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")
@@ -138,4 +137,4 @@
 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/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")
 
@@ -119,4 +118,4 @@
 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/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