Enforce ruff/bugbear rules (B) (#286)

* Enforce ruff/bugbear rule B018

B018 Found useless expression. Either assign it to a variable or remove it.

* Enforce ruff/bugbear rule B009

B009 Do not call `getattr` with a constant attribute value.
     It is not any safer than normal property access.

* Enforce ruff/bugbear rule B010

B010 Do not call `setattr` with a constant attribute value.
     It is not any safer than normal property access.

* Enforce ruff/bugbear rule B032

B032 Possible unintentional type annotation (using `:`).
     Did you mean to assign (using `=`)?

* Enforce ruff/bugbear rule B904

B904 Within an `except` clause, raise exceptions with `raise ... from err` or
     `raise ... from None` to distinguish them from errors in exception handling

* Enforce ruff/bugbear rule B007

B007 Loop control variable not used within loop body

* Enforce ruff/bugbear rule B028

B028 No explicit `stacklevel` keyword argument found

Author: DimitriPapadopoulos

bin/create_iods_modules.py

@@ -102,8 +102,8 @@ def _create_modules(directory):
     # https://github.com/innolitics/dicom-standard/tree/master/standard
     try:
         directory = sys.argv[1]
-    except IndexError:
-        raise ValueError('Path to directory must be provided.')
+    except IndexError as e:
+        raise ValueError('Path to directory must be provided.') from e
     if not os.path.exists(directory):
         raise OSError(f'Path does not exist: "{directory}"')
     if not os.path.isdir(directory):

src/highdicom/_module_utils.py

@@ -92,8 +92,8 @@ def check_required_attributes(
         for p in base_path:
             try:
                 tree = tree['attributes'][p]
-            except KeyError:
-                raise AttributeError(f"Invalid base path: {base_path}.")
+            except KeyError as e:
+                raise AttributeError(f"Invalid base path: {base_path}.") from e
 
     # Define recursive function
     def check(

src/highdicom/ann/content.py

@@ -111,7 +111,7 @@ def get_values(self, number_of_annotations: int) -> np.ndarray:
                 f'annotation indices: {error}. This may either be due to '
                 'incorrect encoding of the measurements or due to incorrectly '
                 'specified "number_of_annotations".'
-            )
+            ) from error
         return values
 
     @classmethod
@@ -339,11 +339,11 @@ def __init__(
 
         try:
             coordinates = np.concatenate(graphic_data, axis=0)
-        except ValueError:
+        except ValueError as e:
             raise ValueError(
                 'Items of argument "graphic_data" must be arrays with the '
                 'same dimensions.'
-            )
+            ) from e
 
         if coordinates.dtype.kind in ('u', 'i'):
             coordinates = coordinates.astype(np.float32)
@@ -420,8 +420,8 @@ def __init__(
                 )
                 try:
                     measured_values = item.get_values(self.NumberOfAnnotations)
-                except IndexError:
-                    raise ValueError(error_message)
+                except IndexError as e:
+                    raise ValueError(error_message) from e
                 if len(measured_values) != self.NumberOfAnnotations:
                     # This should not occur, but safety first.
                     raise ValueError(error_message)
@@ -541,10 +541,10 @@ def get_graphic_data(
                 coordinate_dimensionality = 3
 
             try:
-                coordinates_data = getattr(self, 'DoublePointCoordinatesData')
+                coordinates_data = self.DoublePointCoordinatesData
                 coordinates_dtype = np.float64
             except AttributeError:
-                coordinates_data = getattr(self, 'PointCoordinatesData')
+                coordinates_data = self.PointCoordinatesData
                 coordinates_dtype = np.float32
             decoded_coordinates_data = np.frombuffer(
                 coordinates_data,

src/highdicom/color.py

@@ -87,8 +87,8 @@ def __init__(self, icc_profile: bytes):
         """
         try:
             self._icc_transform = self._build_icc_transform(icc_profile)
-        except OSError:
-            raise ValueError('Could not read ICC Profile.')
+        except OSError as e:
+            raise ValueError('Could not read ICC Profile.') from e
 
     def transform_frame(self, array: np.ndarray) -> np.ndarray:
         """Transforms a frame by applying the ICC profile.
@@ -138,8 +138,10 @@ def _build_icc_transform(icc_profile: bytes) -> ImageCmsTransform:
         profile: bytes
         try:
             profile = ImageCmsProfile(BytesIO(icc_profile))
-        except OSError:
-            raise ValueError('Cannot read ICC Profile in image metadata.')
+        except OSError as e:
+            raise ValueError(
+                'Cannot read ICC Profile in image metadata.'
+            ) from e
         name = getProfileName(profile).strip()
         description = getProfileDescription(profile).strip()
         logger.debug(f'found ICC Profile "{name}": "{description}"')

src/highdicom/content.py

@@ -1352,7 +1352,7 @@ def from_dataset(
             )
         processing_type = processing_type_items[0].value
 
-        instance._processing_procedure: Union[
+        instance._processing_procedure: Union[  # noqa: B032
             SpecimenCollection,
             SpecimenSampling,
             SpecimenStaining,

src/highdicom/io.py

@@ -312,12 +312,14 @@ def open(self) -> None:
         if self._fp is None:
             try:
                 self._fp = DicomFile(str(self._filename), mode='rb')
-            except FileNotFoundError:
-                raise FileNotFoundError(f'File not found: "{self._filename}"')
-            except Exception:
+            except FileNotFoundError as e:
+                raise FileNotFoundError(
+                    f'File not found: "{self._filename}"'
+                ) from e
+            except Exception as e:
                 raise OSError(
                     f'Could not open file for reading: "{self._filename}"'
-                )
+                ) from e
         is_little_endian, is_implicit_VR = self._check_file_format(self._fp)
         self._fp.is_little_endian = is_little_endian
         self._fp.is_implicit_VR = is_implicit_VR
@@ -377,7 +379,9 @@ def _read_metadata(self) -> None:
         try:
             metadata = dcmread(self._fp, stop_before_pixels=True)
         except Exception as err:
-            raise OSError(f'DICOM metadata cannot be read from file: "{err}"')
+            raise OSError(
+                f'DICOM metadata cannot be read from file: "{err}"'
+            ) from err
 
         # Cache Transfer Syntax UID, since we need it to decode frame items
         self._transfer_syntax_uid = UID(metadata.file_meta.TransferSyntaxUID)
@@ -391,10 +395,10 @@ def _read_metadata(self) -> None:
         # Determine whether dataset contains a Pixel Data element
         try:
             tag = TupleTag(self._fp.read_tag())
-        except EOFError:
+        except EOFError as e:
             raise ValueError(
                 'Dataset does not represent an image information entity.'
-            )
+            ) from e
         if int(tag) not in _PIXEL_DATA_TAGS:
             raise ValueError(
                 'Dataset does not represent an image information entity.'
@@ -412,7 +416,9 @@ def _read_metadata(self) -> None:
             try:
                 self._basic_offset_table = _get_bot(self._fp, number_of_frames)
             except Exception as err:
-                raise OSError(f'Failed to build Basic Offset Table: "{err}"')
+                raise OSError(
+                    f'Failed to build Basic Offset Table: "{err}"'
+                ) from err
             self._first_frame_offset = self._fp.tell()
         else:
             if self._fp.is_implicit_VR:

src/highdicom/ko/sop.py

@@ -177,11 +177,11 @@ def resolve_reference(self, sop_instance_uid: str) -> Tuple[str, str, str]:
         """
         try:
             return self._reference_lut[sop_instance_uid]
-        except KeyError:
+        except KeyError as e:
             raise ValueError(
                 'Could not find any evidence for SOP Instance UID '
                 f'"{sop_instance_uid}" in KOS document.'
-            )
+            ) from e
 
     @classmethod
     def from_dataset(cls, dataset: Dataset) -> 'KeyObjectSelectionDocument':

src/highdicom/legacy/sop.py

@@ -62,8 +62,10 @@ def _convert_legacy_to_enhanced(
     from highdicom._modules import MODULE_ATTRIBUTE_MAP
     try:
         ref_ds = sf_datasets[0]
-    except IndexError:
-        raise ValueError('No data sets of single-frame legacy images provided.')
+    except IndexError as e:
+        raise ValueError(
+            'No data sets of single-frame legacy images provided.'
+        ) from e
 
     if mf_dataset is None:
         mf_dataset = Dataset()
@@ -166,7 +168,7 @@ def _convert_legacy_to_enhanced(
 
     # Per-Frame Functional Groups
     perframe_items = []
-    for i, ds in enumerate(sf_datasets):
+    for ds in sf_datasets:
         perframe_item = Dataset()
 
         # Frame Content (M)
@@ -334,7 +336,7 @@ def _convert_legacy_to_enhanced(
         Dataset()
         for _ in range(len(sf_datasets))
     ]
-    for tag, dataelements in unassigned_dataelements.items():
+    for _tag, dataelements in unassigned_dataelements.items():
         values = [str(da.value) for da in dataelements]
         unique_values = set(values)
         if len(unique_values) == 1:
@@ -455,8 +457,8 @@ def __init__(
 
         try:
             ref_ds = legacy_datasets[0]
-        except IndexError:
-            raise ValueError('No DICOM data sets of provided.')
+        except IndexError as e:
+            raise ValueError('No DICOM data sets of provided.') from e
 
         if ref_ds.Modality != 'MR':
             raise ValueError(
@@ -548,8 +550,8 @@ def __init__(
 
         try:
             ref_ds = legacy_datasets[0]
-        except IndexError:
-            raise ValueError('No DICOM data sets of provided.')
+        except IndexError as e:
+            raise ValueError('No DICOM data sets of provided.') from e
 
         if ref_ds.Modality != 'CT':
             raise ValueError(
@@ -627,8 +629,8 @@ def __init__(
 
         try:
             ref_ds = legacy_datasets[0]
-        except IndexError:
-            raise ValueError('No DICOM data sets of provided.')
+        except IndexError as e:
+            raise ValueError('No DICOM data sets of provided.') from e
 
         if ref_ds.Modality != 'PT':
             raise ValueError(

src/highdicom/pm/sop.py

@@ -456,8 +456,8 @@ def __init__(
             sffg_item.RealWorldValueMappingSequence = real_world_value_mappings
             try:
                 real_world_value_mappings[0]
-            except IndexError:
-                raise TypeError(error_message)
+            except IndexError as e:
+                raise TypeError(error_message) from e
             if not isinstance(
                 real_world_value_mappings[0],
                 RealWorldValueMapping
@@ -479,8 +479,8 @@ def __init__(
             )
             try:
                 real_world_value_mappings[0][0]
-            except IndexError:
-                raise TypeError(error_message)
+            except IndexError as e:
+                raise TypeError(error_message) from e
             if not isinstance(
                 real_world_value_mappings[0][0],
                 RealWorldValueMapping
@@ -700,13 +700,8 @@ def __init__(
                 palette_color_lut_transformation,
                 'PaletteColorLookupTableUID'
             ):
-                setattr(
-                    self,
-                    'PaletteColorLookupTableUID',
-                    getattr(
-                        palette_color_lut_transformation,
-                        'PaletteColorLookupTableUID'
-                    )
+                self.PaletteColorLookupTableUID = (
+                    palette_color_lut_transformation.PaletteColorLookupTableUID
                 )
         else:
             self.PixelPresentation = 'MONOCHROME'

src/highdicom/seg/sop.py

@@ -1992,7 +1992,8 @@ def __init__(
                     "Setting workers != 0 or passing an instance of "
                     "concurrent.futures.Executor when using a non-encapsulated "
                     "transfer syntax has no effect.",
-                    UserWarning
+                    UserWarning,
+                    stacklevel=2,
                 )
                 using_multiprocessing = False
 
@@ -2061,7 +2062,7 @@ def __init__(
                             'Could not determine position of plane '
                             f'#{plane_index} in three dimensional coordinate '
                             f'system based on dimension index values: {error}'
-                        )
+                        ) from error
                 else:
                     dimension_index_values = []