Adds release action and rename package to RATpy

.github/workflows/release.yml

@@ -0,0 +1,45 @@
+name: Build and upload to PyPI
+
+on:
+  release:
+    types:
+        - published
+  workflow_dispatch:
+
+jobs:
+  build_wheels:
+    uses: RascalSoftware/python-RAT/.github/workflows/build_wheel.yml@main
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        run: |
+          pip install pybind11
+          python setup.py sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: release
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+      - name: Publish to TestPyPi
+        if: github.event_name == 'workflow_dispatch' 
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+      - name: Publish
+        if: github.event_name == 'release'
+        uses: pypa/gh-action-pypi-publish@release/v1

RATpy/__init__.py

@@ -0,0 +1,8 @@
+from RATpy import events, models
+from RATpy.classlist import ClassList
+from RATpy.controls import set_controls
+from RATpy.project import Project
+from RATpy.run import run
+from RATpy.utils import plotting
+
+__all__ = ["ClassList", "Project", "run", "set_controls", "models", "events", "plotting"]

RAT/controls.py → RATpy/controls.py

@@ -4,8 +4,8 @@
 import prettytable
 from pydantic import BaseModel, Field, ValidationError, field_validator
 
-from RAT.utils.custom_errors import custom_pydantic_validation_error
-from RAT.utils.enums import BoundHandling, Display, Parallel, Procedures, Strategies
+from RATpy.utils.custom_errors import custom_pydantic_validation_error
+from RATpy.utils.enums import BoundHandling, Display, Parallel, Procedures, Strategies
 
 
 @dataclass(frozen=True)

RAT/events.py → RATpy/events.py

@@ -1,6 +1,7 @@
+import os
 from typing import Callable, List, Union
 
-from RAT.rat_core import EventBridge, EventTypes, PlotEventData, ProgressEventData
+from RATpy.rat_core import EventBridge, EventTypes, PlotEventData, ProgressEventData
 
 
 def notify(event_type: EventTypes, data: Union[str, PlotEventData, ProgressEventData]) -> None:
@@ -63,5 +64,7 @@ def clear() -> None:
         __event_callbacks[key] = set()
 
 
+dir_path = os.path.dirname(os.path.realpath(__file__))
+os.environ["RAT_PATH"] = os.path.join(dir_path, "")
 __event_impl = EventBridge(notify)
 __event_callbacks = {EventTypes.Message: set(), EventTypes.Plot: set(), EventTypes.Progress: set()}

RAT/examples/absorption/absorption.py → RATpy/examples/absorption/absorption.py

@@ -5,8 +5,7 @@
 
 import numpy as np
 
-import RAT
-import RAT.utils.plotting
+import RATpy as RAT
 
 problem = RAT.Project(
     name="Absorption example",
@@ -146,4 +145,4 @@
 
 # Run the code and plot the results
 problem, results = RAT.run(problem, controls)
-RAT.utils.plotting.plot_ref_sld(problem, results, True)
+RAT.plotting.plot_ref_sld(problem, results, True)

RAT/examples/domains/domains_custom_XY.py → RATpy/examples/domains/domains_custom_XY.py

@@ -2,8 +2,7 @@
 
 import pathlib
 
-import RAT
-import RAT.utils.plotting
+import RATpy as RAT
 
 problem = RAT.Project(calculation="domains", model="custom xy", geometry="substrate/liquid")
 
@@ -67,4 +66,4 @@
 controls = RAT.set_controls()
 problem, results = RAT.run(problem, controls)
 
-RAT.utils.plotting.plot_ref_sld(problem, results, True)
+RAT.plotting.plot_ref_sld(problem, results, True)

RAT/examples/domains/domains_custom_layers.py → RATpy/examples/domains/domains_custom_layers.py

@@ -2,8 +2,7 @@
 
 import pathlib
 
-import RAT
-import RAT.utils.plotting
+import RATpy as RAT
 
 problem = RAT.Project(calculation="domains", model="custom layers", geometry="substrate/liquid")
 
@@ -44,4 +43,4 @@
 controls = RAT.set_controls()
 
 problem, results = RAT.run(problem, controls)
-RAT.utils.plotting.plot_ref_sld(problem, results, True)
+RAT.plotting.plot_ref_sld(problem, results, True)

RAT/examples/domains/domains_standard_layers.py → RATpy/examples/domains/domains_standard_layers.py

@@ -1,5 +1,4 @@
-import RAT
-import RAT.utils.plotting
+import RATpy as RAT
 
 problem = RAT.Project(calculation="domains")
 
@@ -73,4 +72,4 @@
 controls = RAT.set_controls()
 
 problem, results = RAT.run(problem, controls)
-RAT.utils.plotting.plot_ref_sld(problem, results, True)
+RAT.plotting.plot_ref_sld(problem, results, True)

RAT/examples/languages/run_custom_file_languages.py → RATpy/examples/languages/run_custom_file_languages.py

@@ -5,7 +5,7 @@
 
 import setup_problem
 
-import RAT.utils.plotting
+import RATpy as RAT
 
 path = pathlib.Path(__file__).parent.resolve()
 
@@ -18,7 +18,7 @@
 end = time.time()
 print(f"Python time is: {end-start}s\n")
 
-RAT.utils.plotting.plot_ref_sld(project, results)
+RAT.plotting.plot_ref_sld(project, results)
 
 # Matlab
 project.custom_files.set_fields(0, filename="custom_bilayer.m", language="matlab", path=path)
@@ -28,7 +28,7 @@
 end = time.time()
 print(f"Matlab time is: {end-start}s\n")
 
-RAT.utils.plotting.plot_ref_sld(project, results)
+RAT.plotting.plot_ref_sld(project, results)
 
 # C++
 project.custom_files.set_fields(0, filename="custom_bilayer.dll", language="cpp", path=path)
@@ -38,4 +38,4 @@
 end = time.time()
 print(f"C++ time is: {end-start}s\n")
 
-RAT.utils.plotting.plot_ref_sld(project, results)
+RAT.plotting.plot_ref_sld(project, results)

RAT/examples/languages/setup_problem.py → RATpy/examples/languages/setup_problem.py

@@ -8,7 +8,7 @@
 
 import numpy as np
 
-import RAT
+import RATpy as RAT
 
 
 def make_example_problem():

RAT/examples/non_polarised/DSPC_custom_XY.py → RATpy/examples/non_polarised/DSPC_custom_XY.py

@@ -28,8 +28,7 @@
 
 import numpy as np
 
-import RAT
-import RAT.utils.plotting
+import RATpy as RAT
 
 # Start by making the class and setting it to a custom layers type:
 problem = RAT.Project(name="Orso lipid example - custom XY", model="custom xy", geometry="substrate/liquid")

RAT/examples/non_polarised/DSPC_custom_layers.py → RATpy/examples/non_polarised/DSPC_custom_layers.py

@@ -8,8 +8,7 @@
 
 import numpy as np
 
-import RAT
-import RAT.utils.plotting
+import RATpy as RAT
 
 problem = RAT.Project(name="Orso lipid example - custom layers", model="custom layers", geometry="substrate/liquid")
 

RAT/examples/non_polarised/DSPC_standard_layers.py → RATpy/examples/non_polarised/DSPC_standard_layers.py

@@ -5,8 +5,7 @@
 
 import numpy as np
 
-import RAT
-import RAT.utils.plotting
+import RATpy as RAT
 
 problem = RAT.Project(
     name="original_dspc_bilayer",
@@ -356,4 +355,4 @@
 controls = RAT.set_controls()
 
 problem, results = RAT.run(problem, controls)
-RAT.utils.plotting.plot_ref_sld(problem, results, True)
+RAT.plotting.plot_ref_sld(problem, results, True)

RAT/inputs.py → RATpy/inputs.py

@@ -5,16 +5,18 @@
 import pathlib
 from typing import Callable, Union
 
-import RAT
-import RAT.controls
-import RAT.wrappers
-from RAT.rat_core import Cells, Checks, Control, Limits, Priors, ProblemDefinition
-from RAT.utils.enums import Calculations, Languages, LayerModels, TypeOptions
+import RATpy
+import RATpy.controls
+import RATpy.wrappers
+from RATpy.rat_core import Cells, Checks, Control, Limits, Priors, ProblemDefinition
+from RATpy.utils.enums import Calculations, Languages, LayerModels, TypeOptions
 
 
 def make_input(
-    project: RAT.Project,
-    controls: Union[RAT.controls.Calculate, RAT.controls.Simplex, RAT.controls.DE, RAT.controls.NS, RAT.controls.Dream],
+    project: RATpy.Project,
+    controls: Union[
+        RATpy.controls.Calculate, RATpy.controls.Simplex, RATpy.controls.DE, RATpy.controls.NS, RATpy.controls.Dream
+    ],
 ) -> tuple[ProblemDefinition, Cells, Limits, Priors, Control]:
     """Constructs the inputs required for the compiled RAT code using the data defined in the input project and
     controls.
@@ -68,7 +70,7 @@ def make_input(
     limits = Limits()
     priors = Priors()
 
-    for class_list in RAT.project.parameter_class_lists:
+    for class_list in RATpy.project.parameter_class_lists:
         setattr(checks, checks_field[class_list], [int(element.fit) for element in getattr(project, class_list)])
         setattr(
             limits,
@@ -87,11 +89,11 @@ def make_input(
     priors.qzshift = []
 
     priors.priorNames = [
-        param.name for class_list in RAT.project.parameter_class_lists for param in getattr(project, class_list)
+        param.name for class_list in RATpy.project.parameter_class_lists for param in getattr(project, class_list)
     ]
     priors.priorValues = [
         [prior_id[param.prior_type], param.mu, param.sigma]
-        for class_list in RAT.project.parameter_class_lists
+        for class_list in RATpy.project.parameter_class_lists
         for param in getattr(project, class_list)
     ]
 
@@ -103,7 +105,7 @@ def make_input(
     return problem, cells, limits, priors, cpp_controls
 
 
-def make_problem(project: RAT.Project) -> ProblemDefinition:
+def make_problem(project: RATpy.Project) -> ProblemDefinition:
     """Constructs the problem input required for the compiled RAT code.
 
     Parameters
@@ -181,25 +183,25 @@ def make_problem(project: RAT.Project) -> ProblemDefinition:
     problem.numberOfDomainContrasts = len(project.domain_contrasts)
     problem.fitParams = [
         param.value
-        for class_list in RAT.project.parameter_class_lists
+        for class_list in RATpy.project.parameter_class_lists
         for param in getattr(project, class_list)
         if param.fit
     ]
     problem.fitLimits = [
         [param.min, param.max]
-        for class_list in RAT.project.parameter_class_lists
+        for class_list in RATpy.project.parameter_class_lists
         for param in getattr(project, class_list)
         if param.fit
     ]
     problem.otherParams = [
         param.value
-        for class_list in RAT.project.parameter_class_lists
+        for class_list in RATpy.project.parameter_class_lists
         for param in getattr(project, class_list)
         if not param.fit
     ]
     problem.otherLimits = [
         [param.min, param.max]
-        for class_list in RAT.project.parameter_class_lists
+        for class_list in RATpy.project.parameter_class_lists
         for param in getattr(project, class_list)
         if not param.fit
     ]
@@ -209,7 +211,7 @@ def make_problem(project: RAT.Project) -> ProblemDefinition:
     return problem
 
 
-def make_resample(project: RAT.Project) -> list[int]:
+def make_resample(project: RATpy.Project) -> list[int]:
     """Constructs the "resample" field of the problem input required for the compiled RAT code.
 
     Parameters
@@ -226,7 +228,7 @@ def make_resample(project: RAT.Project) -> list[int]:
     return [contrast.resample for contrast in project.contrasts]
 
 
-def make_data_present(project: RAT.Project) -> list[int]:
+def make_data_present(project: RATpy.Project) -> list[int]:
     """Constructs the "dataPresent" field of the problem input required for the compiled RAT code.
 
     Parameters
@@ -282,7 +284,7 @@ def check_indices(problem: ProblemDefinition) -> None:
             )
 
 
-def make_cells(project: RAT.Project) -> Cells:
+def make_cells(project: RATpy.Project) -> Cells:
     """Constructs the cells input required for the compiled RAT code.
 
     Note that the order of the inputs (i.e, f1 to f20) has been hard--coded into the compiled RAT code.
@@ -353,9 +355,9 @@ def make_cells(project: RAT.Project) -> Cells:
         if custom_file.language == Languages.Python:
             file_handles.append(get_python_handle(custom_file.filename, custom_file.function_name, custom_file.path))
         elif custom_file.language == Languages.Matlab:
-            file_handles.append(RAT.wrappers.MatlabWrapper(full_path).getHandle())
+            file_handles.append(RATpy.wrappers.MatlabWrapper(full_path).getHandle())
         elif custom_file.language == Languages.Cpp:
-            file_handles.append(RAT.wrappers.DylibWrapper(full_path, custom_file.function_name).getHandle())
+            file_handles.append(RATpy.wrappers.DylibWrapper(full_path, custom_file.function_name).getHandle())
 
     # Populate the set of cells
     cells = Cells()
@@ -418,7 +420,9 @@ def get_python_handle(file_name: str, function_name: str, path: Union[str, pathl
 
 
 def make_controls(
-    controls: Union[RAT.controls.Calculate, RAT.controls.Simplex, RAT.controls.DE, RAT.controls.NS, RAT.controls.Dream],
+    controls: Union[
+        RATpy.controls.Calculate, RATpy.controls.Simplex, RATpy.controls.DE, RATpy.controls.NS, RATpy.controls.Dream
+    ],
     checks: Checks,
 ) -> Control:
     """Converts the controls object to the format required by the compiled RAT code.
@@ -436,7 +440,7 @@ def make_controls(
         The controls object used in the compiled RAT code.
 
     """
-    full_controls = RAT.controls.Controls(**controls.model_dump())
+    full_controls = RATpy.controls.Controls(**controls.model_dump())
     cpp_controls = Control()
 
     cpp_controls.procedure = full_controls.procedure

RAT/models.py → RATpy/models.py

@@ -6,7 +6,7 @@
 import numpy as np
 from pydantic import BaseModel, Field, ValidationInfo, field_validator, model_validator
 
-from RAT.utils.enums import BackgroundActions, Hydration, Languages, Priors, TypeOptions
+from RATpy.utils.enums import BackgroundActions, Hydration, Languages, Priors, TypeOptions
 
 try:
     from enum import StrEnum