Update to MADSci v0.8

.pre-commit-config.yaml

@@ -12,12 +12,12 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.9.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.14.1
+    rev: v0.15.14
     hooks:
       # Run the linter.
       - id: ruff

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/ad-sdl/madsci
+FROM ghcr.io/ad-sdl/madsci:v0.8.0
 
 LABEL org.opencontainers.image.source=https://github.com/AD-SDL/ot2_module
 LABEL org.opencontainers.image.description="Drivers and REST API's for the Opentrons OT2 LiquidHandling robots"
@@ -13,10 +13,14 @@ RUN mkdir -p ot2_module
 COPY ./src ot2_module/src
 COPY ./README.md ot2_module/README.md
 COPY ./pyproject.toml ot2_module/pyproject.toml
-COPY ./tests ot2_module/tests
 
+# Install into the madsci venv (system pip would land in /usr/lib site-packages,
+# invisible to the venv interpreter the entrypoint actually runs).
 RUN --mount=type=cache,target=/root/.cache \
-    pip install -e ./ot2_module
+    uv pip install --python ${MADSCI_VENV}/bin/python -e ./ot2_module
+
+# Note: do not switch USER here — the base entrypoint runs userdel/useradd as
+# root to remap UID/GID to the host's, then drops to the madsci user itself.
 
 CMD ["python", "ot2_module/src/ot2_rest_node.py"]
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "ot2_module"
-version = "2.0.0"
+version = "2.0.1"
 description = "Software for automatting an OT2 liquid_handler"
 authors = [
     {name = "Ryan D. Lewis", email="ryan.lewis@anl.gov"},
@@ -9,11 +9,11 @@ authors = [
     {name = "Tobias Ginsburg", email = "tginsburg@anl.gov"},
 ]
 dependencies = [
-    "madsci.node_module~=0.5.0",
-    "madsci.client~=0.5.0",
-    "madsci.common~=0.5.0"
+    "madsci.node_module~=0.8.0",
+    "madsci.client~=0.8.0",
+    "madsci.common~=0.8.0"
 ]
-requires-python = ">=3.9.1"
+requires-python = ">=3.10"
 readme = "README.md"
 license = {text = "MIT"}
 

scripts/delete_all_runs.py

@@ -1,4 +1,5 @@
 """delete all runs"""
+
 from argparse import ArgumentParser
 
 import requests

src/ot2_interface/config.py

@@ -1,4 +1,5 @@
 """Stores dataclasses/args/config for the ot2 drivers"""
+
 import json
 from argparse import ArgumentParser, Namespace
 from pathlib import Path

src/ot2_interface/ot2_driver_http.py

@@ -23,6 +23,7 @@ class RobotStatus(Enum):
     FAILED = "failed"
     PAUSED = "paused"
     OFFLINE = "offline"
+    STOPPED = "stopped"
 
 
 class RunStatus(Enum):

src/ot2_interface/protopiler/config.py

@@ -1,4 +1,5 @@
 """Dataclasses and other configuration used in the protopiler"""
+
 from pathlib import Path
 from typing import List, Literal, Optional, TypeVar, Union
 

src/ot2_interface/protopiler/deconstructor.py

@@ -1,4 +1,5 @@
 """Deconstructor, parses a protocol and turns it into a config"""
+
 import re
 import subprocess
 from argparse import ArgumentParser

src/ot2_interface/protopiler/protopiler.py

@@ -1,4 +1,5 @@
 """Protopiler is designed to compile a config yaml into a working protocol"""
+
 import argparse
 import copy
 from datetime import datetime
@@ -7,6 +8,7 @@
 from typing import Dict, Generator, List, Optional, Tuple, Union
 
 import pandas as pd
+
 from ot2_interface.protopiler.config import (
     Clear_Pipette,
     CommandBase,
@@ -501,7 +503,7 @@ def yaml_to_protocol(
                         "#location#", f'"{location}"'
                     )
                     labware_command = labware_command.replace(
-                        "#nickname#", f'{"module"}'
+                        "#nickname#", f"{'module'}"
                     )
                     labware_command = labware_command.replace(
                         "#labware_name#", f'"{name}"'

src/ot2_interface/protopiler/resource_manager.py

@@ -1,4 +1,5 @@
 """Class to manage/keep track of resources used by a protocol"""
+
 import json
 import re
 from argparse import ArgumentParser

src/ot2_interface/protopiler/test_configs/basic_config.py

@@ -1,4 +1,5 @@
 """basic config module"""
+
 from opentrons import protocol_api
 
 metadata = {

src/ot2_rest_node.py

@@ -9,15 +9,18 @@
 from madsci.common.types.resource_types import Container, Pool, Slot, Stack
 from madsci.node_module.helpers import action
 from madsci.node_module.rest_node_module import RestNode
-from ot2_interface.ot2_driver_http import OT2_Config, OT2_Driver
 from typing_extensions import Annotated
 
+from ot2_interface.ot2_driver_http import OT2_Config, OT2_Driver
+
 
 class OT2NodeConfig(RestNodeConfig):
     """Configuration for the OT2 node module."""
 
     ot2_ip: Optional[str] = None
     "ip of opentrons device"
+    rate_limit_requests: int = 500
+    "max number of requests per minute to the ot2 device"
 
 
 class OT2Node(RestNode):
@@ -33,27 +36,26 @@ def startup_handler(self) -> None:
         temp_dir = Path.home() / ".madsci" / ".ot2_temp"
         temp_dir.mkdir(exist_ok=True)
         self.protocols_folder_path = str(
-            temp_dir / self.node_definition.node_name / "protocols/"
+            temp_dir / self.node_info.node_name / "protocols/"
         )
         # Create templates
         self._create_ot2_templates()
 
         # Create deck instance
         self.deck = self.resource_client.create_resource_from_template(
             template_name="ot2_deck",
-            resource_name=f"ot2_{self.node_definition.node_name}_deck",
+            resource_name=f"{self.node_info.node_name}.deck",
             add_to_database=True,
         )
 
         # Create 12 deck slots (1-11 standard, 12 is trash)
         for i in range(1, 13):
-            slot_name = f"ot2_{self.node_definition.node_name}_deck_slot_{i}"
+            slot_name = f"{self.node_info.node_name}.deck.nest_{i}"
             template_name = "ot2_trash_slot" if i == 12 else "ot2_deck_slot"
 
             slot = self.resource_client.create_resource_from_template(
                 template_name=template_name,
                 resource_name=slot_name,
-                add_to_database=True,
             )
 
             try:
@@ -66,8 +68,7 @@ def startup_handler(self) -> None:
         for mount in ["left", "right"]:
             mount_slot = self.resource_client.create_resource_from_template(
                 template_name="ot2_pipette_mount",
-                resource_name=f"ot2_{self.node_definition.node_name}_{mount}_mount",
-                add_to_database=True,
+                resource_name=f"{self.node_info.node_name}.{mount}_mount",
             )
             self.pipette_slots[mount] = mount_slot
 
@@ -93,7 +94,7 @@ def _create_ot2_templates(self) -> None:
             capacity=12,
             attributes={
                 "deck_type": "OT2",
-                "slot_count": 12,
+                "nest_count": 12,
                 "sbs_compatible": True,
                 "description": "OT2 deck with 11 standard slots plus trash bin",
             },
@@ -105,7 +106,7 @@ def _create_ot2_templates(self) -> None:
             description="Template for OT2 deck container. Holds 11 deck slots plus trash bin.",
             required_overrides=["resource_name"],
             tags=["ot2", "deck", "container"],
-            created_by=self.node_definition.node_id,
+            created_by=self.node_info.node_id,
             version="1.0.0",
         )
 
@@ -127,7 +128,7 @@ def _create_ot2_templates(self) -> None:
             description="Template for OT2 deck slot. Standard SBS-compatible position.",
             required_overrides=["resource_name"],
             tags=["ot2", "deck", "slot"],
-            created_by=self.node_definition.node_id,
+            created_by=self.node_info.node_id,
             version="1.0.0",
         )
 
@@ -148,7 +149,7 @@ def _create_ot2_templates(self) -> None:
             description="Template for OT2 trash bin slot.",
             required_overrides=["resource_name"],
             tags=["ot2", "trash", "stack"],
-            created_by=self.node_definition.node_id,
+            created_by=self.node_info.node_id,
             version="1.0.0",
         )
 
@@ -169,7 +170,7 @@ def _create_ot2_templates(self) -> None:
             description="Template for OT2 pipette mount slot.",
             required_overrides=["resource_name"],
             tags=["ot2", "pipette", "mount", "slot"],
-            created_by=self.node_definition.node_id,
+            created_by=self.node_info.node_id,
             version="1.0.0",
         )
 
@@ -196,7 +197,7 @@ def _create_ot2_templates(self) -> None:
             description="Template for OT2 P20 Single-Channel pipette (1-20 µL).",
             required_overrides=["resource_name"],
             tags=["ot2", "pipette", "p20", "single-channel", "pool"],
-            created_by=self.node_definition.node_id,
+            created_by=self.node_info.node_id,
             version="1.0.0",
         )
 
@@ -229,7 +230,7 @@ def _create_ot2_templates(self) -> None:
             description="Template for OT2 P300 Single-Channel pipette (20-300 µL).",
             required_overrides=["resource_name"],
             tags=["ot2", "pipette", "p300", "single-channel", "pool"],
-            created_by=self.node_definition.node_id,
+            created_by=self.node_info.node_id,
             version="1.0.0",
         )
 
@@ -265,7 +266,7 @@ def _create_ot2_templates(self) -> None:
             description="Template for OT2 P1000 Single-Channel pipette (100-1000 µL).",
             required_overrides=["resource_name"],
             tags=["ot2", "pipette", "p1000", "single-channel", "pool"],
-            created_by=self.node_definition.node_id,
+            created_by=self.node_info.node_id,
             version="1.0.0",
         )
 
@@ -296,7 +297,7 @@ def _create_ot2_templates(self) -> None:
             description="Template for OT2 P20 8-Channel pipette (1-20 µL).",
             required_overrides=["resource_name"],
             tags=["ot2", "pipette", "p20", "8-channel", "multi-channel", "pool"],
-            created_by=self.node_definition.node_id,
+            created_by=self.node_info.node_id,
             version="1.0.0",
         )
 
@@ -333,7 +334,7 @@ def _create_ot2_templates(self) -> None:
             description="Template for OT2 P300 8-Channel pipette (20-300 µL).",
             required_overrides=["resource_name"],
             tags=["ot2", "pipette", "p300", "8-channel", "multi-channel", "pool"],
-            created_by=self.node_definition.node_id,
+            created_by=self.node_info.node_id,
             version="1.0.0",
         )
 
@@ -429,9 +430,7 @@ def execute(self, protocol_path, payload=None, resource_config=None):
         try:
             protocol_id, run_id = self.ot2_interface.transfer(protocol_file_path)
             self.logger.log(
-                "OT2 "
-                + self.node_definition.node_name
-                + " protocol transfer successful"
+                "OT2 " + self.node_info.node_name + " protocol transfer successful"
             )
 
             self.run_id = run_id
@@ -442,39 +441,39 @@ def execute(self, protocol_path, payload=None, resource_config=None):
                 # poll_OT2_until_run_completion()
                 self.logger.log(
                     "OT2 "
-                    + self.node_definition.node_name
+                    + self.node_info.node_name
                     + " succeeded in executing a protocol"
                 )
                 response_msg = (
                     "OT2 "
-                    + self.node_definition.node_name
+                    + self.node_info.node_name
                     + " successfully IDLE running a protocol"
                 )
                 return "succeeded", response_msg, run_id
 
             elif resp["data"]["status"] == "stopped":
                 self.logger.log(
                     "OT2 "
-                    + self.node_definition.node_name
+                    + self.node_info.node_name
                     + " stopped while executing a protocol"
                 )
                 response_msg = (
                     "OT2 "
-                    + self.node_definition.node_name
+                    + self.node_info.node_name
                     + " successfully IDLE after stopping a protocol"
                 )
                 return "stopped", response_msg, run_id
 
             else:
                 self.logger.log(
                     "OT2 "
-                    + self.node_definition.node_name
+                    + self.node_info.node_name
                     + " failed in executing a protocol"
                 )
                 self.logger.log(resp["data"])
                 response_msg = (
                     "OT2 "
-                    + self.node_definition.node_name
+                    + self.node_info.node_name
                     + " failed running a protocol\n"
                     + str(resp["data"])
                 )