Enable more linting rules and adjust the code

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

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.',
     ),

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.
 

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:
         """

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

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]:
         """

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)

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

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,

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,

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:
     """

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

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.

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()

src/easydiffraction/core/validation.py

@@ -122,6 +122,7 @@ def validated(
         name: str,
         default: object = None,
         current: object = None,
+        *,
         allow_none: bool = False,
     ) -> object:
         """

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
 

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

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
 

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(

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

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

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