Enforce ruff rules (RUF) (#290)

* Enforce ruff rule RUF027

RUF027 Possible f-string without an `f` prefix

* Enforce ruff rule RUF013

RUF013 PEP 484 prohibits implicit `Optional`

* Enforce ruff rule RUF022

RUF022 `__all__` is not sorted

Author: DimitriPapadopoulos

src/highdicom/__init__.py

@@ -58,6 +58,9 @@
 from highdicom.version import __version__
 
 __all__ = [
+    'LUT',
+    'UID',
+    'VOILUT',
     'AlgorithmIdentificationSequence',
     'AnatomicalOrientationTypeValues',
     'ContentCreatorIdentificationCodeSequence',
@@ -66,7 +69,6 @@
     'DimensionOrganizationTypeValues',
     'IssuerOfIdentifier',
     'LateralityValues',
-    'LUT',
     'ModalityLUT',
     'ModalityLUTTransformation',
     'PaletteColorLUT',
@@ -85,19 +87,18 @@
     'PresentationLUTTransformation',
     'ReferencedImageSequence',
     'RescaleTypeValues',
+    'SOPClass',
     'SegmentedPaletteColorLUT',
     'SpecimenCollection',
     'SpecimenDescription',
     'SpecimenPreparationStep',
     'SpecimenProcessing',
     'SpecimenSampling',
     'SpecimenStaining',
-    'SOPClass',
-    'UID',
     'UniversalEntityIDTypeValues',
-    'VOILUT',
     'VOILUTFunctionValues',
     'VOILUTTransformation',
+    '__version__',
     'ann',
     'color',
     'frame',
@@ -111,5 +112,4 @@
     'spatial',
     'sr',
     'utils',
-    '__version__',
 ]

src/highdicom/base.py

@@ -264,7 +264,7 @@ def _copy_attribute(
         """
         tag = tag_for_keyword(keyword)
         if tag is None:
-            raise ValueError('No tag not found for keyword "{keyword}".')
+            raise ValueError(f'No tag not found for keyword "{keyword}".')
         try:
             data_element = dataset[tag]
             logger.debug(f'copied attribute "{keyword}"')

src/highdicom/pr/__init__.py

@@ -37,9 +37,9 @@
     'AdvancedBlending',
     'AdvancedBlendingPresentationState',
     'AnnotationUnitsValues',
-    'BlendingModeValues',
     'BlendingDisplay',
     'BlendingDisplayInput',
+    'BlendingModeValues',
     'ColorSoftcopyPresentationState',
     'GraphicAnnotation',
     'GraphicGroup',

src/highdicom/sc/sop.py

@@ -69,7 +69,7 @@ def __init__(
             patient_birth_date: Optional[str] = None,
             patient_sex: Union[str, PatientSexValues, None] = None,
             accession_number: Optional[str] = None,
-            study_id: str = None,
+            study_id: Optional[str] = None,
             study_date: Optional[Union[str, datetime.date]] = None,
             study_time: Optional[Union[str, datetime.time]] = None,
             referring_physician_name: Optional[Union[str, PersonName]] = None,

src/highdicom/seg/__init__.py

@@ -20,14 +20,14 @@
 
 __all__ = [
     'DimensionIndexSequence',
-    'Segmentation',
-    'segread',
     'SegmentAlgorithmTypeValues',
+    'SegmentDescription',
+    'Segmentation',
     'SegmentationFractionalTypeValues',
     'SegmentationTypeValues',
-    'SegmentDescription',
     'SegmentsOverlapValues',
     'SpatialLocationsPreservedValues',
     'create_segmentation_pyramid',
+    'segread',
     'utils',
 ]

src/highdicom/sr/content.py

@@ -1612,7 +1612,7 @@ def from_segmentation(
         for frame_number in frame_numbers:
             if frame_number < 1 or frame_number > number_of_frames:
                 raise ValueError(
-                    'Value {frame_number} is not a valid frame number.'
+                    f'Value {frame_number} is not a valid frame number.'
                 )
             frame_index = frame_number - 1
             item = segmentation.PerFrameFunctionalGroupsSequence[frame_index]

src/highdicom/sr/templates.py

@@ -2572,7 +2572,7 @@ def __init__(
         algorithm_id: Optional[AlgorithmIdentification] = None,
         finding_sites: Optional[Sequence[FindingSite]] = None,
         session: Optional[str] = None,
-        measurements: Sequence[Measurement] = None,
+        measurements: Optional[Sequence[Measurement]] = None,
         qualitative_evaluations: Optional[
             Sequence[QualitativeEvaluation]
         ] = None,
@@ -2969,7 +2969,7 @@ def __init__(
         algorithm_id: Optional[AlgorithmIdentification] = None,
         finding_sites: Optional[Sequence[FindingSite]] = None,
         session: Optional[str] = None,
-        measurements: Sequence[Measurement] = None,
+        measurements: Optional[Sequence[Measurement]] = None,
         qualitative_evaluations: Optional[
             Sequence[QualitativeEvaluation]
         ] = None,
@@ -3079,7 +3079,7 @@ def __init__(
         algorithm_id: Optional[AlgorithmIdentification] = None,
         finding_sites: Optional[Sequence[FindingSite]] = None,
         session: Optional[str] = None,
-        measurements: Sequence[Measurement] = None,
+        measurements: Optional[Sequence[Measurement]] = None,
         qualitative_evaluations: Optional[
             Sequence[QualitativeEvaluation]
         ] = None,
@@ -3235,7 +3235,7 @@ def __init__(
         algorithm_id: Optional[AlgorithmIdentification] = None,
         finding_sites: Optional[Sequence[FindingSite]] = None,
         session: Optional[str] = None,
-        measurements: Sequence[Measurement] = None,
+        measurements: Optional[Sequence[Measurement]] = None,
         qualitative_evaluations: Optional[
             Sequence[QualitativeEvaluation]
         ] = None,
@@ -3519,7 +3519,7 @@ def __init__(
         algorithm_id: Optional[AlgorithmIdentification] = None,
         finding_sites: Optional[Sequence[FindingSite]] = None,
         session: Optional[str] = None,
-        measurements: Sequence[Measurement] = None,
+        measurements: Optional[Sequence[Measurement]] = None,
         qualitative_evaluations: Optional[
             Sequence[QualitativeEvaluation]
         ] = None,

src/highdicom/sr/value_types.py

@@ -60,7 +60,7 @@ def _assert_value_type(
 
     """
     if not hasattr(dataset, 'ValueType'):
-        raise AttributeError('Dataset is not an SR Content Item:\n{dataset}.')
+        raise AttributeError(f'Dataset is not an SR Content Item:\n{dataset}.')
     if not dataset.ValueType == value_type.value:
         raise ValueError(
             'Dataset is not an SR Content Item with value type '