Fix style issues (#910)

* Fix style issues.

* Update eddy.py

docs/conf.py

@@ -367,7 +367,7 @@
 linkcode_resolve = make_linkcode_resolve(
     'qsiprep',
     (
-        'https://github.com/pennlinc/qsiprep/blob/' '{revision}/{package}/{path}#L{lineno}'  # noqa: FS003
+        'https://github.com/pennlinc/qsiprep/blob/{revision}/{package}/{path}#L{lineno}'  # noqa: FS003
     ),
 )
 

qsiprep/_warnings.py

@@ -37,7 +37,7 @@ def _warn(message, category=None, stacklevel=1, source=None):
         category = type(category).__name__
         category = category.replace('type', 'WARNING')
 
-    logging.getLogger('py.warnings').warning(f"{category or 'WARNING'}: {message}")
+    logging.getLogger('py.warnings').warning(f'{category or "WARNING"}: {message}')
 
 
 def _showwarning(message, category, filename, lineno, file=None, line=None):

qsiprep/cli/parser.py

@@ -54,8 +54,8 @@ class DeprecatedAction(Action):
         def __call__(self, parser, namespace, values, option_string=None):
             new_opt, rem_vers = deprecations.get(self.dest, (None, None))
             msg = (
-                f"{self.option_strings} has been deprecated and will be removed in "
-                f"{rem_vers or 'a later version'}."
+                f'{self.option_strings} has been deprecated and will be removed in '
+                f'{rem_vers or "a later version"}.'
             )
             if new_opt:
                 msg += f' Please use `{new_opt}` instead.'
@@ -193,7 +193,7 @@ def _bids_filter(value, parser):
     parser.add_argument(
         'analysis_level',
         choices=['participant'],
-        help='Processing stage to be run, only "participant" in the case of ' 'QSIPrep (for now).',
+        help='Processing stage to be run, only "participant" in the case of QSIPrep (for now).',
     )
 
     g_bids = parser.add_argument_group('Options for filtering BIDS queries')
@@ -507,7 +507,7 @@ def _bids_filter(value, parser):
         action='store',
         default='Affine',
         choices=['Affine', 'Rigid'],
-        help='transformation to be optimized during head motion correction ' '(default: affine)',
+        help='transformation to be optimized during head motion correction (default: affine)',
     )
     g_moco.add_argument(
         '--hmc-model',
@@ -739,7 +739,7 @@ def parse_args(args=None, namespace=None):
 
     # Ensure input and output folders are not the same
     if output_dir == bids_dir:
-        rec_path = output_dir / 'derivatives' / f"qsiprep-{version.split('+')[0]}"
+        rec_path = output_dir / 'derivatives' / f'qsiprep-{version.split("+")[0]}'
         parser.error(
             'The selected output folder is the same as the input BIDS folder. '
             f'Please modify the output path (suggestion: {rec_path}).'
@@ -756,8 +756,7 @@ def parse_args(args=None, namespace=None):
         from ..utils.bids import validate_input_dir
 
         build_log.info(
-            'Making sure the input data is BIDS compliant (warnings can be ignored in most '
-            'cases).'
+            'Making sure the input data is BIDS compliant (warnings can be ignored in most cases).'
         )
         validate_input_dir(
             config.environment.exec_env,
@@ -782,7 +781,7 @@ def parse_args(args=None, namespace=None):
     if missing_subjects:
         parser.error(
             'One or more participant labels were not found in the BIDS directory: '
-            f"{', '.join(missing_subjects)}."
+            f'{", ".join(missing_subjects)}.'
         )
 
     # Determine which sessions to process and group them

qsiprep/cli/workflow.py

@@ -61,11 +61,11 @@ def build_workflow(config_file, retval):
     notice_path = Path(pkgrf('qsiprep', 'data/NOTICE'))
     if notice_path.exists():
         banner[0] += '\n'
-        banner += [f"License NOTICE {'#' * 50}"]
+        banner += [f'License NOTICE {"#" * 50}']
         banner += [f'QSIPrep {version}']
         banner += notice_path.read_text().splitlines(keepends=False)[1:]
         banner += ['#' * len(banner[1])]
-    build_log.log(25, f"\n{' ' * 9}".join(banner))
+    build_log.log(25, f'\n{" " * 9}'.join(banner))
 
     # warn if older results exist: check for dataset_description.json in output folder
     # msg = check_pipeline_version("QSIPrep", version, output_dir / "dataset_description.json")
@@ -112,7 +112,7 @@ def build_workflow(config_file, retval):
         f'Run identifier: {config.execution.run_uuid}.',
     ]
 
-    build_log.log(25, f"\n{' ' * 11}* ".join(init_msg))
+    build_log.log(25, f'\n{" " * 11}* '.join(init_msg))
 
     # If qsiprep is being run on already preprocessed data:
     retval['workflow'] = init_qsiprep_wf()

qsiprep/config.py

@@ -428,7 +428,7 @@ class execution(_Config):
     # the command line) as spatial references for outputs."""
     reports_only = False
     """Only build the reports, based on the reportlets found in a cached working directory."""
-    run_uuid = f"{strftime('%Y%m%d-%H%M%S')}_{uuid4()}"
+    run_uuid = f'{strftime("%Y%m%d-%H%M%S")}_{uuid4()}'
     """Unique identifier of this particular run."""
     participant_label = None
     """List of participant identifiers that are to be preprocessed."""
@@ -766,7 +766,7 @@ def get(flat=False):
     }
     if 'processing_list' in settings['execution']:
         settings['execution']['processing_list'] = [
-            f"{el[0]}:{','.join(el[1])}" for el in settings['execution']['processing_list']
+            f'{el[0]}:{",".join(el[1])}' for el in settings['execution']['processing_list']
         ]
 
     if not flat:

qsiprep/interfaces/dipy.py

@@ -48,7 +48,7 @@ class Patch2SelfInputSpec(SeriesPreprocReportInputSpec):
     shift_intensity = traits.Bool(
         True,
         usedefault=True,
-        desc='Shifts the distribution of intensities per ' 'volume to give non-negative values',
+        desc='Shifts the distribution of intensities per volume to give non-negative values',
     )
     out_report = File(
         'patch2self_report.svg', usedefault=True, desc='filename for the visual report'

qsiprep/interfaces/eddy.py

@@ -318,9 +318,9 @@ def boilerplate_from_eddy_config(eddy_config, fieldmap_type, pepolar_method):
 
     # did you sep_offs_mov?
     if isdefined(ext_eddy.inputs.dont_sep_offs_move) and ext_eddy.inputs.dont_sep_offs_move:
-        desc.append('No attempt was made to separate field offset from ' 'subject movement.')
+        desc.append('No attempt was made to separate field offset from subject movement.')
     else:
-        desc.append('Field offset was attempted to be separated from ' 'subject movement.')
+        desc.append('Field offset was attempted to be separated from subject movement.')
 
     # did you peas?
     if isdefined(ext_eddy.inputs.dont_peas) and ext_eddy.inputs.dont_peas:
@@ -355,7 +355,7 @@ def boilerplate_from_eddy_config(eddy_config, fieldmap_type, pepolar_method):
             if mb_off != 0:
                 offs_txt = {-1: 'bottom', 1: 'top'}
                 offs_txt = f'and slices removed from the {offs_txt} of the volume were'
-            desc.append('A multi-band acceleration factor of %d ' '%s assumed.' % (mbf, offs_txt))
+            desc.append(f'A multi-band acceleration factor of {mbf} {offs_txt} assumed.')
 
         # The threshold for outliers
         std_threshold = (
@@ -420,7 +420,7 @@ def boilerplate_from_eddy_config(eddy_config, fieldmap_type, pepolar_method):
     lsr_ref = ' [@fsllsr]' if ext_eddy.inputs.method == 'lsr' else ''
     if doing_2stage:
         desc.append(
-            'Interpolation after head motion and initial susceptibility ' 'distortion correction'
+            'Interpolation after head motion and initial susceptibility distortion correction'
         )
     else:
         desc.append('Final interpolation')
@@ -450,7 +450,7 @@ def topup_boilerplate(fieldmap_type, pepolar_method):
 
     desc.append('was used to estimate a susceptibility-induced off-resonance field based on')
     if fieldmap_type == 'epi':
-        desc.append('b=0 reference images with reversed ' 'phase encoding directions.')
+        desc.append('b=0 reference images with reversed phase encoding directions.')
     else:
         desc.append(
             'b=0 images extracted from multiple DWI series  '

qsiprep/interfaces/gradients.py

@@ -127,7 +127,7 @@ class SliceQCInputSpec(BaseInterfaceInputSpec):
     min_slice_size_percentile = traits.CFloat(
         10.0,
         usedefault=True,
-        desc='slices bigger than ' 'this percentile are candidates for imputation.',
+        desc='slices bigger than this percentile are candidates for imputation.',
     )
 
 
@@ -351,7 +351,7 @@ class ComposeTransformsInputSpec(ApplyTransformsInputSpec):
     b0_to_intramodal_template_transforms = InputMultiObject(
         File(exists=True),
         mandtory=False,
-        desc='list of transforms to register the b=0 to ' 'the intramodal template.',
+        desc='list of transforms to register the b=0 to the intramodal template.',
     )
     intramodal_template_to_t1_affine = File(
         exists=True, desc='affine from the intramodal template to t1'
@@ -565,8 +565,7 @@ class GradientRotationInputSpec(BaseInterfaceInputSpec):
     )
     bvec_files = InputMultiObject(
         File(exists=True),
-        desc='list of split bvec files, must correspond to a '
-        'non-oblique image/reference frame.',
+        desc='list of split bvec files, must correspond to a non-oblique image/reference frame.',
         mandatory=True,
     )
     bval_files = InputMultiObject(

qsiprep/interfaces/tortoise.py

@@ -723,8 +723,7 @@ def generate_drbuddi_boilerplate(fieldmap_type, t2w_sdc, with_topup=False):
     # Describe what's going on
     if fieldmap_type == 'epi':
         desc.append(
-            'DRBUDDI used b=0 reference images with reversed '
-            'phase encoding directions to estimate'
+            'DRBUDDI used b=0 reference images with reversed phase encoding directions to estimate'
         )
     else:
         desc.append(

qsiprep/tests/run_local_tests.py

@@ -60,7 +60,7 @@ def run_command(command, env=None):
 
     if process.returncode != 0:
         raise RuntimeError(
-            f'Non zero return code: {process.returncode}\n' f'{command}\n\n{process.stdout.read()}'
+            f'Non zero return code: {process.returncode}\n{command}\n\n{process.stdout.read()}'
         )
 
 

qsiprep/tests/utils.py

@@ -47,7 +47,7 @@ def download_test_data(dset, data_dir=None):
         return
 
     if dset not in URLS:
-        raise ValueError(f"dset ({dset}) must be one of: {', '.join(URLS.keys())}")
+        raise ValueError(f'dset ({dset}) must be one of: {", ".join(URLS.keys())}')
 
     if not data_dir:
         data_dir = os.path.join(os.path.dirname(get_test_data_path()), 'test_data')

qsiprep/workflows/dwi/distortion_group_merge.py

@@ -108,7 +108,8 @@ def init_distortion_group_merge_wf(
                 'merged_bval',
                 'merged_bvec',
                 'merged_qc',
-                'merged_cnr_map' 'dwi_mask_t1',
+                'merged_cnr_map',
+                'dwi_mask_t1',
                 'cnr_map_t1',
                 'merged_bval',
                 'bvecs_t1',

qsiprep/workflows/dwi/hmc.py

@@ -161,8 +161,7 @@ def init_dwi_hmc_wf(
     # If we're just aligning based on the b=0 images, compute the b=0 tsnr as the cnr
     if hmc_model.lower() == 'none':
         workflow.__postdesc__ = (
-            'Each b>0 image was transformed based on the registration '
-            ' of the nearest b=0 image. '
+            'Each b>0 image was transformed based on the registration of the nearest b=0 image. '
         )
 
         concat_b0s = pe.Node(afni.TCat(outputtype='NIFTI_GZ'), name='concat_b0s')

qsiprep/workflows/dwi/merge.py

@@ -676,8 +676,7 @@ def gen_denoising_boilerplate():
     no_b0_harmonization = config.workflow.no_b0_harmonization
     b0_threshold = config.workflow.b0_threshold
     desc = [
-        f'Any images with a b-value less than {b0_threshold} s/mm^2 were treated as a '
-        '*b*=0 image.'
+        f'Any images with a b-value less than {b0_threshold} s/mm^2 were treated as a *b*=0 image.'
     ]
     harmonize_b0s = not no_b0_harmonization
     last_step = ''