Renames package to lower case and fixes some build issues

.github/workflows/release.yml

@@ -15,6 +15,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          submodules: true
       - name: Build sdist
         run: |
           pip install pybind11

.github/workflows/run_tests.yml

@@ -54,4 +54,4 @@ jobs:
         run: |
           export PATH="$pythonLocation:$PATH"
           python -m pip install -e .[Dev,Orso]
-          pytest tests/ --cov=RATapi --cov-report=term
+          pytest tests/ --cov=ratapi --cov-report=term

ratapi/__init__.py

@@ -0,0 +1,29 @@
+"""ratapi is a Python package for modelling, fitting and optimising reflectivity problems."""
+
+from contextlib import suppress
+
+import ratapi.examples as examples
+from ratapi import events, models
+from ratapi.classlist import ClassList
+from ratapi.controls import Controls
+from ratapi.outputs import BayesResults, Results
+from ratapi.project import Project
+from ratapi.run import run
+from ratapi.utils import convert, plotting
+
+with suppress(ImportError):  # orsopy is an optional dependency
+    from ratapi.utils import orso as orso
+
+__all__ = [
+    "examples",
+    "models",
+    "events",
+    "ClassList",
+    "Controls",
+    "BayesResults",
+    "Results",
+    "Project",
+    "run",
+    "plotting",
+    "convert",
+]

RATapi/controls.py → ratapi/controls.py

@@ -17,8 +17,8 @@
     model_validator,
 )
 
-from RATapi.utils.custom_errors import custom_pydantic_validation_error
-from RATapi.utils.enums import BoundHandling, Display, Parallel, Procedures, Strategies
+from ratapi.utils.custom_errors import custom_pydantic_validation_error
+from ratapi.utils.enums import BoundHandling, Display, Parallel, Procedures, Strategies
 
 common_fields = ["procedure", "parallel", "calcSldDuringFit", "resampleMinAngle", "resampleNPoints", "display"]
 update_fields = ["updateFreq", "updatePlotFreq"]

RATapi/events.py → ratapi/events.py

@@ -3,7 +3,7 @@
 import os
 from typing import Callable, Union
 
-from RATapi.rat_core import EventBridge, EventTypes, PlotEventData, ProgressEventData
+from ratapi.rat_core import EventBridge, EventTypes, PlotEventData, ProgressEventData
 
 
 def notify(event_type: EventTypes, data: Union[str, PlotEventData, ProgressEventData]) -> None:

ratapi/examples/__init__.py

@@ -0,0 +1,25 @@
+"""Usage examples for the Python RAT API."""
+
+from ratapi.examples.absorption.absorption import absorption
+from ratapi.examples.convert_rascal_project.convert_rascal import convert_rascal
+from ratapi.examples.domains.domains_custom_layers import domains_custom_layers
+from ratapi.examples.domains.domains_custom_XY import domains_custom_XY
+from ratapi.examples.domains.domains_standard_layers import domains_standard_layers
+from ratapi.examples.normal_reflectivity.DSPC_custom_layers import DSPC_custom_layers
+from ratapi.examples.normal_reflectivity.DSPC_custom_XY import DSPC_custom_XY
+from ratapi.examples.normal_reflectivity.DSPC_data_background import DSPC_data_background
+from ratapi.examples.normal_reflectivity.DSPC_function_background import DSPC_function_background
+from ratapi.examples.normal_reflectivity.DSPC_standard_layers import DSPC_standard_layers
+
+__all__ = [
+    "absorption",
+    "domains_custom_layers",
+    "domains_custom_XY",
+    "domains_standard_layers",
+    "DSPC_custom_layers",
+    "DSPC_custom_XY",
+    "DSPC_standard_layers",
+    "DSPC_data_background",
+    "DSPC_function_background",
+    "convert_rascal",
+]

RATapi/examples/absorption/absorption.ipynb → ratapi/examples/absorption/absorption.ipynb

@@ -11,8 +11,8 @@
     "import numpy as np\n",
     "from IPython.display import Code\n",
     "\n",
-    "import RATapi as RAT\n",
-    "from RATapi.models import Parameter"
+    "import ratapi as RAT\n",
+    "from ratapi.models import Parameter"
    ]
   },
   {

RATapi/examples/absorption/absorption.py → ratapi/examples/absorption/absorption.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 def absorption():

RATapi/examples/bayes_benchmark/bayes_benchmark.ipynb → ratapi/examples/bayes_benchmark/bayes_benchmark.ipynb

@@ -41,8 +41,8 @@
    "source": [
     "import numpy as np\n",
     "\n",
-    "import RATapi as RAT\n",
-    "from RATapi.models import Parameter, Background, Resolution, Data, Contrast"
+    "import ratapi as RAT\n",
+    "from ratapi.models import Parameter, Background, Resolution, Data, Contrast"
    ]
   },
   {
@@ -263,7 +263,7 @@
    "source": [
     "import matplotlib.pyplot as plt\n",
     "from matplotlib import colormaps\n",
-    "import RATapi.utils.plotting as RATplot\n",
+    "import ratapi.utils.plotting as RATplot\n",
     "\n",
     "fig, axes = plt.subplots(3, 2, figsize=(6, 9))\n",
     "\n",

RATapi/examples/bayes_benchmark/bayes_benchmark.py → ratapi/examples/bayes_benchmark/bayes_benchmark.py

@@ -24,9 +24,9 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-import RATapi as RAT
-import RATapi.utils.plotting as RATplot
-from RATapi.models import Background, Contrast, Data, Parameter, Resolution
+import ratapi as RAT
+import ratapi.utils.plotting as RATplot
+from ratapi.models import Background, Contrast, Data, Parameter, Resolution
 
 PWD = Path(__file__).parents[0]
 

RATapi/examples/convert_rascal_project/convert_rascal.ipynb → ratapi/examples/convert_rascal_project/convert_rascal.ipynb

@@ -24,7 +24,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from RATapi.utils.convert import r1_to_project\n",
+    "from ratapi.utils.convert import r1_to_project\n",
     "\n",
     "project = r1_to_project(\"R1monolayerVolumeModel.mat\")\n",
     "print(project)"
@@ -99,7 +99,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from RATapi.examples import DSPC_standard_layers\n",
+    "from ratapi.examples import DSPC_standard_layers\n",
     "lipid_bilayer_project = DSPC_standard_layers()[0]\n",
     "print(lipid_bilayer_project)"
    ]
@@ -121,7 +121,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from RATapi.utils.convert import project_to_r1\n",
+    "from ratapi.utils.convert import project_to_r1\n",
     "from pprint import pp  # for printing the struct\n",
     "\n",
     "# save to a file called lipid_bilayer.mat\n",

RATapi/examples/convert_rascal_project/convert_rascal.py → ratapi/examples/convert_rascal_project/convert_rascal.py

@@ -3,7 +3,7 @@
 import pathlib
 from pprint import pp
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 # convert R1 project to Project class

RATapi/examples/domains/domains_custom_XY.ipynb → ratapi/examples/domains/domains_custom_XY.ipynb

@@ -9,8 +9,8 @@
     "import pathlib\n",
     "from IPython.display import Code\n",
     "\n",
-    "import RATapi as RAT\n",
-    "from RATapi.models import Parameter"
+    "import ratapi as RAT\n",
+    "from ratapi.models import Parameter"
    ]
   },
   {

RATapi/examples/domains/domains_custom_XY.py → ratapi/examples/domains/domains_custom_XY.py

@@ -2,7 +2,7 @@
 
 import pathlib
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 def domains_custom_XY():

RATapi/examples/domains/domains_custom_layers.ipynb → ratapi/examples/domains/domains_custom_layers.ipynb

@@ -9,8 +9,8 @@
     "import pathlib\n",
     "from IPython.display import Code\n",
     "\n",
-    "import RATapi as RAT\n",
-    "from RATapi.models import Parameter"
+    "import ratapi as RAT\n",
+    "from ratapi.models import Parameter"
    ]
   },
   {

RATapi/examples/domains/domains_custom_layers.py → ratapi/examples/domains/domains_custom_layers.py

@@ -2,7 +2,7 @@
 
 import pathlib
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 def domains_custom_layers():

RATapi/examples/domains/domains_standard_layers.ipynb → ratapi/examples/domains/domains_standard_layers.ipynb

@@ -6,8 +6,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import RATapi as RAT\n",
-    "from RATapi.models import Layer, Parameter"
+    "import ratapi as RAT\n",
+    "from ratapi.models import Layer, Parameter"
    ]
   },
   {

RATapi/examples/domains/domains_standard_layers.py → ratapi/examples/domains/domains_standard_layers.py

@@ -1,6 +1,6 @@
 """An example using domains with standard layers."""
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 def domains_standard_layers():

RATapi/examples/extras/two_contrast_example.py → ratapi/examples/extras/two_contrast_example.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 def two_contrast_example():

RATapi/examples/languages/run_custom_file_languages.py → ratapi/examples/languages/run_custom_file_languages.py

@@ -5,7 +5,7 @@
 
 import setup_problem
 
-import RATapi as RAT
+import ratapi as RAT
 
 path = pathlib.Path(__file__).parent
 

RATapi/examples/languages/setup_problem.py → ratapi/examples/languages/setup_problem.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 def make_example_problem():

RATapi/examples/normal_reflectivity/DSPC_custom_XY.py → ratapi/examples/normal_reflectivity/DSPC_custom_XY.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 def DSPC_custom_XY():

RATapi/examples/normal_reflectivity/DSPC_custom_layers.ipynb → ratapi/examples/normal_reflectivity/DSPC_custom_layers.ipynb

@@ -12,8 +12,8 @@
     "import numpy as np\n",
     "from IPython.display import Code\n",
     "\n",
-    "import RATapi as RAT\n",
-    "from RATapi.models import Parameter"
+    "import ratapi as RAT\n",
+    "from ratapi.models import Parameter"
    ]
   },
   {
@@ -730,7 +730,7 @@
       "+-------+------------+------------------------+---------------------+----------+-------------------------------------------------------------------------+\n",
       "| index |    name    |        filename        |    function name    | language |                                   path                                  |\n",
       "+-------+------------+------------------------+---------------------+----------+-------------------------------------------------------------------------+\n",
-      "|   0   | DSPC Model | custom_bilayer_DSPC.py | custom_bilayer_DSPC |  python  | /mnt/c/Users/gnn85523/projects/python-RAT/RATapi/examples/non_polarised |\n",
+      "|   0   | DSPC Model | custom_bilayer_DSPC.py | custom_bilayer_DSPC |  python  | /mnt/c/Users/gnn85523/projects/python-RAT/ratapi/examples/non_polarised |\n",
       "+-------+------------+------------------------+---------------------+----------+-------------------------------------------------------------------------+\n",
       "\n",
       "Data: ----------------------------------------------------------------------------------------------\n",

RATapi/examples/normal_reflectivity/DSPC_custom_layers.py → ratapi/examples/normal_reflectivity/DSPC_custom_layers.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 def DSPC_custom_layers():

RATapi/examples/normal_reflectivity/DSPC_custom_xy.ipynb → ratapi/examples/normal_reflectivity/DSPC_custom_xy.ipynb

@@ -12,8 +12,8 @@
     "import numpy as np\n",
     "from IPython.display import Code\n",
     "\n",
-    "import RATapi as RAT\n",
-    "from RATapi.models import Parameter"
+    "import ratapi as RAT\n",
+    "from ratapi.models import Parameter"
    ]
   },
   {

RATapi/examples/normal_reflectivity/DSPC_data_background.py → ratapi/examples/normal_reflectivity/DSPC_data_background.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 def DSPC_data_background():

RATapi/examples/normal_reflectivity/DSPC_function_background.py → ratapi/examples/normal_reflectivity/DSPC_function_background.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 
-import RATapi as RAT
+import ratapi as RAT
 
 
 def DSPC_function_background():