses.
+        add_slave_trigger (optional): add the slave trigger(s)
+        tdm_seq (optional): compile for TDM
+    '''
+    # save input code to file
+    save_code(seqs, fileName + suffix)
+
+    awgData = compile_to_IR(seqs, add_slave_trigger=add_slave_trigger, tdm_seq=tdm_seq)
 
     # convert to hardware formats
     # files = {}
@@ -791,7 +813,7 @@ def __repr__(self):
 
     def __str__(self):
         if self.isRunTime:
-            return f"Hardware-Generated({self.length})"
+            return f"Hardware-Generated({self.label}, {self.length})"
         if self.isTimeAmp:
             TA = 'HIGH' if self.amp != 0 else 'LOW'
             return "Waveform-TA(" + TA + ", " + str(self.length) + ")"
diff --git a/QGL/ControlFlow.py b/QGL/ControlFlow.py
index 719a2964..2aea53ad 100644
--- a/QGL/ControlFlow.py
+++ b/QGL/ControlFlow.py
@@ -151,8 +151,9 @@ def __init__(self, target):
 
 class Call(ControlInstruction):
     # target is a BlockLabel
-    def __init__(self, target):
+    def __init__(self, target, load_addr=False):
         super(Call, self).__init__("CALL", target=target)
+        self.load_addr = load_addr
 
 
 class Return(ControlInstruction):
diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 81c64a96..71df08c6 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -262,6 +262,11 @@ def __eq__(self, other):
     def __ne__(self, other):
         return not self == other
 
+    @property
+    def isRunTime(self):
+        #Check if any of the member pulses contain a run-time pulse
+        return any([hasattr(entry, 'isRunTime') and entry.isRunTime for entry in self.pulses.values()])
+
     @property
     def channel(self):
         return self.pulses.keys()
diff --git a/QGL/TdmInstructions.py b/QGL/TdmInstructions.py
index 4b057d3a..fb0069e7 100644
--- a/QGL/TdmInstructions.py
+++ b/QGL/TdmInstructions.py
@@ -109,5 +109,5 @@ def __ne__(self, other):
         return not self == other
 
 
-# def LoadCmpVram(addr, mask):
-#     return LoadCmpVramInstruction('LOADCMPVRAM', 1, addr, mask)
+def LoadCmpVram(addr, mask, tdm=True):
+    return LoadCmpVramInstruction('LOADCMPVRAM', 1, addr, mask, tdm)
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 851be455..9a3e2290 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -31,6 +31,8 @@
 from QGL import PulseSequencer
 from QGL.PatternUtils import hash_pulse, flatten
 from QGL import TdmInstructions
+from QGL import APS2CustomInstructions
+from QGL.APS2CustomInstructions import APS2_CUSTOM_DECODE
 
 # Python 2/3 compatibility: use 'int' that subclasses 'long'
 from builtins import int
@@ -86,20 +88,17 @@
 
 CMPTABLE = {'==': EQUAL, '!=': NOTEQUAL, '>': GREATERTHAN, '<': LESSTHAN}
 
-# custom OP_CODES
+# custom TDM OP_CODES
 TDM_MAJORITY_VOTE = 0
 TDM_MAJORITY_VOTE_SET_MASK = 1
 TDM_TSM_SET_ROUNDS = 2
 TDM_TSM = 3
 
-APS_CUSTOM_DECODE = ["APS_RAND", "APS_CLIFFORD_RAND","APS_CLIFFORD_SET_SEED" ,"APS_CLIFFORD_SET_OFFSET"
-, "APS_CLIFFORD_SET_SPACING"]
-
 TDM_CUSTOM_DECODE = ["TDM_MAJORITY_VOTE", "TDM_MAJORITY_VOTE_SET_MASK", "TDM_TSM_SET_ROUNDS", "TDM_TSM"]
 
 # Whether we use PHASE_OFFSET modulation commands or bake it into waveform
 # Default to false as we usually don't have many variants
-USE_PHASE_OFFSET_INSTRUCTION = False
+USE_PHASE_OFFSET_INSTRUCTION = True
 
 # Whether to save the waveform offsets for partial compilation
 SAVE_WF_OFFSETS = False
@@ -446,8 +445,8 @@ def Goto(addr, label=None):
     return Command(GOTO, addr, label=label)
 
 
-def Call(addr, label=None):
-    return Command(CALL, addr, label=label)
+def Call(addr, load_addr=False, label=None):
+    return Command(CALL, addr, label=label, write=load_addr)
 
 
 def Return(label=None):
@@ -513,11 +512,11 @@ def LoadCmpVram(addr, mask, label=None):
     return Instruction(header, payload, label=label)
 
 
-def preprocess(seqs, shapeLib):
+def preprocess(seqs, shapeLib, clifford_set=False):
     seqs = PatternUtils.convert_lengths_to_samples(
         seqs, SAMPLING_RATE, ADDRESS_UNIT, Compiler.Waveform)
     wfLib = build_waveforms(seqs, shapeLib)
-    inject_modulation_cmds(seqs)
+    inject_modulation_cmds(seqs, force_phase_update=clifford_set)
     return seqs, wfLib
 
 
@@ -611,7 +610,7 @@ def to_instruction(self, write_flag=True, label=None):
         instr.writeFlag = write_flag
         return instr
 
-def inject_modulation_cmds(seqs):
+def inject_modulation_cmds(seqs, force_phase_update=False):
     """
     Inject modulation commands from phase, frequency and frameChange of waveforms
     in an IQ waveform sequence. Assume up to 2 NCOs for now.
@@ -629,7 +628,7 @@ def inject_modulation_cmds(seqs):
         frame_changes = [entry.frameChange for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
         no_frame_cmds = np.all(np.less(np.abs(frame_changes), 1e-8))
         no_modulation_cmds = no_freq_cmds and no_phase_cmds and no_frame_cmds
-
+        #import pdb; pdb.set_trace()
         if no_modulation_cmds:
             continue
 
@@ -672,10 +671,11 @@ def inject_modulation_cmds(seqs):
                             mod_seq.append( ModulationCommand("MODULATE", nco_select, length = entry.length))
                             pending_frame_update = False
                     #now apply non-zero frame changes after so it is applied at end
+
                     if entry.frameChange != 0:
                         pending_frame_update = True
                         #zero length frame changes (Z pulses) need to be combined with the previous frame change or injected where possible
-                        if entry.length == 0:
+                        if entry.length == 0 and not force_phase_update:
                             #if the last is a frame change then we can add to the frame change
                             if isinstance(mod_seq[-1], ModulationCommand) and mod_seq[-1].instruction == "UPDATE_FRAME":
                                 mod_seq[-1].phase += entry.frameChange
@@ -808,7 +808,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                     isinstance(entry, ControlFlow.ControlInstruction) or
                     isinstance(entry, BlockLabel.BlockLabel) or
                     isinstance(entry, TdmInstructions.CustomInstruction) or
-                    isinstance(entry, TdmInstructions.WriteAddrInstruction) or
+                    isinstance(entry, TdmInstructions.Instruction) or
                     isinstance(entry, TdmInstructions.LoadCmpVramInstruction)):
                 if isinstance(entry, BlockLabel.BlockLabel):
                     # carry label forward to next entry
@@ -827,7 +827,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                 elif isinstance(entry, ControlFlow.Goto):
                     instructions.append(Goto(entry.target, label=label))
                 elif isinstance(entry, ControlFlow.Call):
-                    instructions.append(Call(entry.target, label=label))
+                    instructions.append(Call(entry.target, load_addr = entry.load_addr, label=label))
                 elif isinstance(entry, ControlFlow.Repeat):
                     instructions.append(Repeat(entry.target, label=label))
                 # value argument commands

From 180ecb17e2f5f00969dd5fedfa383a48e0b6560e Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Fri, 22 Feb 2019 17:35:48 -0500
Subject: [PATCH 192/235] More WIP...

---
 QGL/APS2CustomInstructions.py | 74 +++++++++++++++++++++++++++++++++++
 QGL/RandomCliffordTools.py    | 51 ++++++++++++++++++++++++
 2 files changed, 125 insertions(+)
 create mode 100644 QGL/APS2CustomInstructions.py
 create mode 100644 QGL/RandomCliffordTools.py

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
new file mode 100644
index 00000000..cb082dc0
--- /dev/null
+++ b/QGL/APS2CustomInstructions.py
@@ -0,0 +1,74 @@
+'''
+Copyright 2019 Raytheon BBN Technologies
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+   http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+'''
+
+# Instructions for the the prototype APS2-TDM hardware.
+
+from .TdmInstructions import CustomInstruction, WriteAddr, Invalidate, LoadCmpVram
+from .ControlFlow import LoadCmp, Call
+
+##custom APS OP_CODES
+#APS_CLIFFORD_SET_SEED:         Set 32 bit seed for random number generator
+#APS_CLIFFORD_SET_OFFSET:       Stores jump table starting offset
+#APS_CLIFFORD_SET_SPACING:      Stores jump table spacing (integer to shift left),
+#                               including interal address representation
+#APS_CLIFFORD_INVERSE_RESET:    Reset inverse tracker
+#APS_CLIFFORD_RAND:             Choose randomly from set of 24 waveforms,
+#                               returns starting address of jump table entry from RAM
+#APS_CLIFFORD_INVERSE:          Store waveform address of inverse waveform to be jumped to
+
+APS2_CUSTOM_DECODE = {"APS_RAND": 0,
+                     "APS_CLIFFORD_RAND": 2,
+                     "APS_CLIFFORD_INVERSE": 6,
+                     "APS_CLIFFORD_INVERSE_RESET": 7,
+                     "APS_CLIFFORD_SET_SEED": 3,
+                     "APS_CLIFFORD_SET_OFFSET": 4,
+                     "APS_CLIFFORD_SET_SPACING": 5}
+
+##Note that the expected call pattern for the randomizer is:
+
+#   APS_CLIFFORD_RAND / APS_CLIFFORD_INVERSE
+#   LOADCMP
+#   CALL
+
+def RandomCliffordSetOffset(addr, offset):
+    return [Invalidate(addr, 0, tdm=False),
+            WriteAddr(adrr, offset, tdm=False),
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
+            CustomInstruction("APS_CLIFFORD_SET_OFFSET", addr, 0x3)]
+
+def RandomCliffordSetSpacing(addr, spacing):
+    return [Invalidate(addr, 0, tdm=False),
+            WriteAddr(adrr, offset, tdm=False),
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
+            CustomInstruction("APS_CLIFFORD_SET_SPACING", addr, 0x3)]
+
+def RandomClifford(target, addr):
+    return [Invalidate(addr, 0, tdm=False),
+            CustomInstruction("APS_CLIFFORD_RAND", 0x0, addr),
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
+            Call(target, load_addr=True)]
+
+def RandomCliffordInverse(target, addr):
+    return [Invalidate(addr, 0, tdm=False),
+            CustomInstruction("APS_CLIFFORD_RAND", 0x0, addr),
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
+            Call(target, load_addr=True)]
+
+def RandomCliffordInverseReset(addr): #for now don't use addr
+    return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0x0006)
+
+def RandomCliffordSeed(seed):
+    raise NotImplementedError("APS_CLIFFORD_SET_SEED not implemented!")
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
new file mode 100644
index 00000000..6273e063
--- /dev/null
+++ b/QGL/RandomCliffordTools.py
@@ -0,0 +1,51 @@
+'''
+Functions for dealing with random clifford pulse sequences
+
+Copyright 2019 Raytheon BBN Technologies
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+   http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+'''
+
+from . import config
+from . import PatternUtils
+from .PatternUtils import flatten, has_gate
+from . import Channels
+from . import ChannelLibraries
+from . import PulseShapes
+from . import PulsePrimitives
+from .PulsePrimitives import Id, clear_pulse_cache
+from .PulseSequencer import Pulse, PulseBlock, CompositePulse
+from . import ControlFlow
+from . import BlockLabel
+from . import TdmInstructions # only for APS2-TDM
+from . import APS2CustomInstructions
+
+def generate_clifford_jump_table(cliff_wires, jt_label = None):
+    """Generate the jump table that will be used to call into the clifford set"""
+
+    if jt_label is None:
+        jt_label = BlockLabel.BlockLabel("JT")
+    if not isinstance(jt_label, BlockLabel.BlockLabel):
+        raise ValueError("Jump table label must be a BlockLabel.")
+
+    cliff_labels = [f"C{n}" for n in range(24)]
+    jump_table = [jt_label]
+    for cl in cliff_labels:
+        jump_table.append(ControlFlow.Call(cl))
+        jump_table.append(ControlFlow.Return())
+
+    for cliff, cl in zip(cliff_wires, cliff_labels):
+        cliff.insert(0, BlockLabel.BlockLabel(cl))
+        cliff.append(ControlFlow.Return())
+
+    cliff_wires.insert(0, jump_table)

From f6aa67d4fb393b96408b6a8caecd2783df2a8380 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Sat, 23 Feb 2019 18:40:30 -0500
Subject: [PATCH 193/235] Add string representation for custom instructions

---
 QGL/TdmInstructions.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/QGL/TdmInstructions.py b/QGL/TdmInstructions.py
index fb0069e7..76780197 100644
--- a/QGL/TdmInstructions.py
+++ b/QGL/TdmInstructions.py
@@ -36,6 +36,13 @@ def __eq__(self, other):
     def __ne__(self, other):
         return not self == other
 
+    def __str__(self):
+        return f"{self.instruction}({hex(self.in_addr)}, {hex(self.out_addr)})"
+
+    def __repr__(self):
+        return self.__str__()
+
+
 
 def MajorityVote(in_addr, out_addr, nmeas): # alternatively, append the loadcmpvram instruction when compiling (see STOREMEAS)
     return [LoadCmpVramInstruction('LOADCMPVRAM', 1, in_addr, 2**nmeas-1, True), CustomInstruction('MAJORITY', in_addr, out_addr)]
@@ -74,6 +81,12 @@ def __eq__(self, other):
     def __ne__(self, other):
         return not self == other
 
+    def __str__(self):
+        return f"{self.instruction}({hex(self.addr)}, {hex(self.value)})"
+
+    def __repr__(self):
+        return self.__str__()
+
 def WriteAddr(addr, value, channel=None, tdm=True):
     return WriteAddrInstruction('WRITEADDR', channel, 0, addr, value, tdm)
 
@@ -108,6 +121,12 @@ def __eq__(self, other):
     def __ne__(self, other):
         return not self == other
 
+    def __str__(self):
+        return f"{self.instruction}({hex(self.addr)}, {hex(self.mask)})"
+
+    def __repr__(self):
+        return self.__str__()
+
 
 def LoadCmpVram(addr, mask, tdm=True):
     return LoadCmpVramInstruction('LOADCMPVRAM', 1, addr, mask, tdm)

From 7409fe56938ce2f88d7f976a74115b54a187ac8c Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Sat, 23 Feb 2019 18:41:16 -0500
Subject: [PATCH 194/235] Set write flag to CALL to indicate load from VRAM

---
 QGL/ControlFlow.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/QGL/ControlFlow.py b/QGL/ControlFlow.py
index 2aea53ad..daf12587 100644
--- a/QGL/ControlFlow.py
+++ b/QGL/ControlFlow.py
@@ -155,6 +155,13 @@ def __init__(self, target, load_addr=False):
         super(Call, self).__init__("CALL", target=target)
         self.load_addr = load_addr
 
+    def __str__(self):
+        if self.load_addr:
+            return f"{self.instruction}({str(self.target)})"
+        else:
+            return f"{self.instruction}({str(self.target)}, LOAD)"
+
+
 
 class Return(ControlInstruction):
     def __init__(self):

From b6cc8247448fdcfdd15cdb6e17a5459bec731c99 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Sat, 23 Feb 2019 18:41:42 -0500
Subject: [PATCH 195/235] Update APS2 custom instructions for randomizer

---
 QGL/APS2CustomInstructions.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index cb082dc0..285f8685 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -63,12 +63,12 @@ def RandomClifford(target, addr):
 
 def RandomCliffordInverse(target, addr):
     return [Invalidate(addr, 0, tdm=False),
-            CustomInstruction("APS_CLIFFORD_RAND", 0x0, addr),
+            CustomInstruction("APS_CLIFFORD_INVERSE", 0x0, addr),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
             Call(target, load_addr=True)]
 
 def RandomCliffordInverseReset(addr): #for now don't use addr
-    return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0x0006)
+    return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0xF)
 
 def RandomCliffordSeed(seed):
     raise NotImplementedError("APS_CLIFFORD_SET_SEED not implemented!")

From fa7aff84df1ec2310d77c00b9e978910ed144e47 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Sat, 23 Feb 2019 18:42:21 -0500
Subject: [PATCH 196/235] Tools for random clifford sequences.

---
 QGL/RandomCliffordTools.py | 46 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 45 insertions(+), 1 deletion(-)

diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index 6273e063..d7584c34 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -17,18 +17,23 @@
 '''
 
 from . import config
+from functools import reduce
 from . import PatternUtils
 from .PatternUtils import flatten, has_gate
 from . import Channels
 from . import ChannelLibraries
 from . import PulseShapes
 from . import PulsePrimitives
+from . import Compiler
 from .PulsePrimitives import Id, clear_pulse_cache
 from .PulseSequencer import Pulse, PulseBlock, CompositePulse
 from . import ControlFlow
 from . import BlockLabel
 from . import TdmInstructions # only for APS2-TDM
-from . import APS2CustomInstructions
+from .APS2CustomInstructions import *
+from .Cliffords import C1, inverse_clifford, clifford_multiply
+
+VALID_CLIFFORD_TYPES = ('RandomAC',)
 
 def generate_clifford_jump_table(cliff_wires, jt_label = None):
     """Generate the jump table that will be used to call into the clifford set"""
@@ -49,3 +54,42 @@ def generate_clifford_jump_table(cliff_wires, jt_label = None):
         cliff.append(ControlFlow.Return())
 
     cliff_wires.insert(0, jump_table)
+
+def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
+                            inv_addr=0x3, inv_values=[]):
+
+    if jt_label is None:
+        jt_label = BlockLabel.BlockLabel("JT")
+    if not isinstance(jt_label, BlockLabel.BlockLabel):
+        raise ValueError("Jump table label must be a BlockLabel.")
+
+    for idx, seq in enumerate(seqs[:]):
+        if not PatternUtils.contains_runtime_pulses(seq):
+            continue
+        new_seq = []
+        for pulse in seq:
+            if isinstance(pulse, Compiler.Waveform) and pulse.isRunTime \
+                and pulse.label in VALID_CLIFFORD_TYPES:
+                has_random_cliff = True
+                new_seq.extend(RandomClifford(jt_label, cliff_addr))
+                print("Inserting clifford pulse!")
+            else:
+                new_seq.append(pulse)
+
+        if add_inv:
+            #insert reset after first wait
+            w_idx = next(i for i, v in enumerate(new_seq) if isinstance(v, ControlFlow.Wait))
+            new_seq.insert(w_idx+1, RandomCliffordInverseReset(0x0))
+            #insert at end of sequence or before last GOTO
+            if isinstance(new_seq[-1], ControlFlow.Goto):
+                  new_seq[-1:-1] = RandomCliffordInverse(jt_label, inv_addr)
+            else:
+                  new_seq.extend(RandomCliffordInverse(jt_label, inv_addr))
+
+        seqs[idx] = new_seq
+
+def randomize_clifford_sequences(qubit, seqs, clifford_type=PulsePrimitives.RandomAC):
+
+    c_seqs = [[clifford_type(qubit) for _ in seq] for seq in seqs]
+    inverses = [inverse_clifford(C1[reduce(clifford_multiply, seq)]) for seq in seqs]
+    return c_seqs, inverses

From fca2e8132c17694bfdb0d45feac1eeb60f8f5e0b Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 25 Feb 2019 17:35:52 -0500
Subject: [PATCH 197/235] Even more WIP

---
 QGL/APS2CustomInstructions.py |  4 ++-
 QGL/Compiler.py               | 40 ++++++++++++++---------
 QGL/PulsePrimitives.py        |  2 +-
 QGL/RandomCliffordTools.py    |  4 +--
 QGL/TdmInstructions.py        |  7 ++--
 QGL/drivers/APS2Pattern.py    | 61 ++++++++++++++++++++++-------------
 6 files changed, 74 insertions(+), 44 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index 285f8685..6eb22054 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -29,7 +29,7 @@
 #                               returns starting address of jump table entry from RAM
 #APS_CLIFFORD_INVERSE:          Store waveform address of inverse waveform to be jumped to
 
-APS2_CUSTOM_DECODE = {"APS_RAND": 0,
+APS2_CUSTOM = {"APS_RAND": 0,
                      "APS_CLIFFORD_RAND": 2,
                      "APS_CLIFFORD_INVERSE": 6,
                      "APS_CLIFFORD_INVERSE_RESET": 7,
@@ -37,6 +37,8 @@
                      "APS_CLIFFORD_SET_OFFSET": 4,
                      "APS_CLIFFORD_SET_SPACING": 5}
 
+APS2_CUSTOM_DECODE = {v: k for k, v in APS2_CUSTOM.items()}
+
 ##Note that the expected call pattern for the randomizer is:
 
 #   APS_CLIFFORD_RAND / APS_CLIFFORD_INVERSE
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 10e08258..5c7de855 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -36,6 +36,8 @@
 from . import ControlFlow
 from . import BlockLabel
 from . import TdmInstructions # only for APS2-TDM
+from . import APS2CustomInstructions
+from . import RandomCliffordTools
 import gc
 
 logger = logging.getLogger(__name__)
@@ -327,7 +329,7 @@ def setup_awg_channels(physicalChannels):
     return data
 
 
-def bundle_wires(physWires, wfs, cliff_wires=None):
+def bundle_wires(physWires, wfs):
     awgData = setup_awg_channels(physWires.keys())
     for chan in physWires.keys():
         _, awgChan = chan.label.rsplit('-', 1)
@@ -335,8 +337,6 @@ def bundle_wires(physWires, wfs, cliff_wires=None):
             awgChan = 'ch' + awgChan
         awgData[chan.instrument][awgChan]['linkList'] = physWires[chan]
         awgData[chan.instrument][awgChan]['wfLib'] = wfs[chan]
-        if cliff_wires is not None and chan in cliff_wires.keys():
-            awgData[chan.instrument][awgChan]['clifford_set'] = cliff_wires[chan]
         if hasattr(chan, 'correctionT'):
             awgData[chan.instrument][awgChan]['correctionT'] = chan.correctionT
     return awgData
@@ -357,7 +357,7 @@ def collect_specializations(seqs):
             done.append(target)
     return funcs
 
-def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False):
+def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=False):
 
     ChannelLibraries.channelLib.update_channelDict()
     clear_pulse_cache()
@@ -394,7 +394,7 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False):
 
     # Compile all the pulses/pulseblocks to sequences of pulses and control flow
     logger.info("Compiling sequences.")
-    wireSeqs = compile_sequences(seqs, channels)
+    wireSeqs = compile_sequences(seqs, channels, random_cliffords=random_cliffords)
 
     if not validate_linklist_channels(wireSeqs.keys()):
         print("Compile to hardware failed")
@@ -459,11 +459,8 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False):
     wfs = generate_waveforms(physWires)
 
     # If there are run-time pulses add these to the library
-    if PatternUtils.contains_runtime_pulses(seqs):
+    if random_cliffords:
         wfs = add_runtime_pulse_set(physWires, wfs)
-        cliff_wires = create_clifford_waveforms(physWires)
-    else:
-        cliff_wires = None
 
     # replace Pulse objects with Waveforms
     logger.info("Replacing pulses with waveforms")
@@ -472,7 +469,7 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False):
     # bundle wires on instruments, or channels depending
     # on whether we have one sequence per channel
     logger.info("Bundling wires.")
-    awgData = bundle_wires(physWires, wfs, cliff_wires=cliff_wires)
+    awgData = bundle_wires(physWires, wfs)
     return awgData
 
 def compile_to_hardware(seqs,
@@ -590,7 +587,7 @@ def compile_to_hardware(seqs,
     return metafilepath
 
 
-def compile_sequences(seqs, channels=set()):
+def compile_sequences(seqs, channels=set(), random_cliffords=False):
     '''
     Main function to convert sequences to miniLL's and waveform libraries.
     '''
@@ -604,6 +601,16 @@ def compile_sequences(seqs, channels=set()):
     subroutines = collect_specializations(seqs)
     seqs += subroutines
 
+    if random_cliffords:
+        qubits = [q for q in list(channels) if isinstance(q, Channels.Qubit)]
+        if len(qubits) > 1:
+            raise Exception("Too many qubits! Don't know how to deal with this yet.")
+        #replace cliffords with
+        cliffords = [[get_clifford_type(seqs)(n)] for n in range(24)]
+        RandomCliffordTools.generate_clifford_jump_table(cliffords)
+        RandomCliffordTools.insert_clifford_calls(seqs)
+        seqs += cliffords
+
     #expand the channel definitions for anything defined in subroutines
     for func in subroutines:
         channels |= find_unique_channels(subroutines)
@@ -665,10 +672,10 @@ def flatten_to_pulses(obj):
                 wires[chan] += [copy(block)]
             continue
         # control flow broadcasts to all channels if channel attribute is None
-        if (isinstance(block, ControlFlow.ControlInstruction) or
-                isinstance(block, TdmInstructions.WriteAddrInstruction) or
-                isinstance(block, TdmInstructions.CustomInstruction) or
-                isinstance(block, TdmInstructions.LoadCmpVramInstruction)):
+        if isinstance(block, ControlFlow.ControlInstruction): #or
+                #isinstance(block, TdmInstructions.WriteAddrInstruction) or
+                #isinstance(block, TdmInstructions.CustomInstruction) or
+                #isinstance(block, TdmInstructions.LoadCmpVramInstruction)):
             # Need to deal with attaching measurements and edges to control
             # instruction. Until we have a proper solution for that, we will
             # always broadcast control instructions to all channels
@@ -677,6 +684,9 @@ def flatten_to_pulses(obj):
             for chan in block_channels:
                 wires[chan] += [copy(block)]
             continue
+        #Don't propagate VRAM instructions
+        if isinstance(block, TdmInstructions.VRAMInstruction) or isinstance(block, TdmInstructions.CustomInstruction):
+            continue
         # propagate frame change from nodes to edges
         for chan in channels:
             if block.pulses[chan].frameChange == 0:
diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index 596c79d2..a648e044 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -372,7 +372,7 @@ def AC(qubit, cliffNum):
     #Now a big else if chain for to get the specific Clifford
     if cliffNum == 0:
         #Identity gate
-        return Id(qubit, length=0)
+        return Id(qubit)#Id(qubit, length=0)
     elif cliffNum == 1:
         #X90
         return X90(qubit)
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index d7584c34..d4a0d26e 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -68,11 +68,11 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
             continue
         new_seq = []
         for pulse in seq:
-            if isinstance(pulse, Compiler.Waveform) and pulse.isRunTime \
+            if isinstance(pulse, Pulse) and pulse.isRunTime \
                 and pulse.label in VALID_CLIFFORD_TYPES:
                 has_random_cliff = True
                 new_seq.extend(RandomClifford(jt_label, cliff_addr))
-                print("Inserting clifford pulse!")
+                #print("Inserting clifford pulse!")
             else:
                 new_seq.append(pulse)
 
diff --git a/QGL/TdmInstructions.py b/QGL/TdmInstructions.py
index 76780197..cbb919b5 100644
--- a/QGL/TdmInstructions.py
+++ b/QGL/TdmInstructions.py
@@ -58,7 +58,10 @@ def DecodeSetRounds(in_addr, out_addr, value):
 
 # TODO: the rest of the CUSTOM instructions
 
-class WriteAddrInstruction(object):
+class VRAMInstruction(object):
+    pass
+
+class WriteAddrInstruction(VRAMInstruction):
 
     def __init__(self, name, channel, modifier, addr, value, tdm, **kwargs):
         self.instruction = name
@@ -99,7 +102,7 @@ def CrossBar(addr, value, channel=None, tdm=True): # should this be a high-level
 def StoreMeas(addr, value, channel=None, tdm=True):
     return WriteAddrInstruction('STOREMEAS', channel, 5, addr, value, tdm)
 
-class LoadCmpVramInstruction(object):
+class LoadCmpVramInstruction(VRAMInstruction):
 
     def __init__(self, name, use_vram, addr, mask, tdm):
         # TODO: sanity checks on input values
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 9a3e2290..bcf695bc 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -32,7 +32,7 @@
 from QGL.PatternUtils import hash_pulse, flatten
 from QGL import TdmInstructions
 from QGL import APS2CustomInstructions
-from QGL.APS2CustomInstructions import APS2_CUSTOM_DECODE
+from QGL.APS2CustomInstructions import APS2_CUSTOM, APS2_CUSTOM_DECODE
 
 # Python 2/3 compatibility: use 'int' that subclasses 'long'
 from builtins import int
@@ -307,7 +307,10 @@ def __str__(self):
             store_addr = self.payload & 0xFFFF
             load_addr = (self.payload >> 16) & 0xFFFF
             instruction = (self.payload >> 32) & 0xFF
-            instructionAPS = TDM_CUSTOM_DECODE[instruction]
+            if self.decode_as_tdm:
+                instructionAPS = TDM_CUSTOM_DECODE[instruction]
+            else:
+                instructionAPS = APS2_CUSTOM_DECODE[instruction]
             out += " | instruction={0} ({1}), load_addr=0x{2:0x}, store_addr=0x{3:0x}".format(instruction, instructionAPS, load_addr, store_addr)
 
         elif instrOpCode == WRITEADDR:
@@ -511,12 +514,11 @@ def LoadCmpVram(addr, mask, label=None):
     payload = (1 << 48) | (mask << 16) | addr
     return Instruction(header, payload, label=label)
 
-
-def preprocess(seqs, shapeLib, clifford_set=False):
+def preprocess(seqs, shapeLib):
     seqs = PatternUtils.convert_lengths_to_samples(
         seqs, SAMPLING_RATE, ADDRESS_UNIT, Compiler.Waveform)
     wfLib = build_waveforms(seqs, shapeLib)
-    inject_modulation_cmds(seqs, force_phase_update=clifford_set)
+    inject_modulation_cmds(seqs)
     return seqs, wfLib
 
 
@@ -722,7 +724,7 @@ def synchronize_clocks(seqs):
     syncInstructions = [list(filter(
         lambda s: isinstance(s, ControlFlow.ControlInstruction), seq))
                         for seq in seqs if seq]
-
+    #import pdb; pdb.set_trace()
     # Add length to control-flow instructions to make accumulated time match at end of CFI.
     # Keep running tally of how much each channel has been shifted so far.
     localShift = [0 for _ in syncInstructions]
@@ -808,7 +810,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                     isinstance(entry, ControlFlow.ControlInstruction) or
                     isinstance(entry, BlockLabel.BlockLabel) or
                     isinstance(entry, TdmInstructions.CustomInstruction) or
-                    isinstance(entry, TdmInstructions.Instruction) or
+                    #isinstance(entry, TdmInstructions.Instruction) or ??????
                     isinstance(entry, TdmInstructions.LoadCmpVramInstruction)):
                 if isinstance(entry, BlockLabel.BlockLabel):
                     # carry label forward to next entry
@@ -842,11 +844,15 @@ def create_seq_instructions(seqs, offsets, label = None):
                     instructions.append(LoadCmpVram(entry.addr, entry.mask, label=label))
                 # some TDM instructions are ignored by the APS
                 elif isinstance(entry, TdmInstructions.CustomInstruction):
-                    pass
+                    try:
+                        instructions.append(Custom(entry.in_addr, entry.out_addr,
+                                                    APS2_CUSTOM[entry.instruction], label=label))
+                    except KeyError as e:
+                        raise Exception(f"Got unknown APS2 instruction: {e.args[0]} in {str(entry)}.")
                 elif isinstance(entry, TdmInstructions.WriteAddrInstruction):
                     if entry.instruction == 'INVALIDATE' and entry.tdm == False:
                         instructions.append(Invalidate(entry.addr, entry.value, label=label))
-
+                label=None #Reset label to prevent it propagating in a jump table
                 continue
 
             if seq_idx == 0:
@@ -990,20 +996,29 @@ def create_instr_data(seqs, offsets, cache_lines):
 
 
 def resolve_symbols(seq):
-    symbols = {}
-    # create symbol look-up table
-    for ct, entry in enumerate(seq):
-        if entry.label and entry.label not in symbols:
-            symbols[entry.label] = ct
-    # then update
-    for (ct, entry) in enumerate(seq):
-        if entry.target:
-            # find next available label. The TDM may miss some labels if branches only contain waveforms (which are ignored)
-            for k in range(len(seq)-ct):
-                temp = seq[ct+k]
-                if temp.target in symbols:
-                    break
-            entry.address = symbols[temp.target]
+
+    labeled_entries = [(idx, entry.label) for idx, entry in enumerate(seq) if entry.label is not None]
+    import pdb; pdb.set_trace()
+    symbols = {label: idx for idx, label in labeled_entries}
+    print(f"Found labels: {symbols}")
+    for entry in seq:
+        if entry.target is not None and entry.target in symbols.keys():
+            entry.address = symbols[entry.target]
+
+    # symbols = {}
+    # # create symbol look-up table
+    # for ct, entry in enumerate(seq):
+    #     if entry.label and entry.label not in symbols:
+    #         symbols[entry.label] = ct
+    # # then update
+    # for (ct, entry) in enumerate(seq):
+    #     if entry.target:
+    #         # find next available label. The TDM may miss some labels if branches only contain waveforms (which are ignored)
+    #         for k in range(len(seq)-ct):
+    #             temp = seq[ct+k]
+    #             if temp.label in symbols:
+    #                 break
+    #         entry.address = symbols[temp.label]
 
 
 def compress_marker(markerLL):

From 5fe0c19e6f555fd5aaf3d52a97f49486b512f9ea Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 25 Feb 2019 17:56:00 -0500
Subject: [PATCH 198/235] Remove debug.

---
 QGL/drivers/APS2Pattern.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index bcf695bc..b7acdb0f 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -998,7 +998,6 @@ def create_instr_data(seqs, offsets, cache_lines):
 def resolve_symbols(seq):
 
     labeled_entries = [(idx, entry.label) for idx, entry in enumerate(seq) if entry.label is not None]
-    import pdb; pdb.set_trace()
     symbols = {label: idx for idx, label in labeled_entries}
     print(f"Found labels: {symbols}")
     for entry in seq:

From edb89fca03bd5d0b5a0460cd66679507b841fad2 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 25 Feb 2019 21:33:07 -0500
Subject: [PATCH 199/235] Make sure Custom instructions not dropped by pattern
 generator!

---
 QGL/APS2CustomInstructions.py |  4 ++--
 QGL/Compiler.py               | 22 ++++++++++++++--------
 QGL/PulseSequencer.py         |  4 ++++
 QGL/RandomCliffordTools.py    | 14 +++++++++++++-
 QGL/drivers/APS2Pattern.py    |  6 +++---
 5 files changed, 36 insertions(+), 14 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index 6eb22054..3b269884 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -47,13 +47,13 @@
 
 def RandomCliffordSetOffset(addr, offset):
     return [Invalidate(addr, 0, tdm=False),
-            WriteAddr(adrr, offset, tdm=False),
+            WriteAddr(addr, offset, tdm=False),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
             CustomInstruction("APS_CLIFFORD_SET_OFFSET", addr, 0x3)]
 
 def RandomCliffordSetSpacing(addr, spacing):
     return [Invalidate(addr, 0, tdm=False),
-            WriteAddr(adrr, offset, tdm=False),
+            WriteAddr(addr, spacing, tdm=False),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
             CustomInstruction("APS_CLIFFORD_SET_SPACING", addr, 0x3)]
 
diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 5c7de855..930774d8 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -236,7 +236,15 @@ def generate_waveforms(physicalWires):
     return wfs
 
 def get_clifford_type(wire, allowed_types=("RandomAC")):
-    rt_pulses = [pulse for pulse in flatten(wire) if isinstance(pulse, Pulse) and pulse.isRunTime]
+    rt_pulses = []
+    for pulse in flatten(wire):
+        if isinstance(pulse, Pulse) and pulse.isRunTime:
+            rt_pulses.append(pulse)
+        elif isinstance(pulse, PulseBlock) and pulse.isRunTime:
+            for p in pulse.pulses.values():
+                if p.isRunTime:
+                    rt_pulses.append(p)
+
     if len(rt_pulses) == 0:
         return None
     pulse_type = list(set([pulse.label for pulse in rt_pulses]))
@@ -399,7 +407,6 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=
     if not validate_linklist_channels(wireSeqs.keys()):
         print("Compile to hardware failed")
         return
-
     logger.debug('')
     logger.debug("Now after gating constraints:")
     # apply gating constraints
@@ -672,10 +679,9 @@ def flatten_to_pulses(obj):
                 wires[chan] += [copy(block)]
             continue
         # control flow broadcasts to all channels if channel attribute is None
-        if isinstance(block, ControlFlow.ControlInstruction): #or
-                #isinstance(block, TdmInstructions.WriteAddrInstruction) or
-                #isinstance(block, TdmInstructions.CustomInstruction) or
-                #isinstance(block, TdmInstructions.LoadCmpVramInstruction)):
+        if (isinstance(block, ControlFlow.ControlInstruction) or
+                isinstance(block, TdmInstructions.VRAMInstruction) or
+                isinstance(block, TdmInstructions.CustomInstruction)):
             # Need to deal with attaching measurements and edges to control
             # instruction. Until we have a proper solution for that, we will
             # always broadcast control instructions to all channels
@@ -685,8 +691,8 @@ def flatten_to_pulses(obj):
                 wires[chan] += [copy(block)]
             continue
         #Don't propagate VRAM instructions
-        if isinstance(block, TdmInstructions.VRAMInstruction) or isinstance(block, TdmInstructions.CustomInstruction):
-            continue
+        #if isinstance(block, TdmInstructions.VRAMInstruction) or isinstance(block, TdmInstructions.CustomInstruction):
+        #    continue
         # propagate frame change from nodes to edges
         for chan in channels:
             if block.pulses[chan].frameChange == 0:
diff --git a/QGL/PulseSequencer.py b/QGL/PulseSequencer.py
index 71df08c6..e25abac8 100644
--- a/QGL/PulseSequencer.py
+++ b/QGL/PulseSequencer.py
@@ -198,6 +198,10 @@ def frameChange(self):
     def isZero(self):
         return all(p.isZero for p in self.pulses)
 
+    @property
+    def isRunTime(self):
+        return any(hasattr(entry, 'isRunTime') and entry.isRunTime for entry in self.pulses)
+
 
 class PulseBlock(object):
     '''
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index d4a0d26e..6863f0b4 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -66,16 +66,27 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
     for idx, seq in enumerate(seqs[:]):
         if not PatternUtils.contains_runtime_pulses(seq):
             continue
+
         new_seq = []
+
         for pulse in seq:
             if isinstance(pulse, Pulse) and pulse.isRunTime \
                 and pulse.label in VALID_CLIFFORD_TYPES:
                 has_random_cliff = True
                 new_seq.extend(RandomClifford(jt_label, cliff_addr))
-                #print("Inserting clifford pulse!")
+                print("Inserting clifford pulse!")
             else:
                 new_seq.append(pulse)
 
+        info_seqs = []
+        info_seqs.extend(RandomCliffordSetOffset(0x1, 0x0))
+        info_seqs.extend(RandomCliffordSetSpacing(0x2, 0x1))
+
+        if isinstance(seq[0], BlockLabel.BlockLabel):
+            new_seq[1:1] = info_seqs
+        else:
+            new_seq[0:0] = info_seqs
+
         if add_inv:
             #insert reset after first wait
             w_idx = next(i for i, v in enumerate(new_seq) if isinstance(v, ControlFlow.Wait))
@@ -88,6 +99,7 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
 
         seqs[idx] = new_seq
 
+
 def randomize_clifford_sequences(qubit, seqs, clifford_type=PulsePrimitives.RandomAC):
 
     c_seqs = [[clifford_type(qubit) for _ in seq] for seq in seqs]
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index b7acdb0f..fe2f1d1f 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -641,10 +641,10 @@ def inject_modulation_cmds(seqs, force_phase_update=False):
 
             #copies to avoid same object having different timestamps later
             #copy through BlockLabel
-            if isinstance(entry, BlockLabel.BlockLabel):
+            if isinstance(entry, BlockLabel.BlockLabel) or isinstance(entry, TdmInstructions.CustomInstruction):
                 mod_seq.append(copy(entry))
             #mostly copy through control-flow
-            elif isinstance(entry, ControlFlow.ControlInstruction) or isinstance(entry, TdmInstructions.LoadCmpVramInstruction) or isinstance(entry, TdmInstructions.WriteAddrInstruction):
+            elif isinstance(entry, ControlFlow.ControlInstruction) or isinstance(entry, TdmInstructions.VRAMInstruction):
                 #heuristic to insert phase reset before trigger if we have modulation commands
                 if isinstance(entry, ControlFlow.Wait):
                     if not ( no_modulation_cmds and (cur_freq == 0) and (cur_phase == 0)):
@@ -804,7 +804,6 @@ def create_seq_instructions(seqs, offsets, label = None):
 
         write_flags = [True] * len(entries)
         for ct, (entry, seq_idx) in enumerate(entries):
-
             #use first non empty sequence for control flow
             if seq_idx == first_non_empty and (
                     isinstance(entry, ControlFlow.ControlInstruction) or
@@ -844,6 +843,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                     instructions.append(LoadCmpVram(entry.addr, entry.mask, label=label))
                 # some TDM instructions are ignored by the APS
                 elif isinstance(entry, TdmInstructions.CustomInstruction):
+                    print(str(entry))
                     try:
                         instructions.append(Custom(entry.in_addr, entry.out_addr,
                                                     APS2_CUSTOM[entry.instruction], label=label))

From 41e488e09ba732fe237c57ad9817d31cb2fba854 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 10:50:59 -0500
Subject: [PATCH 200/235] Add color for custom instructions

---
 QGL/drivers/APS2Pattern.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index fe2f1d1f..1e564978 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1542,7 +1542,8 @@ def display_raw_file(filename):
 
         colors = {"WFM": QColor(0,200,0),
                   "GOTO": QColor(0,100,100),
-                  "MARKER": QColor(150,150,200)}
+                  "MARKER": QColor(150,150,200),
+                  "CUSTOM": QColor(200,65,200)}
 
         class MatplotlibWidget(QWidget):
             def __init__(self, I, Q, parent=None):

From 6f6530af1123c88020e0e0b0b654deeb50f166ee Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 11:10:54 -0500
Subject: [PATCH 201/235] Don't drop WRITEADDR instructions!

---
 QGL/drivers/APS2Pattern.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 1e564978..158abedf 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -810,7 +810,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                     isinstance(entry, BlockLabel.BlockLabel) or
                     isinstance(entry, TdmInstructions.CustomInstruction) or
                     #isinstance(entry, TdmInstructions.Instruction) or ??????
-                    isinstance(entry, TdmInstructions.LoadCmpVramInstruction)):
+                    isinstance(entry, TdmInstructions.VRAMInstruction)):
                 if isinstance(entry, BlockLabel.BlockLabel):
                     # carry label forward to next entry
                     label = entry
@@ -850,8 +850,11 @@ def create_seq_instructions(seqs, offsets, label = None):
                     except KeyError as e:
                         raise Exception(f"Got unknown APS2 instruction: {e.args[0]} in {str(entry)}.")
                 elif isinstance(entry, TdmInstructions.WriteAddrInstruction):
+                    print(str(entry))
                     if entry.instruction == 'INVALIDATE' and entry.tdm == False:
                         instructions.append(Invalidate(entry.addr, entry.value, label=label))
+                    if entry.instruction == 'WRITEADDR' and entry.tdm == False:
+                        instructions.append(WriteAddr(entry.addr, entry.value, label=label))
                 label=None #Reset label to prevent it propagating in a jump table
                 continue
 
@@ -1543,7 +1546,8 @@ def display_raw_file(filename):
         colors = {"WFM": QColor(0,200,0),
                   "GOTO": QColor(0,100,100),
                   "MARKER": QColor(150,150,200),
-                  "CUSTOM": QColor(200,65,200)}
+                  "CUSTOM": QColor(200,65,200),
+                  "WRITEADDR": QColor(245, 105, 65)}
 
         class MatplotlibWidget(QWidget):
             def __init__(self, I, Q, parent=None):

From 418e1b47ad059c332aa86383e635270a080f3509 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 11:58:32 -0500
Subject: [PATCH 202/235] Add sequence debugger.

---
 QGL/test_helpers.py        |   0
 tests/aps_debug_watcher.py | 219 +++++++++++++++++++++++++++++++++++++
 2 files changed, 219 insertions(+)
 create mode 100644 QGL/test_helpers.py
 create mode 100644 tests/aps_debug_watcher.py

diff --git a/QGL/test_helpers.py b/QGL/test_helpers.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/aps_debug_watcher.py b/tests/aps_debug_watcher.py
new file mode 100644
index 00000000..4f389e8f
--- /dev/null
+++ b/tests/aps_debug_watcher.py
@@ -0,0 +1,219 @@
+#!/usr/bin/env python
+
+import sys
+import socket
+import struct
+try:
+    from QGL.drivers import APS2Pattern
+    haveQGL = True
+except:
+    haveQGL = False
+import numpy as np
+from ansicolor import * # from ansicolors
+
+ip = sys.argv[1]
+port = 0xbb50
+
+short_time = True
+
+raw_mode = '-r' in sys.argv
+tdm_mode = '-tdm' in sys.argv
+
+print("Connecting to APS Debug Port at {0}:{1}".format(ip,port))
+
+PACKET_SIZE=168//8+1
+
+if short_time:
+    PACKET_SIZE -= 2
+
+MODE_UNKNOWN = 0
+MODE_SEQUENCER = 1
+MODE_RAM = 2
+MODE_TRIGGER = 3
+
+def bittest(v, b):
+    if ((v & (1<<b)) == (1<<b)):
+        return red('T')
+    else:
+        return 'F'
+
+def get_bytes(a, s, e):
+    e += s
+    return a[s:e], e
+
+def formatHaltBits(haltBits):
+    haltSync = bittest(haltBits,5)
+    haltCustom = bittest(haltBits,4)
+    haltValid = bittest(haltBits,3)
+    haltWait = bittest(haltBits,2)
+    haltStr = "S:{} V:{} C:{} W:{}".format(haltSync, haltValid, haltCustom, haltWait)
+    return haltStr
+
+
+
+s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+s.connect((ip,port))
+print("Connected")
+print(s)
+extraData = b''
+while 1:
+    data = extraData + s.recv(10*PACKET_SIZE)
+    num_packets = len(data) // PACKET_SIZE
+    num_excess = len(data) % PACKET_SIZE
+    block_size = num_packets*PACKET_SIZE
+    extraData = b''
+    if num_excess > 0:
+        extraData = data[block_size:]
+        data = data[:block_size]
+
+    for cnt in range(num_packets):
+        start = cnt * PACKET_SIZE
+        end = (cnt+1)*PACKET_SIZE
+        packet = data[start:end]
+        packet_bytes = bytearray(packet)
+        if raw_mode:
+            print(packet_bytes)
+            continue
+
+        if packet[0] ==  0x1:
+            mode = MODE_SEQUENCER
+        elif packet[0] in [0x2,0x3, 0x4, 0x5]:
+            mode = MODE_RAM
+        elif packet[0] == 0x6:
+            mode = MODE_TRIGGER
+        else:
+            mode = MODE_UNKNOWN
+
+
+        if short_time:
+            uptime_seconds = packet_bytes[1:3]
+            uptime_nanoseconds = packet_bytes[3:7]
+
+            uptime_seconds = struct.unpack(">H", uptime_seconds)[0]
+        else:
+            uptime_seconds = packet_bytes[1:5]
+            uptime_nanoseconds = packet_bytes[5:9]
+
+            uptime_seconds = struct.unpack(">I", uptime_seconds)[0]
+
+        uptime_nanoseconds = struct.unpack(">I", uptime_nanoseconds)[0]
+
+        #print(uptime_seconds, uptime_nanoseconds)
+
+        uptime_nanoseconds = uptime_nanoseconds/1e9
+        uptime = uptime_seconds + uptime_nanoseconds
+
+        if short_time:
+            start = 8
+        else:
+            start = 10
+
+        if mode == MODE_SEQUENCER:
+
+            if short_time:
+                triggerWord = packet[7]
+            else:
+                triggerWord = packet[9]
+
+            haltBits = packet[start]
+
+            haltStr = formatHaltBits(haltBits)
+
+            instructionAddr, start = get_bytes(packet, start, 4)
+            instructionAddr = bytearray(instructionAddr)
+            # clear halt bits, only the first two bits are part of the Addr
+            instructionAddr[0] = instructionAddr[0] & 0x3
+            instructionAddr = struct.unpack(">I", instructionAddr)[0]
+
+            seq_debug_data, start = get_bytes(packet, start, 8)
+            seq_debug_data = np.fromstring(seq_debug_data[::-1], dtype=np.uint64)
+
+            if haveQGL:
+                instruction = APS2Pattern.Instruction.unflatten(seq_debug_data, decode_as_tdm = tdm_mode)
+            else:
+                instruction = ''
+
+            h = "{:016x}".format(seq_debug_data[0]).upper()
+
+            print(red("{:10}".format("Sequencer")), \
+                  white(": {:4}".format(instructionAddr)),\
+                  blue("0x{}".format(h)), \
+                  yellow(" {:6.8f}".format(uptime)), \
+                  haltStr, \
+                  "T:0x{:x}".format(triggerWord), \
+                  " {} ".format(instruction))
+            # if instructionAddr > 100:
+            #    sys.exit()
+        elif mode == MODE_RAM:
+
+            zeros, start = get_bytes(packet, start, 4)
+            vram_addr, start = get_bytes(packet, start, 4)
+            vram_data, start = get_bytes(packet, start, 4)
+
+            vram_header = struct.unpack(">I", zeros)[0]
+            vram_addr = struct.unpack(">I", vram_addr)[0]
+            vram_data = struct.unpack(">I", vram_data)[0]
+
+            if packet[0] == 0x2:
+                ram_mode = "Valid"
+
+            if packet[0] == 0x3:
+                ram_mode = "Write"
+
+            if packet[0] == 0x4:
+                ram_mode = "Send"
+
+            if packet[0] == 0x5:
+                ram_mode = "Recv"
+
+            print(green("{:10}".format("RAM")), \
+                  white(": {:>23}".format(ram_mode)),\
+                  yellow(" {:6.8f}".format(uptime)), \
+                  "addr = 0x{:08X} data = 0x{:08X}".format(vram_addr, vram_data))
+
+        elif mode == MODE_TRIGGER:
+
+            zeros, start = get_bytes(packet, start, 8)
+            syncBits, start = get_bytes(packet,start,1)
+            haltBits, start = get_bytes(packet, start, 1)
+            triggers, start = get_bytes(packet, start, 1)
+            triggerWord, start = get_bytes(packet,start,1)
+
+            for z in zeros:
+                if z != 0:
+                    print("Error expected 0 not", z)
+
+            haltBits = haltBits[0]
+            syncBits = syncBits[0]
+            triggers = triggers[0]
+            triggerWord = triggerWord[0]
+
+            haltStr = formatHaltBits(haltBits)
+
+            syncWF = (syncBits >> 3) & 0xF
+            syncMarker = (syncBits >> 1) & 0x3
+            syncMod = syncBits & 0x1
+
+
+            halt = bittest(syncBits,4)
+            pc_jump = bittest(syncBits, 5)
+            tready = bittest(syncBits, 6)
+            tvalid = bittest(syncBits, 7)
+
+            syncStr = "TV: {} TR: {} PJ: {} H: {} SWF: 0x{} SMa: 0x{} SMo: 0x{}".format(tvalid, tready, pc_jump, halt, syncWF, syncMarker, syncMod)
+
+            trigger = bittest(triggers,1)
+            triggerWordValid = bittest(triggers,0)
+
+            triggerStr = "t = {} tWV = {} tW = 0x{:0X}".format(trigger,triggerWordValid, triggerWord)
+
+            print(green("{:10}".format("Trigger")), \
+                  white(": {:>23}".format('')),\
+                  yellow(" {:6.8f}".format(uptime)), \
+                  haltStr, \
+                  syncStr, \
+                  triggerStr)
+        elif mode == MODE_UNKNOWN:
+            print(green("{:10}".format("Unknown")),packet_bytes)
+
+s.close()

From 3c8608d4b645c377671c46ad395b06a4594ece68 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 14:31:14 -0500
Subject: [PATCH 203/235] Properly set indirect mode on CALL

---
 QGL/APS2CustomInstructions.py |  4 ++--
 QGL/ControlFlow.py            |  6 +++---
 QGL/drivers/APS2Pattern.py    | 25 ++++++++++++++++++-------
 3 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index 3b269884..1d93cf38 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -61,13 +61,13 @@ def RandomClifford(target, addr):
     return [Invalidate(addr, 0, tdm=False),
             CustomInstruction("APS_CLIFFORD_RAND", 0x0, addr),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
-            Call(target, load_addr=True)]
+            Call(target, indirect=True)]
 
 def RandomCliffordInverse(target, addr):
     return [Invalidate(addr, 0, tdm=False),
             CustomInstruction("APS_CLIFFORD_INVERSE", 0x0, addr),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
-            Call(target, load_addr=True)]
+            Call(target, indirect=True)]
 
 def RandomCliffordInverseReset(addr): #for now don't use addr
     return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0xF)
diff --git a/QGL/ControlFlow.py b/QGL/ControlFlow.py
index daf12587..19d764dc 100644
--- a/QGL/ControlFlow.py
+++ b/QGL/ControlFlow.py
@@ -151,15 +151,15 @@ def __init__(self, target):
 
 class Call(ControlInstruction):
     # target is a BlockLabel
-    def __init__(self, target, load_addr=False):
+    def __init__(self, target, indirect=False):
         super(Call, self).__init__("CALL", target=target)
-        self.load_addr = load_addr
+        self.indirect = indirect
 
     def __str__(self):
         if self.load_addr:
             return f"{self.instruction}({str(self.target)})"
         else:
-            return f"{self.instruction}({str(self.target)}, LOAD)"
+            return f"{self.instruction}({str(self.target)}, INDIRECT)"
 
 
 
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 158abedf..bf48e0b1 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -342,12 +342,11 @@ def __str__(self):
         elif instrOpCode == LOADCMP:
             addr = self.payload & 0xFFFF
             mask = (self.payload >> 16) & 0xFFFF
-            use_ram = (self.payload >> 48) & 0x1
-            if self.decode_as_tdm and not use_ram:
+            if self.decode_as_tdm and not self.use_ram:
                 out += "WAITMEAS"
             else:
                 src = "EXT"
-                if use_ram:
+                if self.use_ram:
                     src = "RAM"
                 out += "LOADCMP | source={0}, addr=0x{1:0x}, read_mask=0x{2:0x}".format(src, addr, mask)
         return out
@@ -375,7 +374,17 @@ def writeFlag(self):
 
     @writeFlag.setter
     def writeFlag(self, value):
-        self.header |= value & 0x1
+        self.header &= ~(0x1 << 0) #clear bit
+        self.header |= (value & 0x1) #set bit
+
+    @property
+    def use_ram(self):
+        return ((self.payload >> 48) & 0x1)
+
+    @use_ram.setter
+    def use_ram(self, value):
+        self.payload &= ~(0x1 << 48) #clear bit
+        self.payload |= ((value & 0x1) << 48)
 
     @property
     def opcode(self):
@@ -448,8 +457,10 @@ def Goto(addr, label=None):
     return Command(GOTO, addr, label=label)
 
 
-def Call(addr, load_addr=False, label=None):
-    return Command(CALL, addr, label=label, write=load_addr)
+def Call(addr, indirect=False, label=None):
+    cmd = Command(CALL, addr, label=label)
+    cmd.use_ram = indirect
+    return cmd
 
 
 def Return(label=None):
@@ -828,7 +839,7 @@ def create_seq_instructions(seqs, offsets, label = None):
                 elif isinstance(entry, ControlFlow.Goto):
                     instructions.append(Goto(entry.target, label=label))
                 elif isinstance(entry, ControlFlow.Call):
-                    instructions.append(Call(entry.target, load_addr = entry.load_addr, label=label))
+                    instructions.append(Call(entry.target, indirect = entry.indirect, label=label))
                 elif isinstance(entry, ControlFlow.Repeat):
                     instructions.append(Repeat(entry.target, label=label))
                 # value argument commands

From 40fc869cb5e25818501227519200ccb5bd3646fe Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 14:55:27 -0500
Subject: [PATCH 204/235] Fix block labels on Calls.

---
 QGL/RandomCliffordTools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index 6863f0b4..d4fc97bb 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -43,14 +43,14 @@ def generate_clifford_jump_table(cliff_wires, jt_label = None):
     if not isinstance(jt_label, BlockLabel.BlockLabel):
         raise ValueError("Jump table label must be a BlockLabel.")
 
-    cliff_labels = [f"C{n}" for n in range(24)]
+    cliff_labels = [BlockLabel.BlockLabel(f"C{n}") for n in range(24)]
     jump_table = [jt_label]
     for cl in cliff_labels:
         jump_table.append(ControlFlow.Call(cl))
         jump_table.append(ControlFlow.Return())
 
     for cliff, cl in zip(cliff_wires, cliff_labels):
-        cliff.insert(0, BlockLabel.BlockLabel(cl))
+        cliff.insert(0, cl)
         cliff.append(ControlFlow.Return())
 
     cliff_wires.insert(0, jump_table)

From 20a83a72975badfbf87b0ae466cd01da4a403ad7 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 14:55:40 -0500
Subject: [PATCH 205/235] Make more pretty

---
 QGL/drivers/APS2Pattern.py | 33 +++++++++++++++++++++++++++++++--
 1 file changed, 31 insertions(+), 2 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index bf48e0b1..f3f6a97e 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1546,6 +1546,7 @@ def display_raw_file(filename):
 if __name__ == '__main__':
     if len(sys.argv) == 2:
 
+<<<<<<< HEAD
         from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView, QPushButton
         from PyQt5.QtGui import QIcon, QColor, QFont
 
@@ -1553,12 +1554,23 @@ def display_raw_file(filename):
         from matplotlib.figure import Figure
 
         table_font = QFont("Arial", weight=QFont.Bold)
+=======
+        from PyQt5.QtWidgets import QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView
+        from PyQt5.QtGui import QIcon, QColor, QFont
+
+        table_font = QFont("Arial", weight=57)
+>>>>>>> Make more pretty
 
         colors = {"WFM": QColor(0,200,0),
                   "GOTO": QColor(0,100,100),
                   "MARKER": QColor(150,150,200),
                   "CUSTOM": QColor(200,65,200),
-                  "WRITEADDR": QColor(245, 105, 65)}
+                  "WRITEADDR": QColor(245, 105, 65),
+                  "INVALIDATE": QColor(245, 105, 65),
+                  "CALL": QColor(65, 205, 245),
+                  "RET": QColor(65, 205, 245),
+                  "LOADCMP": QColor(245, 225, 65),
+                  "MODULATION": QColor(175, 255, 185)}
 
         class MatplotlibWidget(QWidget):
             def __init__(self, I, Q, parent=None):
@@ -1587,7 +1599,12 @@ def __init__(self, I, Q, parent=None):
         class App(QWidget):
 
             COLUMN_COUNT = 7
+<<<<<<< HEAD
             def __init__(self, instructions, waveforms):
+=======
+
+            def __init__(self, instructions):
+>>>>>>> Make more pretty
                 super().__init__()
                 self.title = 'APS2 Disassembled Instructions'
                 self.left = 100
@@ -1616,7 +1633,7 @@ def createTable(self):
                # Create table
                 self.tableWidget = QTableWidget()
                 self.tableWidget.setRowCount(len(self.instructions))
-                self.tableWidget.setColumnCount(7)
+                self.tableWidget.setColumnCount(self.COLUMN_COUNT)
 
                 for k, instr in enumerate(self.instructions):
                     fields = str(instr).replace(',','').replace(';', '').split(" ")
@@ -1628,6 +1645,7 @@ def createTable(self):
                         color = None
                     for l, f in enumerate(fields):
                         text = fields[l]
+<<<<<<< HEAD
                         if text == "GOTO":
                             btn = QPushButton(self.tableWidget)
                             btn.setText('GOTO')
@@ -1653,12 +1671,23 @@ def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.wavefor
                             if color:
                                 item.setBackground(color)
                             self.tableWidget.setItem(k, l, item)
+=======
+                        item = QTableWidgetItem(text)
+                        item.setFont(table_font)
+                        if color:
+                            item.setBackground(color)
+                        self.tableWidget.setItem(k,l, item)
+>>>>>>> Make more pretty
                     if l < self.COLUMN_COUNT-1:
                         for j in range(l+1, self.COLUMN_COUNT):
                             item = QTableWidgetItem("")
                             if color:
                                 item.setBackground(color)
                             self.tableWidget.setItem(k, j, item)
+<<<<<<< HEAD
+=======
+
+>>>>>>> Make more pretty
                 self.tableWidget.move(0,0)
                 self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
 

From dc7d2be1ed379872b5c55f912ce4fd2fd616e312 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Tue, 26 Feb 2019 14:59:42 -0500
Subject: [PATCH 206/235] Bold font

---
 QGL/drivers/APS2Pattern.py | 46 +-------------------------------------
 1 file changed, 1 insertion(+), 45 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index f3f6a97e..20f98b60 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1546,20 +1546,11 @@ def display_raw_file(filename):
 if __name__ == '__main__':
     if len(sys.argv) == 2:
 
-<<<<<<< HEAD
-        from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView, QPushButton
+        from PyQt5.QtWidgets import QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView
         from PyQt5.QtGui import QIcon, QColor, QFont
 
-        from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg
-        from matplotlib.figure import Figure
-
         table_font = QFont("Arial", weight=QFont.Bold)
-=======
-        from PyQt5.QtWidgets import QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView
-        from PyQt5.QtGui import QIcon, QColor, QFont
 
-        table_font = QFont("Arial", weight=57)
->>>>>>> Make more pretty
 
         colors = {"WFM": QColor(0,200,0),
                   "GOTO": QColor(0,100,100),
@@ -1599,12 +1590,8 @@ def __init__(self, I, Q, parent=None):
         class App(QWidget):
 
             COLUMN_COUNT = 7
-<<<<<<< HEAD
-            def __init__(self, instructions, waveforms):
-=======
 
             def __init__(self, instructions):
->>>>>>> Make more pretty
                 super().__init__()
                 self.title = 'APS2 Disassembled Instructions'
                 self.left = 100
@@ -1645,49 +1632,18 @@ def createTable(self):
                         color = None
                     for l, f in enumerate(fields):
                         text = fields[l]
-<<<<<<< HEAD
-                        if text == "GOTO":
-                            btn = QPushButton(self.tableWidget)
-                            btn.setText('GOTO')
-                            target_row = int(fields[1].split("=")[1])
-                            def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
-                                tab.scrollToItem(tab.item(row, 0))
-                            btn.clicked.connect(scroll_to_goto_target)
-                            self.tableWidget.setCellWidget(k, l, btn)
-                        if text == "WFM" and int(fields[4].split("=")[1])==0:
-                            # Not a TA pair
-                            btn = QPushButton(self.tableWidget)
-                            btn.setText('WFM')
-                            addr = int(fields[6].split("=")[1])
-                            count = int(fields[5].split("=")[1])
-                            def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
-                                w = MatplotlibWidget(I,Q)
-                                self.plotters.append(w)
-                            btn.clicked.connect(open_plotter)
-                            self.tableWidget.setCellWidget(k, l, btn)
-                        else:
-                            item = QTableWidgetItem(text)
-                            item.setFont(table_font)
-                            if color:
-                                item.setBackground(color)
-                            self.tableWidget.setItem(k, l, item)
-=======
                         item = QTableWidgetItem(text)
                         item.setFont(table_font)
                         if color:
                             item.setBackground(color)
                         self.tableWidget.setItem(k,l, item)
->>>>>>> Make more pretty
                     if l < self.COLUMN_COUNT-1:
                         for j in range(l+1, self.COLUMN_COUNT):
                             item = QTableWidgetItem("")
                             if color:
                                 item.setBackground(color)
                             self.tableWidget.setItem(k, j, item)
-<<<<<<< HEAD
-=======
 
->>>>>>> Make more pretty
                 self.tableWidget.move(0,0)
                 self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
 

From 8ea186dc8716830293d2a98237010b7c3e70cb9b Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 26 Feb 2019 15:57:16 -0500
Subject: [PATCH 207/235] Added goto buttons and waveform plotters to APS2
 disassembler

---
 QGL/drivers/APS2Pattern.py | 39 ++++++++++++++++++++++++++++++--------
 1 file changed, 31 insertions(+), 8 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 20f98b60..4f17a509 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1546,9 +1546,12 @@ def display_raw_file(filename):
 if __name__ == '__main__':
     if len(sys.argv) == 2:
 
-        from PyQt5.QtWidgets import QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView
+        from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView, QPushButton
         from PyQt5.QtGui import QIcon, QColor, QFont
 
+        from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg
+        from matplotlib.figure import Figure
+
         table_font = QFont("Arial", weight=QFont.Bold)
 
 
@@ -1591,7 +1594,7 @@ class App(QWidget):
 
             COLUMN_COUNT = 7
 
-            def __init__(self, instructions):
+            def __init__(self, instructions, waveforms):
                 super().__init__()
                 self.title = 'APS2 Disassembled Instructions'
                 self.left = 100
@@ -1632,11 +1635,31 @@ def createTable(self):
                         color = None
                     for l, f in enumerate(fields):
                         text = fields[l]
-                        item = QTableWidgetItem(text)
-                        item.setFont(table_font)
-                        if color:
-                            item.setBackground(color)
-                        self.tableWidget.setItem(k,l, item)
+                        if text == "GOTO":
+                            btn = QPushButton(self.tableWidget)
+                            btn.setText('GOTO')
+                            target_row = int(fields[1].split("=")[1])
+                            def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
+                                tab.scrollToItem(tab.item(row, 0))
+                            btn.clicked.connect(scroll_to_goto_target)
+                            self.tableWidget.setCellWidget(k, l, btn)
+                        if text == "WFM" and int(fields[4].split("=")[1])==0:
+                            # Not a TA pair
+                            btn = QPushButton(self.tableWidget)
+                            btn.setText('WFM')
+                            addr = int(fields[6].split("=")[1])
+                            count = int(fields[5].split("=")[1])
+                            def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
+                                w = MatplotlibWidget(I,Q)
+                                self.plotters.append(w)
+                            btn.clicked.connect(open_plotter)
+                            self.tableWidget.setCellWidget(k, l, btn)
+                        else:
+                            item = QTableWidgetItem(text)
+                            item.setFont(table_font)
+                            if color:
+                                item.setBackground(color)
+                            self.tableWidget.setItem(k, l, item)
                     if l < self.COLUMN_COUNT-1:
                         for j in range(l+1, self.COLUMN_COUNT):
                             item = QTableWidgetItem("")
@@ -1646,7 +1669,7 @@ def createTable(self):
 
                 self.tableWidget.move(0,0)
                 self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
-
+        
         app = QApplication(sys.argv[:1])
         ex = App(read_instructions(sys.argv[1]), read_waveforms(sys.argv[1]))
         sys.exit(app.exec_())

From c55f7e709bd43905080efe4d07d98cca512655fc Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Tue, 26 Feb 2019 21:34:53 -0500
Subject: [PATCH 208/235] Nice looking buttons for WFM and GOTO in disassembler

---
 QGL/drivers/APS2Pattern.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 4f17a509..801d95b2 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1603,7 +1603,6 @@ def __init__(self, instructions, waveforms):
                 self.height = 1200
                 self.instructions = instructions
                 self.waveforms = waveforms
-                print(self.waveforms)
                 self.initUI()
                 self.plotters = []
 
@@ -1642,17 +1641,19 @@ def createTable(self):
                             def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
                                 tab.scrollToItem(tab.item(row, 0))
                             btn.clicked.connect(scroll_to_goto_target)
+                            btn.setStyleSheet("background-color: #006464; color: white; font-weight: bold; text-align: left;")
                             self.tableWidget.setCellWidget(k, l, btn)
                         if text == "WFM" and int(fields[4].split("=")[1])==0:
                             # Not a TA pair
                             btn = QPushButton(self.tableWidget)
-                            btn.setText('WFM')
+                            btn.setText(' WFM')
                             addr = int(fields[6].split("=")[1])
                             count = int(fields[5].split("=")[1])
                             def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
                                 w = MatplotlibWidget(I,Q)
                                 self.plotters.append(w)
                             btn.clicked.connect(open_plotter)
+                            btn.setStyleSheet("background-color: #00C800; color: white; font-weight: bold; text-align: left;")
                             self.tableWidget.setCellWidget(k, l, btn)
                         else:
                             item = QTableWidgetItem(text)

From 19abc55a63b9751fc64835f2b1cb3fd1a163d9f3 Mon Sep 17 00:00:00 2001
From: Graham Rowlands <grahamrow@gmail.com>
Date: Wed, 27 Feb 2019 10:21:02 -0500
Subject: [PATCH 209/235] Move disassembler to utils directory

---
 QGL/drivers/APS2Pattern.py | 132 -------------------------------
 utils/disassemble_aps.py   | 157 +++++++++++++++++++++++++++++++++++++
 2 files changed, 157 insertions(+), 132 deletions(-)
 create mode 100755 utils/disassemble_aps.py

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 801d95b2..f2e7090d 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1542,135 +1542,3 @@ def display_raw_instructions(raw):
 def display_raw_file(filename):
     raw = raw_instructions(filename)
     display_raw_instructions(raw)
-
-if __name__ == '__main__':
-    if len(sys.argv) == 2:
-
-        from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView, QPushButton
-        from PyQt5.QtGui import QIcon, QColor, QFont
-
-        from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg
-        from matplotlib.figure import Figure
-
-        table_font = QFont("Arial", weight=QFont.Bold)
-
-
-        colors = {"WFM": QColor(0,200,0),
-                  "GOTO": QColor(0,100,100),
-                  "MARKER": QColor(150,150,200),
-                  "CUSTOM": QColor(200,65,200),
-                  "WRITEADDR": QColor(245, 105, 65),
-                  "INVALIDATE": QColor(245, 105, 65),
-                  "CALL": QColor(65, 205, 245),
-                  "RET": QColor(65, 205, 245),
-                  "LOADCMP": QColor(245, 225, 65),
-                  "MODULATION": QColor(175, 255, 185)}
-
-        class MatplotlibWidget(QWidget):
-            def __init__(self, I, Q, parent=None):
-                super(MatplotlibWidget, self).__init__(parent)
-                self.title = 'Waveform'
-                self.left = 100
-                self.top = 100
-                self.width = 800
-                self.height = 600
-                self.setWindowTitle(self.title)
-                self.setGeometry(self.left, self.top, self.width, self.height)
-
-                self.figure = Figure()
-                self.canvas = FigureCanvasQTAgg(self.figure)
-
-                self.axis = self.figure.add_subplot(111)
-                self.axis.plot(I)
-                self.axis.plot(Q)
-                self.layout = QVBoxLayout(self)
-                self.layout.addWidget(self.canvas)
-                self.setLayout(self.layout)
-                self.canvas.draw()
-                self.show()
-
-
-        class App(QWidget):
-
-            COLUMN_COUNT = 7
-
-            def __init__(self, instructions, waveforms):
-                super().__init__()
-                self.title = 'APS2 Disassembled Instructions'
-                self.left = 100
-                self.top = 100
-                self.width = 1000
-                self.height = 1200
-                self.instructions = instructions
-                self.waveforms = waveforms
-                self.initUI()
-                self.plotters = []
-
-            def initUI(self):
-                self.setWindowTitle(self.title)
-                self.setGeometry(self.left, self.top, self.width, self.height)
-
-                self.createTable()
-                self.layout = QVBoxLayout()
-                self.layout.addWidget(self.tableWidget)
-                self.setLayout(self.layout)
-
-                # Show widget
-                self.show()
-
-            def createTable(self):
-               # Create table
-                self.tableWidget = QTableWidget()
-                self.tableWidget.setRowCount(len(self.instructions))
-                self.tableWidget.setColumnCount(self.COLUMN_COUNT)
-
-                for k, instr in enumerate(self.instructions):
-                    fields = str(instr).replace(',','').replace(';', '').split(" ")
-                    if "|" in fields:
-                        fields.remove("|")
-                    if fields[0] in colors:
-                        color = colors[fields[0]]
-                    else:
-                        color = None
-                    for l, f in enumerate(fields):
-                        text = fields[l]
-                        if text == "GOTO":
-                            btn = QPushButton(self.tableWidget)
-                            btn.setText('GOTO')
-                            target_row = int(fields[1].split("=")[1])
-                            def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
-                                tab.scrollToItem(tab.item(row, 0))
-                            btn.clicked.connect(scroll_to_goto_target)
-                            btn.setStyleSheet("background-color: #006464; color: white; font-weight: bold; text-align: left;")
-                            self.tableWidget.setCellWidget(k, l, btn)
-                        if text == "WFM" and int(fields[4].split("=")[1])==0:
-                            # Not a TA pair
-                            btn = QPushButton(self.tableWidget)
-                            btn.setText(' WFM')
-                            addr = int(fields[6].split("=")[1])
-                            count = int(fields[5].split("=")[1])
-                            def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
-                                w = MatplotlibWidget(I,Q)
-                                self.plotters.append(w)
-                            btn.clicked.connect(open_plotter)
-                            btn.setStyleSheet("background-color: #00C800; color: white; font-weight: bold; text-align: left;")
-                            self.tableWidget.setCellWidget(k, l, btn)
-                        else:
-                            item = QTableWidgetItem(text)
-                            item.setFont(table_font)
-                            if color:
-                                item.setBackground(color)
-                            self.tableWidget.setItem(k, l, item)
-                    if l < self.COLUMN_COUNT-1:
-                        for j in range(l+1, self.COLUMN_COUNT):
-                            item = QTableWidgetItem("")
-                            if color:
-                                item.setBackground(color)
-                            self.tableWidget.setItem(k, j, item)
-
-                self.tableWidget.move(0,0)
-                self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
-        
-        app = QApplication(sys.argv[:1])
-        ex = App(read_instructions(sys.argv[1]), read_waveforms(sys.argv[1]))
-        sys.exit(app.exec_())
diff --git a/utils/disassemble_aps.py b/utils/disassemble_aps.py
new file mode 100755
index 00000000..1b7919c4
--- /dev/null
+++ b/utils/disassemble_aps.py
@@ -0,0 +1,157 @@
+#!/usr/bin/env python
+
+import numpy as np
+import sys
+import os.path
+
+from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView, QPushButton
+from PyQt5.QtGui import QIcon, QColor, QFont
+from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg
+from matplotlib.figure import Figure
+
+colors = {"WFM": QColor(0,200,0),
+          "GOTO": QColor(0,100,100),
+          "MARKER": QColor(150,150,200),
+          "CUSTOM": QColor(200,65,200),
+          "WRITEADDR": QColor(245, 105, 65),
+          "INVALIDATE": QColor(245, 105, 65),
+          "CALL": QColor(65, 205, 245),
+          "RET": QColor(65, 205, 245),
+          "LOADCMP": QColor(245, 225, 65),
+          "MODULATION": QColor(175, 255, 185)}
+
+table_font = QFont("Arial", weight=QFont.Bold)
+
+class MatplotlibWidget(QWidget):
+    def __init__(self, I, Q, parent=None):
+        super(MatplotlibWidget, self).__init__(parent)
+        self.title  = 'Waveform'
+        self.left   = 100
+        self.top    = 100
+        self.width  = 800
+        self.height = 600
+        self.setWindowTitle(self.title)
+        self.setGeometry(self.left, self.top, self.width, self.height)
+
+        self.figure = Figure()
+        self.canvas = FigureCanvasQTAgg(self.figure)
+
+        self.axis = self.figure.add_subplot(111)
+        self.axis.plot(I)
+        self.axis.plot(Q)
+        self.layout = QVBoxLayout(self)
+        self.layout.addWidget(self.canvas)
+        self.setLayout(self.layout)
+        self.canvas.draw()
+        self.show()
+
+
+class DisassemblerApp(QWidget):
+
+    COLUMN_COUNT = 7
+
+    def __init__(self, instructions, waveforms):
+        super().__init__()
+        self.title  = 'APS2 Disassembled Instructions'
+        self.left   = 100
+        self.top    = 100
+        self.width  = 1000
+        self.height = 1200
+        self.instructions = instructions
+        self.waveforms = waveforms
+        self.initUI()
+        self.plotters = []
+
+    def initUI(self):
+        self.setWindowTitle(self.title)
+        self.setGeometry(self.left, self.top, self.width, self.height)
+
+        self.createTable()
+        self.layout = QVBoxLayout()
+        self.layout.addWidget(self.tableWidget)
+        self.setLayout(self.layout)
+
+        # Show widget
+        self.show()
+
+    def createTable(self):
+       # Create table
+        self.tableWidget = QTableWidget()
+        self.tableWidget.setRowCount(len(self.instructions))
+        self.tableWidget.setColumnCount(self.COLUMN_COUNT)
+
+        for k, instr in enumerate(self.instructions):
+            fields = str(instr).replace(',','').replace(';', '').split(" ")
+            if "|" in fields:
+                fields.remove("|")
+            if fields[0] in colors:
+                color = colors[fields[0]]
+            else:
+                color = None
+            for l, f in enumerate(fields):
+                text = fields[l]
+                if text == "GOTO":
+                    btn = QPushButton(self.tableWidget)
+                    btn.setText('GOTO')
+                    target_row = int(fields[1].split("=")[1])
+                    def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
+                        tab.scrollToItem(tab.item(row, 0))
+                    btn.clicked.connect(scroll_to_goto_target)
+                    btn.setStyleSheet("background-color: #006464; color: white; font-weight: bold; text-align: left;")
+                    self.tableWidget.setCellWidget(k, l, btn)
+                if text == "WFM" and int(fields[4].split("=")[1])==0:
+                    # Not a TA pair
+                    btn = QPushButton(self.tableWidget)
+                    btn.setText(' WFM')
+                    addr = int(fields[6].split("=")[1])
+                    count = int(fields[5].split("=")[1])
+                    def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
+                        w = MatplotlibWidget(I,Q)
+                        self.plotters.append(w)
+                    btn.clicked.connect(open_plotter)
+                    btn.setStyleSheet("background-color: #00C800; color: white; font-weight: bold; text-align: left;")
+                    self.tableWidget.setCellWidget(k, l, btn)
+                else:
+                    item = QTableWidgetItem(text)
+                    item.setFont(table_font)
+                    if color:
+                        item.setBackground(color)
+                    self.tableWidget.setItem(k, l, item)
+            if l < self.COLUMN_COUNT-1:
+                for j in range(l+1, self.COLUMN_COUNT):
+                    item = QTableWidgetItem("")
+                    if color:
+                        item.setBackground(color)
+                    self.tableWidget.setItem(k, j, item)
+
+        self.tableWidget.move(0,0)
+        self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
+
+def get_target_hardware(filename):
+    with open(filename, 'rb') as FID:
+        target_hw = FID.read(4).decode('utf-8')
+    return target_hw
+
+if __name__ == '__main__':
+    if len(sys.argv) == 2:
+        filename = sys.argv[1]
+        try:
+            hw = get_target_hardware(filename)
+            if hw == "APS2":
+                from QGL.drivers.APS2Pattern import read_instructions, read_waveforms
+                app = QApplication(sys.argv[:1])
+                ex  = DisassemblerApp(read_instructions(sys.argv[1]), read_waveforms(sys.argv[1]))
+                sys.exit(app.exec_())
+            elif hw == "APS1":
+                print("APS1 disassmbler not yet implemented")
+            else:
+                raise Exception("Unknown hardware target.")
+        except:
+            print(f"The supplied file {filename} does not appear to be APS1 or APS2 format.")
+        
+    else:
+        print("Expected single file (.aps1 or .aps2 format) as an argument.")
+
+        
+
+

From 9ba81a6156e28f0710469ba74134027c3d2cd672 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:54:39 -0500
Subject: [PATCH 210/235] Add jump table indicator to block label.

---
 QGL/BlockLabel.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/QGL/BlockLabel.py b/QGL/BlockLabel.py
index 52db8b63..6725cd13 100644
--- a/QGL/BlockLabel.py
+++ b/QGL/BlockLabel.py
@@ -2,8 +2,10 @@
 
 
 class BlockLabel(object):
-    def __init__(self, label):
+    def __init__(self, label, jump_table=False, table_size=0):
         self.label = label
+        self.jump_table = jump_table
+        self.table_size = table_size
 
     def __repr__(self):
         return self.__str__()

From 79fffaaec19a68267a4a4c381d27446b8e898d26 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:56:09 -0500
Subject: [PATCH 211/235] Only set up clifford generator once per sequence
 file.

---
 QGL/RandomCliffordTools.py | 34 +++++++++++++++++++++++-----------
 1 file changed, 23 insertions(+), 11 deletions(-)

diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index d4fc97bb..9317b3e2 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -33,13 +33,15 @@
 from .APS2CustomInstructions import *
 from .Cliffords import C1, inverse_clifford, clifford_multiply
 
+default_clifford_options = {"offset": 0x0, "spacing": 0x1, "seed": 0x31}
+
 VALID_CLIFFORD_TYPES = ('RandomAC',)
 
 def generate_clifford_jump_table(cliff_wires, jt_label = None):
     """Generate the jump table that will be used to call into the clifford set"""
 
     if jt_label is None:
-        jt_label = BlockLabel.BlockLabel("JT")
+        jt_label = BlockLabel.BlockLabel("JT", jump_table=True, table_size=48)
     if not isinstance(jt_label, BlockLabel.BlockLabel):
         raise ValueError("Jump table label must be a BlockLabel.")
 
@@ -55,14 +57,22 @@ def generate_clifford_jump_table(cliff_wires, jt_label = None):
 
     cliff_wires.insert(0, jump_table)
 
+    return jt_label
+
 def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
-                            inv_addr=0x3, inv_values=[]):
+                            inv_addr=0x3, inv_values=[],
+                            clifford_options=default_clifford_options):
 
     if jt_label is None:
         jt_label = BlockLabel.BlockLabel("JT")
     if not isinstance(jt_label, BlockLabel.BlockLabel):
         raise ValueError("Jump table label must be a BlockLabel.")
 
+    #Insert defaults
+    for k,v in default_clifford_options.items():
+        if k not in clifford_options.keys():
+            cliford_options[k] = v
+
     for idx, seq in enumerate(seqs[:]):
         if not PatternUtils.contains_runtime_pulses(seq):
             continue
@@ -74,18 +84,14 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
                 and pulse.label in VALID_CLIFFORD_TYPES:
                 has_random_cliff = True
                 new_seq.extend(RandomClifford(jt_label, cliff_addr))
-                print("Inserting clifford pulse!")
+                #print("Inserting clifford pulse!")
             else:
                 new_seq.append(pulse)
 
-        info_seqs = []
-        info_seqs.extend(RandomCliffordSetOffset(0x1, 0x0))
-        info_seqs.extend(RandomCliffordSetSpacing(0x2, 0x1))
-
-        if isinstance(seq[0], BlockLabel.BlockLabel):
-            new_seq[1:1] = info_seqs
-        else:
-            new_seq[0:0] = info_seqs
+        # if isinstance(seq[0], BlockLabel.BlockLabel):
+        #     new_seq[1:1] = info_seqs
+        # else:
+        #     new_seq[0:0] = info_seqs
 
         if add_inv:
             #insert reset after first wait
@@ -99,6 +105,12 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
 
         seqs[idx] = new_seq
 
+    info_seqs = []
+    info_seqs.extend(RandomCliffordSetOffset(0x1, clifford_options["offset"]))
+    info_seqs.extend(RandomCliffordSetSpacing(0x2, clifford_options["spacing"]))
+    info_seqs.extend(RandomCliffordSeed(clifford_options["seed"]))
+    seqs.insert(0, info_seqs)
+
 
 def randomize_clifford_sequences(qubit, seqs, clifford_type=PulsePrimitives.RandomAC):
 

From 0545e72a84742235aca874c7fda0f55410aac55b Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:56:42 -0500
Subject: [PATCH 212/235] Correct __str__ for indicrect CALL

---
 QGL/ControlFlow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/ControlFlow.py b/QGL/ControlFlow.py
index 19d764dc..692958ff 100644
--- a/QGL/ControlFlow.py
+++ b/QGL/ControlFlow.py
@@ -156,7 +156,7 @@ def __init__(self, target, indirect=False):
         self.indirect = indirect
 
     def __str__(self):
-        if self.load_addr:
+        if not self.indirect:
             return f"{self.instruction}({str(self.target)})"
         else:
             return f"{self.instruction}({str(self.target)}, INDIRECT)"

From 0b588e99a609df4b1bb5189841973510f40dcdf4 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:57:20 -0500
Subject: [PATCH 213/235] Correct implementation of APS2_SET_SEED

---
 QGL/APS2CustomInstructions.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index 1d93cf38..ae9c4221 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -48,14 +48,14 @@
 def RandomCliffordSetOffset(addr, offset):
     return [Invalidate(addr, 0, tdm=False),
             WriteAddr(addr, offset, tdm=False),
-            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
-            CustomInstruction("APS_CLIFFORD_SET_OFFSET", addr, 0x3)]
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False), #
+            CustomInstruction("APS_CLIFFORD_SET_OFFSET", addr, 0xA)]
 
 def RandomCliffordSetSpacing(addr, spacing):
     return [Invalidate(addr, 0, tdm=False),
             WriteAddr(addr, spacing, tdm=False),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
-            CustomInstruction("APS_CLIFFORD_SET_SPACING", addr, 0x3)]
+            CustomInstruction("APS_CLIFFORD_SET_SPACING", addr, 0xA)]
 
 def RandomClifford(target, addr):
     return [Invalidate(addr, 0, tdm=False),
@@ -73,4 +73,7 @@ def RandomCliffordInverseReset(addr): #for now don't use addr
     return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0xF)
 
 def RandomCliffordSeed(seed):
-    raise NotImplementedError("APS_CLIFFORD_SET_SEED not implemented!")
+    return [Invalidate(0xB, 0, tdm=False),
+        WriteAddr(0xB, seed, tdm=False),
+        LoadCmpVram(0xB, 0xFFFFFFFF, tdm=False),
+        CustomInstruction("APS_CLIFFORD_SET_SEED", 0xB, 0xA)]

From 5382f144e380aa7ab255c7a205c5cd379ef18e11 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:58:15 -0500
Subject: [PATCH 214/235] Keep modulation commands explicitly in subroutines to
 prevent eliding Z pulses

---
 QGL/Compiler.py | 29 +++++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 930774d8..4071ae6d 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -37,6 +37,7 @@
 from . import BlockLabel
 from . import TdmInstructions # only for APS2-TDM
 from . import APS2CustomInstructions
+from .RandomCliffordTools import default_clifford_options
 from . import RandomCliffordTools
 import gc
 
@@ -365,7 +366,8 @@ def collect_specializations(seqs):
             done.append(target)
     return funcs
 
-def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=False):
+def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=False,
+                    clifford_options=default_clifford_options):
 
     ChannelLibraries.channelLib.update_channelDict()
     clear_pulse_cache()
@@ -402,7 +404,7 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=
 
     # Compile all the pulses/pulseblocks to sequences of pulses and control flow
     logger.info("Compiling sequences.")
-    wireSeqs = compile_sequences(seqs, channels, random_cliffords=random_cliffords)
+    wireSeqs = compile_sequences(seqs, channels, random_cliffords=random_cliffords, clifford_options=clifford_options)
 
     if not validate_linklist_channels(wireSeqs.keys()):
         print("Compile to hardware failed")
@@ -594,7 +596,8 @@ def compile_to_hardware(seqs,
     return metafilepath
 
 
-def compile_sequences(seqs, channels=set(), random_cliffords=False):
+def compile_sequences(seqs, channels=set(), random_cliffords=False,
+                            clifford_options=default_clifford_options):
     '''
     Main function to convert sequences to miniLL's and waveform libraries.
     '''
@@ -609,14 +612,21 @@ def compile_sequences(seqs, channels=set(), random_cliffords=False):
     seqs += subroutines
 
     if random_cliffords:
+
         qubits = [q for q in list(channels) if isinstance(q, Channels.Qubit)]
         if len(qubits) > 1:
             raise Exception("Too many qubits! Don't know how to deal with this yet.")
         #replace cliffords with
         cliffords = [[get_clifford_type(seqs)(n)] for n in range(24)]
-        RandomCliffordTools.generate_clifford_jump_table(cliffords)
-        RandomCliffordTools.insert_clifford_calls(seqs)
+        jt_label = RandomCliffordTools.generate_clifford_jump_table(cliffords)
+        RandomCliffordTools.insert_clifford_calls(seqs, jt_label=jt_label, clifford_options=clifford_options)
+
+        # if not isinstance(seqs[0][0], BlockLabel.BlockLabel):
+        #     raise Exception("Fist instruciton must be block label!")
+        # start_label = seqs[0][0]
         seqs += cliffords
+        #seqs[0:0] = cliffords
+        #seqs[0].insert(0, ControlFlow.Goto(start_label))
 
     #expand the channel definitions for anything defined in subroutines
     for func in subroutines:
@@ -702,7 +712,14 @@ def flatten_to_pulses(obj):
                 wires = propagate_node_frame_to_edges(
                     wires, chan, block.pulses[chan].frameChange)
         # drop length 0 blocks but push nonzero frame changes onto previous entries
-        if block.length == 0:
+
+        is_subroutine = False
+        if isinstance(seq[-1], ControlFlow.Return):
+            #Make sure we do not drop frame update instructions for subroutines that are only Z pulses
+            is_subroutine = True
+
+
+        if block.length == 0 and not is_subroutine:
             for chan in channels:
                 if block.pulses[chan].frameChange == 0:
                     continue

From 3a2236954a22f2504cbf4ad3685e99396314538b Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 16:59:01 -0500
Subject: [PATCH 215/235] Proper prefetching for jump-table based subroutines

---
 QGL/drivers/APS2Pattern.py | 43 ++++++++++++++++++++++++++++----------
 1 file changed, 32 insertions(+), 11 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index f2e7090d..507da11d 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -298,8 +298,11 @@ def __str__(self):
 
         elif any(
             [instrOpCode == op for op in [GOTO, CALL, RET, REPEAT, PREFETCH]]):
+            if self.use_ram:
+                out += " RAM"
             out += " | target_addr={}".format(self.payload & 2**26 - 1)
 
+
         elif instrOpCode == LOAD:
             out += " | count={}".format(self.payload)
 
@@ -360,6 +363,9 @@ def __ne__(self, other):
     def __hash__(self):
         return hash((self.header, self.payload, self.label))
 
+    def isa(self, value):
+        return (self.header >> 4) == value
+
     @property
     def address(self):
         return self.payload & 0xffffffff  # bottom 32-bits of payload
@@ -623,7 +629,7 @@ def to_instruction(self, write_flag=True, label=None):
         instr.writeFlag = write_flag
         return instr
 
-def inject_modulation_cmds(seqs, force_phase_update=False):
+def inject_modulation_cmds(seqs):
     """
     Inject modulation commands from phase, frequency and frameChange of waveforms
     in an IQ waveform sequence. Assume up to 2 NCOs for now.
@@ -641,13 +647,17 @@ def inject_modulation_cmds(seqs, force_phase_update=False):
         frame_changes = [entry.frameChange for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
         no_frame_cmds = np.all(np.less(np.abs(frame_changes), 1e-8))
         no_modulation_cmds = no_freq_cmds and no_phase_cmds and no_frame_cmds
-        #import pdb; pdb.set_trace()
         if no_modulation_cmds:
             continue
 
         mod_seq = []
         pending_frame_update = False
 
+        #check to see if we are in a subroutine by using last instruction as return as a tell
+        #if so, ensure frame updates do not get dropped
+        if isinstance(seq[-1], ControlFlow.Return):
+            force_phase_update = True
+
         for entry in seq:
 
             #copies to avoid same object having different timestamps later
@@ -735,7 +745,6 @@ def synchronize_clocks(seqs):
     syncInstructions = [list(filter(
         lambda s: isinstance(s, ControlFlow.ControlInstruction), seq))
                         for seq in seqs if seq]
-    #import pdb; pdb.set_trace()
     # Add length to control-flow instructions to make accumulated time match at end of CFI.
     # Keep running tally of how much each channel has been shifted so far.
     localShift = [0 for _ in syncInstructions]
@@ -854,14 +863,14 @@ def create_seq_instructions(seqs, offsets, label = None):
                     instructions.append(LoadCmpVram(entry.addr, entry.mask, label=label))
                 # some TDM instructions are ignored by the APS
                 elif isinstance(entry, TdmInstructions.CustomInstruction):
-                    print(str(entry))
+                    #print(str(entry))
                     try:
                         instructions.append(Custom(entry.in_addr, entry.out_addr,
                                                     APS2_CUSTOM[entry.instruction], label=label))
                     except KeyError as e:
                         raise Exception(f"Got unknown APS2 instruction: {e.args[0]} in {str(entry)}.")
                 elif isinstance(entry, TdmInstructions.WriteAddrInstruction):
-                    print(str(entry))
+                    #print(str(entry))
                     if entry.instruction == 'INVALIDATE' and entry.tdm == False:
                         instructions.append(Invalidate(entry.addr, entry.value, label=label))
                     if entry.instruction == 'WRITEADDR' and entry.tdm == False:
@@ -946,7 +955,6 @@ def create_instr_data(seqs, offsets, cache_lines):
         except:
             pass
         instructions += seq
-
     #if we have any subroutines then group in cache lines
     if subroutines_start >= 0:
         subroutine_instrs = []
@@ -974,12 +982,25 @@ def create_instr_data(seqs, offsets, cache_lines):
             CACHE_LINE_LENGTH))
         #inject prefetch commands before waits
         wait_idx = [idx for idx, instr in enumerate(instructions)
-                    if (instr.header >> 4) == WAIT] + [len(instructions)]
+                    if instr.isa(WAIT)] + [len(instructions)]
         instructions_with_prefetch = instructions[:wait_idx[0]]
         last_prefetch = None
+
         for start, stop in zip(wait_idx[:-1], wait_idx[1:]):
             call_targets = [instr.target for instr in instructions[start:stop]
-                            if (instr.header >> 4) == CALL]
+                           if instr.isa(CALL)]
+
+            #Check if we call into any jump tables
+            jump_tables = [label for label in call_targets if label.jump_table]
+            if len(jump_tables) > 0:
+                for jt in set(jump_tables):
+                    #Find the start of the jump table
+                    start_idx = next(j for j, instr in enumerate(subroutine_instrs)
+                                        if instr.label == jt)
+                    stop_idx = start_idx + jt.table_size
+                    call_targets.extend([instr.target for instr in
+                                            subroutine_instrs[start_idx:stop_idx]
+                                                if instr.isa(CALL)])
             needed_lines = set()
             for target in call_targets:
                 needed_lines.add(subroutine_cache_line[target])
@@ -996,9 +1017,9 @@ def create_instr_data(seqs, offsets, cache_lines):
         #pad out instruction vector to ensure circular cache never loads a subroutine
         pad_instrs = 7 * 128 + (128 - ((len(instructions) + 128) % 128))
         instructions += [NoOp()] * pad_instrs
-
         instructions += subroutine_instrs
 
+
     #turn symbols into integers addresses
     resolve_symbols(instructions)
 
@@ -1013,7 +1034,7 @@ def resolve_symbols(seq):
 
     labeled_entries = [(idx, entry.label) for idx, entry in enumerate(seq) if entry.label is not None]
     symbols = {label: idx for idx, label in labeled_entries}
-    print(f"Found labels: {symbols}")
+    #print(f"Found labels: {symbols}")
     for entry in seq:
         if entry.target is not None and entry.target in symbols.keys():
             entry.address = symbols[entry.target]
@@ -1215,7 +1236,7 @@ def start_new_seq():
                 chan_select_bits = ((instr.header >> 2) & 0x1,
                                     (instr.header >> 3) & 0x1)
                 #On older firmware we broadcast by default whereas on newer we respect the engine select
-                for chan, select_bit in zip(('ch1', 'ch2'), chan_select_bits):
+                for chan, select_bit in zip(('ch1', 'ch2'), chan_select_bits):plot_pulse
                     if (file_version < 4) or select_bit:
                         if isTA:
                             seqs[chan][-1].append((count, wf_lib[chan][addr]))

From d45839b505510820943924b6ddf48eb44db32f95 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 17:00:52 -0500
Subject: [PATCH 216/235] Fix typo.

---
 QGL/drivers/APS2Pattern.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 507da11d..c5b0762f 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1236,7 +1236,7 @@ def start_new_seq():
                 chan_select_bits = ((instr.header >> 2) & 0x1,
                                     (instr.header >> 3) & 0x1)
                 #On older firmware we broadcast by default whereas on newer we respect the engine select
-                for chan, select_bit in zip(('ch1', 'ch2'), chan_select_bits):plot_pulse
+                for chan, select_bit in zip(('ch1', 'ch2'), chan_select_bits):
                     if (file_version < 4) or select_bit:
                         if isTA:
                             seqs[chan][-1].append((count, wf_lib[chan][addr]))

From bd19ab381ab30ec42fc21152ded61a0af4e5522a Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 17:05:06 -0500
Subject: [PATCH 217/235] Remove debug watcher from QGL (now in libaps2)

---
 tests/aps_debug_watcher.py | 219 -------------------------------------
 thing.txt                  |   3 +
 2 files changed, 3 insertions(+), 219 deletions(-)
 delete mode 100644 tests/aps_debug_watcher.py
 create mode 100644 thing.txt

diff --git a/tests/aps_debug_watcher.py b/tests/aps_debug_watcher.py
deleted file mode 100644
index 4f389e8f..00000000
--- a/tests/aps_debug_watcher.py
+++ /dev/null
@@ -1,219 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-import socket
-import struct
-try:
-    from QGL.drivers import APS2Pattern
-    haveQGL = True
-except:
-    haveQGL = False
-import numpy as np
-from ansicolor import * # from ansicolors
-
-ip = sys.argv[1]
-port = 0xbb50
-
-short_time = True
-
-raw_mode = '-r' in sys.argv
-tdm_mode = '-tdm' in sys.argv
-
-print("Connecting to APS Debug Port at {0}:{1}".format(ip,port))
-
-PACKET_SIZE=168//8+1
-
-if short_time:
-    PACKET_SIZE -= 2
-
-MODE_UNKNOWN = 0
-MODE_SEQUENCER = 1
-MODE_RAM = 2
-MODE_TRIGGER = 3
-
-def bittest(v, b):
-    if ((v & (1<<b)) == (1<<b)):
-        return red('T')
-    else:
-        return 'F'
-
-def get_bytes(a, s, e):
-    e += s
-    return a[s:e], e
-
-def formatHaltBits(haltBits):
-    haltSync = bittest(haltBits,5)
-    haltCustom = bittest(haltBits,4)
-    haltValid = bittest(haltBits,3)
-    haltWait = bittest(haltBits,2)
-    haltStr = "S:{} V:{} C:{} W:{}".format(haltSync, haltValid, haltCustom, haltWait)
-    return haltStr
-
-
-
-s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
-s.connect((ip,port))
-print("Connected")
-print(s)
-extraData = b''
-while 1:
-    data = extraData + s.recv(10*PACKET_SIZE)
-    num_packets = len(data) // PACKET_SIZE
-    num_excess = len(data) % PACKET_SIZE
-    block_size = num_packets*PACKET_SIZE
-    extraData = b''
-    if num_excess > 0:
-        extraData = data[block_size:]
-        data = data[:block_size]
-
-    for cnt in range(num_packets):
-        start = cnt * PACKET_SIZE
-        end = (cnt+1)*PACKET_SIZE
-        packet = data[start:end]
-        packet_bytes = bytearray(packet)
-        if raw_mode:
-            print(packet_bytes)
-            continue
-
-        if packet[0] ==  0x1:
-            mode = MODE_SEQUENCER
-        elif packet[0] in [0x2,0x3, 0x4, 0x5]:
-            mode = MODE_RAM
-        elif packet[0] == 0x6:
-            mode = MODE_TRIGGER
-        else:
-            mode = MODE_UNKNOWN
-
-
-        if short_time:
-            uptime_seconds = packet_bytes[1:3]
-            uptime_nanoseconds = packet_bytes[3:7]
-
-            uptime_seconds = struct.unpack(">H", uptime_seconds)[0]
-        else:
-            uptime_seconds = packet_bytes[1:5]
-            uptime_nanoseconds = packet_bytes[5:9]
-
-            uptime_seconds = struct.unpack(">I", uptime_seconds)[0]
-
-        uptime_nanoseconds = struct.unpack(">I", uptime_nanoseconds)[0]
-
-        #print(uptime_seconds, uptime_nanoseconds)
-
-        uptime_nanoseconds = uptime_nanoseconds/1e9
-        uptime = uptime_seconds + uptime_nanoseconds
-
-        if short_time:
-            start = 8
-        else:
-            start = 10
-
-        if mode == MODE_SEQUENCER:
-
-            if short_time:
-                triggerWord = packet[7]
-            else:
-                triggerWord = packet[9]
-
-            haltBits = packet[start]
-
-            haltStr = formatHaltBits(haltBits)
-
-            instructionAddr, start = get_bytes(packet, start, 4)
-            instructionAddr = bytearray(instructionAddr)
-            # clear halt bits, only the first two bits are part of the Addr
-            instructionAddr[0] = instructionAddr[0] & 0x3
-            instructionAddr = struct.unpack(">I", instructionAddr)[0]
-
-            seq_debug_data, start = get_bytes(packet, start, 8)
-            seq_debug_data = np.fromstring(seq_debug_data[::-1], dtype=np.uint64)
-
-            if haveQGL:
-                instruction = APS2Pattern.Instruction.unflatten(seq_debug_data, decode_as_tdm = tdm_mode)
-            else:
-                instruction = ''
-
-            h = "{:016x}".format(seq_debug_data[0]).upper()
-
-            print(red("{:10}".format("Sequencer")), \
-                  white(": {:4}".format(instructionAddr)),\
-                  blue("0x{}".format(h)), \
-                  yellow(" {:6.8f}".format(uptime)), \
-                  haltStr, \
-                  "T:0x{:x}".format(triggerWord), \
-                  " {} ".format(instruction))
-            # if instructionAddr > 100:
-            #    sys.exit()
-        elif mode == MODE_RAM:
-
-            zeros, start = get_bytes(packet, start, 4)
-            vram_addr, start = get_bytes(packet, start, 4)
-            vram_data, start = get_bytes(packet, start, 4)
-
-            vram_header = struct.unpack(">I", zeros)[0]
-            vram_addr = struct.unpack(">I", vram_addr)[0]
-            vram_data = struct.unpack(">I", vram_data)[0]
-
-            if packet[0] == 0x2:
-                ram_mode = "Valid"
-
-            if packet[0] == 0x3:
-                ram_mode = "Write"
-
-            if packet[0] == 0x4:
-                ram_mode = "Send"
-
-            if packet[0] == 0x5:
-                ram_mode = "Recv"
-
-            print(green("{:10}".format("RAM")), \
-                  white(": {:>23}".format(ram_mode)),\
-                  yellow(" {:6.8f}".format(uptime)), \
-                  "addr = 0x{:08X} data = 0x{:08X}".format(vram_addr, vram_data))
-
-        elif mode == MODE_TRIGGER:
-
-            zeros, start = get_bytes(packet, start, 8)
-            syncBits, start = get_bytes(packet,start,1)
-            haltBits, start = get_bytes(packet, start, 1)
-            triggers, start = get_bytes(packet, start, 1)
-            triggerWord, start = get_bytes(packet,start,1)
-
-            for z in zeros:
-                if z != 0:
-                    print("Error expected 0 not", z)
-
-            haltBits = haltBits[0]
-            syncBits = syncBits[0]
-            triggers = triggers[0]
-            triggerWord = triggerWord[0]
-
-            haltStr = formatHaltBits(haltBits)
-
-            syncWF = (syncBits >> 3) & 0xF
-            syncMarker = (syncBits >> 1) & 0x3
-            syncMod = syncBits & 0x1
-
-
-            halt = bittest(syncBits,4)
-            pc_jump = bittest(syncBits, 5)
-            tready = bittest(syncBits, 6)
-            tvalid = bittest(syncBits, 7)
-
-            syncStr = "TV: {} TR: {} PJ: {} H: {} SWF: 0x{} SMa: 0x{} SMo: 0x{}".format(tvalid, tready, pc_jump, halt, syncWF, syncMarker, syncMod)
-
-            trigger = bittest(triggers,1)
-            triggerWordValid = bittest(triggers,0)
-
-            triggerStr = "t = {} tWV = {} tW = 0x{:0X}".format(trigger,triggerWordValid, triggerWord)
-
-            print(green("{:10}".format("Trigger")), \
-                  white(": {:>23}".format('')),\
-                  yellow(" {:6.8f}".format(uptime)), \
-                  haltStr, \
-                  syncStr, \
-                  triggerStr)
-        elif mode == MODE_UNKNOWN:
-            print(green("{:10}".format("Unknown")),packet_bytes)
-
-s.close()
diff --git a/thing.txt b/thing.txt
new file mode 100644
index 00000000..5e24153f
--- /dev/null
+++ b/thing.txt
@@ -0,0 +1,3 @@
+1.222 4.0+5.0i
+1.32 4.1+5.6i
+1.55 4.2+6.7i

From d34bb118e5f7ef17e14438e152fec784dc27a358 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 27 Feb 2019 17:05:49 -0500
Subject: [PATCH 218/235] Remove junk

---
 thing.txt | 3 ---
 1 file changed, 3 deletions(-)
 delete mode 100644 thing.txt

diff --git a/thing.txt b/thing.txt
deleted file mode 100644
index 5e24153f..00000000
--- a/thing.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-1.222 4.0+5.0i
-1.32 4.1+5.6i
-1.55 4.2+6.7i

From 8d75d89cf9557ab3a59aef00f36cc410ca78386b Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Wed, 24 Apr 2019 17:36:37 -0400
Subject: [PATCH 219/235] Update to latest sqlalchemy syntax

---
 QGL/Compiler.py | 64 +++++++++++++++++++++++++++++--------------------
 1 file changed, 38 insertions(+), 26 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 4071ae6d..04a6bfe8 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -432,26 +432,32 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=
     physWires = map_logical_to_physical(wireSeqs)
 
     # Pave the way for composite instruments, not useful yet...
-    files = {}
-    label_to_inst   = {}
-    label_to_chan   = {}
-    old_wire_names  = {}
-    old_wire_instrs = {}
+    extra_info = {}
+    extra_info["files"]             = {}
+    extra_info["label_to_inst"]     = {}
+    extra_info["label_to_chan"]     = {}
+    extra_info["old_wire_names"]    = {}
+    extra_info["old_wire_instrs"]   = {}
+
+    extra_info["num_measurements"] = num_measurements
+    extra_info["wire_measurements"] = wire_measurements
+    extra_info["channels"] = channels
+
     for wire, pulses in physWires.items():
         pattern_module = import_module('QGL.drivers.' + wire.translator)
         if pattern_module.SEQFILE_PER_CHANNEL:
             inst_name = wire.transmitter.label
             chan_name = wire.label
             has_non_id_pulses = any([len([p for p in ps if isinstance(p,Pulse) and p.label!="Id"]) > 0 for ps in pulses])
-            label_to_inst[wire.label] = inst_name
+            extra_info["label_to_inst"][wire.label] = inst_name
             if has_non_id_pulses:
-                label_to_chan[wire.label] = chan_name
+                extra_info["label_to_chan"][wire.label] = chan_name
             # Change the name/inst for uniqueness, but we must restore this later!
-            old_wire_names[wire] = wire.label
-            old_wire_instrs[wire] = wire.instrument
+            extra_info["old_wire_names"][wire] = wire.label
+            extra_info["old_wire_instrs"][wire] = wire.instrument
             wire.instrument = wire.label
             wire.label = chan_name
-            #files[inst_name] = {}
+            extra_info["files"][inst_name] = {}
 
     # construct channel delay map
     logger.info("Constructing delay map.")
@@ -479,7 +485,7 @@ def compile_to_IR(seqs, add_slave_trigger=True, tdm_seq=False, random_cliffords=
     # on whether we have one sequence per channel
     logger.info("Bundling wires.")
     awgData = bundle_wires(physWires, wfs)
-    return awgData
+    return awgData, extra_info
 
 def compile_to_hardware(seqs,
                         fileName,
@@ -505,9 +511,15 @@ def compile_to_hardware(seqs,
         tdm_seq (optional): compile for TDM
     '''
     # save input code to file
+
     save_code(seqs, fileName + suffix)
 
-    awgData = compile_to_IR(seqs, add_slave_trigger=add_slave_trigger, tdm_seq=tdm_seq)
+    if any([p.isRunTime for p in flatten(seqs)]):
+        random_cliffords = True
+    else:
+        random_cliffords = False
+
+    awgData, extra_info = compile_to_IR(seqs, add_slave_trigger=add_slave_trigger, tdm_seq=tdm_seq, random_cliffords=random_cliffords)
 
     # convert to hardware formats
     # files = {}
@@ -529,11 +541,11 @@ def compile_to_hardware(seqs,
             ChannelLibraries.channelLib[awgName].extra_meta = new_meta
 
         # Allow for per channel and per AWG seq files
-        if awgName in label_to_inst:
-            if awgName in label_to_chan:
-                files[label_to_chan[awgName]] = fullFileName
+        if awgName in extra_info["label_to_inst"]:
+            if awgName in extra_info["label_to_chan"]:
+                files[extra_info["label_to_inst"][awgName]][extra_info["label_to_chan"][awgName]] = fullFileName
         else:
-            files[awgName] = fullFileName
+            extra_info["files"][awgName] = fullFileName
 
         del data
         del awgData[awgName]
@@ -563,21 +575,21 @@ def compile_to_hardware(seqs,
         axis_descriptor = [{
             'name': 'segment',
             'unit': None,
-            'points': list(range(1, 1 + num_measurements)),
+            'points': list(range(1, 1 + extra_info["num_measurements"])),
             'partition': 1
         }]
     receiver_measurements = {}
-    for wire, n in wire_measurements.items():
+    for wire, n in extra_info["wire_measurements"].items():
         if wire.receiver_chan and n>0:
             receiver_measurements[wire.receiver_chan.label] = n
     meta = {
         'database_info': db_info,
-        'instruments': files,
+        'instruments': extra_info["files"],
         'num_sequences': len(seqs),
-        'num_measurements': num_measurements,
+        'num_measurements': extra_info["num_measurements"],
         'axis_descriptor': axis_descriptor,
-        'qubits': [c.label for c in channels if isinstance(c, Channels.Qubit)],
-        'measurements': [c.label for c in channels if isinstance(c, Channels.Measurement)],
+        'qubits': [c.label for c in extra_info["channels"] if isinstance(c, Channels.Qubit)],
+        'measurements': [c.label for c in extra_info["channels"] if isinstance(c, Channels.Measurement)],
         'receivers': receiver_measurements
     }
     if extra_meta:
@@ -587,10 +599,10 @@ def compile_to_hardware(seqs,
         json.dump(meta, FID, indent=2, sort_keys=True)
 
     # Restore the wire info
-    for wire in old_wire_names.keys():
-        wire.label = old_wire_names[wire]
-    for wire in old_wire_instrs.keys():
-        wire.instrument = old_wire_instrs[wire]
+    for wire in extra_info["old_wire_names"].keys():
+        wire.label = extra_info["old_wire_names"][wire]
+    for wire in extra_info["old_wire_instrs"].keys():
+        wire.instrument = extra_info["old_wire_instrs"][wire]
 
     # Return the filenames we wrote
     return metafilepath

From dba195f27bcf1611f5c4a5059f87f47cb4d61301 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Fri, 26 Apr 2019 16:06:16 -0400
Subject: [PATCH 220/235] Add python egg file to gitignore

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index fcfad9a8..7150e5b0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,5 @@
 *.h5
 *.py~
 *.py#
+*.egg-info
+QGL.egg-info/

From dcde87bdc6705f264c5e4dba4af7bc4649827c3c Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Fri, 26 Apr 2019 16:07:25 -0400
Subject: [PATCH 221/235] Update Inverse Reset instruction sequence.

---
 QGL/APS2CustomInstructions.py | 7 +++++--
 QGL/RandomCliffordTools.py    | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index ae9c4221..9b8268f9 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -69,8 +69,11 @@ def RandomCliffordInverse(target, addr):
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
             Call(target, indirect=True)]
 
-def RandomCliffordInverseReset(addr): #for now don't use addr
-    return CustomInstruction("APS_CLIFFORD_INVERSE_RESET", 0x0, 0xF)
+def RandomCliffordInverseReset(val=0x0, addr=0xD): #for now don't use addr
+    return [Invalidate(addr, 0, tdm=False),
+            WriteAddr(addr, val, tdm=False),
+            LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
+            CustomInstruction("APS_CLIFFORD_INVERSE_RESET", addr, 0xA)]
 
 def RandomCliffordSeed(seed):
     return [Invalidate(0xB, 0, tdm=False),
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index 9317b3e2..82288031 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -60,7 +60,7 @@ def generate_clifford_jump_table(cliff_wires, jt_label = None):
     return jt_label
 
 def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
-                            inv_addr=0x3, inv_values=[],
+                            inv_addr=0x4, inv_values=[],
                             clifford_options=default_clifford_options):
 
     if jt_label is None:

From 8c6630bd65ed720f4bd7930395bc5476714f886e Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Fri, 26 Apr 2019 16:08:56 -0400
Subject: [PATCH 222/235] Output label names and address for debug.

---
 QGL/drivers/APS2Pattern.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index c5b0762f..a833780f 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1034,7 +1034,7 @@ def resolve_symbols(seq):
 
     labeled_entries = [(idx, entry.label) for idx, entry in enumerate(seq) if entry.label is not None]
     symbols = {label: idx for idx, label in labeled_entries}
-    #print(f"Found labels: {symbols}")
+    logger.info(f"Found labels: {symbols}")
     for entry in seq:
         if entry.target is not None and entry.target in symbols.keys():
             entry.address = symbols[entry.target]

From e7b6aacf1a3359d142ffdab691aeb8534c9b4b07 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Fri, 19 Jul 2019 19:15:50 -0400
Subject: [PATCH 223/235] Add RandomClifford to set of random pulses. -GR

---
 QGL/Compiler.py            |  2 +-
 QGL/PulsePrimitives.py     | 12 ++++++++++--
 QGL/RandomCliffordTools.py |  2 +-
 QGL/drivers/APS2Pattern.py |  1 +
 4 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 04a6bfe8..612357bd 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -236,7 +236,7 @@ def generate_waveforms(physicalWires):
                     wfs[ch][pulse.hashshape()] = pulse.shape
     return wfs
 
-def get_clifford_type(wire, allowed_types=("RandomAC")):
+def get_clifford_type(wire, allowed_types=("RandomAC", "RandomClifford")):
     rt_pulses = []
     for pulse in flatten(wire):
         if isinstance(pulse, Pulse) and pulse.isRunTime:
diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index a648e044..a4c879a3 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -24,7 +24,6 @@
 from .PulseSequencer import Pulse, TAPulse, CompoundGate, align
 from functools import wraps, reduce
 
-
 def overrideDefaults(chan, updateParams, ignoredStrParams=['isRunTime', 'maddr', 'moffset']):
     '''Helper function to update any parameters passed in and fill in the defaults otherwise.'''
     # The default parameter list depends on the channel type so pull out of channel
@@ -116,7 +115,7 @@ def Utheta(qubit,
         else:
             # linearly scale based upon the 'pi/2' amplitude
             amp  = (angle / (pi/2)) * qubit.pulse_params['pi2Amp']
-    return Pulse(label, qubit, params, amp, phase, 0.0, ignoredStrParams, frequency=frequency, **kwargs)
+    return Pulse(label, qubit, params, amp, phase, 0.0, ignoredStrParams, frequency=frequency)
 
 
 # generic pulses around X, Y, and Z axes
@@ -340,6 +339,10 @@ def arb_axis_drag(qubit,
     return Pulse(kwargs["label"] if "label" in kwargs else "ArbAxis", qubit,
                  params, 1.0, aziAngle, frameChange)
 
+def RandomClifford(qubit):
+    params = overrideDefaults(qubit, {})
+    return Pulse("RandomClifford", qubit, params, isRunTime=True)
+
 def RandomAC(qubit):
     params = overrideDefaults(qubit, {})
     return Pulse("RandomAC", qubit, params, isRunTime=True)
@@ -349,6 +352,11 @@ def RandomDiAC(qubit):
     params["length"] *= 2.0
     return Pulse("RandomDiAC", qubit, params, isRunTime=True)
 
+from . import Cliffords
+
+def Clifford(qubit, cliffNum):
+    return reduce(operator.add, [p for p in Cliffords.clifford_seq(cliffNum, qubit)])
+
 def AC(qubit, cliffNum):
     """
 
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index 82288031..6d202835 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -35,7 +35,7 @@
 
 default_clifford_options = {"offset": 0x0, "spacing": 0x1, "seed": 0x31}
 
-VALID_CLIFFORD_TYPES = ('RandomAC',)
+VALID_CLIFFORD_TYPES = ('RandomAC', 'RandomClifford')
 
 def generate_clifford_jump_table(cliff_wires, jt_label = None):
     """Generate the jump table that will be used to call into the clifford set"""
diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index a833780f..20bb84fc 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -652,6 +652,7 @@ def inject_modulation_cmds(seqs):
 
         mod_seq = []
         pending_frame_update = False
+        force_phase_update = False
 
         #check to see if we are in a subroutine by using last instruction as return as a tell
         #if so, ensure frame updates do not get dropped

From e44559201c988c6c54d02851003f5919e8819e6b Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Wed, 24 Jul 2019 17:18:40 -0400
Subject: [PATCH 224/235] Revert 4-NCO changes to APS2Pattern.py

---
 QGL/drivers/APS2Pattern.py | 29 +++++++++++------------------
 1 file changed, 11 insertions(+), 18 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 20bb84fc..863e78ae 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -599,19 +599,13 @@ def to_instruction(self, write_flag=True, label=None):
         NCO_SELECT_OP_OFFSET = 40
         MODULATION_CLOCK = 300e6
 
-        nco_select_bits = {1 : 0b0001,
-                           2 : 0b0010,
-                           3 : 0b0100,
-                           4 : 0b1000,
-                           15: 0b1111}[self.nco_select]
-
         op_code_map = {"MODULATE": 0x0,
                        "RESET_PHASE": 0x2,
                        "SET_FREQ": 0x6,
                        "SET_PHASE": 0xa,
                        "UPDATE_FRAME": 0xe}
         payload = (op_code_map[self.instruction] << MODULATOR_OP_OFFSET) | (
-            (nco_select_bits) << NCO_SELECT_OP_OFFSET)
+            (self.nco_select) << NCO_SELECT_OP_OFFSET)
         if self.instruction == "MODULATE":
             #zero-indexed quad count
             payload |= np.uint32(self.length / ADDRESS_UNIT - 1)
@@ -639,9 +633,9 @@ def inject_modulation_cmds(seqs):
     for ct,seq in enumerate(seqs):
         #check whether we have modulation commands
         freqs = np.unique([entry.frequency for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)])
-        if len(freqs) > NUM_NCO:
-            raise Exception("Max {} frequencies on the same channel allowed.".format(NUM_NCO))
-        no_freq_cmds = np.allclose(freqs, 0)
+        if len(freqs) > 2:
+            raise Exception("Max {} frequencies on the same channel allowed.".format(2))
+        no_freq_cmds = np.all(np.less(np.abs(freqs), 1e-8))
         phases = [entry.phase for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
         no_phase_cmds = np.all(np.less(np.abs(phases), 1e-8))
         frame_changes = [entry.frameChange for entry in filter(lambda s: isinstance(s,Compiler.Waveform), seq)]
@@ -670,7 +664,7 @@ def inject_modulation_cmds(seqs):
                 #heuristic to insert phase reset before trigger if we have modulation commands
                 if isinstance(entry, ControlFlow.Wait):
                     if not ( no_modulation_cmds and (cur_freq == 0) and (cur_phase == 0)):
-                        mod_seq.append(ModulationCommand("RESET_PHASE", 0xF))
+                        mod_seq.append(ModulationCommand("RESET_PHASE", 0x3))
                         for nco_ind, freq in enumerate(freqs):
                             mod_seq.append( ModulationCommand("SET_FREQ", nco_ind + 1, frequency = -freq) )
                 elif isinstance(entry, ControlFlow.Return):
@@ -1191,13 +1185,12 @@ def start_new_seq():
         instructions = np.frombuffer(FID.read(8*inst_len), dtype=np.uint64)
 
         wf_lib = {}
-        wf_lib['ch1'] = (
-            1.0 /
-            MAX_WAVEFORM_VALUE) * FID['/chan_1/waveforms'].value.flatten()
-        wf_lib['ch2'] = (
-            1.0 /
-            MAX_WAVEFORM_VALUE) * FID['/chan_2/waveforms'].value.flatten()
-        instructions = FID['/chan_1/instructions'].value.flatten()
+        for i in range(num_chans):
+            wf_len = struct.unpack('<Q', FID.read(8))[0]
+            wf_dat = np.frombuffer(FID.read(2*wf_len), dtype=np.int16)
+            wf_lif[f'ch{i+1}'] = ( 1.0 / MAX_WAVEFORM_VALUE) * wf_dat.flatten()
+
+        NUM_NCO = 2
         freq = np.zeros(NUM_NCO)  #radians per timestep
         phase = np.zeros(NUM_NCO)
         frame = np.zeros(NUM_NCO)

From 86566f448db6fc532e02b486423fb094222b4380 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Wed, 24 Jul 2019 17:20:26 -0400
Subject: [PATCH 225/235] Remove RandomClifford name collison

---
 QGL/Compiler.py            | 4 ++--
 QGL/PulsePrimitives.py     | 4 ++--
 QGL/RandomCliffordTools.py | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index 612357bd..a104e066 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -37,7 +37,7 @@
 from . import BlockLabel
 from . import TdmInstructions # only for APS2-TDM
 from . import APS2CustomInstructions
-from .RandomCliffordTools import default_clifford_options
+from .RandomCliffordTools import default_clifford_options, VALID_CLIFFORD_TYPES
 from . import RandomCliffordTools
 import gc
 
@@ -236,7 +236,7 @@ def generate_waveforms(physicalWires):
                     wfs[ch][pulse.hashshape()] = pulse.shape
     return wfs
 
-def get_clifford_type(wire, allowed_types=("RandomAC", "RandomClifford")):
+def get_clifford_type(wire, allowed_types=VALID_CLIFFORD_TYPES):
     rt_pulses = []
     for pulse in flatten(wire):
         if isinstance(pulse, Pulse) and pulse.isRunTime:
diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index a4c879a3..5627d6d3 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -339,9 +339,9 @@ def arb_axis_drag(qubit,
     return Pulse(kwargs["label"] if "label" in kwargs else "ArbAxis", qubit,
                  params, 1.0, aziAngle, frameChange)
 
-def RandomClifford(qubit):
+def RandomCliff(qubit):
     params = overrideDefaults(qubit, {})
-    return Pulse("RandomClifford", qubit, params, isRunTime=True)
+    return Pulse("RandomCliff", qubit, params, isRunTime=True)
 
 def RandomAC(qubit):
     params = overrideDefaults(qubit, {})
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index 6d202835..df848aa2 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -35,7 +35,7 @@
 
 default_clifford_options = {"offset": 0x0, "spacing": 0x1, "seed": 0x31}
 
-VALID_CLIFFORD_TYPES = ('RandomAC', 'RandomClifford')
+VALID_CLIFFORD_TYPES = ('RandomAC', 'RandomCliff')
 
 def generate_clifford_jump_table(cliff_wires, jt_label = None):
     """Generate the jump table that will be used to call into the clifford set"""

From 2589b4426a384448c1adbbf1392dccc0044ebacd Mon Sep 17 00:00:00 2001
From: Matthew Ware <matt.ware@raytheon.com>
Date: Thu, 25 Jul 2019 10:27:49 -0400
Subject: [PATCH 226/235] typo in APS2pattern.py  -MW

---
 QGL/drivers/APS2Pattern.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 863e78ae..f5ff31de 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1188,7 +1188,7 @@ def start_new_seq():
         for i in range(num_chans):
             wf_len = struct.unpack('<Q', FID.read(8))[0]
             wf_dat = np.frombuffer(FID.read(2*wf_len), dtype=np.int16)
-            wf_lif[f'ch{i+1}'] = ( 1.0 / MAX_WAVEFORM_VALUE) * wf_dat.flatten()
+            wf_lib[f'ch{i+1}'] = ( 1.0 / MAX_WAVEFORM_VALUE) * wf_dat.flatten()
 
         NUM_NCO = 2
         freq = np.zeros(NUM_NCO)  #radians per timestep

From 8fd7909049cf7a4db2d51feea71a065c6ea6f500 Mon Sep 17 00:00:00 2001
From: Matthew Ware <matt.ware@raytheon.com>
Date: Thu, 25 Jul 2019 10:31:52 -0400
Subject: [PATCH 227/235] Let's be honest about what we're doing  -MW

---
 QGL/drivers/APS2Pattern.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index f5ff31de..669f4563 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -1,5 +1,5 @@
 '''
-Module for writing hdf5 APS2 files from sequences and patterns
+Module for writing .aps APS2 files from sequences and patterns
 
 Copyright 2014 Raytheon BBN Technologies
 
@@ -1158,7 +1158,7 @@ def write_sequence_file(awgData, fileName):
 
 def read_sequence_file(fileName):
     """
-    Reads a HDF5 sequence file and returns a dictionary of lists.
+    Reads a .aps sequence file and returns a dictionary of lists.
     Dictionary keys are channel strings such as ch1, m1
     Lists are or tuples of time-amplitude pairs (time, output)
     """

From 4a53e7bc8b3b12af522f1854ac3d305654e7f187 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Mon, 29 Jul 2019 13:36:18 -0400
Subject: [PATCH 228/235] Load to comparison register after custom instruction
 to block sequencer.

---
 QGL/APS2CustomInstructions.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/QGL/APS2CustomInstructions.py b/QGL/APS2CustomInstructions.py
index 9b8268f9..971bd16b 100644
--- a/QGL/APS2CustomInstructions.py
+++ b/QGL/APS2CustomInstructions.py
@@ -49,13 +49,15 @@ def RandomCliffordSetOffset(addr, offset):
     return [Invalidate(addr, 0, tdm=False),
             WriteAddr(addr, offset, tdm=False),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False), #
-            CustomInstruction("APS_CLIFFORD_SET_OFFSET", addr, 0xA)]
+            CustomInstruction("APS_CLIFFORD_SET_OFFSET", addr, 0xA),
+            LoadCmpVram(0xA, 0xFFFFFFFF, tdm=False)]
 
 def RandomCliffordSetSpacing(addr, spacing):
     return [Invalidate(addr, 0, tdm=False),
             WriteAddr(addr, spacing, tdm=False),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
-            CustomInstruction("APS_CLIFFORD_SET_SPACING", addr, 0xA)]
+            CustomInstruction("APS_CLIFFORD_SET_SPACING", addr, 0xA),
+            LoadCmpVram(0xA, 0xFFFFFFFF, tdm=False)]
 
 def RandomClifford(target, addr):
     return [Invalidate(addr, 0, tdm=False),
@@ -73,10 +75,12 @@ def RandomCliffordInverseReset(val=0x0, addr=0xD): #for now don't use addr
     return [Invalidate(addr, 0, tdm=False),
             WriteAddr(addr, val, tdm=False),
             LoadCmpVram(addr, 0xFFFFFFFF, tdm=False),
-            CustomInstruction("APS_CLIFFORD_INVERSE_RESET", addr, 0xA)]
+            CustomInstruction("APS_CLIFFORD_INVERSE_RESET", addr, 0xA),
+            LoadCmpVram(0xA, 0xFFFFFFFF, tdm=False)]
 
 def RandomCliffordSeed(seed):
     return [Invalidate(0xB, 0, tdm=False),
         WriteAddr(0xB, seed, tdm=False),
         LoadCmpVram(0xB, 0xFFFFFFFF, tdm=False),
-        CustomInstruction("APS_CLIFFORD_SET_SEED", 0xB, 0xA)]
+        CustomInstruction("APS_CLIFFORD_SET_SEED", 0xB, 0xA),
+        LoadCmpVram(0xA, 0xFFFFFFFF, tdm=False)]

From fa544b83af70268a3fadb74bcd620ef2abebb998 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Mon, 29 Jul 2019 13:37:27 -0400
Subject: [PATCH 229/235] Add explicit random inverse pulse.

---
 QGL/Compiler.py            |  2 ++
 QGL/RandomCliffordTools.py | 26 +++++++++++++++-----------
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index a104e066..c41e64f1 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -249,6 +249,8 @@ def get_clifford_type(wire, allowed_types=VALID_CLIFFORD_TYPES):
     if len(rt_pulses) == 0:
         return None
     pulse_type = list(set([pulse.label for pulse in rt_pulses]))
+    if 'RandomInverse' in pulse_type:
+        pulse_type.remove('RandomInverse')
     pulse_logical_chan = list(set([pulse.channel for pulse in rt_pulses]))
     if len(pulse_type) > 1:
         raise Exception(f"All run-time pulses must have the same label. Found: {pulse_type}.")
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index df848aa2..a494364f 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -35,7 +35,7 @@
 
 default_clifford_options = {"offset": 0x0, "spacing": 0x1, "seed": 0x31}
 
-VALID_CLIFFORD_TYPES = ('RandomAC', 'RandomCliff')
+VALID_CLIFFORD_TYPES = ('RandomAC', 'RandomCliff', 'RandomTestCliff')
 
 def generate_clifford_jump_table(cliff_wires, jt_label = None):
     """Generate the jump table that will be used to call into the clifford set"""
@@ -80,10 +80,14 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
         new_seq = []
 
         for pulse in seq:
-            if isinstance(pulse, Pulse) and pulse.isRunTime \
-                and pulse.label in VALID_CLIFFORD_TYPES:
-                has_random_cliff = True
-                new_seq.extend(RandomClifford(jt_label, cliff_addr))
+            if isinstance(pulse, Pulse) and pulse.isRunTime:
+                if pulse.label in VALID_CLIFFORD_TYPES:
+                    has_random_cliff = True
+                    new_seq.extend(RandomClifford(jt_label, cliff_addr))
+                elif pulse.label == 'RandomInverse':
+                    new_seq.extend(RandomCliffordInverse(jt_label, inv_addr))
+                else:
+                    raise Exception(f"Unhandled run-time pulse: {pulse.label}")
                 #print("Inserting clifford pulse!")
             else:
                 new_seq.append(pulse)
@@ -94,14 +98,14 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
         #     new_seq[0:0] = info_seqs
 
         if add_inv:
-            #insert reset after first wait
+            #insert reset before first wait
             w_idx = next(i for i, v in enumerate(new_seq) if isinstance(v, ControlFlow.Wait))
-            new_seq.insert(w_idx+1, RandomCliffordInverseReset(0x0))
+            new_seq.insert(w_idx, RandomCliffordInverseReset(0x0))
             #insert at end of sequence or before last GOTO
-            if isinstance(new_seq[-1], ControlFlow.Goto):
-                  new_seq[-1:-1] = RandomCliffordInverse(jt_label, inv_addr)
-            else:
-                  new_seq.extend(RandomCliffordInverse(jt_label, inv_addr))
+            #if isinstance(new_seq[-1], ControlFlow.Goto):
+            #      new_seq[-1:-1] = RandomCliffordInverse(jt_label, inv_addr)
+            #else:
+            #      new_seq.extend(RandomCliffordInverse(jt_label, inv_addr))
 
         seqs[idx] = new_seq
 

From 751345142bc48854f92eb47875536027e0ad886b Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Mon, 29 Jul 2019 13:38:42 -0400
Subject: [PATCH 230/235] Add TestClifford pulse for testing randomizer output.

---
 QGL/PulsePrimitives.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index 5627d6d3..4efd5f6c 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -352,9 +352,23 @@ def RandomDiAC(qubit):
     params["length"] *= 2.0
     return Pulse("RandomDiAC", qubit, params, isRunTime=True)
 
+def RandomInverse(qubit):
+    params = overrideDefaults(qubit, {})
+    return Pulse("RandomInverse", qubit, params, isRunTime=True)
+
 from . import Cliffords
 
-def Clifford(qubit, cliffNum):
+def RandomTestCliff(qubit):
+    params = overrideDefaults(qubit, {})
+    return Pulse("RandomTestCliff", qubit, params, isRunTime=True)
+
+def TestCliff(qubit, cliffNum):
+    params = overrideDefaults(qubit, {'shape_fun': 'constant'})
+    amp = cliffNum * (1.0/24.0) + (1.0/24.0)
+    return Pulse("TCPulse", qubit, params, amp, 0.0, 0.0, frequency=0.0)
+
+
+def Cliff(qubit, cliffNum):
     return reduce(operator.add, [p for p in Cliffords.clifford_seq(cliffNum, qubit)])
 
 def AC(qubit, cliffNum):

From ab5b379f9daa9736e66714f25cfc8e0593b9c37c Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Mon, 29 Jul 2019 13:39:15 -0400
Subject: [PATCH 231/235] Restore sequence file viewer code that got nuked at
 some point

---
 QGL/drivers/APS2Pattern.py | 123 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 122 insertions(+), 1 deletion(-)

diff --git a/QGL/drivers/APS2Pattern.py b/QGL/drivers/APS2Pattern.py
index 669f4563..6ece1645 100644
--- a/QGL/drivers/APS2Pattern.py
+++ b/QGL/drivers/APS2Pattern.py
@@ -98,7 +98,7 @@
 
 # Whether we use PHASE_OFFSET modulation commands or bake it into waveform
 # Default to false as we usually don't have many variants
-USE_PHASE_OFFSET_INSTRUCTION = True
+USE_PHASE_OFFSET_INSTRUCTION = False
 
 # Whether to save the waveform offsets for partial compilation
 SAVE_WF_OFFSETS = False
@@ -1557,3 +1557,124 @@ def display_raw_instructions(raw):
 def display_raw_file(filename):
     raw = raw_instructions(filename)
     display_raw_instructions(raw)
+
+if __name__ == '__main__':
+    if len(sys.argv) == 2:
+
+        from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QTableWidget, QTableWidgetItem, QVBoxLayout, QAbstractItemView, QPushButton
+        from PyQt5.QtGui import QIcon, QColor, QFont
+
+        from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg
+        from matplotlib.figure import Figure
+
+        table_font = QFont("Arial", weight=QFont.Bold)
+
+        colors = {"WFM": QColor(0,200,0),
+                  "GOTO": QColor(0,100,100),
+                  "MARKER": QColor(150,150,200)}
+
+        class MatplotlibWidget(QWidget):
+            def __init__(self, I, Q, parent=None):
+                super(MatplotlibWidget, self).__init__(parent)
+                self.title = 'Waveform'
+                self.left = 100
+                self.top = 100
+                self.width = 800
+                self.height = 600
+                self.setWindowTitle(self.title)
+                self.setGeometry(self.left, self.top, self.width, self.height)
+
+                self.figure = Figure()
+                self.canvas = FigureCanvasQTAgg(self.figure)
+
+                self.axis = self.figure.add_subplot(111)
+                self.axis.plot(I)
+                self.axis.plot(Q)
+                self.layout = QVBoxLayout(self)
+                self.layout.addWidget(self.canvas)
+                self.setLayout(self.layout)
+                self.canvas.draw()
+                self.show()
+
+
+        class App(QWidget):
+
+            COLUMN_COUNT = 7
+            def __init__(self, instructions, waveforms):
+                super().__init__()
+                self.title = 'APS2 Disassembled Instructions'
+                self.left = 100
+                self.top = 100
+                self.width = 1000
+                self.height = 1200
+                self.instructions = instructions
+                self.waveforms = waveforms
+                print(self.waveforms)
+                self.initUI()
+                self.plotters = []
+
+            def initUI(self):
+                self.setWindowTitle(self.title)
+                self.setGeometry(self.left, self.top, self.width, self.height)
+
+                self.createTable()
+                self.layout = QVBoxLayout()
+                self.layout.addWidget(self.tableWidget)
+                self.setLayout(self.layout)
+
+                # Show widget
+                self.show()
+
+            def createTable(self):
+               # Create table
+                self.tableWidget = QTableWidget()
+                self.tableWidget.setRowCount(len(self.instructions))
+                self.tableWidget.setColumnCount(7)
+
+                for k, instr in enumerate(self.instructions):
+                    fields = str(instr).replace(',','').replace(';', '').split(" ")
+                    if "|" in fields:
+                        fields.remove("|")
+                    if fields[0] in colors:
+                        color = colors[fields[0]]
+                    else:
+                        color = None
+                    for l, f in enumerate(fields):
+                        text = fields[l]
+                        if text == "GOTO":
+                            btn = QPushButton(self.tableWidget)
+                            btn.setText('GOTO')
+                            target_row = int(fields[1].split("=")[1])
+                            def scroll_to_goto_target(row=target_row, tab=self.tableWidget):
+                                tab.scrollToItem(tab.item(row, 0))
+                            btn.clicked.connect(scroll_to_goto_target)
+                            self.tableWidget.setCellWidget(k, l, btn)
+                        if text == "WFM" and int(fields[4].split("=")[1])==0:
+                            # Not a TA pair
+                            btn = QPushButton(self.tableWidget)
+                            btn.setText('WFM')
+                            addr = int(fields[6].split("=")[1])
+                            count = int(fields[5].split("=")[1])
+                            def open_plotter(addr=None, I=self.waveforms[0][addr:addr+count], Q=self.waveforms[1][addr:addr+count]):
+                                w = MatplotlibWidget(I,Q)
+                                self.plotters.append(w)
+                            btn.clicked.connect(open_plotter)
+                            self.tableWidget.setCellWidget(k, l, btn)
+                        else:
+                            item = QTableWidgetItem(text)
+                            item.setFont(table_font)
+                            if color:
+                                item.setBackground(color)
+                            self.tableWidget.setItem(k, l, item)
+                    if l < self.COLUMN_COUNT-1:
+                        for j in range(l+1, self.COLUMN_COUNT):
+                            item = QTableWidgetItem("")
+                            if color:
+                                item.setBackground(color)
+                            self.tableWidget.setItem(k, j, item)
+                self.tableWidget.move(0,0)
+                self.tableWidget.setSelectionBehavior(QAbstractItemView.SelectRows)
+
+        app = QApplication(sys.argv[:1])
+        ex = App(read_instructions(sys.argv[1]), read_waveforms(sys.argv[1]))
+        sys.exit(app.exec_())

From 1cdf53b4b4f6e5163a16cc7cc00e8569158f47e4 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 29 Jul 2019 13:59:49 -0400
Subject: [PATCH 232/235] Add ability to reset inverse tracker to other than
 identity.

---
 QGL/Compiler.py            |  7 +++++--
 QGL/PulsePrimitives.py     | 22 +++++++++++++++++++++-
 QGL/RandomCliffordTools.py | 18 +++++-------------
 3 files changed, 31 insertions(+), 16 deletions(-)

diff --git a/QGL/Compiler.py b/QGL/Compiler.py
index c41e64f1..f6538f88 100644
--- a/QGL/Compiler.py
+++ b/QGL/Compiler.py
@@ -249,8 +249,11 @@ def get_clifford_type(wire, allowed_types=VALID_CLIFFORD_TYPES):
     if len(rt_pulses) == 0:
         return None
     pulse_type = list(set([pulse.label for pulse in rt_pulses]))
-    if 'RandomInverse' in pulse_type:
-        pulse_type.remove('RandomInverse')
+    #Remove pulses that are not the actual cliffords we want to play.
+    #We assume the RandomInverse is of the same type as the RandomCliffords!
+    for p in ('RandomInverse', 'RandomInverseReset'):
+        if p in pulse_type:
+            pulse_type.remove(p)
     pulse_logical_chan = list(set([pulse.channel for pulse in rt_pulses]))
     if len(pulse_type) > 1:
         raise Exception(f"All run-time pulses must have the same label. Found: {pulse_type}.")
diff --git a/QGL/PulsePrimitives.py b/QGL/PulsePrimitives.py
index 4efd5f6c..b9d66f2a 100644
--- a/QGL/PulsePrimitives.py
+++ b/QGL/PulsePrimitives.py
@@ -340,22 +340,43 @@ def arb_axis_drag(qubit,
                  params, 1.0, aziAngle, frameChange)
 
 def RandomCliff(qubit):
+    """A randomly generated clifford gate, using the standard clifford library.
+    """
     params = overrideDefaults(qubit, {})
     return Pulse("RandomCliff", qubit, params, isRunTime=True)
 
 def RandomAC(qubit):
+    """A randomly generated clifford gate, using the diatomic clifford library.
+    """
     params = overrideDefaults(qubit, {})
     return Pulse("RandomAC", qubit, params, isRunTime=True)
 
 def RandomDiAC(qubit):
+    """A randomly generated clifford gate, using the atomic clifford library.
+    """
     params = overrideDefaults(qubit, {})
     params["length"] *= 2.0
     return Pulse("RandomDiAC", qubit, params, isRunTime=True)
 
 def RandomInverse(qubit):
+    """The currently-stored `Inverse` clifford generated by the on-board frame
+        tracking hardware.
+    """
     params = overrideDefaults(qubit, {})
     return Pulse("RandomInverse", qubit, params, isRunTime=True)
 
+def RandomInverseReset(qubit, reset_value=0):
+    """Reset the on-board frame tracker to the given value (clifford index).
+    NOTE: Because of potential timing issues with the random clifford firmware,
+    this "pulse" will be played in the "dead time" between sequences (i.e.
+    BEFORE the first WAIT of a sequence.) No guarantees as to what will happen if
+    you try to put this pulse inside of a sequence...
+    """
+    params = overrideDefaults(qubit, {})
+    #note that we store the reset value in the `maddr` paramter, otherwise unused
+    #TODO: this is a bit hacky and should probably be changed.
+    return Pulse("RandomInverseReset", qubit, params, isRunTime=True, maddr=reset_value)
+
 from . import Cliffords
 
 def RandomTestCliff(qubit):
@@ -367,7 +388,6 @@ def TestCliff(qubit, cliffNum):
     amp = cliffNum * (1.0/24.0) + (1.0/24.0)
     return Pulse("TCPulse", qubit, params, amp, 0.0, 0.0, frequency=0.0)
 
-
 def Cliff(qubit, cliffNum):
     return reduce(operator.add, [p for p in Cliffords.clifford_seq(cliffNum, qubit)])
 
diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index a494364f..8fae9f73 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -78,6 +78,7 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
             continue
 
         new_seq = []
+        inverse_val = 0
 
         for pulse in seq:
             if isinstance(pulse, Pulse) and pulse.isRunTime:
@@ -86,29 +87,20 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
                     new_seq.extend(RandomClifford(jt_label, cliff_addr))
                 elif pulse.label == 'RandomInverse':
                     new_seq.extend(RandomCliffordInverse(jt_label, inv_addr))
+                elif pulse.label == 'RandomInverseReset':
+                    inverse_val = pulse.maddr
                 else:
                     raise Exception(f"Unhandled run-time pulse: {pulse.label}")
                 #print("Inserting clifford pulse!")
             else:
                 new_seq.append(pulse)
 
-        # if isinstance(seq[0], BlockLabel.BlockLabel):
-        #     new_seq[1:1] = info_seqs
-        # else:
-        #     new_seq[0:0] = info_seqs
-
         if add_inv:
-            #insert reset before first wait
             w_idx = next(i for i, v in enumerate(new_seq) if isinstance(v, ControlFlow.Wait))
-            new_seq.insert(w_idx, RandomCliffordInverseReset(0x0))
-            #insert at end of sequence or before last GOTO
-            #if isinstance(new_seq[-1], ControlFlow.Goto):
-            #      new_seq[-1:-1] = RandomCliffordInverse(jt_label, inv_addr)
-            #else:
-            #      new_seq.extend(RandomCliffordInverse(jt_label, inv_addr))
-
+            new_seq.insert(w_idx, RandomCliffordInverseReset(val=inverse_val))
         seqs[idx] = new_seq
 
+    #Helper "sequence" to set the random clifford settings.
     info_seqs = []
     info_seqs.extend(RandomCliffordSetOffset(0x1, clifford_options["offset"]))
     info_seqs.extend(RandomCliffordSetSpacing(0x2, clifford_options["spacing"]))

From 602dd1f819466d7818332104b9571602aa77bcd7 Mon Sep 17 00:00:00 2001
From: gribeill <guilhem.ribeill@gmail.com>
Date: Mon, 29 Jul 2019 14:18:17 -0400
Subject: [PATCH 233/235] Update random clifford sequence builder

---
 QGL/RandomCliffordTools.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index 8fae9f73..ebcfcfaa 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -108,8 +108,14 @@ def insert_clifford_calls(seqs, jt_label=None, cliff_addr=0x3, add_inv = True,
     seqs.insert(0, info_seqs)
 
 
-def randomize_clifford_sequences(qubit, seqs, clifford_type=PulsePrimitives.RandomAC):
-
-    c_seqs = [[clifford_type(qubit) for _ in seq] for seq in seqs]
-    inverses = [inverse_clifford(C1[reduce(clifford_multiply, seq)]) for seq in seqs]
-    return c_seqs, inverses
+def randomize_clifford_sequences(qubit, seqs, clifford_type=PulsePrimitives.RandomCliff):
+    """Randomize a sequence of cliffords (given as integers).
+    """
+    rseqs = []
+    for seq in seqs:
+        inverse = reduce(clifford_multiply, seq)
+        rseq = ([PulsePrimitives.RandomCliffordInverse(qubit, reset_value=inverse)] +
+                [clifford_type(qubit)]*len(seq) +
+                [RandomInverse(qubit), MEAS(qubit)])
+        rseqs.append(rseq)
+    return rseqs

From eacf5beb9175c6bc63678079af40fbd8cddf6fd3 Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Thu, 25 Jul 2019 13:43:33 -0400
Subject: [PATCH 234/235] Modify GST code for newest pygsti stuff.

---
 QGL/GSTTools.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/QGL/GSTTools.py b/QGL/GSTTools.py
index 0052b1c6..49ad9749 100644
--- a/QGL/GSTTools.py
+++ b/QGL/GSTTools.py
@@ -28,7 +28,7 @@
 
 PYGSTI_PRESENT = False
 try:
-   from pygsti.objects import GateString
+   from pygsti.objects.circuit import Circuit
    PYGSTI_PRESENT = True
 except:
    pass
@@ -51,11 +51,11 @@ def gst_map_1Q(gst_list, qubit, qgl_map=gst_gate_map, append_meas=True):
     Returns:
         QGL sequences, preserving the input list nesting (as a generator)
     """
-    if isinstance(gst_list, GateString):
+    if isinstance(gst_list, Circuit):
         gst_list = [gst_list]
     for item in gst_list:
-        if isinstance(item, GateString):
-            mapped = map(lambda x: qgl_map[x](qubit), item.tup)
+        if isinstance(item, Circuit):
+            mapped = map(lambda x: qgl_map[str(x)](qubit), item.tup)
             if append_meas:
                 yield list(chain(mapped, [MEAS(qubit)]))
             else:

From 242118d6f680de457a2ca79672895b10d211854e Mon Sep 17 00:00:00 2001
From: Guilhem Ribeill <guilhem.ribeill@gmail.com>
Date: Thu, 29 Aug 2019 17:04:32 -0400
Subject: [PATCH 235/235] Support Random diatomic pulses

---
 QGL/RandomCliffordTools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QGL/RandomCliffordTools.py b/QGL/RandomCliffordTools.py
index ebcfcfaa..1f61c34e 100644
--- a/QGL/RandomCliffordTools.py
+++ b/QGL/RandomCliffordTools.py
@@ -35,7 +35,7 @@
 
 default_clifford_options = {"offset": 0x0, "spacing": 0x1, "seed": 0x31}
 
-VALID_CLIFFORD_TYPES = ('RandomAC', 'RandomCliff', 'RandomTestCliff')
+VALID_CLIFFORD_TYPES = ('RandomAC', 'RandomCliff', 'RandomTestCliff', 'RandomDiAC')
 
 def generate_clifford_jump_table(cliff_wires, jt_label = None):
     """Generate the jump table that will be used to call into the clifford set"""
@@ -114,7 +114,7 @@ def randomize_clifford_sequences(qubit, seqs, clifford_type=PulsePrimitives.Rand
     rseqs = []
     for seq in seqs:
         inverse = reduce(clifford_multiply, seq)
-        rseq = ([PulsePrimitives.RandomCliffordInverse(qubit, reset_value=inverse)] +
+        rseq = ([PulsePrimitives.RandomInverse(qubit, reset_value=inverse)] +
                 [clifford_type(qubit)]*len(seq) +
                 [RandomInverse(qubit), MEAS(qubit)])
         rseqs.append(rseq)