Adds to "pyproject.toml" to enable setup of uv environment (#182)

* Adds code to enable setup of uv environment

* Fixes linting errors

* Sorts dependencies into groups

* Moves dev dependencies into optional requirements

* Adds conflicts for uv

* Updates submodule with empty layers bug fix

* Fixes code hanging bug

* Reverts typing change

Author: DrPaulSharp

.github/workflows/run_tests.yml

@@ -63,5 +63,5 @@ jobs:
       - name: Install and Test with pytest
         run: |
           export PATH="$pythonLocation:$PATH"
-          python -m pip install -e .[Dev,Orso]
+          python -m pip install -e .[dev,orso]
           pytest tests/ --cov=ratapi --cov-report=term

.gitignore

@@ -40,3 +40,6 @@ dist/*
 
 # Jupyter notebook checkpoints
 .ipynb_checkpoints/*
+
+# Lock file for uv env
+uv.lock

README.md

@@ -12,11 +12,11 @@ To install in local directory:
 
 matlabengine is an optional dependency only required for Matlab custom functions. The version of matlabengine should match the version of Matlab installed on the machine. This can be installed as shown below:
 
-    pip install -e .[Matlab-2023a]
+    pip install -e .[matlab-2023a]
 
 Development dependencies can be installed as shown below
 
-    pip install -e .[Dev]    
+    pip install -e .[dev]
 
 To build wheel:
 

cpp/RAT

@@ -6,6 +6,53 @@ requires = [
 ]
 build-backend = 'setuptools.build_meta'
 
+[project]
+name = "ratapi"
+version = "0.0.0.dev8"
+description = "Python extension for the Reflectivity Analysis Toolbox (RAT)"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "matplotlib>=3.8.3",
+    "numpy>=1.20",
+    "prettytable>=3.9.0",
+    "pydantic>=2.7.2",
+    "scipy>=1.13.1",
+    "strenum>=0.4.15 ; python_full_version < '3.11'",
+    "tqdm>=4.66.5",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.4.0",
+    "pytest-cov>=4.1.0",
+    "ruff>=0.4.10"
+]
+orso = [
+    "orsopy>=1.2.1",
+    "pint>=0.24.4"
+]
+matlab_latest = ["matlabengine"]
+matlab_2025b = ["matlabengine == 25.2.*"]
+matlab_2025a = ["matlabengine == 25.1.2"]
+matlab_2024b = ["matlabengine == 24.2.2"]
+matlab_2024a = ["matlabengine == 24.1.4"]
+matlab_2023b = ["matlabengine == 23.2.3"]
+matlab_2023a = ["matlabengine == 9.14.3"]
+
+[tool.uv]
+conflicts = [
+    [
+        { extra = "matlab_latest" },
+        { extra = "matlab_2025b" },
+        { extra = "matlab_2025a" },
+        { extra = "matlab_2024b" },
+        { extra = "matlab_2024a" },
+        { extra = "matlab_2023b" },
+        { extra = "matlab_2023a" },
+    ],
+]
+
 [tool.ruff]
 line-length = 120
 extend-exclude = ["*.ipynb"]
@@ -24,7 +71,8 @@ ignore = ["SIM103", # needless bool
           "D105",   # undocumented __init__
           "D107",   # undocumented magic method
           "D203",   # blank line before class docstring
-          "D213"]   # multi line summary should start at second line
+          "D213",   # multi line summary should start at second line
+          "UP038"]  # non pep604 isinstance - to be removed
 
 # ignore docstring lints in the tests and install script
 [tool.ruff.lint.per-file-ignores]

pyproject.toml

@@ -5,7 +5,7 @@
 import importlib
 import warnings
 from collections.abc import Sequence
-from typing import Any, Generic, TypeVar, Union
+from typing import Any, Generic, TypeVar
 
 import numpy as np
 import prettytable
@@ -38,7 +38,7 @@ class ClassList(collections.UserList, Generic[T]):
 
     """
 
-    def __init__(self, init_list: Union[Sequence[T], T] = None, name_field: str = "name") -> None:
+    def __init__(self, init_list: Sequence[T] | T = None, name_field: str = "name") -> None:
         self.name_field = name_field
 
         # Set input as list if necessary
@@ -114,7 +114,7 @@ def __str__(self):
                 output = str(self.data)
         return output
 
-    def __getitem__(self, index: Union[int, slice, str, T]) -> T:
+    def __getitem__(self, index: int | slice | str | T) -> T:
         """Get an item by its index, name, a slice, or the object itself."""
         if isinstance(index, (int, slice)):
             return self.data[index]
@@ -262,12 +262,12 @@ def insert(self, index: int, obj: T = None, **kwargs) -> None:
             self._validate_name_field(kwargs)
             self.data.insert(index, self._class_handle(**kwargs))
 
-    def remove(self, item: Union[T, str]) -> None:
+    def remove(self, item: T | str) -> None:
         """Remove an object from the ClassList using either the object itself or its ``name_field`` value."""
         item = self._get_item_from_name_field(item)
         self.data.remove(item)
 
-    def count(self, item: Union[T, str]) -> int:
+    def count(self, item: T | str) -> int:
         """Return the number of times an object appears in the ClassList.
 
         This method can use either the object itself or its ``name_field`` value.
@@ -276,7 +276,7 @@ def count(self, item: Union[T, str]) -> int:
         item = self._get_item_from_name_field(item)
         return self.data.count(item)
 
-    def index(self, item: Union[T, str], offset: bool = False, *args) -> int:
+    def index(self, item: T | str, offset: bool = False, *args) -> int:
         """Return the index of a particular object in the ClassList.
 
         This method can use either the object itself or its ``name_field`` value.
@@ -309,7 +309,7 @@ def union(self, other: Sequence[T]) -> None:
             ]
         )
 
-    def set_fields(self, index: Union[int, slice, str, T], **kwargs) -> None:
+    def set_fields(self, index: int | slice | str | T, **kwargs) -> None:
         """Assign the values of an existing object's attributes using keyword arguments."""
         self._validate_name_field(kwargs)
         pydantic_object = False
@@ -519,7 +519,7 @@ def _check_classes(self, input_list: Sequence[T]) -> None:
                 f"In the input list:\n{newline.join(error for error in error_list)}\n"
             )
 
-    def _get_item_from_name_field(self, value: Union[T, str]) -> Union[T, str]:
+    def _get_item_from_name_field(self, value: T | str) -> T | str:
         """Return the object with the given value of the ``name_field`` attribute in the ClassList.
 
         Parameters
@@ -577,11 +577,12 @@ def _determine_class_handle(input_list: Sequence[T]):
     @classmethod
     def __get_pydantic_core_schema__(cls, source: Any, handler):
         # import here so that the ClassList can be instantiated and used without Pydantic installed
+        from typing import get_args, get_origin
+
         from pydantic import ValidatorFunctionWrapHandler
         from pydantic.types import (
             core_schema,  # import core_schema through here rather than making pydantic_core a dependency
         )
-        from typing_extensions import get_args, get_origin
 
         # if annotated with a class, get the item type of that class
         origin = get_origin(source)

ratapi/classlist.py

@@ -5,7 +5,6 @@
 import tempfile
 import warnings
 from pathlib import Path
-from typing import Union
 
 import prettytable
 from pydantic import (
@@ -233,7 +232,7 @@ def delete_IPC(self):
             os.remove(self._IPCFilePath)
         return None
 
-    def save(self, filepath: Union[str, Path] = "./controls.json"):
+    def save(self, filepath: str | Path = "./controls.json"):
         """Save a controls object to a JSON file.
 
         Parameters
@@ -245,7 +244,7 @@ def save(self, filepath: Union[str, Path] = "./controls.json"):
         filepath.write_text(self.model_dump_json())
 
     @classmethod
-    def load(cls, path: Union[str, Path]) -> "Controls":
+    def load(cls, path: str | Path) -> "Controls":
         """Load a controls object from file.
 
         Parameters

ratapi/controls.py

@@ -1,12 +1,12 @@
 """Hooks for connecting to run callback events."""
 
 import os
-from typing import Callable, Union
+from collections.abc import Callable
 
 from ratapi.rat_core import EventBridge, EventTypes, PlotEventData, ProgressEventData
 
 
-def notify(event_type: EventTypes, data: Union[str, PlotEventData, ProgressEventData]) -> None:
+def notify(event_type: EventTypes, data: str | PlotEventData | ProgressEventData) -> None:
     """Call registered callbacks with data when event type has been triggered.
 
     Parameters
@@ -22,7 +22,7 @@ def notify(event_type: EventTypes, data: Union[str, PlotEventData, ProgressEvent
         callback(data)
 
 
-def get_event_callback(event_type: EventTypes) -> list[Callable[[Union[str, PlotEventData, ProgressEventData]], None]]:
+def get_event_callback(event_type: EventTypes) -> list[Callable[[str | PlotEventData | ProgressEventData], None]]:
     """Return all callbacks registered for the given event type.
 
     Parameters
@@ -39,7 +39,7 @@ def get_event_callback(event_type: EventTypes) -> list[Callable[[Union[str, Plot
     return list(__event_callbacks[event_type])
 
 
-def register(event_type: EventTypes, callback: Callable[[Union[str, PlotEventData, ProgressEventData]], None]) -> None:
+def register(event_type: EventTypes, callback: Callable[[str | PlotEventData | ProgressEventData], None]) -> None:
     """Register a new callback for the event type.
 
     Parameters

ratapi/events.py

@@ -3,7 +3,7 @@
 import importlib
 import os
 import pathlib
-from typing import Callable, Union
+from collections.abc import Callable
 
 import numpy as np
 
@@ -23,7 +23,7 @@
 }
 
 
-def get_python_handle(file_name: str, function_name: str, path: Union[str, pathlib.Path] = "") -> Callable:
+def get_python_handle(file_name: str, function_name: str, path: str | pathlib.Path = "") -> Callable:
     """Get the function handle from a function defined in a python module located anywhere within the filesystem.
 
     Parameters

ratapi/inputs.py

@@ -3,7 +3,7 @@
 import json
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any, Union
 
 import numpy as np
 
@@ -244,7 +244,7 @@ def __str__(self):
             output += get_field_string(key, value, 100)
         return output
 
-    def save(self, filepath: Union[str, Path] = "./results.json"):
+    def save(self, filepath: str | Path = "./results.json"):
         """Save the Results object to a JSON file.
 
         Parameters
@@ -258,7 +258,7 @@ def save(self, filepath: Union[str, Path] = "./results.json"):
         filepath.write_text(json.dumps(json_dict))
 
     @classmethod
-    def load(cls, path: Union[str, Path]) -> Union["Results", "BayesResults"]:
+    def load(cls, path: str | Path) -> Union["Results", "BayesResults"]:
         """Load a Results object from file.
 
         Parameters
@@ -538,7 +538,7 @@ class BayesResults(Results):
     nestedSamplerOutput: NestedSamplerOutput
     chain: np.ndarray
 
-    def save(self, filepath: Union[str, Path] = "./results.json"):
+    def save(self, filepath: str | Path = "./results.json"):
         """Save the BayesResults object to a JSON file.
 
         Parameters
@@ -574,7 +574,7 @@ def save(self, filepath: Union[str, Path] = "./results.json"):
         filepath.write_text(json.dumps(json_dict))
 
 
-def write_core_results_fields(results: Union[Results, BayesResults], json_dict: Optional[dict] = None) -> dict:
+def write_core_results_fields(results: Results | BayesResults, json_dict: dict | None = None) -> dict:
     """Modify the values of the fields that appear in both Results and BayesResults when saving to a json file.
 
     Parameters
@@ -684,8 +684,8 @@ def read_bayes_results_fields(results_dict: dict) -> dict:
 def make_results(
     procedure: Procedures,
     output_results: ratapi.rat_core.OutputResult,
-    bayes_results: Optional[ratapi.rat_core.OutputBayesResult] = None,
-) -> Union[Results, BayesResults]:
+    bayes_results: ratapi.rat_core.OutputBayesResult | None = None,
+) -> Results | BayesResults:
     """Initialise a python Results or BayesResults object using the outputs from a RAT calculation.
 
     Parameters