Add RUF, NPY and several other linting rules

docs/docs/tutorials/analysis.ipynb

@@ -213,10 +213,7 @@
     "    instrument_model=instrument_model,\n",
     ")\n",
     "\n",
-    "# We need to hack in the resolution model from the vanadium analysis,\n",
-    "# since the setters and getters overwrite the model. This will be fixed\n",
-    "# asap.\n",
-    "diffusion_analysis.instrument_model._resolution_model = (\n",
+    "diffusion_analysis.instrument_model.resolution_model = (\n",
     "    vanadium_analysis.instrument_model.resolution_model\n",
     ")\n",
     "\n",
@@ -305,10 +302,7 @@
     "    instrument_model=instrument_model,\n",
     ")\n",
     "\n",
-    "# We again need to hack in the resolution model from the vanadium\n",
-    "# analysis, since the setters and getters overwrite the model. This will\n",
-    "# be fixed asap.\n",
-    "diffusion_model_analysis.instrument_model._resolution_model = (\n",
+    "diffusion_model_analysis.instrument_model.resolution_model = (\n",
     "    vanadium_analysis.instrument_model.resolution_model\n",
     ")\n",
     "diffusion_model_analysis.instrument_model.resolution_model.fix_all_parameters()\n",

docs/docs/tutorials/tutorial2_nanoparticles.ipynb

@@ -34,7 +34,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "bca91d3c",
    "metadata": {},
    "outputs": [],
@@ -70,15 +70,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "4fbb90da",
    "metadata": {},
    "outputs": [],
    "source": [
     "resolution_experiment = Experiment(display_name='Nanoparticles, 1.5 K')\n",
     "\n",
     "file_path = pooch.retrieve(\n",
-    "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/tutorial2/docs/docs/tutorials/data/nano_1p5K.h5',\n",
+    "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/master/docs/docs/tutorials/data/nano_1p5K.h5',\n",
     "    known_hash='32935cfaa5e623137ea5f4ba972d0c921bca8d0e067486666cdcf23abf27823e',\n",
     ")\n",
     "\n",
@@ -216,7 +216,7 @@
     "resolution_experiment = Experiment(display_name='Nanoparticles, 1.5 K')\n",
     "\n",
     "file_path = pooch.retrieve(\n",
-    "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/tutorial2/docs/docs/tutorials/data/nano_150K.h5',\n",
+    "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/master/docs/docs/tutorials/data/nano_150K.h5',\n",
     "    known_hash='dc3abdaf6d2165f4dbc5df4e0de1890af8d4cd290f2c79ac7b319ccbe44117b8',\n",
     ")\n",
     "\n",

pyproject.toml

@@ -202,11 +202,11 @@ select = [
   #'FURB', # https://docs.astral.sh/ruff/rules/#refurb-furb
   'I', # https://docs.astral.sh/ruff/rules/#isort-i
   #'N',    # https://docs.astral.sh/ruff/rules/#pep8-naming-n
-  #'NPY',  # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy
+  'NPY', # https://docs.astral.sh/ruff/rules/#numpy-specific-rules-npy
   #'PGH',  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
-  #'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
+  '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 # overly restrictive
   'UP', # https://docs.astral.sh/ruff/rules/#pyupgrade-up
   # pycodestyle (E, W) rules
   'E', # https://docs.astral.sh/ruff/rules/#error-e
@@ -215,49 +215,48 @@ select = [
   #'PLC', # https://docs.astral.sh/ruff/rules/#convention-plc
   #'PLE', # https://docs.astral.sh/ruff/rules/#error-ple
   #'PLR', # https://docs.astral.sh/ruff/rules/#refactor-plr
-  #'PLW', # https://docs.astral.sh/ruff/rules/#warning-plw
+  #'PLW', # https://docs.astral.sh/ruff/rules/#warning-plw # Good to enable
   # flake8 rules
-  'A',   # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
-  '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
-  #'BLE',   # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble
+  'A',     # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+  '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
+  #'BLE',   # https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble # enable when base classes have been merged in
   'C4',  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
   'COM', # https://docs.astral.sh/ruff/rules/#flake8-commas-com
-  #'DTZ',   # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-  #'EM',    # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+  'DTZ', # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+  #'EM',    # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em # Unsure if I want it - requires all error messages to be rewritten
   'FA', # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa
-  #'FBT',   # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt
-  #'FIX',   # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix
-  #'G',     # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
-  #'ICN',   # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn
-  #'INP',   # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
-  #'ISC',   # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
-  #'LOG',   # https://docs.astral.sh/ruff/rules/#flake8-logging-log
-  #'PIE',   # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
-  #'PT',    # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
-  'PTH', # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
-  #'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
-  #'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
-  'TC', # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc
-  #'TD',    # https://docs.astral.sh/ruff/rules/#flake8-todos-td
-  'TID', # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid
+  #'FBT',   # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt # should eventually be enabled, but may break serialization
+  'FIX', # https://docs.astral.sh/ruff/rules/#flake8-fixme-fix
+  'G',   # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+  'ICN', # https://docs.astral.sh/ruff/rules/#flake8-import-conventions-icn
+  'INP', # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
+  'ISC', # https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
+  'LOG', # https://docs.astral.sh/ruff/rules/#flake8-logging-log
+  'PIE', # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+  #'PT',    # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt # Should eventually be enabled, but quite a few errors to fix
+  'PTH',  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+  '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
+  '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
+  'TC',   # https://docs.astral.sh/ruff/rules/#flake8-type-checking-tc
+  'TD',   # https://docs.astral.sh/ruff/rules/#flake8-todos-td
+  'TID',  # https://docs.astral.sh/ruff/rules/#flake8-tidy-imports-tid
 ]
 
 # Exceptions to the linting rules
 
 # Ignore specific rules globally
 ignore = [
   'COM812', # https://docs.astral.sh/ruff/rules/missing-trailing-comma/
-  # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint]
-  'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc
+  # The following is replaced by 'D'/[tool.ruff.lint.pydocstyle] and [tool.pydoclint]  'DOC', # https://docs.astral.sh/ruff/rules/#pydoclint-doc
   # Disable, as [tool.format_docstring] split one-line docstrings into the canonical multi-line layout
   'D200', # https://docs.astral.sh/ruff/rules/unnecessary-multiline-docstring/
 ]
@@ -273,6 +272,7 @@ ignore = [
   'DOC',    # https://docs.astral.sh/ruff/rules/#pydoclint-doc
   'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/
   'S101',   # https://docs.astral.sh/ruff/rules/assert/
+  'SLF',    # https://docs.astral.sh/ruff/rules/#flake8-self-slf # may want to eventually enable it, but accessing private methods is quite useful in tests
 ]
 'docs/**' = [
   'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/

src/easydynamics/analysis/analysis.py

@@ -567,14 +567,18 @@ def _fit_all_Q_simultaneously(self) -> FitResults:
         ys = []
         ws = []
 
-        for analysis in self.analysis_list:
-            x, y, weight, _ = self.experiment._extract_x_y_weights_only_finite(analysis.Q_index)
+        for analysis1d in self.analysis_list:
+            x, y, weight, _ = self.experiment._extract_x_y_weights_only_finite(  # noqa: SLF001
+                analysis1d.Q_index
+            )
             xs.append(x)
             ys.append(y)
             ws.append(weight)
 
             # Make sure the convolver is up to date for this Q index
-            analysis._convolver = analysis._create_convolver(energy=x)
+            analysis1d._convolver = analysis1d._create_convolver(  # noqa: SLF001
+                energy=x
+            )
 
         mf = MultiFitter(
             fit_objects=self.analysis_list,
@@ -655,10 +659,10 @@ def _create_components_dataset(
             energy = self.energy
 
         datasets = [
-            analysis._create_components_dataset_single_Q(
+            analysis1d._create_components_dataset_single_Q(  # noqa: SLF001
                 add_background=add_background, energy=energy
             )
-            for analysis in self.analysis_list
+            for analysis1d in self.analysis_list
         ]
 
         return sc.concat(datasets, dim='Q')

src/easydynamics/analysis/analysis1d.py

@@ -195,7 +195,7 @@ def fit(self) -> FitResults:
             fit_function=self.as_fit_function(),
         )
 
-        x, y, weights, _ = self.experiment._extract_x_y_weights_only_finite(
+        x, y, weights, _ = self.experiment._extract_x_y_weights_only_finite(  # noqa: SLF001
             Q_index=self._require_Q_index()
         )
         fit_result = fitter.fit(x=x, y=y, weights=weights)
@@ -671,7 +671,6 @@ def _create_convolver(
         if resolution_components.is_empty:
             return None
 
-        # TODO: allow convolution options to be set.
         return Convolution(
             sample_components=sample_components,
             resolution_components=resolution_components,

src/easydynamics/convolution/analytical_convolution.py

@@ -1,6 +1,8 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
 
+from typing import ClassVar
+
 import numpy as np
 import scipp as sc
 from easyscience.variable import Parameter
@@ -26,7 +28,7 @@ class AnalyticalConvolution(ConvolutionBase):
 
     # Mapping of supported component type pairs to convolution methods.
     # Delta functions are handled separately.
-    _CONVOLUTIONS = {
+    _CONVOLUTIONS: ClassVar[dict[str, object]] = {
         ('Gaussian', 'Gaussian'): '_convolute_gaussian_gaussian',
         ('Gaussian', 'Lorentzian'): '_convolute_gaussian_lorentzian',
         ('Gaussian', 'Voigt'): '_convolute_gaussian_voigt',

src/easydynamics/convolution/convolution.py

@@ -1,6 +1,8 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
 
+from typing import ClassVar
+
 import numpy as np
 import scipp as sc
 from easyscience.variable import Parameter
@@ -33,7 +35,7 @@ class Convolution(NumericalConvolutionBase):
 
     # When these attributes are changed, the convolution plan
     # needs to be rebuilt
-    _invalidate_plan_on_change = {
+    _invalidate_plan_on_change: ClassVar[dict[str, object]] = {
         'energy',
         '_energy',
         '_energy_grid',
@@ -231,11 +233,10 @@ def _build_convolution_plan(self) -> None:
             # If temperature is not set, check if all
             # resolution components can be convolved analytically with
             # this sample component
-            pair_is_analytic = []
-            for resolution_component in self._resolution_components.components:
-                pair_is_analytic.append(
-                    self._check_if_pair_is_analytic(sample_component, resolution_component)
-                )
+            pair_is_analytic = [
+                self._check_if_pair_is_analytic(sample_component, resolution_component)
+                for resolution_component in self._resolution_components.components
+            ]
             # If all resolution components can be convolved analytically
             # with this sample component, add it to analytical
             # sample model. If not, it goes to numerical sample model.

src/easydynamics/convolution/convolution_base.py

@@ -222,7 +222,7 @@ 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.'
-        )  # noqa: E501
+        )
 
     def convert_energy_unit(self, energy_unit: str | sc.Unit) -> None:
         """

src/easydynamics/convolution/numerical_convolution_base.py

@@ -432,8 +432,8 @@ def __repr__(self) -> str:
         return (
             f'{self.__class__.__name__}('
             f'energy=array of shape {self.energy.values.shape},\n '
-            f'sample_components={repr(self.sample_components)}, \n'
-            f'resolution_components={repr(self.resolution_components)},\n '
+            f'sample_components={self.sample_components!r}, \n'
+            f'resolution_components={self.resolution_components!r},\n '
             f'energy_unit={self._energy_unit}, '
             f'upsample_factor={self.upsample_factor}, '
             f'extension_factor={self.extension_factor}, '

src/easydynamics/sample_model/__init__.py

@@ -21,18 +21,18 @@
 from easydynamics.sample_model.sample_model import SampleModel
 
 __all__ = [
+    'BackgroundModel',
+    'BrownianTranslationalDiffusion',
     'ComponentCollection',
+    'DampedHarmonicOscillator',
+    'DeltaFunction',
+    'Exponential',
+    'ExpressionComponent',
     'Gaussian',
+    'InstrumentModel',
     'Lorentzian',
-    'Voigt',
-    'DeltaFunction',
-    'DampedHarmonicOscillator',
     'Polynomial',
-    'Exponential',
-    'BrownianTranslationalDiffusion',
-    'SampleModel',
     'ResolutionModel',
-    'BackgroundModel',
-    'InstrumentModel',
-    'ExpressionComponent',
+    'SampleModel',
+    'Voigt',
 ]

src/easydynamics/sample_model/component_collection.py

@@ -173,7 +173,7 @@ 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.'
-        )  # noqa: E501
+        )
 
     def convert_unit(self, unit: str | sc.Unit) -> None:
         """

src/easydynamics/sample_model/components/__init__.py

@@ -13,12 +13,12 @@
 from easydynamics.sample_model.components.voigt import Voigt
 
 __all__ = [
-    'Gaussian',
-    'Lorentzian',
-    'Voigt',
-    'DeltaFunction',
     'DampedHarmonicOscillator',
-    'Polynomial',
+    'DeltaFunction',
     'Exponential',
     'ExpressionComponent',
+    'Gaussian',
+    'Lorentzian',
+    'Polynomial',
+    'Voigt',
 ]

src/easydynamics/sample_model/components/expression_component.py

@@ -4,6 +4,7 @@
 from __future__ import annotations
 
 from typing import TYPE_CHECKING
+from typing import ClassVar
 
 import sympy as sp
 from easyscience.variable import Parameter
@@ -29,7 +30,7 @@ class ExpressionComponent(ModelComponent):
     # -------------------------
     # Allowed symbolic functions
     # -------------------------
-    _ALLOWED_FUNCS = {
+    _ALLOWED_FUNCS: ClassVar[dict[str, object]] = {
         # Exponentials & logs
         'exp': sp.exp,
         'log': sp.log,
@@ -62,12 +63,12 @@ class ExpressionComponent(ModelComponent):
     # -------------------------
     # Allowed constants
     # -------------------------
-    _ALLOWED_CONSTANTS = {
+    _ALLOWED_CONSTANTS: ClassVar[dict[str, object]] = {
         'pi': sp.pi,
         'E': sp.E,
     }
 
-    _RESERVED_NAMES = {'x'}
+    _RESERVED_NAMES: ClassVar[dict[str, object]] = {'x'}
 
     def __init__(
         self,