Fixes linting errors

Author: DrPaulSharp

pyproject.toml

@@ -46,7 +46,8 @@ 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]

ratapi/classlist.py

@@ -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/controls.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/events.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/inputs.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/outputs.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

ratapi/project.py

@@ -5,10 +5,11 @@
 import functools
 import json
 import warnings
+from collections.abc import Callable
 from enum import Enum
 from pathlib import Path
 from textwrap import indent
-from typing import Annotated, Any, Callable, Union
+from typing import Annotated, Any, get_args, get_origin
 
 import numpy as np
 from pydantic import (
@@ -21,7 +22,6 @@
     field_validator,
     model_validator,
 )
-from typing_extensions import get_args, get_origin
 
 import ratapi.models
 from ratapi.classlist import ClassList
@@ -248,10 +248,10 @@ class Project(BaseModel, validate_assignment=True, extra="forbid", use_attribute
     data: ClassList[ratapi.models.Data] = ClassList()
     """Experimental data for a model."""
 
-    layers: Union[
-        Annotated[ClassList[ratapi.models.Layer], Tag("no_abs")],
-        Annotated[ClassList[ratapi.models.AbsorptionLayer], Tag("abs")],
-    ] = Field(
+    layers: (
+        Annotated[ClassList[ratapi.models.Layer], Tag("no_abs")]
+        | Annotated[ClassList[ratapi.models.AbsorptionLayer], Tag("abs")]
+    ) = Field(
         default=ClassList(),
         discriminator=Discriminator(
             discriminate_layers,
@@ -265,10 +265,10 @@ class Project(BaseModel, validate_assignment=True, extra="forbid", use_attribute
     domain_contrasts: ClassList[ratapi.models.DomainContrast] = ClassList()
     """The groups of layers required by each domain in a domains model."""
 
-    contrasts: Union[
-        Annotated[ClassList[ratapi.models.Contrast], Tag("no_ratio")],
-        Annotated[ClassList[ratapi.models.ContrastWithRatio], Tag("ratio")],
-    ] = Field(
+    contrasts: (
+        Annotated[ClassList[ratapi.models.Contrast], Tag("no_ratio")]
+        | Annotated[ClassList[ratapi.models.ContrastWithRatio], Tag("ratio")]
+    ) = Field(
         default=ClassList(),
         discriminator=Discriminator(
             discriminate_contrasts,
@@ -577,7 +577,7 @@ def update_renamed_models(self) -> "Project":
             old_names = self._all_names[class_list]
             new_names = getattr(self, class_list).get_names()
             if len(old_names) == len(new_names):
-                name_diff = [(old, new) for (old, new) in zip(old_names, new_names) if old != new]
+                name_diff = [(old, new) for (old, new) in zip(old_names, new_names, strict=False) if old != new]
                 for old_name, new_name in name_diff:
                     for field in fields_to_update:
                         project_field = getattr(self, field.attribute)
@@ -927,7 +927,7 @@ def classlist_script(name, classlist):
             + "\n)"
         )
 
-    def save(self, filepath: Union[str, Path] = "./project.json"):
+    def save(self, filepath: str | Path = "./project.json"):
         """Save a project to a JSON file.
 
         Parameters
@@ -973,7 +973,7 @@ def make_custom_file_dict(item):
         filepath.write_text(json.dumps(json_dict))
 
     @classmethod
-    def load(cls, path: Union[str, Path]) -> "Project":
+    def load(cls, path: str | Path) -> "Project":
         """Load a project from file.
 
         Parameters

ratapi/utils/convert.py

@@ -4,7 +4,6 @@
 from collections.abc import Iterable
 from os import PathLike
 from pathlib import Path
-from typing import Union
 
 from numpy import array, empty
 from scipy.io.matlab import MatlabOpaque, loadmat
@@ -15,7 +14,7 @@
 from ratapi.utils.enums import Geometries, Languages, LayerModels
 
 
-def r1_to_project(filename: Union[str, PathLike]) -> Project:
+def r1_to_project(filename: str | PathLike) -> Project:
     """Read a RasCAL1 project struct as a Python `Project`.
 
     Parameters
@@ -43,7 +42,7 @@ def r1_to_project(filename: Union[str, PathLike]) -> Project:
         layer_model = LayerModels.CustomXY
     layer_model = LayerModels(layer_model)
 
-    def zip_if_several(*params) -> Union[tuple, list[tuple]]:
+    def zip_if_several(*params) -> tuple | list[tuple]:
         """Zips parameters if necessary, but can handle single-item parameters.
 
         Examples
@@ -64,7 +63,7 @@ def zip_if_several(*params) -> Union[tuple, list[tuple]]:
 
         """
         if all(isinstance(param, Iterable) and not isinstance(param, str) for param in params):
-            return zip(*params)
+            return zip(*params, strict=False)
         return [params]
 
     def read_param(names, constrs, values, fits):
@@ -319,8 +318,8 @@ def fix_invalid_constraints(name: str, constrs: tuple[float, float], value: floa
 
 
 def project_to_r1(
-    project: Project, filename: Union[str, PathLike] = "RAT_project", return_struct: bool = False
-) -> Union[dict, None]:
+    project: Project, filename: str | PathLike = "RAT_project", return_struct: bool = False
+) -> dict | None:
     """Convert a RAT Project to a RasCAL1 project struct.
 
     Parameters

ratapi/utils/custom_errors.py

@@ -1,13 +1,11 @@
 """Defines routines for custom error handling in RAT."""
 
-from typing import Optional
-
 import pydantic_core
 
 
 def custom_pydantic_validation_error(
     error_list: list[pydantic_core.ErrorDetails],
-    custom_error_msgs: Optional[dict[str, str]] = None,
+    custom_error_msgs: dict[str, str] | None = None,
 ) -> list[pydantic_core.ErrorDetails]:
     """Give Pydantic errors a better custom message with extraneous information removed.
 

ratapi/utils/enums.py

@@ -1,7 +1,5 @@
 """The Enum values used in the parameters of various ratapi classes and functions."""
 
-from typing import Union
-
 try:
     from enum import StrEnum
 except ImportError:
@@ -92,7 +90,7 @@ class Strategies(RATEnum):
     or a pure recombination of parent parameter values."""
 
     @classmethod
-    def _missing_(cls, value: Union[int, str]):
+    def _missing_(cls, value: int | str):
         # legacy compatibility with strategies being 1-indexed ints under the hood
         if isinstance(value, int):
             if value < 1 or value > 6: