Introduces ruff as linter and formatter (#38)

* Adds ruff and resolves linting errors on standard rule set

* Resolves automatically fixable linting errors on advanced rule set

* Resolves most manually fixable linting errors on advanced rule set

* Switches code to use double quotes

* Resolves automatically fixable linting errors on full rule set

* Applies ruff formatter

* Finalises rule selection and tidies up code

* Adds "requirements-dev.txt"

* Adds "requirements-dev.txt"

* Adds new github action for linter and formatter

* Addresses review comments

Author: DrPaulSharp

.github/workflows/run_ruff.yml

@@ -0,0 +1,18 @@
+name: Ruff
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: 'format --check'
+          

.gitignore

@@ -28,3 +28,6 @@ docs/*.inv
 build/*
 dist/*
 *.whl
+
+# Local pre-commit hooks
+.pre-commit-config.yaml

RAT/__init__.py

@@ -1,9 +1,12 @@
 import os
+
+from RAT import models
 from RAT.classlist import ClassList
-from RAT.project import Project
 from RAT.controls import set_controls
+from RAT.project import Project
 from RAT.run import run
-import RAT.models
+
+__all__ = ["ClassList", "Project", "run", "set_controls", "models"]
 
 dir_path = os.path.dirname(os.path.realpath(__file__))
-os.environ["RAT_PATH"] = os.path.join(dir_path, '')
+os.environ["RAT_PATH"] = os.path.join(dir_path, "")

RAT/classlist.py

@@ -1,12 +1,14 @@
-"""The classlist module. Contains the ClassList class, which defines a list containing instances of a particular class.
+"""The classlist module. Contains the ClassList class, which defines a list containing instances of a particular
+class.
 """
 
 import collections
-from collections.abc import Iterable, Sequence
 import contextlib
-import prettytable
-from typing import Any, Union
 import warnings
+from collections.abc import Iterable, Sequence
+from typing import Any, Union
+
+import prettytable
 
 
 class ClassList(collections.UserList):
@@ -31,7 +33,9 @@ class ClassList(collections.UserList):
         An instance, or list of instance(s), of the class to be used in this ClassList.
     name_field : str, optional
         The field used to define unique objects in the ClassList (default is "name").
+
     """
+
     def __init__(self, init_list: Union[Sequence[object], object] = None, name_field: str = "name") -> None:
         self.name_field = name_field
 
@@ -56,7 +60,7 @@ def __repr__(self):
         else:
             if any(model.__dict__ for model in self.data):
                 table = prettytable.PrettyTable()
-                table.field_names = ['index'] + [key.replace('_', ' ') for key in self.data[0].__dict__.keys()]
+                table.field_names = ["index"] + [key.replace("_", " ") for key in self.data[0].__dict__]
                 table.add_rows([[index] + list(model.__dict__.values()) for index, model in enumerate(self.data)])
                 output = table.get_string()
             else:
@@ -81,15 +85,15 @@ def _delitem(self, index: int) -> None:
         """Auxiliary routine of "__delitem__" used to enable wrapping."""
         del self.data[index]
 
-    def __iadd__(self, other: Sequence[object]) -> 'ClassList':
+    def __iadd__(self, other: Sequence[object]) -> "ClassList":
         """Define in-place addition using the "+=" operator."""
         return self._iadd(other)
 
-    def _iadd(self, other: Sequence[object]) -> 'ClassList':
+    def _iadd(self, other: Sequence[object]) -> "ClassList":
         """Auxiliary routine of "__iadd__" used to enable wrapping."""
         if other and not (isinstance(other, Sequence) and not isinstance(other, str)):
             other = [other]
-        if not hasattr(self, '_class_handle'):
+        if not hasattr(self, "_class_handle"):
             self._class_handle = self._determine_class_handle(self + other)
         self._check_classes(self + other)
         self._check_unique_name_fields(self + other)
@@ -129,20 +133,27 @@ def append(self, obj: object = None, **kwargs) -> None:
         SyntaxWarning
             Raised if the input arguments contain BOTH an object and keyword arguments. In this situation the object is
             appended to the ClassList and the keyword arguments are discarded.
+
         """
         if obj and kwargs:
-            warnings.warn('ClassList.append() called with both an object and keyword arguments. '
-                          'The keyword arguments will be ignored.', SyntaxWarning)
+            warnings.warn(
+                "ClassList.append() called with both an object and keyword arguments. "
+                "The keyword arguments will be ignored.",
+                SyntaxWarning,
+                stacklevel=2,
+            )
         if obj:
-            if not hasattr(self, '_class_handle'):
+            if not hasattr(self, "_class_handle"):
                 self._class_handle = type(obj)
             self._check_classes(self + [obj])
             self._check_unique_name_fields(self + [obj])
             self.data.append(obj)
         else:
-            if not hasattr(self, '_class_handle'):
-                raise TypeError('ClassList.append() called with keyword arguments for a ClassList without a class '
-                                'defined. Call ClassList.append() with an object to define the class.')
+            if not hasattr(self, "_class_handle"):
+                raise TypeError(
+                    "ClassList.append() called with keyword arguments for a ClassList without a class "
+                    "defined. Call ClassList.append() with an object to define the class.",
+                )
             self._validate_name_field(kwargs)
             self.data.append(self._class_handle(**kwargs))
 
@@ -169,20 +180,27 @@ def insert(self, index: int, obj: object = None, **kwargs) -> None:
         SyntaxWarning
             Raised if the input arguments contain both an object and keyword arguments. In this situation the object is
             inserted into the ClassList and the keyword arguments are discarded.
+
         """
         if obj and kwargs:
-            warnings.warn('ClassList.insert() called with both an object and keyword arguments. '
-                          'The keyword arguments will be ignored.', SyntaxWarning)
+            warnings.warn(
+                "ClassList.insert() called with both an object and keyword arguments. "
+                "The keyword arguments will be ignored.",
+                SyntaxWarning,
+                stacklevel=2,
+            )
         if obj:
-            if not hasattr(self, '_class_handle'):
+            if not hasattr(self, "_class_handle"):
                 self._class_handle = type(obj)
             self._check_classes(self + [obj])
             self._check_unique_name_fields(self + [obj])
             self.data.insert(index, obj)
         else:
-            if not hasattr(self, '_class_handle'):
-                raise TypeError('ClassList.insert() called with keyword arguments for a ClassList without a class '
-                                'defined. Call ClassList.insert() with an object to define the class.')
+            if not hasattr(self, "_class_handle"):
+                raise TypeError(
+                    "ClassList.insert() called with keyword arguments for a ClassList without a class "
+                    "defined. Call ClassList.insert() with an object to define the class.",
+                )
             self._validate_name_field(kwargs)
             self.data.insert(index, self._class_handle(**kwargs))
 
@@ -209,7 +227,7 @@ def extend(self, other: Sequence[object]) -> None:
         """Extend the ClassList by adding another sequence."""
         if other and not (isinstance(other, Sequence) and not isinstance(other, str)):
             other = [other]
-        if not hasattr(self, '_class_handle'):
+        if not hasattr(self, "_class_handle"):
             self._class_handle = self._determine_class_handle(self + other)
         self._check_classes(self + other)
         self._check_unique_name_fields(self + other)
@@ -229,6 +247,7 @@ def get_names(self) -> list[str]:
         -------
         names : list [str]
             The value of the name_field attribute of each object in the ClassList.
+
         """
         return [getattr(model, self.name_field) for model in self.data if hasattr(model, self.name_field)]
 
@@ -244,9 +263,14 @@ def get_all_matches(self, value: Any) -> list[tuple]:
         -------
          : list [tuple]
             A list of (index, field) tuples matching the given value.
+
         """
-        return [(index, field) for index, element in enumerate(self.data) for field in vars(element)
-                if getattr(element, field) == value]
+        return [
+            (index, field)
+            for index, element in enumerate(self.data)
+            for field in vars(element)
+            if getattr(element, field) == value
+        ]
 
     def _validate_name_field(self, input_args: dict[str, Any]) -> None:
         """Raise a ValueError if the name_field attribute is passed as an object parameter, and its value is already
@@ -261,12 +285,15 @@ def _validate_name_field(self, input_args: dict[str, Any]) -> None:
         ------
         ValueError
             Raised if the input arguments contain a name_field value already defined in the ClassList.
+
         """
         names = self.get_names()
         with contextlib.suppress(KeyError):
             if input_args[self.name_field] in names:
-                raise ValueError(f"Input arguments contain the {self.name_field} '{input_args[self.name_field]}', "
-                                 f"which is already specified in the ClassList")
+                raise ValueError(
+                    f"Input arguments contain the {self.name_field} '{input_args[self.name_field]}', "
+                    f"which is already specified in the ClassList",
+                )
 
     def _check_unique_name_fields(self, input_list: Iterable[object]) -> None:
         """Raise a ValueError if any value of the name_field attribute is used more than once in a list of class
@@ -281,6 +308,7 @@ def _check_unique_name_fields(self, input_list: Iterable[object]) -> None:
         ------
         ValueError
             Raised if the input list defines more than one object with the same value of name_field.
+
         """
         names = [getattr(model, self.name_field) for model in input_list if hasattr(model, self.name_field)]
         if len(set(names)) != len(names):
@@ -298,6 +326,7 @@ def _check_classes(self, input_list: Iterable[object]) -> None:
         ------
         ValueError
             Raised if the input list defines objects of different types.
+
         """
         if not (all(isinstance(element, self._class_handle) for element in input_list)):
             raise ValueError(f"Input list contains elements of type other than '{self._class_handle.__name__}'")
@@ -315,6 +344,7 @@ def _get_item_from_name_field(self, value: Union[object, str]) -> Union[object,
         instance : object or str
             Either the object with the value of the name_field attribute given by value, or the input value if an
             object with that value of the name_field attribute cannot be found.
+
         """
         return next((model for model in self.data if getattr(model, self.name_field) == value), value)
 
@@ -333,6 +363,7 @@ def _determine_class_handle(input_list: Sequence[object]):
         class_handle : type
             The type object of the element fulfilling the condition of satisfying "issubclass" for all of the other
             elements.
+
         """
         for this_element in input_list:
             if all([issubclass(type(instance), type(this_element)) for instance in input_list]):

RAT/controls.py

@@ -1,15 +1,17 @@
 from dataclasses import dataclass, field
-import prettytable
-from pydantic import BaseModel, Field, field_validator, ValidationError
 from typing import Literal, Union
 
-from RAT.utils.enums import Parallel, Procedures, Display, BoundHandling, Strategies
+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
 
 
 @dataclass(frozen=True)
 class Controls:
     """The full set of controls parameters required for the compiled RAT code."""
+
     # All Procedures
     procedure: Procedures = Procedures.Calculate
     parallel: Parallel = Parallel.Single
@@ -44,8 +46,9 @@ class Controls:
     adaptPCR: bool = False
 
 
-class Calculate(BaseModel, validate_assignment=True, extra='forbid'):
+class Calculate(BaseModel, validate_assignment=True, extra="forbid"):
     """Defines the class for the calculate procedure, which includes the properties used in all five procedures."""
+
     procedure: Literal[Procedures.Calculate] = Procedures.Calculate
     parallel: Parallel = Parallel.Single
     calcSldDuringFit: bool = False
@@ -56,20 +59,21 @@ class Calculate(BaseModel, validate_assignment=True, extra='forbid'):
     @classmethod
     def check_resample_params(cls, resampleParams):
         if not 0 < resampleParams[0] < 1:
-            raise ValueError('resampleParams[0] must be between 0 and 1')
+            raise ValueError("resampleParams[0] must be between 0 and 1")
         if resampleParams[1] < 0:
-            raise ValueError('resampleParams[1] must be greater than or equal to 0')
+            raise ValueError("resampleParams[1] must be greater than or equal to 0")
         return resampleParams
 
     def __repr__(self) -> str:
         table = prettytable.PrettyTable()
-        table.field_names = ['Property', 'Value']
+        table.field_names = ["Property", "Value"]
         table.add_rows([[k, v] for k, v in self.__dict__.items()])
         return table.get_string()
 
 
 class Simplex(Calculate):
     """Defines the additional fields for the simplex procedure."""
+
     procedure: Literal[Procedures.Simplex] = Procedures.Simplex
     xTolerance: float = Field(1.0e-6, gt=0.0)
     funcTolerance: float = Field(1.0e-6, gt=0.0)
@@ -81,6 +85,7 @@ class Simplex(Calculate):
 
 class DE(Calculate):
     """Defines the additional fields for the Differential Evolution procedure."""
+
     procedure: Literal[Procedures.DE] = Procedures.DE
     populationSize: int = Field(20, ge=1)
     fWeight: float = 0.5
@@ -92,6 +97,7 @@ class DE(Calculate):
 
 class NS(Calculate):
     """Defines the additional fields for the Nested Sampler procedure."""
+
     procedure: Literal[Procedures.NS] = Procedures.NS
     nLive: int = Field(150, ge=1)
     nMCMC: float = Field(0.0, ge=0.0)
@@ -101,6 +107,7 @@ class NS(Calculate):
 
 class Dream(Calculate):
     """Defines the additional fields for the Dream procedure."""
+
     procedure: Literal[Procedures.Dream] = Procedures.Dream
     nSamples: int = Field(50000, ge=0)
     nChains: int = Field(10, gt=0)
@@ -110,28 +117,31 @@ class Dream(Calculate):
     adaptPCR: bool = False
 
 
-def set_controls(procedure: Procedures = Procedures.Calculate, **properties)\
-        -> Union[Calculate, Simplex, DE, NS, Dream]:
+def set_controls(
+    procedure: Procedures = Procedures.Calculate,
+    **properties,
+) -> Union[Calculate, Simplex, DE, NS, Dream]:
     """Returns the appropriate controls model given the specified procedure."""
     controls = {
         Procedures.Calculate: Calculate,
         Procedures.Simplex: Simplex,
         Procedures.DE: DE,
         Procedures.NS: NS,
-        Procedures.Dream: Dream
+        Procedures.Dream: Dream,
     }
 
     try:
         model = controls[procedure](**properties)
     except KeyError:
         members = list(Procedures.__members__.values())
         allowed_values = f'{", ".join([repr(member.value) for member in members[:-1]])} or {members[-1].value!r}'
-        raise ValueError(f'The controls procedure must be one of: {allowed_values}') from None
+        raise ValueError(f"The controls procedure must be one of: {allowed_values}") from None
     except ValidationError as exc:
-        custom_error_msgs = {'extra_forbidden': f'Extra inputs are not permitted. The fields for the {procedure}'
-                                                f' controls procedure are:\n    '
-                                                f'{", ".join(controls[procedure].model_fields.keys())}\n'
-                             }
+        custom_error_msgs = {
+            "extra_forbidden": f'Extra inputs are not permitted. The fields for the {procedure}'
+            f' controls procedure are:\n    '
+            f'{", ".join(controls[procedure].model_fields.keys())}\n',
+        }
         custom_error_list = custom_pydantic_validation_error(exc.errors(), custom_error_msgs)
         raise ValidationError.from_exception_data(exc.title, custom_error_list) from None