Add B, UP and SIM linting rules

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.10.1-23-g55e8e0e
+_commit: v0.10.1-25-ga5301e9
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/dynamics-app
 app_doi: 10.5281/zenodo.18877180

.github/workflows/test.yml

@@ -74,7 +74,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, macos-14, windows-2022]
+        os: [ubuntu-24.04, macos-15, windows-2022]
 
     runs-on: ${{ matrix.os }}
 
@@ -163,7 +163,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, macos-14, windows-2022]
+        os: [ubuntu-24.04, macos-15, windows-2022]
 
     runs-on: ${{ matrix.os }}
 
@@ -202,11 +202,8 @@ jobs:
             echo "Adding Python $py_ver"
             pixi add "python=$py_ver"
 
-            echo "Adding Conda dependencies"
-            pixi add gsl
-
-            #echo "Adding PyPI dependencies"
-            #pixi add --pypi pytest pytest-xdist
+            echo "Setting macOS 14.0 as minimum required"
+            pixi project system-requirements add macos 14.0
 
             echo "Looking for wheel in ../dist/py$py_ver/"
             ls -l "../dist/py$py_ver/"

docs/docs/tutorials/analysis1d.ipynb

@@ -81,8 +81,7 @@
     ")\n",
     "\n",
     "fit_result = my_analysis.fit()\n",
-    "fig = my_analysis.plot_data_and_model()\n",
-    "fig"
+    "my_analysis.plot_data_and_model()"
    ]
   }
  ],
@@ -102,7 +101,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.13"
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,

docs/docs/tutorials/convolution.ipynb

@@ -30,7 +30,7 @@
     "from easydynamics.sample_model import Gaussian\n",
     "from easydynamics.sample_model import Lorentzian\n",
     "from easydynamics.sample_model.component_collection import ComponentCollection\n",
-    "from easydynamics.utils import _detailed_balance_factor as detailed_balance_factor\n",
+    "from easydynamics.utils import detailed_balance_factor\n",
     "\n",
     "%matplotlib widget"
    ]

docs/docs/tutorials/detailed_balance.ipynb

@@ -25,7 +25,7 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "\n",
-    "from easydynamics.utils import _detailed_balance_factor as detailed_balance_factor\n",
+    "from easydynamics.utils import detailed_balance_factor\n",
     "\n",
     "%matplotlib widget"
    ]

pixi.toml

@@ -119,6 +119,7 @@ check = 'pre-commit run --hook-stage manual --all-files'
 docs-format-fix = 'docformatter --in-place src/ docs/docs/tutorials/'
 notebook-lint-fix = 'nbqa ruff --fix docs/docs/tutorials/'
 py-lint-fix = 'ruff check --fix src/ tests/ docs/docs/tutorials/'
+py-lint-fix-unsafe = 'ruff check --fix --unsafe-fixes src/ tests/ docs/docs/tutorials/'
 py-format-fix = "ruff format src/ tests/ docs/docs/tutorials/"
 nonpy-format-fix = 'npx prettier --write --list-different --config=prettierrc.toml --ignore-unknown .'
 nonpy-format-fix-modified = "python tools/nonpy_prettier_modified.py --write"

pyproject.toml

@@ -204,7 +204,7 @@ select = [
   #'PERF', # https://docs.astral.sh/ruff/rules/#perflint-perf
   #'RUF',  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
   #'TRY',  # https://docs.astral.sh/ruff/rules/#tryceratops-try
-  #'UP',   # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+  'UP', # https://docs.astral.sh/ruff/rules/#pyupgrade-up
   # pycodestyle (E, W) rules
   'E', # https://docs.astral.sh/ruff/rules/#error-e
   'W', # https://docs.astral.sh/ruff/rules/#warning-w
@@ -218,7 +218,7 @@ select = [
   'ANN', # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
   #'ARG',   # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
   #'ASYNC', # https://docs.astral.sh/ruff/rules/#flake8-async-async
-  #'B',     # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+  'B', # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
   #'BLE',   # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble
   #'C4',    # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
   #'COM',   # https://docs.astral.sh/ruff/rules/#flake8-commas-com
@@ -238,8 +238,8 @@ select = [
   #'PYI',   # https://docs.astral.sh/ruff/rules/#flake8-pyi-pyi
   #'RET',   # https://docs.astral.sh/ruff/rules/#flake8-return-ret
   #'RSE',   # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
-  'S', # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
-  #'SIM',   # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+  'S',   # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+  'SIM', # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
   #'SLF',   # https://docs.astral.sh/ruff/rules/#flake8-self-slf
   #'SLOT',  # https://docs.astral.sh/ruff/rules/#flake8-slots-slot
   #'T20',   # https://docs.astral.sh/ruff/rules/#flake8-print-t20

src/easydynamics/analysis/analysis.py

@@ -284,7 +284,7 @@ def plot_data_and_model(
             components = self._create_components_dataset(
                 add_background=add_background, energy=energy
             )
-            for key in components.keys():
+            for key in components:
                 data_and_model[key] = components[key]
                 plot_kwargs_defaults['linestyle'][key] = '--'
                 plot_kwargs_defaults['marker'][key] = None
@@ -362,7 +362,7 @@ def parameters_to_dataset(self) -> sc.Dataset:
                 dims=['Q'],
                 values=np.asarray(values[name], dtype=float),
                 variances=np.asarray(variances[name], dtype=float),
-                unit=units.get(name, None),
+                unit=units.get(name),
             )
 
         return ds

src/easydynamics/analysis/analysis1d.py

@@ -292,7 +292,7 @@ def plot_data_and_model(
         }
 
         if plot_components:
-            for comp_name in component_dataset.keys():
+            for comp_name in component_dataset:
                 plot_kwargs_defaults['linestyle'][comp_name] = '--'
                 plot_kwargs_defaults['marker'][comp_name] = None
 

src/easydynamics/analysis/analysis_base.py

@@ -325,13 +325,12 @@ def _verify_Q_index(self, Q_index: int | None) -> int | None:
         Raises:
             IndexError: If the Q index is not valid.
         """
-        if Q_index is not None:
-            if (
-                not isinstance(Q_index, int)
-                or Q_index < 0
-                or (self.Q is not None and Q_index >= len(self.Q))
-            ):
-                raise IndexError('Q_index must be a valid index for the Q values.')
+        if Q_index is not None and (
+            not isinstance(Q_index, int)
+            or Q_index < 0
+            or (self.Q is not None and Q_index >= len(self.Q))
+        ):
+            raise IndexError('Q_index must be a valid index for the Q values.')
         return Q_index
 
     #############

src/easydynamics/convolution/convolution.py

@@ -198,12 +198,10 @@ def _check_if_pair_is_analytic(
             )
 
         analytical_types = (Gaussian, Lorentzian, Voigt)
-        if isinstance(sample_component, analytical_types) and isinstance(
-            resolution_component, analytical_types
-        ):
-            return True
-
-        return False
+        return bool(
+            isinstance(sample_component, analytical_types)
+            and isinstance(resolution_component, analytical_types)
+        )
 
     def _build_convolution_plan(self) -> None:
         """Separate sample model components into analytical pairs, delta

src/easydynamics/convolution/convolution_base.py

@@ -70,8 +70,7 @@ def __init__(
         self._energy_offset = energy_offset
 
         if sample_components is not None and not (
-            isinstance(sample_components, ComponentCollection)
-            or isinstance(sample_components, ModelComponent)
+            isinstance(sample_components, (ComponentCollection, ModelComponent))
         ):
             raise TypeError(
                 f'`sample_components` is an instance of {type(sample_components).__name__}, but must be a ComponentCollection or ModelComponent.'  # noqa: E501
@@ -81,8 +80,7 @@ def __init__(
         self._sample_components = sample_components
 
         if resolution_components is not None and not (
-            isinstance(resolution_components, ComponentCollection)
-            or isinstance(resolution_components, ModelComponent)
+            isinstance(resolution_components, (ComponentCollection, ModelComponent))
         ):
             raise TypeError(
                 f'`resolution_components` is an instance of {type(resolution_components).__name__}, but must be a ComponentCollection or ModelComponent.'  # noqa: E501
@@ -196,10 +194,8 @@ def energy_unit(self) -> str:
     @energy_unit.setter
     def energy_unit(self, unit_str: str) -> None:
         raise AttributeError(
-            (
-                f'Unit is read-only. Use convert_unit to change the unit between allowed types '
-                f'or create a new {self.__class__.__name__} with the desired unit.'
-            )
+            f'Unit is read-only. Use convert_unit to change the unit between allowed types '
+            f'or create a new {self.__class__.__name__} with the desired unit.'
         )  # noqa: E501
 
     def convert_energy_unit(self, energy_unit: str | sc.Unit) -> None:

src/easydynamics/convolution/numerical_convolution.py

@@ -9,7 +9,7 @@
 from easydynamics.convolution.numerical_convolution_base import NumericalConvolutionBase
 from easydynamics.sample_model.component_collection import ComponentCollection
 from easydynamics.sample_model.components.model_component import ModelComponent
-from easydynamics.utils.detailed_balance import _detailed_balance_factor as detailed_balance_factor
+from easydynamics.utils.detailed_balance import detailed_balance_factor
 from easydynamics.utils.utils import Numeric
 
 

src/easydynamics/convolution/numerical_convolution_base.py

@@ -4,8 +4,6 @@
 import warnings
 
 # from dataclasses import dataclass
-from typing import Optional
-
 import numpy as np
 import scipp as sc
 from easyscience.variable import Parameter
@@ -194,11 +192,11 @@ def extension_factor(self, factor: Numeric) -> None:
         self._energy_grid = self._create_energy_grid()
 
     @property
-    def temperature(self) -> Optional[Parameter]:
+    def temperature(self) -> Parameter | None:
         """Get the temperature.
 
         Returns:
-            Optional[Parameter]: The temperature parameter, or None if
+            Parameter | None: The temperature parameter, or None if
                 detailed balance correction is disabled.
         """
 
@@ -322,10 +320,7 @@ def _create_energy_grid(
         # select the 4 central points we either get
         # indices [2,3,4,5] or [1,2,3,4], both of which are offset by
         # 0.5*dx from the true center at index 3.5.
-        if len(energy_dense) % 2 == 0:
-            energy_even_length_offset = -0.5 * energy_dense_step
-        else:
-            energy_even_length_offset = 0.0
+        energy_even_length_offset = -0.5 * energy_dense_step if len(energy_dense) % 2 == 0 else 0.0
 
         # Handle the case when energy_dense is not symmetric around 0.
         # The resolution is still centered around zero (or close to it),
@@ -367,10 +362,7 @@ def _check_width_thresholds(
         """
 
         # Handle ComponentCollection or ModelComponent
-        if isinstance(model, ComponentCollection):
-            components = model.components
-        else:
-            components = [model]  # Treat single ModelComponent as a list
+        components = model.components if isinstance(model, ComponentCollection) else [model]
 
         for comp in components:
             if hasattr(comp, 'width'):
@@ -382,6 +374,7 @@ def _check_width_thresholds(
                             This may lead to inaccuracies in the convolution. \
                                 Increase extension_factor to improve accuracy.',
                         UserWarning,
+                        stacklevel=3,
                     )
                 if comp.width.value < SMALL_WIDTH_THRESHOLD * self._energy_grid.energy_dense_step:
                     warnings.warn(
@@ -391,6 +384,7 @@ def _check_width_thresholds(
                             This may lead to inaccuracies in the convolution. \
                                 Increase upsample_factor to improve accuracy.',
                         UserWarning,
+                        stacklevel=3,
                     )
 
     def __repr__(self) -> str:

src/easydynamics/experiment/experiment.py

@@ -306,7 +306,7 @@ def rebin(self, dimensions: dict[str, int | sc.Variable]) -> None:
                 # This line can be removed when scipp resize support
                 # resizing with coordinates
                 dimensions[dim] = value
-            if not (isinstance(value, int) or isinstance(value, sc.Variable)):
+            if not (isinstance(value, (int, sc.Variable))):
                 raise TypeError(
                     f'Dimension values must be integers or sc.Variable. '
                     f"Got {type(value)} for dimension '{dim}' instead."

src/easydynamics/sample_model/component_collection.py

@@ -4,7 +4,6 @@
 from __future__ import annotations
 
 import warnings
-from typing import List
 
 import numpy as np
 import scipp as sc
@@ -146,10 +145,8 @@ def unit(self, unit_str: str) -> None:
         """
 
         raise AttributeError(
-            (
-                f'Unit is read-only. Use convert_unit to change the unit between allowed types '
-                f'or create a new {self.__class__.__name__} with the desired unit.'
-            )
+            f'Unit is read-only. Use convert_unit to change the unit between allowed types '
+            f'or create a new {self.__class__.__name__} with the desired unit.'
         )  # noqa: E501
 
     def convert_unit(self, unit: str | sc.Unit) -> None:
@@ -187,7 +184,7 @@ def convert_unit(self, unit: str | sc.Unit) -> None:
     # Component management
     # ------------------------------------------------------------------
 
-    def append_component(self, component: ModelComponent | 'ComponentCollection') -> None:
+    def append_component(self, component: ModelComponent | ComponentCollection) -> None:
         """Append a model component or the components from another
         ComponentCollection to this ComponentCollection.
 
@@ -302,11 +299,11 @@ def is_empty(self, value: bool) -> None:
             'whether the collection has components.'
         )
 
-    def list_component_names(self) -> List[str]:
+    def list_component_names(self) -> list[str]:
         """List the names of all components in the model.
 
         Returns:
-            List[str]: List of unique names of the components in the
+            list[str]: List of unique names of the components in the
                 collection.
         """
 
@@ -340,6 +337,7 @@ def normalize_area(self) -> None:
                     f"Component '{component.unique_name}' does not have an 'area' attribute "
                     f'and will be skipped in normalization.',
                     UserWarning,
+                    stacklevel=2,
                 )
 
         if total_area.value == 0:
@@ -404,7 +402,7 @@ def evaluate_component(
 
         if not isinstance(unique_name, str):
             raise TypeError(
-                (f'Component unique name must be a string, got {type(unique_name)} instead.')
+                f'Component unique name must be a string, got {type(unique_name)} instead.'
             )
 
         matches = [comp for comp in self.components if comp.unique_name == unique_name]

src/easydynamics/sample_model/components/delta_function.py

@@ -140,13 +140,13 @@ def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray)
             i = np.argmin(np.abs(x - center))
 
             # left half-width
-            if i == 0:
+            if i == 0:  # noqa: SIM108
                 left = x[1] - x[0] if x.size > 1 else 0.5
             else:
                 left = x[i] - x[i - 1]
 
             # right half-width
-            if i == x.size - 1:
+            if i == x.size - 1:  # noqa: SIM108
                 right = x[-1] - x[-2] if x.size > 1 else 0.5
             else:
                 right = x[i + 1] - x[i]

src/easydynamics/sample_model/components/mixins.py

@@ -62,7 +62,9 @@ def _create_area_parameter(
 
         if area.value < 0:
             warnings.warn(
-                f'The area of {name} is negative, which may not be physically meaningful.'
+                f'The area of {name} is negative, which may not be physically meaningful.',
+                UserWarning,
+                stacklevel=3,
             )
         else:
             area.min = minimum_area