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+- pypi: https://files.pythonhosted.org/packages/f2/c0/4ac978fe874d0618c7da647862afe697b281c2806f13ce904ad652fa87e4/ruff-0.15.10-py3-none-macosx_11_0_arm64.whl
name: ruff
- version: 0.15.9
- sha256: 2b0c7c341f68adb01c488c3b7d4b49aa8ea97409eae6462d860a79cf55f431b6
+ version: 0.15.10
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name: sciline
diff --git a/pyproject.toml b/pyproject.toml
index a2b9456d..08b13256 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -257,7 +257,7 @@ select = [
'DTZ', # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
'EM', # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
'FA', # https://docs.astral.sh/ruff/rules/#flake8-future-annotations-fa
- #'FBT', # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt
+ '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
@@ -268,7 +268,7 @@ select = [
'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
+ '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
diff --git a/src/easydiffraction/__main__.py b/src/easydiffraction/__main__.py
index f0b5ab12..edb8b877 100644
--- a/src/easydiffraction/__main__.py
+++ b/src/easydiffraction/__main__.py
@@ -18,8 +18,8 @@
@app.callback(invoke_without_command=True)
def main(
ctx: typer.Context,
- version: bool = typer.Option(
- False,
+ version: bool = typer.Option( # noqa: FBT001
+ False, # noqa: FBT003
'--version',
'-V',
help='Show easydiffraction version and exit.',
@@ -52,8 +52,8 @@ def download_tutorial(
'-d',
help='Directory to save the tutorial into.',
),
- overwrite: bool = typer.Option(
- False,
+ overwrite: bool = typer.Option( # noqa: FBT001
+ False, # noqa: FBT003
'--overwrite',
'-o',
help='Overwrite existing file if present.',
@@ -71,8 +71,8 @@ def download_all_tutorials(
'-d',
help='Directory to save the tutorials into.',
),
- overwrite: bool = typer.Option(
- False,
+ overwrite: bool = typer.Option( # noqa: FBT001
+ False, # noqa: FBT003
'--overwrite',
'-o',
help='Overwrite existing files if present.',
@@ -88,8 +88,8 @@ def fit(
...,
help='Path to the project directory (must contain project.cif).',
),
- dry: bool = typer.Option(
- False,
+ dry: bool = typer.Option( # noqa: FBT001
+ False, # noqa: FBT003
'--dry',
help='Run fitting without saving results back to the project directory.',
),
diff --git a/src/easydiffraction/analysis/analysis.py b/src/easydiffraction/analysis/analysis.py
index b23df608..8a641bc9 100644
--- a/src/easydiffraction/analysis/analysis.py
+++ b/src/easydiffraction/analysis/analysis.py
@@ -905,6 +905,7 @@ def fit_sequential(
file_pattern: str = '*',
extract_diffrn: object = None,
verbosity: str | None = None,
+ *,
reverse: bool = False,
) -> None:
"""
@@ -966,7 +967,11 @@ def fit_sequential(
if original_verbosity is not None:
self.project.verbosity = original_verbosity
- def _update_categories(self, called_by_minimizer: bool = False) -> None:
+ def _update_categories(
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
"""
Update all categories owned by Analysis.
diff --git a/src/easydiffraction/analysis/calculators/base.py b/src/easydiffraction/analysis/calculators/base.py
index ed36991d..5ef47e3b 100644
--- a/src/easydiffraction/analysis/calculators/base.py
+++ b/src/easydiffraction/analysis/calculators/base.py
@@ -29,6 +29,7 @@ def calculate_structure_factors(
self,
structure: Structure,
experiment: ExperimentBase,
+ *,
called_by_minimizer: bool,
) -> None:
"""Calculate structure factors for one experiment."""
@@ -38,6 +39,7 @@ def calculate_pattern(
self,
structure: Structures, # TODO: Structure?
experiment: ExperimentBase,
+ *,
called_by_minimizer: bool,
) -> np.ndarray:
"""
diff --git a/src/easydiffraction/analysis/calculators/crysfml.py b/src/easydiffraction/analysis/calculators/crysfml.py
index aaaa537e..1fcc4087 100644
--- a/src/easydiffraction/analysis/calculators/crysfml.py
+++ b/src/easydiffraction/analysis/calculators/crysfml.py
@@ -68,6 +68,7 @@ def calculate_pattern(
self,
structure: Structures,
experiment: ExperimentBase,
+ *,
called_by_minimizer: bool = False,
) -> np.ndarray | list[float]:
"""
@@ -231,7 +232,7 @@ def _convert_experiment_to_dict( # noqa: PLR6301
# TODO: Process default values on the experiment creation
# instead of here
- exp_dict = {
+ return {
'NPD': {
'_diffrn_radiation_probe': expt_type.radiation_probe.value
if expt_type
@@ -258,5 +259,3 @@ def _convert_experiment_to_dict( # noqa: PLR6301
/ (len(x_data) - 1 + 1e-9),
}
}
-
- return exp_dict
diff --git a/src/easydiffraction/analysis/calculators/cryspy.py b/src/easydiffraction/analysis/calculators/cryspy.py
index d60c5629..adb72668 100644
--- a/src/easydiffraction/analysis/calculators/cryspy.py
+++ b/src/easydiffraction/analysis/calculators/cryspy.py
@@ -58,6 +58,7 @@ def calculate_structure_factors(
self,
structure: Structure,
experiment: ExperimentBase,
+ *,
called_by_minimizer: bool = False,
) -> None:
"""
@@ -117,6 +118,7 @@ def calculate_pattern(
self,
structure: Structure,
experiment: ExperimentBase,
+ *,
called_by_minimizer: bool = False,
) -> np.ndarray | list[float]:
"""
diff --git a/src/easydiffraction/analysis/calculators/pdffit.py b/src/easydiffraction/analysis/calculators/pdffit.py
index 67864cea..ed071753 100644
--- a/src/easydiffraction/analysis/calculators/pdffit.py
+++ b/src/easydiffraction/analysis/calculators/pdffit.py
@@ -88,6 +88,7 @@ def calculate_pattern( # noqa: PLR6301
self,
structure: Structure,
experiment: ExperimentBase,
+ *,
called_by_minimizer: bool = False,
) -> None:
"""
@@ -165,6 +166,4 @@ def calculate_pattern( # noqa: PLR6301
# Get the calculated PDF pattern
pattern = calculator.getpdf_fit()
- pattern = np.array(pattern)
-
- return pattern
+ return np.array(pattern)
diff --git a/src/easydiffraction/analysis/categories/fit_mode/enums.py b/src/easydiffraction/analysis/categories/fit_mode/enums.py
index ffae6a2c..80b8d1de 100644
--- a/src/easydiffraction/analysis/categories/fit_mode/enums.py
+++ b/src/easydiffraction/analysis/categories/fit_mode/enums.py
@@ -24,3 +24,4 @@ def description(self) -> str:
return 'Independent fitting of each experiment; no shared parameters'
if self is FitModeEnum.JOINT:
return 'Simultaneous fitting of all experiments; some parameters are shared'
+ return None
diff --git a/src/easydiffraction/analysis/fit_helpers/reporting.py b/src/easydiffraction/analysis/fit_helpers/reporting.py
index 91e21718..f11cd7b1 100644
--- a/src/easydiffraction/analysis/fit_helpers/reporting.py
+++ b/src/easydiffraction/analysis/fit_helpers/reporting.py
@@ -21,6 +21,7 @@ class FitResults:
def __init__(
self,
+ *,
success: bool = False,
parameters: list[object] | None = None,
reduced_chi_square: float | None = None,
diff --git a/src/easydiffraction/analysis/minimizers/base.py b/src/easydiffraction/analysis/minimizers/base.py
index fd4387ea..ee08ee55 100644
--- a/src/easydiffraction/analysis/minimizers/base.py
+++ b/src/easydiffraction/analysis/minimizers/base.py
@@ -168,9 +168,7 @@ def fit(
self._stop_tracking()
- result = self._finalize_fit(parameters, raw_result)
-
- return result
+ return self._finalize_fit(parameters, raw_result)
def _objective_function(
self,
diff --git a/src/easydiffraction/analysis/sequential.py b/src/easydiffraction/analysis/sequential.py
index e95eeb0a..3be80ba4 100644
--- a/src/easydiffraction/analysis/sequential.py
+++ b/src/easydiffraction/analysis/sequential.py
@@ -811,6 +811,7 @@ def fit_sequential(
chunk_size: int | None = None,
file_pattern: str = '*',
extract_diffrn: Callable | None = None,
+ *,
reverse: bool = False,
) -> None:
"""
diff --git a/src/easydiffraction/core/category.py b/src/easydiffraction/core/category.py
index 1d8710ed..0804d7d4 100644
--- a/src/easydiffraction/core/category.py
+++ b/src/easydiffraction/core/category.py
@@ -30,7 +30,11 @@ def __str__(self) -> str:
return f'<{name} ({params})>'
# TODO: Common for all categories
- def _update(self, called_by_minimizer: bool = False) -> None: # noqa: PLR6301
+ def _update( # noqa: PLR6301
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
del called_by_minimizer
@property
@@ -193,7 +197,11 @@ def __str__(self) -> str:
return f'<{name} collection ({size} items)>'
# TODO: Common for all categories
- def _update(self, called_by_minimizer: bool = False) -> None: # noqa: PLR6301
+ def _update( # noqa: PLR6301
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
del called_by_minimizer
@property
diff --git a/src/easydiffraction/core/datablock.py b/src/easydiffraction/core/datablock.py
index ac49fbc2..f6f7ae05 100644
--- a/src/easydiffraction/core/datablock.py
+++ b/src/easydiffraction/core/datablock.py
@@ -33,6 +33,7 @@ def __repr__(self) -> str:
def _update_categories(
self,
+ *,
called_by_minimizer: bool = False,
) -> None:
# TODO: Make abstract method and implement in subclasses.
diff --git a/src/easydiffraction/core/guard.py b/src/easydiffraction/core/guard.py
index 096ec9f9..ff259d3f 100644
--- a/src/easydiffraction/core/guard.py
+++ b/src/easydiffraction/core/guard.py
@@ -113,7 +113,11 @@ def _public_writable_attrs(cls) -> set[str]:
"""Public properties with a setter."""
return {key for key, prop in cls._iter_properties() if prop.fset is not None}
- def _allowed_attrs(self, writable_only: bool = False) -> set[str]:
+ def _allowed_attrs(
+ self,
+ *,
+ writable_only: bool = False,
+ ) -> set[str]:
cls = type(self)
if writable_only:
return cls._public_writable_attrs()
diff --git a/src/easydiffraction/core/validation.py b/src/easydiffraction/core/validation.py
index a5e4ffba..3fd88208 100644
--- a/src/easydiffraction/core/validation.py
+++ b/src/easydiffraction/core/validation.py
@@ -122,6 +122,7 @@ def validated(
name: str,
default: object = None,
current: object = None,
+ *,
allow_none: bool = False,
) -> object:
"""
diff --git a/src/easydiffraction/datablocks/experiment/categories/background/chebyshev.py b/src/easydiffraction/datablocks/experiment/categories/background/chebyshev.py
index 4980541a..35c09a22 100644
--- a/src/easydiffraction/datablocks/experiment/categories/background/chebyshev.py
+++ b/src/easydiffraction/datablocks/experiment/categories/background/chebyshev.py
@@ -151,7 +151,11 @@ class ChebyshevPolynomialBackground(BackgroundBase):
def __init__(self) -> None:
super().__init__(item_type=PolynomialTerm)
- def _update(self, called_by_minimizer: bool = False) -> None:
+ def _update(
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
"""Evaluate polynomial background over x data."""
del called_by_minimizer
diff --git a/src/easydiffraction/datablocks/experiment/categories/background/enums.py b/src/easydiffraction/datablocks/experiment/categories/background/enums.py
index 2755b649..c0e325a7 100644
--- a/src/easydiffraction/datablocks/experiment/categories/background/enums.py
+++ b/src/easydiffraction/datablocks/experiment/categories/background/enums.py
@@ -25,3 +25,4 @@ def description(self) -> str:
return 'Linear interpolation between points'
if self is BackgroundTypeEnum.CHEBYSHEV:
return 'Chebyshev polynomial background'
+ return None
diff --git a/src/easydiffraction/datablocks/experiment/categories/background/line_segment.py b/src/easydiffraction/datablocks/experiment/categories/background/line_segment.py
index ad4a5246..83e202b4 100644
--- a/src/easydiffraction/datablocks/experiment/categories/background/line_segment.py
+++ b/src/easydiffraction/datablocks/experiment/categories/background/line_segment.py
@@ -148,7 +148,11 @@ class LineSegmentBackground(BackgroundBase):
def __init__(self) -> None:
super().__init__(item_type=LineSegment)
- def _update(self, called_by_minimizer: bool = False) -> None:
+ def _update(
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
"""Interpolate background points over x data."""
del called_by_minimizer
diff --git a/src/easydiffraction/datablocks/experiment/categories/data/bragg_pd.py b/src/easydiffraction/datablocks/experiment/categories/data/bragg_pd.py
index d52de4f0..7f973f53 100644
--- a/src/easydiffraction/datablocks/experiment/categories/data/bragg_pd.py
+++ b/src/easydiffraction/datablocks/experiment/categories/data/bragg_pd.py
@@ -369,7 +369,11 @@ def _calc_items(self) -> list:
# Misc
- def _update(self, called_by_minimizer: bool = False) -> None:
+ def _update(
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
experiment = self._parent
experiments = experiment._parent
project = experiments._parent
@@ -452,8 +456,7 @@ def intensity_meas_su(self) -> np.ndarray:
dtype=float, # TODO: needed? DataTypes.NUMERIC?
)
# Replace values smaller than _MIN_UNCERTAINTY with 1.0
- modified = np.where(original < _MIN_UNCERTAINTY, 1.0, original)
- return modified
+ return np.where(original < _MIN_UNCERTAINTY, 1.0, original)
@property
def intensity_calc(self) -> np.ndarray:
@@ -514,8 +517,12 @@ def _create_items_set_xcoord_and_id(self, values: object) -> None:
# Misc
- def _update(self, called_by_minimizer: bool = False) -> None:
- super()._update(called_by_minimizer)
+ def _update(
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
+ super()._update(called_by_minimizer=called_by_minimizer)
experiment = self._parent
d_spacing = twotheta_to_d(
@@ -589,8 +596,12 @@ def _create_items_set_xcoord_and_id(self, values: object) -> None:
# Misc
- def _update(self, called_by_minimizer: bool = False) -> None:
- super()._update(called_by_minimizer)
+ def _update(
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
+ super()._update(called_by_minimizer=called_by_minimizer)
experiment = self._parent
d_spacing = tof_to_d(
diff --git a/src/easydiffraction/datablocks/experiment/categories/data/bragg_sc.py b/src/easydiffraction/datablocks/experiment/categories/data/bragg_sc.py
index d19eb75f..84376f5d 100644
--- a/src/easydiffraction/datablocks/experiment/categories/data/bragg_sc.py
+++ b/src/easydiffraction/datablocks/experiment/categories/data/bragg_sc.py
@@ -323,7 +323,11 @@ def _set_intensity_calc(self, values: object) -> None:
# Misc
- def _update(self, called_by_minimizer: bool = False) -> None:
+ def _update(
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
experiment = self._parent
experiments = experiment._parent
project = experiments._parent
diff --git a/src/easydiffraction/datablocks/experiment/categories/data/total_pd.py b/src/easydiffraction/datablocks/experiment/categories/data/total_pd.py
index 8d465bb7..5f0ebedf 100644
--- a/src/easydiffraction/datablocks/experiment/categories/data/total_pd.py
+++ b/src/easydiffraction/datablocks/experiment/categories/data/total_pd.py
@@ -237,7 +237,11 @@ def _calc_items(self) -> list:
# Misc
- def _update(self, called_by_minimizer: bool = False) -> None:
+ def _update(
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
experiment = self._parent
experiments = experiment._parent
project = experiments._parent
diff --git a/src/easydiffraction/datablocks/experiment/categories/excluded_regions/default.py b/src/easydiffraction/datablocks/experiment/categories/excluded_regions/default.py
index 21dda1d9..2f4170bb 100644
--- a/src/easydiffraction/datablocks/experiment/categories/excluded_regions/default.py
+++ b/src/easydiffraction/datablocks/experiment/categories/excluded_regions/default.py
@@ -135,7 +135,11 @@ class ExcludedRegions(CategoryCollection):
def __init__(self) -> None:
super().__init__(item_type=ExcludedRegion)
- def _update(self, called_by_minimizer: bool = False) -> None:
+ def _update(
+ self,
+ *,
+ called_by_minimizer: bool = False,
+ ) -> None:
del called_by_minimizer
data = self._parent.data
diff --git a/src/easydiffraction/datablocks/experiment/item/enums.py b/src/easydiffraction/datablocks/experiment/item/enums.py
index 3fb217cf..1c73f521 100644
--- a/src/easydiffraction/datablocks/experiment/item/enums.py
+++ b/src/easydiffraction/datablocks/experiment/item/enums.py
@@ -36,6 +36,7 @@ def description(self) -> str:
return 'Powdered or polycrystalline sample.'
if self is SampleFormEnum.SINGLE_CRYSTAL:
return 'Single crystal sample.'
+ return None
class ScatteringTypeEnum(StrEnum):
@@ -69,6 +70,7 @@ def description(self) -> str:
return 'Bragg diffraction for conventional structure refinement.'
if self is ScatteringTypeEnum.TOTAL:
return 'Total scattering for pair distribution function analysis (PDF).'
+ return None
class RadiationProbeEnum(StrEnum):
@@ -102,6 +104,7 @@ def description(self) -> str:
return 'Neutron diffraction.'
if self is RadiationProbeEnum.XRAY:
return 'X-ray diffraction.'
+ return None
class BeamModeEnum(StrEnum):
@@ -136,6 +139,7 @@ def description(self) -> str:
return 'Constant wavelength (CW) diffraction.'
if self is BeamModeEnum.TIME_OF_FLIGHT:
return 'Time-of-flight (TOF) diffraction.'
+ return None
class CalculatorEnum(StrEnum):
@@ -199,7 +203,7 @@ def default(
(ScatteringTypeEnum.TOTAL, BeamModeEnum.TIME_OF_FLIGHT): cls.GAUSSIAN_DAMPED_SINC,
}[scattering_type, beam_mode]
- def description(self) -> str:
+ def description(self) -> str: # noqa: PLR0911
"""
Return a human-readable description of this peak profile type.
@@ -220,3 +224,4 @@ def description(self) -> str:
return 'Pseudo-Voigt profile with Back-to-Back Exponential asymmetry correction.'
if self is PeakProfileTypeEnum.GAUSSIAN_DAMPED_SINC:
return 'Gaussian-damped sinc profile for pair distribution function (PDF) analysis.'
+ return None
diff --git a/src/easydiffraction/datablocks/experiment/item/factory.py b/src/easydiffraction/datablocks/experiment/item/factory.py
index c4310f4f..d722d572 100644
--- a/src/easydiffraction/datablocks/experiment/item/factory.py
+++ b/src/easydiffraction/datablocks/experiment/item/factory.py
@@ -172,8 +172,7 @@ def from_scratch(
scattering_type=scattering_type,
)
expt_class = cls._resolve_class(expt_type)
- expt_obj = expt_class(name=name, type=expt_type)
- return expt_obj
+ return expt_class(name=name, type=expt_type)
# TODO: add minimal default configuration for missing parameters
@classmethod
diff --git a/src/easydiffraction/datablocks/structure/categories/atom_sites/default.py b/src/easydiffraction/datablocks/structure/categories/atom_sites/default.py
index 265c3c62..6bc85eee 100644
--- a/src/easydiffraction/datablocks/structure/categories/atom_sites/default.py
+++ b/src/easydiffraction/datablocks/structure/categories/atom_sites/default.py
@@ -364,6 +364,7 @@ def _apply_atomic_coordinates_symmetry_constraints(self) -> None:
def _update(
self,
+ *,
called_by_minimizer: bool = False,
) -> None:
"""
diff --git a/src/easydiffraction/datablocks/structure/categories/cell/default.py b/src/easydiffraction/datablocks/structure/categories/cell/default.py
index 53cc98ee..e08761c9 100644
--- a/src/easydiffraction/datablocks/structure/categories/cell/default.py
+++ b/src/easydiffraction/datablocks/structure/categories/cell/default.py
@@ -131,6 +131,7 @@ def _apply_cell_symmetry_constraints(self) -> None:
def _update(
self,
+ *,
called_by_minimizer: bool = False,
) -> None:
"""
diff --git a/src/easydiffraction/display/plotters/ascii.py b/src/easydiffraction/display/plotters/ascii.py
index 9ef5484b..1874faca 100644
--- a/src/easydiffraction/display/plotters/ascii.py
+++ b/src/easydiffraction/display/plotters/ascii.py
@@ -50,8 +50,7 @@ def _get_legend_item(label: str) -> str:
color_end = asciichartpy.reset
line = '────'
name = SERIES_CONFIG[label]['name']
- item = f'{color_start}{line}{color_end} {name}'
- return item
+ return f'{color_start}{line}{color_end} {name}'
def plot_powder(
self,
diff --git a/src/easydiffraction/display/plotters/plotly.py b/src/easydiffraction/display/plotters/plotly.py
index af09c437..a876cff7 100644
--- a/src/easydiffraction/display/plotters/plotly.py
+++ b/src/easydiffraction/display/plotters/plotly.py
@@ -349,7 +349,7 @@ def _get_powder_trace(
color = DEFAULT_COLORS[label]
line = {'color': color}
- trace = go.Scatter(
+ return go.Scatter(
x=x,
y=y,
line=line,
@@ -357,8 +357,6 @@ def _get_powder_trace(
name=name,
)
- return trace
-
@staticmethod
def _get_single_crystal_trace(
x_calc: object,
@@ -383,7 +381,7 @@ def _get_single_crystal_trace(
A configured :class:`plotly.graph_objects.Scatter` trace
with markers and error bars.
"""
- trace = go.Scatter(
+ return go.Scatter(
x=x_calc,
y=y_meas,
mode='markers',
@@ -401,8 +399,6 @@ def _get_single_crystal_trace(
hovertemplate='calc: %{x}
meas: %{y}
',
)
- return trace
-
@staticmethod
def _get_diagonal_shape() -> dict:
"""
diff --git a/src/easydiffraction/display/plotting.py b/src/easydiffraction/display/plotting.py
index fc0fd919..bf610183 100644
--- a/src/easydiffraction/display/plotting.py
+++ b/src/easydiffraction/display/plotting.py
@@ -172,9 +172,7 @@ def _filtered_y_array(
x_max = self.x_max
mask = (x_array >= x_min) & (x_array <= x_max)
- filtered_y_array = y_array[mask]
-
- return filtered_y_array
+ return y_array[mask]
@staticmethod
def _get_axes_labels(
@@ -424,6 +422,7 @@ def plot_meas_vs_calc(
expt_name: str,
x_min: float | None = None,
x_max: float | None = None,
+ *,
show_residual: bool = False,
x: object | None = None,
) -> None:
@@ -641,6 +640,7 @@ def _mask_correlation_lower_triangle(
@staticmethod
def _trim_correlation_display_dataframe(
corr_df: pd.DataFrame,
+ *,
preserve_all_rows: bool,
) -> tuple[pd.DataFrame, list[int], list[int]]:
"""
@@ -1065,6 +1065,7 @@ def _plot_meas_vs_calc_data(
expt_name: str,
x_min: object = None,
x_max: object = None,
+ *,
show_residual: bool = False,
x: object = None,
) -> None:
diff --git a/src/easydiffraction/display/tablers/base.py b/src/easydiffraction/display/tablers/base.py
index 49e3fa0e..75922fce 100644
--- a/src/easydiffraction/display/tablers/base.py
+++ b/src/easydiffraction/display/tablers/base.py
@@ -86,8 +86,7 @@ def _rich_to_hex(color: str) -> str:
"""
c = Color.parse(color)
rgb = c.get_truecolor()
- hex_value = '#{:02x}{:02x}{:02x}'.format(*rgb)
- return hex_value
+ return '#{:02x}{:02x}{:02x}'.format(*rgb)
@property
def _rich_border_color(self) -> str:
diff --git a/src/easydiffraction/display/tablers/rich.py b/src/easydiffraction/display/tablers/rich.py
index 903b33ef..8daafb6b 100644
--- a/src/easydiffraction/display/tablers/rich.py
+++ b/src/easydiffraction/display/tablers/rich.py
@@ -61,11 +61,10 @@ def _to_html(table: Table) -> str:
tmp.print(table)
html = tmp.export_html(inline_styles=True)
# Remove margins inside pre blocks and adjust font size
- html = html.replace(
+ return html.replace(
' Table:
"""
diff --git a/src/easydiffraction/project/project.py b/src/easydiffraction/project/project.py
index e4e15f80..c22ea202 100644
--- a/src/easydiffraction/project/project.py
+++ b/src/easydiffraction/project/project.py
@@ -387,6 +387,7 @@ def save(self) -> None:
def save_as(
self,
dir_path: str,
+ *,
temporary: bool = False,
) -> None:
"""Save the project into a new directory."""
diff --git a/src/easydiffraction/utils/utils.py b/src/easydiffraction/utils/utils.py
index 88bdede1..39ec9443 100644
--- a/src/easydiffraction/utils/utils.py
+++ b/src/easydiffraction/utils/utils.py
@@ -125,6 +125,7 @@ def _fetch_tutorials_index() -> dict:
def download_data(
id: int | str,
destination: str = 'data',
+ *,
overwrite: bool = False,
) -> str:
"""
@@ -381,6 +382,7 @@ def list_tutorials() -> None:
def download_tutorial(
id: int | str,
destination: str = 'tutorials',
+ *,
overwrite: bool = False,
) -> str:
"""
@@ -455,6 +457,7 @@ def download_tutorial(
def download_all_tutorials(
destination: str = 'tutorials',
+ *,
overwrite: bool = False,
) -> list[str]:
"""
@@ -676,9 +679,7 @@ def twotheta_to_d(twotheta: object, wavelength: float) -> object:
theta_rad = np.radians(twotheta / 2)
# Calculate d-spacing using Bragg's law
- d = wavelength / (2 * np.sin(theta_rad))
-
- return d
+ return wavelength / (2 * np.sin(theta_rad))
def sin_theta_over_lambda_to_d_spacing(sin_theta_over_lambda: object) -> object:
@@ -699,8 +700,7 @@ def sin_theta_over_lambda_to_d_spacing(sin_theta_over_lambda: object) -> object:
with np.errstate(divide='ignore', invalid='ignore'):
d = 1 / (2 * sin_theta_over_lambda)
# Set non-positive inputs to NaN
- d = np.where(sin_theta_over_lambda > 0, d, np.nan)
- return d
+ return np.where(sin_theta_over_lambda > 0, d, np.nan)
def str_to_ufloat(s: str | None, default: float | None = None) -> UFloat:
diff --git a/tests/unit/easydiffraction/analysis/fit_helpers/test_metrics.py b/tests/unit/easydiffraction/analysis/fit_helpers/test_metrics.py
index 83de8900..d87f2461 100644
--- a/tests/unit/easydiffraction/analysis/fit_helpers/test_metrics.py
+++ b/tests/unit/easydiffraction/analysis/fit_helpers/test_metrics.py
@@ -42,7 +42,7 @@ class Expt:
def __init__(self):
self.data = DS()
- def _update_categories(self, called_by_minimizer=False):
+ def _update_categories(self, *, called_by_minimizer=False):
pass
class DummyStructures(collections.UserDict):
diff --git a/tests/unit/easydiffraction/analysis/minimizers/test_base.py b/tests/unit/easydiffraction/analysis/minimizers/test_base.py
index f4d6c387..bfe7240e 100644
--- a/tests/unit/easydiffraction/analysis/minimizers/test_base.py
+++ b/tests/unit/easydiffraction/analysis/minimizers/test_base.py
@@ -18,7 +18,7 @@ def __init__(self, v):
self.value = v
class DummyResult:
- def __init__(self, success=True):
+ def __init__(self, *, success=True):
self.success = success
class DummyMinimizer(MinimizerBase):
diff --git a/tests/unit/easydiffraction/analysis/minimizers/test_lmfit.py b/tests/unit/easydiffraction/analysis/minimizers/test_lmfit.py
index 8c35a0ca..f41e9896 100644
--- a/tests/unit/easydiffraction/analysis/minimizers/test_lmfit.py
+++ b/tests/unit/easydiffraction/analysis/minimizers/test_lmfit.py
@@ -17,7 +17,7 @@ def test_lmfit_prepare_and_sync(monkeypatch):
from easydiffraction.analysis.minimizers.lmfit import LmfitMinimizer
class P:
- def __init__(self, name, value, free=True, lo=-np.inf, hi=np.inf):
+ def __init__(self, name, value, *, free=True, lo=-np.inf, hi=np.inf):
self._minimizer_uid = name
self._value = value
self.free = free