From 57afb48676231d907cef57fa0370297d095eb41b Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Wed, 18 Mar 2026 11:49:19 +0100 Subject: [PATCH 1/9] Enable B (flake8-bugbear) rules --- docs/docs/tutorials/analysis1d.ipynb | 5 +- pixi.lock | 4 +- pyproject.toml | 2 +- .../convolution/numerical_convolution.py | 2 +- .../convolution/numerical_convolution_base.py | 2 + .../sample_model/component_collection.py | 1 + .../sample_model/components/mixins.py | 4 +- .../components/model_component.py | 4 +- .../sample_model/components/polynomial.py | 1 + src/easydynamics/sample_model/sample_model.py | 8 +-- src/easydynamics/utils/__init__.py | 4 +- src/easydynamics/utils/detailed_balance.py | 16 +++--- .../convolution_width_thresholds.ipynb | 2 +- .../easydynamics/analysis/test_analysis.py | 16 +++--- .../convolution/test_numerical_convolution.py | 2 +- .../components/test_polynomial.py | 4 +- .../sample_model/test_component_collection.py | 16 ++++-- .../sample_model/test_model_base.py | 3 +- .../sample_model/test_sample_model.py | 2 +- .../utils/test_detailed_balance.py | 50 ++++++++----------- 20 files changed, 81 insertions(+), 67 deletions(-) diff --git a/docs/docs/tutorials/analysis1d.ipynb b/docs/docs/tutorials/analysis1d.ipynb index 55edc76f..326e4522 100644 --- a/docs/docs/tutorials/analysis1d.ipynb +++ b/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, diff --git a/pixi.lock b/pixi.lock index f827c396..f2c000a5 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4074,8 +4074,8 @@ packages: requires_python: '>=3.5' - pypi: ./ name: easydynamics - version: 0.2.1+devdirty31 - sha256: 173a472b278902a0a8f520f54a773fa824d5d033443bd820536c6d6c60fe492f + version: 0.3.0+devdirty1 + sha256: 575879f715efce68a2be6c70a4918f7e1776943463e5908b41c9e3c7a757a5f6 requires_dist: - darkdetect - easyscience diff --git a/pyproject.toml b/pyproject.toml index 18d90607..f4e550dc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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 diff --git a/src/easydynamics/convolution/numerical_convolution.py b/src/easydynamics/convolution/numerical_convolution.py index b2f45b45..05e64200 100644 --- a/src/easydynamics/convolution/numerical_convolution.py +++ b/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 as detailed_balance_factor from easydynamics.utils.utils import Numeric diff --git a/src/easydynamics/convolution/numerical_convolution_base.py b/src/easydynamics/convolution/numerical_convolution_base.py index 54ccac6d..c949a580 100644 --- a/src/easydynamics/convolution/numerical_convolution_base.py +++ b/src/easydynamics/convolution/numerical_convolution_base.py @@ -382,6 +382,7 @@ 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 +392,7 @@ 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: diff --git a/src/easydynamics/sample_model/component_collection.py b/src/easydynamics/sample_model/component_collection.py index 24548bf5..fe95fd71 100644 --- a/src/easydynamics/sample_model/component_collection.py +++ b/src/easydynamics/sample_model/component_collection.py @@ -340,6 +340,7 @@ 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: diff --git a/src/easydynamics/sample_model/components/mixins.py b/src/easydynamics/sample_model/components/mixins.py index 97c32422..b5125767 100644 --- a/src/easydynamics/sample_model/components/mixins.py +++ b/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 diff --git a/src/easydynamics/sample_model/components/model_component.py b/src/easydynamics/sample_model/components/model_component.py index 176d32e4..e46d8995 100644 --- a/src/easydynamics/sample_model/components/model_component.py +++ b/src/easydynamics/sample_model/components/model_component.py @@ -131,7 +131,9 @@ def _prepare_x_for_evaluate( warnings.warn( f'Input x has unit {x.unit}, but {self.__class__.__name__} component \ has unit {self_unit_for_warning}. \ - Converting {self.__class__.__name__} to {x.unit}.' + Converting {self.__class__.__name__} to {x.unit}.', + UserWarning, + stacklevel=3, ) else: x_in = x diff --git a/src/easydynamics/sample_model/components/polynomial.py b/src/easydynamics/sample_model/components/polynomial.py index 554fb254..c611dd49 100644 --- a/src/easydynamics/sample_model/components/polynomial.py +++ b/src/easydynamics/sample_model/components/polynomial.py @@ -163,6 +163,7 @@ def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray) f'The Polynomial with unique_name {self.unique_name} has negative values, ' 'which may not be physically meaningful.', UserWarning, + stacklevel=2, ) return result diff --git a/src/easydynamics/sample_model/sample_model.py b/src/easydynamics/sample_model/sample_model.py index 5cf9bf77..29630c45 100644 --- a/src/easydynamics/sample_model/sample_model.py +++ b/src/easydynamics/sample_model/sample_model.py @@ -7,7 +7,7 @@ from easydynamics.sample_model.diffusion_model.diffusion_model_base import DiffusionModelBase from easydynamics.sample_model.model_base import ModelBase -from easydynamics.utils import _detailed_balance_factor +from easydynamics.utils import detailed_balance_factor from easydynamics.utils.utils import Numeric from easydynamics.utils.utils import Q_type @@ -351,7 +351,7 @@ def evaluate( y = super().evaluate(x) if self._temperature is not None: - DBF = _detailed_balance_factor( + DBF = detailed_balance_factor( energy=x, temperature=self._temperature, divide_by_temperature=self._divide_by_temperature, @@ -407,7 +407,9 @@ def _generate_component_collections(self) -> None: # and add to component collections for diffusion_model in self._diffusion_models: diffusion_collections = diffusion_model.create_component_collections(Q=self._Q) - for target, source in zip(self._component_collections, diffusion_collections): + for target, source in zip( + self._component_collections, diffusion_collections, strict=True + ): for component in source.components: target.append_component(component) diff --git a/src/easydynamics/utils/__init__.py b/src/easydynamics/utils/__init__.py index 68d324ce..6792d72e 100644 --- a/src/easydynamics/utils/__init__.py +++ b/src/easydynamics/utils/__init__.py @@ -1,6 +1,6 @@ # SPDX-FileCopyrightText: 2025 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -from .detailed_balance import _detailed_balance_factor +from .detailed_balance import detailed_balance_factor -__all__ = ['_detailed_balance_factor'] +__all__ = ['detailed_balance_factor'] diff --git a/src/easydynamics/utils/detailed_balance.py b/src/easydynamics/utils/detailed_balance.py index 086917fa..f2cfb675 100644 --- a/src/easydynamics/utils/detailed_balance.py +++ b/src/easydynamics/utils/detailed_balance.py @@ -22,7 +22,7 @@ LARGE_THRESHOLD = 100 -def _detailed_balance_factor( +def detailed_balance_factor( energy: int | float | list | np.ndarray | sc.Variable, temperature: int | float | sc.Variable | Parameter, energy_unit: str | sc.Unit = 'meV', @@ -112,13 +112,14 @@ def _detailed_balance_factor( except Exception as e: raise UnitError( f'The unit of energy is wrong: {energy.unit}: {e} Check that energy has a valid unit.' - ) + ) from e # We give users the option to specify the unit of the energy, # but if the input has a unit, they might clash if energy.unit != energy_unit: warnings.warn( f'Input energy has unit {energy.unit}, but energy_unit was set to {energy_unit}. ' - f'Using {energy.unit}.' + f'Using {energy.unit}.', + stacklevel=2, ) # Same for temperature @@ -128,12 +129,13 @@ def _detailed_balance_factor( raise UnitError( f'The unit of temperature is wrong: {temperature.unit}: {e} ' f'Check that temperature has a valid unit.' - ) + ) from e if temperature.unit != temperature_unit: warnings.warn( f'Input temperature has unit {temperature.unit}, ' - f'but temperature_unit was set to {temperature_unit}. Using {temperature.unit}.' + f'but temperature_unit was set to {temperature_unit}. Using {temperature.unit}.', + stacklevel=2, ) # Zero temperature deserves special treatment. @@ -242,10 +244,10 @@ def _convert_to_scipp_variable( try: return sc.scalar(value=float(array_value.flat[0]), unit=unit) except UnitError as e: - raise UnitError(f"Invalid unit string '{unit}' for {name}: {e}") + raise UnitError(f"Invalid unit string '{unit}' for {name}: {e}") from e else: # Multi-element array try: return sc.array(dims=['x'], values=array_value, unit=unit) except UnitError as e: - raise UnitError(f"Invalid unit string '{unit}' for {name}: {e}") + raise UnitError(f"Invalid unit string '{unit}' for {name}: {e}") from e diff --git a/tests/performance_tests/convolution/convolution_width_thresholds.ipynb b/tests/performance_tests/convolution/convolution_width_thresholds.ipynb index 7bb81f70..323c6378 100644 --- a/tests/performance_tests/convolution/convolution_width_thresholds.ipynb +++ b/tests/performance_tests/convolution/convolution_width_thresholds.ipynb @@ -115,7 +115,7 @@ " upsample_factor=None,\n", ")\n", "\n", - "for gwidth, gcenter in zip(gaussian_widths, gaussian_centers):\n", + "for gwidth, gcenter in zip(gaussian_widths, gaussian_centers, strict=True):\n", " sample_components.components[0].width = gwidth\n", " sample_components.components[0].center = gcenter\n", " y_analytical = analytical_convolver.convolution()\n", diff --git a/tests/unit/easydynamics/analysis/test_analysis.py b/tests/unit/easydynamics/analysis/test_analysis.py index 6e18be7a..5052cc8f 100644 --- a/tests/unit/easydynamics/analysis/test_analysis.py +++ b/tests/unit/easydynamics/analysis/test_analysis.py @@ -495,8 +495,8 @@ def test_on_experiment_changed(self, analysis): # EXPECT assert np.array_equal(analysis.Q.values, [2, 3, 4]) assert len(analysis.analysis_list) == 3 - for analysis in analysis.analysis_list: - assert analysis.experiment is new_experiment + for analysis1d in analysis.analysis_list: + assert analysis1d.experiment is new_experiment def test_on_sample_model_changed(self, analysis): # WHEN @@ -508,8 +508,8 @@ def test_on_sample_model_changed(self, analysis): # EXPECT assert analysis.sample_model is new_sample_model - for analysis in analysis.analysis_list: - assert analysis.sample_model is new_sample_model + for analysis1d in analysis.analysis_list: + assert analysis1d.sample_model is new_sample_model def test_on_instrument_model_changed(self, analysis): # WHEN @@ -521,8 +521,8 @@ def test_on_instrument_model_changed(self, analysis): # EXPECT assert analysis.instrument_model is new_instrument_model - for analysis in analysis.analysis_list: - assert analysis.instrument_model is new_instrument_model + for analysis1d in analysis.analysis_list: + assert analysis1d.instrument_model is new_instrument_model def test_fit_single_Q_valid(self, analysis): # WHEN @@ -590,8 +590,8 @@ def test_fit_all_Q_simultaneously(self, analysis): expected_xs = [] expected_ys = [] expected_ws = [] - for analysis in analysis.analysis_list: - data = analysis.experiment.data['Q', analysis.Q_index] + for analysis1d in analysis.analysis_list: + data = analysis1d.experiment.data['Q', analysis1d.Q_index] expected_xs.append(data.coords['energy'].values) expected_ys.append(data.values) diff --git a/tests/unit/easydynamics/convolution/test_numerical_convolution.py b/tests/unit/easydynamics/convolution/test_numerical_convolution.py index 082ac096..7094f3dd 100644 --- a/tests/unit/easydynamics/convolution/test_numerical_convolution.py +++ b/tests/unit/easydynamics/convolution/test_numerical_convolution.py @@ -10,7 +10,7 @@ from easydynamics.convolution.numerical_convolution import NumericalConvolution from easydynamics.sample_model import Gaussian from easydynamics.sample_model.component_collection import ComponentCollection -from easydynamics.utils.detailed_balance import _detailed_balance_factor as detailed_balance_factor +from easydynamics.utils.detailed_balance import detailed_balance_factor as detailed_balance_factor class TestNumericalConvolution: diff --git a/tests/unit/easydynamics/sample_model/components/test_polynomial.py b/tests/unit/easydynamics/sample_model/components/test_polynomial.py index 7d5de9db..82d88d66 100644 --- a/tests/unit/easydynamics/sample_model/components/test_polynomial.py +++ b/tests/unit/easydynamics/sample_model/components/test_polynomial.py @@ -184,7 +184,9 @@ def test_copy(self, polynomial: Polynomial): assert polynomial_copy.display_name == polynomial.display_name assert len(polynomial_copy.coefficients) == len(polynomial.coefficients) for original_coeff, copied_coeff in zip( - polynomial.get_all_parameters(), polynomial_copy.get_all_parameters() + polynomial.get_all_parameters(), + polynomial_copy.get_all_parameters(), + strict=True, ): assert copied_coeff.value == original_coeff.value assert copied_coeff.fixed == original_coeff.fixed diff --git a/tests/unit/easydynamics/sample_model/test_component_collection.py b/tests/unit/easydynamics/sample_model/test_component_collection.py index fcc65b6f..378f0abb 100644 --- a/tests/unit/easydynamics/sample_model/test_component_collection.py +++ b/tests/unit/easydynamics/sample_model/test_component_collection.py @@ -438,7 +438,9 @@ def test_to_dict(self, component_collection): assert model_dict['unit'] == component_collection.unit assert len(model_dict['components']) == len(component_collection.components) - for comp, comp_dict in zip(component_collection.components, model_dict['components']): + for comp, comp_dict in zip( + component_collection.components, model_dict['components'], strict=True + ): assert comp_dict['@class'] == type(comp).__name__ assert comp_dict['display_name'] == comp.display_name assert comp_dict['unit'] == comp.unit @@ -455,7 +457,9 @@ def test_from_dict(self, component_collection): assert len(new_model.components) == len(component_collection.components) # Compare each component and its parameters - for orig_comp, new_comp in zip(component_collection.components, new_model.components): + for orig_comp, new_comp in zip( + component_collection.components, new_model.components, strict=True + ): assert type(new_comp) is type(orig_comp) assert new_comp.display_name == orig_comp.display_name assert new_comp.unit == orig_comp.unit @@ -463,7 +467,7 @@ def test_from_dict(self, component_collection): orig_params = orig_comp.get_all_parameters() new_params = new_comp.get_all_parameters() assert len(orig_params) == len(new_params) - for param_orig, param_new in zip(orig_params, new_params): + for param_orig, param_new in zip(orig_params, new_params, strict=True): assert param_new.name == param_orig.name assert param_new.value == param_orig.value assert param_new.fixed == param_orig.fixed @@ -479,7 +483,9 @@ def test_copy(self, component_collection): assert len(model_copy.components) == len(component_collection.components) # EXPECT: deep copy, same order - for orig_comp, copied_comp in zip(component_collection.components, model_copy.components): + for orig_comp, copied_comp in zip( + component_collection.components, model_copy.components, strict=True + ): # New object assert copied_comp is not orig_comp @@ -494,7 +500,7 @@ def test_copy(self, component_collection): assert len(orig_params) == len(copied_params) - for param_orig, param_copy in zip(orig_params, copied_params): + for param_orig, param_copy in zip(orig_params, copied_params, strict=True): assert param_copy is not param_orig assert param_copy.value == param_orig.value assert param_copy.min == param_orig.min diff --git a/tests/unit/easydynamics/sample_model/test_model_base.py b/tests/unit/easydynamics/sample_model/test_model_base.py index 4368823a..9de4c138 100644 --- a/tests/unit/easydynamics/sample_model/test_model_base.py +++ b/tests/unit/easydynamics/sample_model/test_model_base.py @@ -5,6 +5,7 @@ import numpy as np import pytest +from scipp import UnitError from easydynamics.sample_model import ComponentCollection from easydynamics.sample_model import Gaussian @@ -263,7 +264,7 @@ def test_convert_unit(self, model_base): def test_convert_unit_invalid_raises(self, model_base): # WHEN / THEN / EXPECT - with pytest.raises(Exception): + with pytest.raises(UnitError): model_base.convert_unit('invalid_unit') def test_convert_unit_incorrect_unit_raises(self, model_base): diff --git a/tests/unit/easydynamics/sample_model/test_sample_model.py b/tests/unit/easydynamics/sample_model/test_sample_model.py index e1f7223e..673368e8 100644 --- a/tests/unit/easydynamics/sample_model/test_sample_model.py +++ b/tests/unit/easydynamics/sample_model/test_sample_model.py @@ -317,7 +317,7 @@ def test_evaluate_calls_dbf(self, sample_model): sample_model._component_collections = [collection1, collection2] - with patch('easydynamics.sample_model.sample_model._detailed_balance_factor') as mock_dbf: + with patch('easydynamics.sample_model.sample_model.detailed_balance_factor') as mock_dbf: mock_dbf.return_value = np.array([10.0, 10.0, 10.0]) # simplified DBF # THEN result = sample_model.evaluate(x) diff --git a/tests/unit/easydynamics/utils/test_detailed_balance.py b/tests/unit/easydynamics/utils/test_detailed_balance.py index 4dfe196d..06aa7f02 100644 --- a/tests/unit/easydynamics/utils/test_detailed_balance.py +++ b/tests/unit/easydynamics/utils/test_detailed_balance.py @@ -8,7 +8,7 @@ from scipp import UnitError from scipp.constants import Boltzmann as kB -from easydynamics.utils import _detailed_balance_factor as _detailed_balance_factor +from easydynamics.utils import detailed_balance_factor kB_meV_per_K = sc.to_unit(kB, 'meV/K').value @@ -22,7 +22,7 @@ def test_energy_unit_not_string_error(self): energy_unit = 5 # Then Expect with pytest.raises(TypeError, match='energy_unit must be a string.'): - _detailed_balance_factor(energy, T, energy_unit=energy_unit) + detailed_balance_factor(energy, T, energy_unit=energy_unit) @pytest.mark.parametrize('temperature_unit', [5, 5.0, dict(), list()]) def test_temperature_unit_not_string_error(self, temperature_unit): @@ -31,7 +31,7 @@ def test_temperature_unit_not_string_error(self, temperature_unit): T = 100 # Then Expect with pytest.raises(TypeError, match='temperature_unit must be a string.'): - _detailed_balance_factor(energy, T, temperature_unit=temperature_unit) + detailed_balance_factor(energy, T, temperature_unit=temperature_unit) def test_divide_by_temperature_not_bool_error(self): # When @@ -40,7 +40,7 @@ def test_divide_by_temperature_not_bool_error(self): divide_by_temperature = 'yes' # Then Expect with pytest.raises(TypeError, match='divide_by_temperature must be True or False.'): - _detailed_balance_factor(energy, T, divide_by_temperature=divide_by_temperature) + detailed_balance_factor(energy, T, divide_by_temperature=divide_by_temperature) @pytest.mark.parametrize( 'energy', @@ -63,7 +63,7 @@ def test_energy_inputs(self, energy): # When T = 100 # Then - result = _detailed_balance_factor(energy, T) + result = detailed_balance_factor(energy, T) # Expect if isinstance(energy, (np.ndarray)): energy_array = energy @@ -83,7 +83,7 @@ def test_scipp_variable_input(self): energy = sc.array(dims=['x'], values=[1.0, 2.0, 3.0], unit='meV') T = sc.scalar(value=100, unit='K') # Then - result = _detailed_balance_factor(energy, T) + result = detailed_balance_factor(energy, T) # Expect expected_values = ( np.array([1.0, 2.0, 3.0]) @@ -100,7 +100,7 @@ def test_parameter_temperature(self): energy = np.array([1.0, 2.0, 3.0]) T_param = Parameter(name='T', value=150, unit='K') # Then - result = _detailed_balance_factor(energy, T_param) + result = detailed_balance_factor(energy, T_param) # Expect expected = energy / (1 - np.exp(-energy / (kB_meV_per_K * 150))) / (kB_meV_per_K * 150) @@ -114,7 +114,7 @@ def test_zero_temperature(self): temperature = 0 energy = np.array([-1.0, 0.0, 1.0]) # Then - result = _detailed_balance_factor(energy, temperature, divide_by_temperature=False) + result = detailed_balance_factor(energy, temperature, divide_by_temperature=False) # Expect expected = np.maximum(energy, 0.0) np.testing.assert_array_equal(result, expected) @@ -125,14 +125,14 @@ def test_zero_temperature_divide_by_T_error(self): energy = np.array([-1.0, 0.0, 1.0]) # Then Expect with pytest.raises(ZeroDivisionError, match='Cannot divide by T when T = 0'): - _detailed_balance_factor(energy, temperature, divide_by_temperature=True) + detailed_balance_factor(energy, temperature, divide_by_temperature=True) def test_zero_temperature_single_value(self): # When temperature = 0 energy = 2.0 # Then - result = _detailed_balance_factor(energy, temperature, divide_by_temperature=False) + result = detailed_balance_factor(energy, temperature, divide_by_temperature=False) # Expect expected = 2.0 assert result == expected @@ -140,7 +140,7 @@ def test_zero_temperature_single_value(self): def test_negative_temperature_raises(self): # When Then Expect with pytest.raises(ValueError, match='Temperature must be non-negative'): - _detailed_balance_factor(1.0, -10) + detailed_balance_factor(1.0, -10) # Numerical tests def test_small_energy_limit(self): @@ -148,9 +148,7 @@ def test_small_energy_limit(self): T = 300 energy = np.array([1e-5, 1e-6, 1e-7, 1e-8, 1e-9]) # Then - result = _detailed_balance_factor( - energy=energy, temperature=T, divide_by_temperature=False - ) + result = detailed_balance_factor(energy=energy, temperature=T, divide_by_temperature=False) # Expect x = energy / (kB_meV_per_K * T) expected = (1 + x / 2 + x**2 / 12) * (kB_meV_per_K * T) @@ -161,9 +159,7 @@ def test_large_energy_limit(self): energy = np.linspace(1e2, 1e3, 5) T = 1 # Then - result = _detailed_balance_factor( - energy=energy, temperature=T, divide_by_temperature=False - ) + result = detailed_balance_factor(energy=energy, temperature=T, divide_by_temperature=False) # Expect np.testing.assert_allclose(result, energy, atol=1e-10) @@ -172,9 +168,7 @@ def test_intermediate_energy(self): energy = np.linspace(1, 10, 100) T = 100 # Then - result = _detailed_balance_factor( - energy=energy, temperature=T, divide_by_temperature=False - ) + result = detailed_balance_factor(energy=energy, temperature=T, divide_by_temperature=False) # Expect expected = energy / (1 - np.exp(-energy / (kB_meV_per_K * T))) np.testing.assert_allclose(result, expected, rtol=1e-5) @@ -186,10 +180,10 @@ def test_detailed_balance_is_fulfilled(self, divide_by_T): T = 10 energy = np.linspace(0.01, 100, 101) # Then - detailed_balance_positive = _detailed_balance_factor( + detailed_balance_positive = detailed_balance_factor( energy=energy, temperature=T, divide_by_temperature=divide_by_T ) - detailed_balance_negative = _detailed_balance_factor( + detailed_balance_negative = detailed_balance_factor( energy=-energy, temperature=T, divide_by_temperature=divide_by_T ) ratio = detailed_balance_positive / detailed_balance_negative @@ -206,7 +200,7 @@ def test_energy_unit(self, energy_unit): energy = np.linspace(1e3, 10 * 1e3, 100) T = 100 # Then - result = _detailed_balance_factor( + result = detailed_balance_factor( energy=energy, temperature=T, divide_by_temperature=False, @@ -227,7 +221,7 @@ def test_energy_unit_warning(self): UserWarning, match='Input energy has unit µeV, but energy_unit was set to meV. Using µeV.', ): - result = _detailed_balance_factor( + result = detailed_balance_factor( energy=energy, temperature=T, divide_by_temperature=False, @@ -244,7 +238,7 @@ def test_temperature_unit(self, temperature_unit): temperature = 100 * 1000 temperature_unit = 'mK' # Then - result = _detailed_balance_factor( + result = detailed_balance_factor( energy=energy, temperature=temperature, temperature_unit=temperature_unit, @@ -264,7 +258,7 @@ def test_temperature_unit_warning(self): UserWarning, match='Input temperature has unit mK, but temperature_unit was set to K. Using mK.', ): - result = _detailed_balance_factor( + result = detailed_balance_factor( energy=energy, temperature=temperature, temperature_unit=temperature_unit, @@ -286,7 +280,7 @@ def test_incompatible_energy_unit_raises(self): UnitError, match='The unit of energy is wrong', ): - _detailed_balance_factor( + detailed_balance_factor( energy, T, energy_unit=energy_unit, @@ -305,7 +299,7 @@ def test_incompatible_temperature_unit_raises(self): UnitError, match='The unit of temperature is wrong', ): - _detailed_balance_factor( + detailed_balance_factor( energy, T, energy_unit=energy_unit, From 67ddcb8c0591c87725b20fff56d26eb341d09d83 Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Wed, 18 Mar 2026 11:53:38 +0100 Subject: [PATCH 2/9] Add UP (pyupgrade) rules --- pixi.lock | 4 +- pyproject.toml | 2 +- .../convolution/convolution_base.py | 6 +- .../convolution/numerical_convolution_base.py | 74 ++++++++++--------- .../sample_model/component_collection.py | 13 ++-- .../components/model_component.py | 6 +- .../sample_model/components/polynomial.py | 2 +- .../brownian_translational_diffusion.py | 8 +- .../diffusion_model/diffusion_model_base.py | 6 +- .../jump_translational_diffusion.py | 8 +- .../sample_model/instrument_model.py | 6 +- src/easydynamics/sample_model/model_base.py | 6 +- .../convolution_width_thresholds.ipynb | 8 +- 13 files changed, 69 insertions(+), 80 deletions(-) diff --git a/pixi.lock b/pixi.lock index f2c000a5..1c09e96a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4074,8 +4074,8 @@ packages: requires_python: '>=3.5' - pypi: ./ name: easydynamics - version: 0.3.0+devdirty1 - sha256: 575879f715efce68a2be6c70a4918f7e1776943463e5908b41c9e3c7a757a5f6 + version: 0.3.0+devdirty2 + sha256: 7913c970e279247603131a441c0393e93ed3896434095530226cf3ce36e8fb00 requires_dist: - darkdetect - easyscience diff --git a/pyproject.toml b/pyproject.toml index f4e550dc..12cf9c51 100644 --- a/pyproject.toml +++ b/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 diff --git a/src/easydynamics/convolution/convolution_base.py b/src/easydynamics/convolution/convolution_base.py index 1ace459c..1c6c68ff 100644 --- a/src/easydynamics/convolution/convolution_base.py +++ b/src/easydynamics/convolution/convolution_base.py @@ -196,10 +196,8 @@ 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: diff --git a/src/easydynamics/convolution/numerical_convolution_base.py b/src/easydynamics/convolution/numerical_convolution_base.py index c949a580..98fb05ca 100644 --- a/src/easydynamics/convolution/numerical_convolution_base.py +++ b/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 @@ -44,8 +42,8 @@ def __init__( upsample_factor: Numeric | None = 5, extension_factor: Numeric | None = 0.2, temperature: Parameter | Numeric | None = None, - temperature_unit: str | sc.Unit = 'K', - energy_unit: str | sc.Unit = 'meV', + temperature_unit: str | sc.Unit = "K", + energy_unit: str | sc.Unit = "meV", normalize_detailed_balance: bool = True, ) -> None: """Initialize the NumericalConvolutionBase. @@ -85,11 +83,13 @@ def __init__( energy_offset=energy_offset, ) - if temperature is not None and not isinstance(temperature, (Numeric, Parameter)): - raise TypeError('Temperature must be None, a number or a Parameter.') + if temperature is not None and not isinstance( + temperature, (Numeric, Parameter) + ): + raise TypeError("Temperature must be None, a number or a Parameter.") if not isinstance(temperature_unit, (str, sc.Unit)): - raise TypeError('Temperature_unit must be a string or sc.Unit.') + raise TypeError("Temperature_unit must be a string or sc.Unit.") self._temperature_unit = temperature_unit self._temperature = None self.temperature = temperature @@ -142,10 +142,10 @@ def upsample_factor(self, factor: Numeric | None) -> None: return if not isinstance(factor, Numeric): - raise TypeError('Upsample factor must be a numerical value or None.') + raise TypeError("Upsample factor must be a numerical value or None.") factor = float(factor) if factor <= 1.0: - raise ValueError('Upsample factor must be greater than 1.') + raise ValueError("Upsample factor must be greater than 1.") self._upsample_factor = factor @@ -185,20 +185,20 @@ def extension_factor(self, factor: Numeric) -> None: """ if not isinstance(factor, Numeric): - raise TypeError('Extension factor must be a number.') + raise TypeError("Extension factor must be a number.") if factor < 0.0: - raise ValueError('Extension factor must be non-negative.') + raise ValueError("Extension factor must be non-negative.") self._extension_factor = float(factor) # Recreate dense grid when extension factor is updated 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. """ @@ -227,7 +227,7 @@ def temperature(self, temp: Parameter | Numeric | None) -> None: self._temperature.value = float(temp) else: self._temperature = Parameter( - name='temperature', + name="temperature", value=float(temp), unit=self._temperature_unit, fixed=True, @@ -235,7 +235,7 @@ def temperature(self, temp: Parameter | Numeric | None) -> None: elif isinstance(temp, Parameter): self._temperature = temp else: - raise TypeError('Temperature must be None, a float or a Parameter.') + raise TypeError("Temperature must be None, a float or a Parameter.") @property def normalize_detailed_balance(self) -> bool: @@ -264,7 +264,7 @@ def normalize_detailed_balance(self, normalize: bool) -> None: """ if not isinstance(normalize, bool): - raise TypeError('normalize_detailed_balance must be True or False.') + raise TypeError("normalize_detailed_balance must be True or False.") self._normalize_detailed_balance = normalize @@ -292,7 +292,7 @@ def _create_energy_grid( is_uniform = np.allclose(energy_diff, energy_diff[0]) if not is_uniform: raise ValueError( - 'Input array `energy` must be uniformly spaced if upsample_factor is not given.' # noqa: E501 + "Input array `energy` must be uniformly spaced if upsample_factor is not given." # noqa: E501 ) energy_dense = self.energy.values @@ -309,7 +309,7 @@ def _create_energy_grid( energy_span_dense = extended_max - extended_min if len(energy_dense) < 2: - raise ValueError('Energy array must have at least two points.') + raise ValueError("Energy array must have at least two points.") energy_dense_step = energy_dense[1] - energy_dense[0] # Handle offset for even length of energy_dense in convolution. @@ -373,24 +373,30 @@ def _check_width_thresholds( components = [model] # Treat single ModelComponent as a list for comp in components: - if hasattr(comp, 'width'): - if comp.width.value > LARGE_WIDTH_THRESHOLD * self._energy_grid.energy_span_dense: + if hasattr(comp, "width"): + if ( + comp.width.value + > LARGE_WIDTH_THRESHOLD * self._energy_grid.energy_span_dense + ): warnings.warn( f"The width of the {model_name} component '{comp.unique_name}' \ ({comp.width.value}) is large compared to the span of the input " - f'array ({self._energy_grid.energy_span_dense}). \ + f"array ({self._energy_grid.energy_span_dense}). \ This may lead to inaccuracies in the convolution. \ - Increase extension_factor to improve accuracy.', + Increase extension_factor to improve accuracy.", UserWarning, stacklevel=3, ) - if comp.width.value < SMALL_WIDTH_THRESHOLD * self._energy_grid.energy_dense_step: + if ( + comp.width.value + < SMALL_WIDTH_THRESHOLD * self._energy_grid.energy_dense_step + ): warnings.warn( f"The width of the {model_name} component '{comp.unique_name}' \ ({comp.width.value}) is small compared to the spacing of the input " - f'array ({self._energy_grid.energy_dense_step}). \ + f"array ({self._energy_grid.energy_dense_step}). \ This may lead to inaccuracies in the convolution. \ - Increase upsample_factor to improve accuracy.', + Increase upsample_factor to improve accuracy.", UserWarning, stacklevel=3, ) @@ -404,13 +410,13 @@ def __repr__(self) -> str: NumericalConvolutionBase. """ 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'energy_unit={self._energy_unit}, ' - f'upsample_factor={self.upsample_factor}, ' - f'extension_factor={self.extension_factor}, ' - f'temperature={self.temperature}, ' - f'normalize_detailed_balance={self.normalize_detailed_balance})' + 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"energy_unit={self._energy_unit}, " + f"upsample_factor={self.upsample_factor}, " + f"extension_factor={self.extension_factor}, " + f"temperature={self.temperature}, " + f"normalize_detailed_balance={self.normalize_detailed_balance})" ) diff --git a/src/easydynamics/sample_model/component_collection.py b/src/easydynamics/sample_model/component_collection.py index fe95fd71..ecfc21d7 100644 --- a/src/easydynamics/sample_model/component_collection.py +++ b/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. @@ -302,7 +299,7 @@ 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: @@ -405,7 +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] diff --git a/src/easydynamics/sample_model/components/model_component.py b/src/easydynamics/sample_model/components/model_component.py index e46d8995..62691dff 100644 --- a/src/easydynamics/sample_model/components/model_component.py +++ b/src/easydynamics/sample_model/components/model_component.py @@ -58,10 +58,8 @@ def unit(self, unit_str: str) -> None: AttributeError: Always raised since unit is read-only. """ 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 fix_all_parameters(self) -> None: diff --git a/src/easydynamics/sample_model/components/polynomial.py b/src/easydynamics/sample_model/components/polynomial.py index c611dd49..446c15e1 100644 --- a/src/easydynamics/sample_model/components/polynomial.py +++ b/src/easydynamics/sample_model/components/polynomial.py @@ -4,7 +4,7 @@ from __future__ import annotations import warnings -from typing import Sequence +from collections.abc import Sequence import numpy as np import scipp as sc diff --git a/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py b/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py index dd4ae3df..66ed574c 100644 --- a/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py +++ b/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py @@ -1,8 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -from typing import Dict -from typing import List import numpy as np import scipp as sc @@ -179,7 +177,7 @@ def create_component_collections( self, Q: Q_type, component_display_name: str = 'Brownian diffusion', - ) -> List[ComponentCollection]: + ) -> list[ComponentCollection]: r"""Create ComponentCollection components for the Brownian translational diffusion model at given Q values. @@ -265,7 +263,7 @@ def _write_width_dependency_expression(self, Q: float) -> str: # Q is given as a float, so we need to add the units return f'hbar * D* {Q} **2*1/(angstrom**2)' - def _write_width_dependency_map_expression(self) -> Dict[str, DescriptorNumber]: + def _write_width_dependency_map_expression(self) -> dict[str, DescriptorNumber]: """Write the dependency map expression to make dependent Parameters. @@ -296,7 +294,7 @@ def _write_area_dependency_expression(self, QISF: float) -> str: return f'{QISF} * scale' - def _write_area_dependency_map_expression(self) -> Dict[str, DescriptorNumber]: + def _write_area_dependency_map_expression(self) -> dict[str, DescriptorNumber]: """Write the dependency map expression to make dependent Parameters. diff --git a/src/easydynamics/sample_model/diffusion_model/diffusion_model_base.py b/src/easydynamics/sample_model/diffusion_model/diffusion_model_base.py index 6acc6cac..1721fdc8 100644 --- a/src/easydynamics/sample_model/diffusion_model/diffusion_model_base.py +++ b/src/easydynamics/sample_model/diffusion_model/diffusion_model_base.py @@ -81,10 +81,8 @@ def unit(self, unit_str: str) -> None: AttributeError: Always, since the unit is read-only. """ 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 @property diff --git a/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py b/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py index adb45bc7..18475624 100644 --- a/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py +++ b/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py @@ -1,8 +1,6 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause -from typing import Dict -from typing import List import numpy as np import scipp as sc @@ -232,7 +230,7 @@ def create_component_collections( self, Q: Q_type, component_display_name: str = 'Jump translational diffusion', - ) -> List[ComponentCollection]: + ) -> list[ComponentCollection]: """Create ComponentCollection components for the diffusion model at given Q values. @@ -316,7 +314,7 @@ def _write_width_dependency_expression(self, Q: float) -> str: # Q is given as a float, so we need to add the units return f'hbar * D* {Q} **2/(angstrom**2)/(1 + (D * t* {Q} **2/(angstrom**2)))' - def _write_width_dependency_map_expression(self) -> Dict[str, DescriptorNumber]: + def _write_width_dependency_map_expression(self) -> dict[str, DescriptorNumber]: """Write the dependency map expression to make dependent Parameters. @@ -349,7 +347,7 @@ def _write_area_dependency_expression(self, QISF: float) -> str: return f'{QISF} * scale' - def _write_area_dependency_map_expression(self) -> Dict[str, DescriptorNumber]: + def _write_area_dependency_map_expression(self) -> dict[str, DescriptorNumber]: """Write the dependency map expression to make dependent Parameters. diff --git a/src/easydynamics/sample_model/instrument_model.py b/src/easydynamics/sample_model/instrument_model.py index 2768cb62..3f451de9 100644 --- a/src/easydynamics/sample_model/instrument_model.py +++ b/src/easydynamics/sample_model/instrument_model.py @@ -206,10 +206,8 @@ def unit(self, unit_str: str) -> None: AttributeError: Always, as the unit is read-only. """ 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 @property diff --git a/src/easydynamics/sample_model/model_base.py b/src/easydynamics/sample_model/model_base.py index 88f95c76..e92e5861 100644 --- a/src/easydynamics/sample_model/model_base.py +++ b/src/easydynamics/sample_model/model_base.py @@ -156,10 +156,8 @@ def unit(self, unit_str: str) -> None: read-only. """ 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: diff --git a/tests/performance_tests/convolution/convolution_width_thresholds.ipynb b/tests/performance_tests/convolution/convolution_width_thresholds.ipynb index 323c6378..8b72d888 100644 --- a/tests/performance_tests/convolution/convolution_width_thresholds.ipynb +++ b/tests/performance_tests/convolution/convolution_width_thresholds.ipynb @@ -57,13 +57,13 @@ " plt.plot(\n", " x,\n", " y_analytical,\n", - " label='Analytical, width = {}'.format(gwidth),\n", + " label=f'Analytical, width = {gwidth}',\n", " color=plt.cm.viridis(gaussian_widths.index(gwidth) / len(gaussian_widths)),\n", " )\n", " plt.plot(\n", " x,\n", " y_numerical,\n", - " label='Numerical, width = {}'.format(gwidth),\n", + " label=f'Numerical, width = {gwidth}',\n", " color=plt.cm.viridis(gaussian_widths.index(gwidth) / len(gaussian_widths)),\n", " linestyle='--',\n", " )\n", @@ -125,13 +125,13 @@ " plt.plot(\n", " x,\n", " y_analytical,\n", - " label='Analytical, width = {}'.format(gwidth),\n", + " label=f'Analytical, width = {gwidth}',\n", " color=plt.cm.viridis(gaussian_widths.index(gwidth) / len(gaussian_widths)),\n", " )\n", " plt.plot(\n", " x,\n", " y_numerical,\n", - " label='Numerical, width = {}'.format(gwidth),\n", + " label=f'Numerical, width = {gwidth}',\n", " color=plt.cm.viridis(gaussian_widths.index(gwidth) / len(gaussian_widths)),\n", " linestyle='--',\n", " )\n", From f5ded0b1bd31d1f4198d2837eb5479fe6e7b955d Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Wed, 18 Mar 2026 11:57:55 +0100 Subject: [PATCH 3/9] Add SIM (flake8-simplify) rules part 1 --- pixi.lock | 4 +- pyproject.toml | 2 +- src/easydynamics/analysis/analysis.py | 2 +- .../convolution/numerical_convolution_base.py | 68 ++++++++----------- src/easydynamics/utils/detailed_balance.py | 4 +- .../easydynamics/analysis/test_analysis.py | 22 +++--- 6 files changed, 45 insertions(+), 57 deletions(-) diff --git a/pixi.lock b/pixi.lock index 1c09e96a..5dc0b96a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4074,8 +4074,8 @@ packages: requires_python: '>=3.5' - pypi: ./ name: easydynamics - version: 0.3.0+devdirty2 - sha256: 7913c970e279247603131a441c0393e93ed3896434095530226cf3ce36e8fb00 + version: 0.3.0+devdirty3 + sha256: 51e9a125f4b5de0279d6c15f7664e394527e0a1f17f01ca3edc8bc9a5a898f15 requires_dist: - darkdetect - easyscience diff --git a/pyproject.toml b/pyproject.toml index 12cf9c51..2da4ad1f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -239,7 +239,7 @@ select = [ #'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 + '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 diff --git a/src/easydynamics/analysis/analysis.py b/src/easydynamics/analysis/analysis.py index c4cb9bcb..b344ef90 100644 --- a/src/easydynamics/analysis/analysis.py +++ b/src/easydynamics/analysis/analysis.py @@ -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 diff --git a/src/easydynamics/convolution/numerical_convolution_base.py b/src/easydynamics/convolution/numerical_convolution_base.py index 98fb05ca..c6b626a3 100644 --- a/src/easydynamics/convolution/numerical_convolution_base.py +++ b/src/easydynamics/convolution/numerical_convolution_base.py @@ -42,8 +42,8 @@ def __init__( upsample_factor: Numeric | None = 5, extension_factor: Numeric | None = 0.2, temperature: Parameter | Numeric | None = None, - temperature_unit: str | sc.Unit = "K", - energy_unit: str | sc.Unit = "meV", + temperature_unit: str | sc.Unit = 'K', + energy_unit: str | sc.Unit = 'meV', normalize_detailed_balance: bool = True, ) -> None: """Initialize the NumericalConvolutionBase. @@ -83,13 +83,11 @@ def __init__( energy_offset=energy_offset, ) - if temperature is not None and not isinstance( - temperature, (Numeric, Parameter) - ): - raise TypeError("Temperature must be None, a number or a Parameter.") + if temperature is not None and not isinstance(temperature, (Numeric, Parameter)): + raise TypeError('Temperature must be None, a number or a Parameter.') if not isinstance(temperature_unit, (str, sc.Unit)): - raise TypeError("Temperature_unit must be a string or sc.Unit.") + raise TypeError('Temperature_unit must be a string or sc.Unit.') self._temperature_unit = temperature_unit self._temperature = None self.temperature = temperature @@ -142,10 +140,10 @@ def upsample_factor(self, factor: Numeric | None) -> None: return if not isinstance(factor, Numeric): - raise TypeError("Upsample factor must be a numerical value or None.") + raise TypeError('Upsample factor must be a numerical value or None.') factor = float(factor) if factor <= 1.0: - raise ValueError("Upsample factor must be greater than 1.") + raise ValueError('Upsample factor must be greater than 1.') self._upsample_factor = factor @@ -185,9 +183,9 @@ def extension_factor(self, factor: Numeric) -> None: """ if not isinstance(factor, Numeric): - raise TypeError("Extension factor must be a number.") + raise TypeError('Extension factor must be a number.') if factor < 0.0: - raise ValueError("Extension factor must be non-negative.") + raise ValueError('Extension factor must be non-negative.') self._extension_factor = float(factor) # Recreate dense grid when extension factor is updated @@ -227,7 +225,7 @@ def temperature(self, temp: Parameter | Numeric | None) -> None: self._temperature.value = float(temp) else: self._temperature = Parameter( - name="temperature", + name='temperature', value=float(temp), unit=self._temperature_unit, fixed=True, @@ -235,7 +233,7 @@ def temperature(self, temp: Parameter | Numeric | None) -> None: elif isinstance(temp, Parameter): self._temperature = temp else: - raise TypeError("Temperature must be None, a float or a Parameter.") + raise TypeError('Temperature must be None, a float or a Parameter.') @property def normalize_detailed_balance(self) -> bool: @@ -264,7 +262,7 @@ def normalize_detailed_balance(self, normalize: bool) -> None: """ if not isinstance(normalize, bool): - raise TypeError("normalize_detailed_balance must be True or False.") + raise TypeError('normalize_detailed_balance must be True or False.') self._normalize_detailed_balance = normalize @@ -292,7 +290,7 @@ def _create_energy_grid( is_uniform = np.allclose(energy_diff, energy_diff[0]) if not is_uniform: raise ValueError( - "Input array `energy` must be uniformly spaced if upsample_factor is not given." # noqa: E501 + 'Input array `energy` must be uniformly spaced if upsample_factor is not given.' # noqa: E501 ) energy_dense = self.energy.values @@ -309,7 +307,7 @@ def _create_energy_grid( energy_span_dense = extended_max - extended_min if len(energy_dense) < 2: - raise ValueError("Energy array must have at least two points.") + raise ValueError('Energy array must have at least two points.') energy_dense_step = energy_dense[1] - energy_dense[0] # Handle offset for even length of energy_dense in convolution. @@ -373,30 +371,24 @@ def _check_width_thresholds( components = [model] # Treat single ModelComponent as a list for comp in components: - if hasattr(comp, "width"): - if ( - comp.width.value - > LARGE_WIDTH_THRESHOLD * self._energy_grid.energy_span_dense - ): + if hasattr(comp, 'width'): + if comp.width.value > LARGE_WIDTH_THRESHOLD * self._energy_grid.energy_span_dense: warnings.warn( f"The width of the {model_name} component '{comp.unique_name}' \ ({comp.width.value}) is large compared to the span of the input " - f"array ({self._energy_grid.energy_span_dense}). \ + f'array ({self._energy_grid.energy_span_dense}). \ This may lead to inaccuracies in the convolution. \ - Increase extension_factor to improve accuracy.", + Increase extension_factor to improve accuracy.', UserWarning, stacklevel=3, ) - if ( - comp.width.value - < SMALL_WIDTH_THRESHOLD * self._energy_grid.energy_dense_step - ): + if comp.width.value < SMALL_WIDTH_THRESHOLD * self._energy_grid.energy_dense_step: warnings.warn( f"The width of the {model_name} component '{comp.unique_name}' \ ({comp.width.value}) is small compared to the spacing of the input " - f"array ({self._energy_grid.energy_dense_step}). \ + f'array ({self._energy_grid.energy_dense_step}). \ This may lead to inaccuracies in the convolution. \ - Increase upsample_factor to improve accuracy.", + Increase upsample_factor to improve accuracy.', UserWarning, stacklevel=3, ) @@ -410,13 +402,13 @@ def __repr__(self) -> str: NumericalConvolutionBase. """ 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"energy_unit={self._energy_unit}, " - f"upsample_factor={self.upsample_factor}, " - f"extension_factor={self.extension_factor}, " - f"temperature={self.temperature}, " - f"normalize_detailed_balance={self.normalize_detailed_balance})" + 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'energy_unit={self._energy_unit}, ' + f'upsample_factor={self.upsample_factor}, ' + f'extension_factor={self.extension_factor}, ' + f'temperature={self.temperature}, ' + f'normalize_detailed_balance={self.normalize_detailed_balance})' ) diff --git a/src/easydynamics/utils/detailed_balance.py b/src/easydynamics/utils/detailed_balance.py index f2cfb675..a99ad391 100644 --- a/src/easydynamics/utils/detailed_balance.py +++ b/src/easydynamics/utils/detailed_balance.py @@ -221,9 +221,7 @@ def _convert_to_scipp_variable( return value # Convert to numpy array first for consistent handling - if isinstance(value, (int, float)): - array_value = np.array(value) - elif isinstance(value, (list)): + if isinstance(value, (int, float)) or isinstance(value, (list)): array_value = np.array(value) elif isinstance(value, np.ndarray): array_value = value diff --git a/tests/unit/easydynamics/analysis/test_analysis.py b/tests/unit/easydynamics/analysis/test_analysis.py index 5052cc8f..935cd371 100644 --- a/tests/unit/easydynamics/analysis/test_analysis.py +++ b/tests/unit/easydynamics/analysis/test_analysis.py @@ -228,24 +228,22 @@ def test_plot_data_and_model_invalid_plot_components_raises(self, analysis): # WHEN / THEN / EXPECT with ( - patch('easydynamics.analysis.analysis._in_notebook', return_value=True), + patch('easydynamics.analysis.analysis._in_notebook', return_value=True), pytest.raises( + TypeError, + match='plot_components must be True or False', + ) ): - with pytest.raises( - TypeError, - match='plot_components must be True or False', - ): - analysis.plot_data_and_model(plot_components='not_a_boolean') + analysis.plot_data_and_model(plot_components='not_a_boolean') def test_plot_data_and_model_invalid_add_background_raises(self, analysis): # WHEN / THEN / EXPECT with ( - patch('easydynamics.analysis.analysis._in_notebook', return_value=True), + patch('easydynamics.analysis.analysis._in_notebook', return_value=True), pytest.raises( + TypeError, + match='add_background must be True or False', + ) ): - with pytest.raises( - TypeError, - match='add_background must be True or False', - ): - analysis.plot_data_and_model(add_background='not_a_boolean') + analysis.plot_data_and_model(add_background='not_a_boolean') def test_plot_data_and_model_defaults(self, analysis): From e77b7f647d6f3d8326834c4eb49ffd5ba8e61ef7 Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Wed, 18 Mar 2026 12:12:05 +0100 Subject: [PATCH 4/9] Add SIM (flake8-simplify) rules part 2 --- pixi.lock | 1392 ++++++++--------- pixi.toml | 1 + pyproject.toml | 4 +- src/easydynamics/analysis/analysis.py | 2 +- src/easydynamics/analysis/analysis1d.py | 2 +- src/easydynamics/analysis/analysis_base.py | 13 +- src/easydynamics/convolution/convolution.py | 10 +- .../convolution/convolution_base.py | 6 +- .../convolution/numerical_convolution_base.py | 10 +- src/easydynamics/experiment/experiment.py | 2 +- .../sample_model/components/delta_function.py | 10 +- .../components/model_component.py | 5 +- src/easydynamics/sample_model/sample_model.py | 10 +- src/easydynamics/utils/detailed_balance.py | 12 +- .../easydynamics/analysis/test_analysis.py | 30 +- .../test_analytical_convolution.py | 5 +- .../experiment/test_experiment.py | 11 +- .../components/test_polynomial.py | 5 +- 18 files changed, 697 insertions(+), 833 deletions(-) diff --git a/pixi.lock b/pixi.lock index 5dc0b96a..df61e49b 100644 --- a/pixi.lock +++ b/pixi.lock @@ -13,7 +13,7 @@ environments: - 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mypy ; extra == 'test' - pretend ; extra == 'test' - pytest ; extra == 'test' -- pypi: https://files.pythonhosted.org/packages/78/55/896b06bf93a49bec0f4ae2a6f1ed12bd05c8860744ac3a70eda041064e4d/virtualenv-21.1.0-py3-none-any.whl +- pypi: https://files.pythonhosted.org/packages/c6/59/7d02447a55b2e55755011a647479041bc92a82e143f96a8195cb33bd0a1c/virtualenv-21.2.0-py3-none-any.whl name: virtualenv - version: 21.1.0 - sha256: 164f5e14c5587d170cf98e60378eb91ea35bf037be313811905d3a24ea33cc07 + version: 21.2.0 + sha256: 1bd755b504931164a5a496d217c014d098426cddc79363ad66ac78125f9d908f requires_dist: - distlib>=0.3.7,<1 - filelock>=3.24.2,<4 ; python_full_version >= '3.10' @@ -10398,30 +10312,6 @@ packages: - multidict>=4.0 - propcache>=0.2.1 requires_python: '>=3.10' -- pypi: https://files.pythonhosted.org/packages/2e/54/647ade08bf0db230bfea292f893923872fd20be6ac6f53b2b936ba839d75/zipp-3.23.0-py3-none-any.whl - name: zipp - version: 3.23.0 - sha256: 071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e - requires_dist: - - pytest>=6,!=8.1.* ; extra == 'test' - - jaraco-itertools ; extra == 'test' - - jaraco-functools ; extra == 'test' - - more-itertools ; extra == 'test' - - big-o ; extra == 'test' - - pytest-ignore-flaky ; extra == 'test' - - jaraco-test ; extra == 'test' - - sphinx>=3.5 ; extra == 'doc' - - jaraco-packaging>=9.3 ; extra == 'doc' - - rst-linker>=1.9 ; extra == 'doc' - - furo ; extra == 'doc' - - sphinx-lint ; extra == 'doc' - - jaraco-tidelift>=1.4 ; extra == 'doc' - - pytest-checkdocs>=2.4 ; extra == 'check' - - pytest-ruff>=0.2.1 ; sys_platform != 'cygwin' and extra == 'check' - - pytest-cov ; extra == 'cover' - - pytest-enabler>=2.2 ; extra == 'enabler' - - pytest-mypy ; extra == 'type' - requires_python: '>=3.9' - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7 md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829 diff --git a/pixi.toml b/pixi.toml index e35cbaf1..ab15262f 100644 --- a/pixi.toml +++ b/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" diff --git a/pyproject.toml b/pyproject.toml index 2da4ad1f..f761197a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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 diff --git a/src/easydynamics/analysis/analysis.py b/src/easydynamics/analysis/analysis.py index b344ef90..136cc5be 100644 --- a/src/easydynamics/analysis/analysis.py +++ b/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 diff --git a/src/easydynamics/analysis/analysis1d.py b/src/easydynamics/analysis/analysis1d.py index d2802a4a..ec6c3c8d 100644 --- a/src/easydynamics/analysis/analysis1d.py +++ b/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 diff --git a/src/easydynamics/analysis/analysis_base.py b/src/easydynamics/analysis/analysis_base.py index b5daa54d..c3dc213e 100644 --- a/src/easydynamics/analysis/analysis_base.py +++ b/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 ############# diff --git a/src/easydynamics/convolution/convolution.py b/src/easydynamics/convolution/convolution.py index 7cd742f5..3f3f1ef3 100644 --- a/src/easydynamics/convolution/convolution.py +++ b/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 diff --git a/src/easydynamics/convolution/convolution_base.py b/src/easydynamics/convolution/convolution_base.py index 1c6c68ff..f9cfc9fd 100644 --- a/src/easydynamics/convolution/convolution_base.py +++ b/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 diff --git a/src/easydynamics/convolution/numerical_convolution_base.py b/src/easydynamics/convolution/numerical_convolution_base.py index c6b626a3..913726f6 100644 --- a/src/easydynamics/convolution/numerical_convolution_base.py +++ b/src/easydynamics/convolution/numerical_convolution_base.py @@ -320,10 +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), @@ -365,10 +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'): diff --git a/src/easydynamics/experiment/experiment.py b/src/easydynamics/experiment/experiment.py index 50bbed8f..a86c8ffd 100644 --- a/src/easydynamics/experiment/experiment.py +++ b/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." diff --git a/src/easydynamics/sample_model/components/delta_function.py b/src/easydynamics/sample_model/components/delta_function.py index 4dbf8044..ea85543e 100644 --- a/src/easydynamics/sample_model/components/delta_function.py +++ b/src/easydynamics/sample_model/components/delta_function.py @@ -140,16 +140,10 @@ 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: - left = x[1] - x[0] if x.size > 1 else 0.5 - else: - left = x[i] - x[i - 1] + left = (x[1] - x[0] if x.size > 1 else 0.5) if i == 0 else x[i] - x[i - 1] # right half-width - if i == x.size - 1: - right = x[-1] - x[-2] if x.size > 1 else 0.5 - else: - right = x[i + 1] - x[i] + right = (x[-1] - x[-2] if x.size > 1 else 0.5) if i == x.size - 1 else x[i + 1] - x[i] # effective bin width: half left + half right bin_width = 0.5 * (left + right) diff --git a/src/easydynamics/sample_model/components/model_component.py b/src/easydynamics/sample_model/components/model_component.py index 62691dff..7fc63880 100644 --- a/src/easydynamics/sample_model/components/model_component.py +++ b/src/easydynamics/sample_model/components/model_component.py @@ -111,10 +111,7 @@ def _prepare_x_for_evaluate( if isinstance(x, sc.Variable): # Need to check if the units are consistent, # and convert if not. - if x.sizes == {}: # scalar - x_in = x.value - else: # array - x_in = x.values + x_in = x.value if x.sizes == {} else x.values if self._unit is not None and x.unit != self._unit: self_unit_for_warning = self._unit try: diff --git a/src/easydynamics/sample_model/sample_model.py b/src/easydynamics/sample_model/sample_model.py index 29630c45..b9947712 100644 --- a/src/easydynamics/sample_model/sample_model.py +++ b/src/easydynamics/sample_model/sample_model.py @@ -1,6 +1,8 @@ # SPDX-FileCopyrightText: 2026 EasyScience contributors # SPDX-License-Identifier: BSD-3-Clause +from contextlib import suppress + import numpy as np import scipp as sc from easyscience.variable import Parameter @@ -295,13 +297,11 @@ def convert_temperature_unit(self, unit: str | sc.Unit) -> None: try: self._temperature.convert_unit(unit) self._temperature_unit = unit - except Exception as e: + except Exception: # Attempt to rollback on failure - try: + with suppress(Exception): self._temperature.convert_unit(old_unit) - except Exception: # noqa: S110 - pass # Best effort rollback - raise e + raise @property def divide_by_temperature(self) -> bool: diff --git a/src/easydynamics/utils/detailed_balance.py b/src/easydynamics/utils/detailed_balance.py index a99ad391..f61f4349 100644 --- a/src/easydynamics/utils/detailed_balance.py +++ b/src/easydynamics/utils/detailed_balance.py @@ -145,10 +145,7 @@ def detailed_balance_factor( raise ZeroDivisionError('Cannot divide by T when T = 0.') DBF = sc.where(energy < 0.0 * energy.unit, 0.0 * energy.unit, energy) - if DBF.sizes == {}: - DBF_values = np.array([DBF.value]) - else: - DBF_values = DBF.values + DBF_values = np.array([DBF.value]) if DBF.sizes == {} else DBF.values return DBF_values # Now work with finite temperatures. @@ -182,10 +179,7 @@ def detailed_balance_factor( DBF = DBF * (kB * temperature) DBF = sc.to_unit(DBF, unit=energy.unit) - if DBF.sizes == {}: - DBF_values = np.array([DBF.value]) - else: - DBF_values = DBF.values + DBF_values = np.array([DBF.value]) if DBF.sizes == {} else DBF.values return DBF_values @@ -221,7 +215,7 @@ def _convert_to_scipp_variable( return value # Convert to numpy array first for consistent handling - if isinstance(value, (int, float)) or isinstance(value, (list)): + if isinstance(value, (int, float, list)): array_value = np.array(value) elif isinstance(value, np.ndarray): array_value = value diff --git a/tests/unit/easydynamics/analysis/test_analysis.py b/tests/unit/easydynamics/analysis/test_analysis.py index 935cd371..6fafc09a 100644 --- a/tests/unit/easydynamics/analysis/test_analysis.py +++ b/tests/unit/easydynamics/analysis/test_analysis.py @@ -185,12 +185,14 @@ def test_fit_with_invalid_fit_method(self, analysis): def test_plot_data_and_model_not_in_notebook_raises(self, analysis): # WHEN / THEN / EXPECT - with patch('easydynamics.analysis.analysis._in_notebook', return_value=False): - with pytest.raises( + with ( + patch('easydynamics.analysis.analysis._in_notebook', return_value=False), + pytest.raises( RuntimeError, - match=' can only be used in a Jupyter notebook environment', - ): - analysis.plot_data_and_model() + match=r'can only be used in a Jupyter notebook environment', + ), + ): + analysis.plot_data_and_model() def test_plot_data_and_model_Q_index(self, analysis): @@ -228,20 +230,22 @@ def test_plot_data_and_model_invalid_plot_components_raises(self, analysis): # WHEN / THEN / EXPECT with ( - patch('easydynamics.analysis.analysis._in_notebook', return_value=True), pytest.raises( - TypeError, - match='plot_components must be True or False', - ) + patch('easydynamics.analysis.analysis._in_notebook', return_value=True), + pytest.raises( + TypeError, + match='plot_components must be True or False', + ), ): analysis.plot_data_and_model(plot_components='not_a_boolean') def test_plot_data_and_model_invalid_add_background_raises(self, analysis): # WHEN / THEN / EXPECT with ( - patch('easydynamics.analysis.analysis._in_notebook', return_value=True), pytest.raises( - TypeError, - match='add_background must be True or False', - ) + patch('easydynamics.analysis.analysis._in_notebook', return_value=True), + pytest.raises( + TypeError, + match='add_background must be True or False', + ), ): analysis.plot_data_and_model(add_background='not_a_boolean') diff --git a/tests/unit/easydynamics/convolution/test_analytical_convolution.py b/tests/unit/easydynamics/convolution/test_analytical_convolution.py index 3bc8ec09..06d76431 100644 --- a/tests/unit/easydynamics/convolution/test_analytical_convolution.py +++ b/tests/unit/easydynamics/convolution/test_analytical_convolution.py @@ -271,10 +271,7 @@ def test_convolute_analytic_pair_calls_correct_helper( return_value='mocked_result', ) as mocked_func: result = default_analytical_convolution._convolute_analytic_pair(function1, function2) - if swapped: - expected_args = (function2, function1) - else: - expected_args = (function1, function2) + expected_args = (function2, function1) if swapped else (function1, function2) mocked_func.assert_called_once_with(*expected_args) assert result == 'mocked_result' diff --git a/tests/unit/easydynamics/experiment/test_experiment.py b/tests/unit/easydynamics/experiment/test_experiment.py index a27fb252..84d09059 100644 --- a/tests/unit/easydynamics/experiment/test_experiment.py +++ b/tests/unit/easydynamics/experiment/test_experiment.py @@ -368,13 +368,14 @@ def test_plot_data_not_in_notebook_raises(self, experiment): "Test plotting data raises RuntimeError" 'when not in notebook environment' # WHEN - with patch(f'{Experiment.__module__}._in_notebook', return_value=False): - # THEN EXPECT - with pytest.raises( + with ( + patch(f'{Experiment.__module__}._in_notebook', return_value=False), + pytest.raises( RuntimeError, match='plot_data\\(\\) can only be used in a Jupyter notebook environment', - ): - experiment.plot_data() + ), + ): + experiment.plot_data() ############## # test private methods diff --git a/tests/unit/easydynamics/sample_model/components/test_polynomial.py b/tests/unit/easydynamics/sample_model/components/test_polynomial.py index 82d88d66..aa7790d2 100644 --- a/tests/unit/easydynamics/sample_model/components/test_polynomial.py +++ b/tests/unit/easydynamics/sample_model/components/test_polynomial.py @@ -110,10 +110,7 @@ def test_set_coefficients(self, polynomial: Polynomial, values): # THEN EXPECT: Parameter values match the new inputs for i, val in enumerate(values): - if isinstance(val, Parameter): - expected = val.value - else: - expected = val + expected = val.value if isinstance(val, Parameter) else val assert np.isclose(polynomial.coefficients[i].value, expected) def test_set_coefficients_wrong_length_raises(self, polynomial: Polynomial): From dae81482546bbd475ca31db261c33ac62a04a9aa Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Wed, 18 Mar 2026 12:16:36 +0100 Subject: [PATCH 5/9] final linting --- pixi.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.lock b/pixi.lock index df61e49b..4e837163 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4038,7 +4038,7 @@ packages: requires_python: '>=3.5' - pypi: ./ name: easydynamics - version: 0.3.0+devdirty4 + version: 0.3.0+devdirty5 sha256: 15b8ce320faf7bc1e8397b7808fcc52ae412edca87654e7457d78381219a93c7 requires_dist: - darkdetect From 804729740b662980f8d1d67d5d2d5c0102771da2 Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Wed, 18 Mar 2026 12:20:59 +0100 Subject: [PATCH 6/9] fix docstrings --- src/easydynamics/sample_model/component_collection.py | 2 +- .../diffusion_model/brownian_translational_diffusion.py | 6 +++--- .../diffusion_model/jump_translational_diffusion.py | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/easydynamics/sample_model/component_collection.py b/src/easydynamics/sample_model/component_collection.py index ecfc21d7..c3bd3c56 100644 --- a/src/easydynamics/sample_model/component_collection.py +++ b/src/easydynamics/sample_model/component_collection.py @@ -303,7 +303,7 @@ 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. """ diff --git a/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py b/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py index 66ed574c..dfeac401 100644 --- a/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py +++ b/src/easydynamics/sample_model/diffusion_model/brownian_translational_diffusion.py @@ -187,7 +187,7 @@ def create_component_collections( Name of the Lorentzian component. Returns: - List[ComponentCollection]: List of ComponentCollections with + list[ComponentCollection]: List of ComponentCollections with Lorentzian components for each Q value. Each Lorentzian has a width given by $D*Q^2$ and an area given by the scale parameter multiplied by the QISF (which is 1 for @@ -268,7 +268,7 @@ def _write_width_dependency_map_expression(self) -> dict[str, DescriptorNumber]: Parameters. Returns: - Dict[str, DescriptorNumber]: Dependency map for the width. + dict[str, DescriptorNumber]: Dependency map for the width. """ return { 'D': self.diffusion_coefficient, @@ -299,7 +299,7 @@ def _write_area_dependency_map_expression(self) -> dict[str, DescriptorNumber]: Parameters. Returns: - Dict[str, DescriptorNumber]: Dependency map for the area. + dict[str, DescriptorNumber]: Dependency map for the area. """ return { 'scale': self.scale, diff --git a/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py b/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py index 18475624..f306aae4 100644 --- a/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py +++ b/src/easydynamics/sample_model/diffusion_model/jump_translational_diffusion.py @@ -241,7 +241,7 @@ def create_component_collections( Name of the Jump Diffusion Lorentzian component. Returns: - List[ComponentCollection]: List of ComponentCollections with + list[ComponentCollection]: List of ComponentCollections with Jump Diffusion Lorentzian components. Raises: @@ -319,7 +319,7 @@ def _write_width_dependency_map_expression(self) -> dict[str, DescriptorNumber]: Parameters. Returns: - Dict[str, DescriptorNumber]: Dependency map for the width. + dict[str, DescriptorNumber]: Dependency map for the width. """ return { 'D': self._diffusion_coefficient, @@ -352,7 +352,7 @@ def _write_area_dependency_map_expression(self) -> dict[str, DescriptorNumber]: Parameters. Returns: - Dict[str, DescriptorNumber]: Dependency map for the area. + dict[str, DescriptorNumber]: Dependency map for the area. """ return { 'scale': self._scale, From 60bb2ebe9d57507ac5b0f126aa0f9b1ec00907d2 Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Wed, 18 Mar 2026 14:05:21 +0100 Subject: [PATCH 7/9] fix notebook imports --- docs/docs/tutorials/convolution.ipynb | 2 +- docs/docs/tutorials/detailed_balance.ipynb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/docs/tutorials/convolution.ipynb b/docs/docs/tutorials/convolution.ipynb index b13d7973..8b106ebd 100644 --- a/docs/docs/tutorials/convolution.ipynb +++ b/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" ] diff --git a/docs/docs/tutorials/detailed_balance.ipynb b/docs/docs/tutorials/detailed_balance.ipynb index 135894d3..12d926a6 100644 --- a/docs/docs/tutorials/detailed_balance.ipynb +++ b/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" ] From cae19e2af0d0d32f72d7897f5c1097ccaccec500 Mon Sep 17 00:00:00 2001 From: henrikjacobsenfys Date: Thu, 19 Mar 2026 14:11:20 +0100 Subject: [PATCH 8/9] Respond to PR comments --- src/easydynamics/convolution/numerical_convolution.py | 2 +- .../sample_model/components/delta_function.py | 10 ++++++++-- .../convolution/test_numerical_convolution.py | 2 +- 3 files changed, 10 insertions(+), 4 deletions(-) diff --git a/src/easydynamics/convolution/numerical_convolution.py b/src/easydynamics/convolution/numerical_convolution.py index 05e64200..10a55c81 100644 --- a/src/easydynamics/convolution/numerical_convolution.py +++ b/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 diff --git a/src/easydynamics/sample_model/components/delta_function.py b/src/easydynamics/sample_model/components/delta_function.py index ea85543e..820a039b 100644 --- a/src/easydynamics/sample_model/components/delta_function.py +++ b/src/easydynamics/sample_model/components/delta_function.py @@ -140,10 +140,16 @@ def evaluate(self, x: Numeric | list | np.ndarray | sc.Variable | sc.DataArray) i = np.argmin(np.abs(x - center)) # left half-width - left = (x[1] - x[0] if x.size > 1 else 0.5) if i == 0 else x[i] - x[i - 1] + 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 - right = (x[-1] - x[-2] if x.size > 1 else 0.5) if i == x.size - 1 else x[i + 1] - x[i] + 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] # effective bin width: half left + half right bin_width = 0.5 * (left + right) diff --git a/tests/unit/easydynamics/convolution/test_numerical_convolution.py b/tests/unit/easydynamics/convolution/test_numerical_convolution.py index 7094f3dd..29e5dfd6 100644 --- a/tests/unit/easydynamics/convolution/test_numerical_convolution.py +++ b/tests/unit/easydynamics/convolution/test_numerical_convolution.py @@ -10,7 +10,7 @@ from easydynamics.convolution.numerical_convolution import NumericalConvolution from easydynamics.sample_model import Gaussian from easydynamics.sample_model.component_collection import ComponentCollection -from easydynamics.utils.detailed_balance import detailed_balance_factor as detailed_balance_factor +from easydynamics.utils.detailed_balance import detailed_balance_factor class TestNumericalConvolution: From e62b24ebd6232b116155689d548e3b501c03a49a Mon Sep 17 00:00:00 2001 From: Andrew Sazonov Date: Fri, 20 Mar 2026 09:31:26 +0100 Subject: [PATCH 9/9] Fix package test step on macOS --- .copier-answers.yml | 2 +- .github/workflows/test.yml | 11 ++++------- 2 files changed, 5 insertions(+), 8 deletions(-) diff --git a/.copier-answers.yml b/.copier-answers.yml index b8de5ab8..7b414c16 100644 --- a/.copier-answers.yml +++ b/.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 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 3d23363d..ce03715c 100644 --- a/.github/workflows/test.yml +++ b/.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/"