Run ruff format (#484)

.maint/update_authors.py

@@ -132,7 +132,7 @@ def get_git_lines(fname='line-contributors.txt'):
 def _namelast(inlist):
     retval = []
     for i in inlist:
-        i['name'] = (f"{i.pop('name', '')} {i.pop('lastname', '')}").strip()
+        i['name'] = (f'{i.pop("name", "")} {i.pop("lastname", "")}').strip()
         retval.append(i)
     return retval
 
@@ -187,7 +187,7 @@ def zenodo(
     misses = set(miss_creators).intersection(miss_contributors)
     if misses:
         print(
-            f"Some people made commits, but are missing in .maint/ files: {', '.join(misses)}",
+            f'Some people made commits, but are missing in .maint/ files: {", ".join(misses)}',
             file=sys.stderr,
         )
 
@@ -268,7 +268,7 @@ def _aslist(value):
 
     if misses:
         print(
-            f"Some people made commits, but are missing in .maint/ files: {', '.join(misses)}",
+            f'Some people made commits, but are missing in .maint/ files: {", ".join(misses)}',
             file=sys.stderr,
         )
 

aslprep/_warnings.py

@@ -13,7 +13,7 @@ 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):

aslprep/cli/parser.py

@@ -171,11 +171,11 @@ def _bids_filter(value, parser):
         type=BIDSFilter,
         metavar='FILE',
         help=(
-            "A JSON file describing custom BIDS input filters using PyBIDS. "
-            "For further details, please check out "
-            "https://aslprep.readthedocs.io/en/"
-            f"{currentv.base_version if is_release else 'latest'}/faq.html#"
-            "how-do-I-select-only-certain-files-to-be-input-to-ASLPrep"
+            'A JSON file describing custom BIDS input filters using PyBIDS. '
+            'For further details, please check out '
+            'https://aslprep.readthedocs.io/en/'
+            f'{currentv.base_version if is_release else "latest"}/faq.html#'
+            'how-do-I-select-only-certain-files-to-be-input-to-ASLPrep'
         ),
     )
     g_bids.add_argument(
@@ -771,7 +771,7 @@ def parse_args(args=None, namespace=None):
 
     # Ensure input and output folders are not the same
     if output_dir == bids_dir:
-        rec_path = bids_dir / 'derivatives' / f"aslprep-{version.split('+')[0]}"
+        rec_path = bids_dir / 'derivatives' / f'aslprep-{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}).'
@@ -788,8 +788,7 @@ def parse_args(args=None, namespace=None):
         from fmriprep.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,
@@ -815,8 +814,8 @@ def parse_args(args=None, namespace=None):
     missing_subjects = participant_label - set(all_subjects)
     if missing_subjects:
         parser.error(
-            "One or more participant labels were not found in the BIDS directory: "
-            f"{', '.join(missing_subjects)}."
+            'One or more participant labels were not found in the BIDS directory: '
+            f'{", ".join(missing_subjects)}.'
         )
 
     config.execution.participant_label = sorted(participant_label)

aslprep/cli/workflow.py

@@ -33,11 +33,11 @@ def build_workflow(config_file, retval):
     notice_path = data.load.readable('NOTICE')
     if notice_path.exists():
         banner[0] += '\n'
-        banner += [f"License NOTICE {'#' * 50}"]
+        banner += [f'License NOTICE {"#" * 50}']
         banner += [f'ASLPrep {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(
@@ -96,7 +96,7 @@ def build_workflow(config_file, retval):
     if config.execution.fs_subjects_dir:
         init_msg += [f"Pre-run FreeSurfer's SUBJECTS_DIR: {config.execution.fs_subjects_dir}."]
 
-    build_log.log(25, f"\n{' ' * 11}* ".join(init_msg))
+    build_log.log(25, f'\n{" " * 11}* '.join(init_msg))
 
     retval['workflow'] = init_aslprep_wf()
 

aslprep/config.py

@@ -199,7 +199,7 @@
             if _proc_oc_kbytes.exists():
                 _oc_limit = _proc_oc_kbytes.read_text().strip()
             if _oc_limit in ('0', 'n/a') and Path('/proc/sys/vm/overcommit_ratio').exists():
-                _oc_limit = f"{Path('/proc/sys/vm/overcommit_ratio').read_text().strip()}%"
+                _oc_limit = f'{Path("/proc/sys/vm/overcommit_ratio").read_text().strip()}%'
 except Exception:  # noqa: S110, BLE001
     pass
 
@@ -420,7 +420,7 @@ 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."""

aslprep/interfaces/cbf.py

@@ -587,7 +587,7 @@ def _run_interface(self, runtime):
 
             else:
                 raise ValueError(
-                    f"Unknown BolusCutOffTechnique {metadata['BolusCutOffTechnique']}"
+                    f'Unknown BolusCutOffTechnique {metadata["BolusCutOffTechnique"]}'
                 )
 
             # Q2TIPS uses TI2 instead of w (PLD), see Noguchi 2015 for this info.

aslprep/interfaces/reports.py

@@ -229,36 +229,36 @@ class CBFSummary(SummaryInterface):
     def _generate_segment(self):
         qcfile = pd.read_table(self.inputs.qc_file)
         motionparam = (
-            f"FD : {round(qcfile['mean_fd'][0], 4)}, rmsd: {round(qcfile['rmsd'][0], 4)} "
+            f'FD : {round(qcfile["mean_fd"][0], 4)}, rmsd: {round(qcfile["rmsd"][0], 4)} '
         )
         coregindex = (
-            f" Dice Index: {round(qcfile['coreg_dice'][0], 4)}, "
-            f"Correlation: {round(qcfile['coreg_correlation'][0], 4)}, "
-            f"Coverage: {round(qcfile['coreg_overlap'][0], 4)} "
+            f' Dice Index: {round(qcfile["coreg_dice"][0], 4)}, '
+            f'Correlation: {round(qcfile["coreg_correlation"][0], 4)}, '
+            f'Coverage: {round(qcfile["coreg_overlap"][0], 4)} '
         )
         normindex = (
-            f" Dice Index: {round(qcfile['norm_dice'][0], 4)}, "
-            f"Correlation: {round(qcfile['norm_correlation'][0], 4)}, "
-            f"Coverage: {round(qcfile['norm_overlap'][0], 4)} "
+            f' Dice Index: {round(qcfile["norm_dice"][0], 4)}, '
+            f'Correlation: {round(qcfile["norm_correlation"][0], 4)}, '
+            f'Coverage: {round(qcfile["norm_overlap"][0], 4)} '
         )
         qei = (
-            f"cbf: {round(qcfile['qei_cbf'][0], 4)}, "
-            f"score: {round(qcfile['qei_cbf_score'][0], 4)}, "
-            f"scrub: {round(qcfile['qei_cbf_scrub'][0], 4)}, "
-            f"basil: {round(qcfile['qei_cbf_basil'][0], 4)}, "
-            f"pvc: {round(qcfile['qei_cbf_basil_gm'][0], 4)} "
+            f'cbf: {round(qcfile["qei_cbf"][0], 4)}, '
+            f'score: {round(qcfile["qei_cbf_score"][0], 4)}, '
+            f'scrub: {round(qcfile["qei_cbf_scrub"][0], 4)}, '
+            f'basil: {round(qcfile["qei_cbf_basil"][0], 4)}, '
+            f'pvc: {round(qcfile["qei_cbf_basil_gm"][0], 4)} '
         )
         mean_cbf = (
-            f"GM CBF: {round(qcfile['mean_gm_cbf'][0], 2)}, "
-            f"WM CBF: {round(qcfile['mean_wm_cbf'][0], 2)}, "
-            f"GM/WM CBF ratio: {round(qcfile['ratio_gm_wm_cbf'][0], 2)} "
+            f'GM CBF: {round(qcfile["mean_gm_cbf"][0], 2)}, '
+            f'WM CBF: {round(qcfile["mean_wm_cbf"][0], 2)}, '
+            f'GM/WM CBF ratio: {round(qcfile["ratio_gm_wm_cbf"][0], 2)} '
         )
         negvoxel = (
-            f"cbf: {round(qcfile['percentage_negative_cbf'][0], 2)}, "
-            f"score: {round(qcfile['percentage_negative_cbf_score'][0], 2)}, "
-            f"scrub: {round(qcfile['percentage_negative_cbf_scrub'][0], 2)}, "
-            f"basil: {round(qcfile['percentage_negative_cbf_basil'][0], 2)}, "
-            f"pvc: {round(qcfile['percentage_negative_cbf_basil_gm'][0], 2)} "
+            f'cbf: {round(qcfile["percentage_negative_cbf"][0], 2)}, '
+            f'score: {round(qcfile["percentage_negative_cbf_score"][0], 2)}, '
+            f'scrub: {round(qcfile["percentage_negative_cbf_scrub"][0], 2)}, '
+            f'basil: {round(qcfile["percentage_negative_cbf_basil"][0], 2)}, '
+            f'pvc: {round(qcfile["percentage_negative_cbf_basil_gm"][0], 2)} '
         )
 
         if isdefined(self.inputs.confounds_file):

aslprep/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()}'
         )
 
 

aslprep/tests/test_cli.py

@@ -50,9 +50,9 @@ def test_examples_pasl_multipld(data_dir, output_dir, working_dir):
         '--use-syn-sdc',
         '--m0_scale=10',
         '--fs-no-reconall',
-        f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",
+        f'--fs-subjects-dir={os.path.join(data_dir, "anatomical/freesurfer")}',
         '--derivatives',
-        f"{os.path.join(data_dir, 'anatomical/smriprep')}",
+        f'{os.path.join(data_dir, "anatomical/smriprep")}',
     ]
 
     _run_and_fail(parameters)
@@ -86,9 +86,9 @@ def test_examples_pcasl_multipld(data_dir, output_dir, working_dir):
         '--basil',
         '--m0_scale=10',
         '--fs-no-reconall',
-        f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",
+        f'--fs-subjects-dir={os.path.join(data_dir, "anatomical/freesurfer")}',
         '--derivatives',
-        f"{os.path.join(data_dir, 'anatomical/smriprep')}",
+        f'{os.path.join(data_dir, "anatomical/smriprep")}',
     ]
 
     _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir)
@@ -124,9 +124,9 @@ def test_examples_pcasl_singlepld_ge(data_dir, output_dir, working_dir):
         '--basil',
         '--m0_scale=96',
         '--fs-no-reconall',
-        f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",
+        f'--fs-subjects-dir={os.path.join(data_dir, "anatomical/freesurfer")}',
         '--derivatives',
-        f"{os.path.join(data_dir, 'anatomical/smriprep')}",
+        f'{os.path.join(data_dir, "anatomical/smriprep")}',
     ]
 
     _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir)
@@ -163,9 +163,9 @@ def test_examples_pcasl_singlepld_philips(data_dir, output_dir, working_dir):
         'fsaverage:den-10k',
         '--scorescrub',
         '--basil',
-        f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",
+        f'--fs-subjects-dir={os.path.join(data_dir, "anatomical/freesurfer")}',
         '--derivatives',
-        f"{os.path.join(data_dir, 'anatomical/smriprep')}",
+        f'{os.path.join(data_dir, "anatomical/smriprep")}',
     ]
 
     _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir)
@@ -201,9 +201,9 @@ def test_examples_pcasl_singlepld_siemens(data_dir, output_dir, working_dir):
         '--basil',
         '--m0_scale=10',
         '--fs-no-reconall',
-        f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",
+        f'--fs-subjects-dir={os.path.join(data_dir, "anatomical/freesurfer")}',
         '--derivatives',
-        f"{os.path.join(data_dir, 'anatomical/smriprep')}",
+        f'{os.path.join(data_dir, "anatomical/smriprep")}',
     ]
 
     _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir)
@@ -239,9 +239,9 @@ def test_qtab(data_dir, output_dir, working_dir):
         '--use-syn-sdc',
         '--force-no-ge',
         '--fs-no-reconall',
-        f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",
+        f'--fs-subjects-dir={os.path.join(data_dir, "anatomical/freesurfer")}',
         '--derivatives',
-        f"{os.path.join(data_dir, 'anatomical/smriprep')}",
+        f'{os.path.join(data_dir, "anatomical/smriprep")}',
     ]
 
     _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir)
@@ -276,9 +276,9 @@ def test_test_001(data_dir, output_dir, working_dir):
         '--scorescrub',
         '--force-no-ge',
         '--fs-no-reconall',
-        f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",
+        f'--fs-subjects-dir={os.path.join(data_dir, "anatomical/freesurfer")}',
         '--derivatives',
-        f"{os.path.join(data_dir, 'anatomical/smriprep')}",
+        f'{os.path.join(data_dir, "anatomical/smriprep")}',
     ]
 
     _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir)
@@ -315,9 +315,9 @@ def test_test_002(data_dir, output_dir, working_dir):
         '--m0_scale=96',
         '--force-ge',
         '--fs-no-reconall',
-        f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",
+        f'--fs-subjects-dir={os.path.join(data_dir, "anatomical/freesurfer")}',
         '--derivatives',
-        f"{os.path.join(data_dir, 'anatomical/smriprep')}",
+        f'{os.path.join(data_dir, "anatomical/smriprep")}',
     ]
 
     _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir)
@@ -385,9 +385,9 @@ def base_test_003(data_dir, output_dir, working_dir, level, extra_params):
         'asl',
         '--use-syn-sdc',
         '--m0_scale=10',
-        f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",
+        f'--fs-subjects-dir={os.path.join(data_dir, "anatomical/freesurfer")}',
         '--derivatives',
-        f"{os.path.join(data_dir, 'anatomical/smriprep')}",
+        f'{os.path.join(data_dir, "anatomical/smriprep")}',
         f'--level={level}',
     ]
     parameters += extra_params

aslprep/tests/utils.py

@@ -45,7 +45,7 @@ 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')

aslprep/utils/bids.py

@@ -101,11 +101,11 @@ def collect_run_data(layout, asl_file):
     elif asl_metadata['M0Type'] == 'Separate':
         m0scan_metadata = layout.get_file(run_data['m0scan']).get_metadata()
         if not m0scan_metadata:
-            raise Exception(f"No metadata for m0scan: {run_data['m0scan']}")
+            raise Exception(f'No metadata for m0scan: {run_data["m0scan"]}')
     elif run_data['m0scan']:
         raise ValueError(
-            f"M0Type is {run_data['asl_metadata']['M0Type']}, "
-            f"but an M0 scan was found at {run_data['m0scan']}"
+            f'M0Type is {run_data["asl_metadata"]["M0Type"]}, '
+            f'but an M0 scan was found at {run_data["m0scan"]}'
         )
 
     config.loggers.workflow.info(
@@ -222,7 +222,7 @@ def write_derivative_description(bids_dir, deriv_dir):
             orig_desc = json.load(fobj)
 
     if 'DatasetDOI' in orig_desc:
-        desc['SourceDatasetsURLs'] = [f"https://doi.org/{orig_desc['DatasetDOI']}"]
+        desc['SourceDatasetsURLs'] = [f'https://doi.org/{orig_desc["DatasetDOI"]}']
 
     if 'License' in orig_desc:
         desc['License'] = orig_desc['License']

aslprep/utils/cbf.py

@@ -806,8 +806,8 @@ def estimate_t1(metadata):
     t1blood = T1BLOOD_DICT.get(metadata['MagneticFieldStrength'])
     if not t1blood:
         config.loggers.interface.warning(
-            f"T1blood cannot be inferred for {metadata['MagneticFieldStrength']}T data. "
-            "Defaulting to formula from Zhang et al. (2013)."
+            f'T1blood cannot be inferred for {metadata["MagneticFieldStrength"]}T data. '
+            'Defaulting to formula from Zhang et al. (2013).'
         )
         t1blood = (110 * metadata['MagneticFieldStrength'] + 1316) / 1000
 
@@ -820,7 +820,7 @@ def estimate_t1(metadata):
     t1tissue = T1TISSUE_DICT.get(metadata['MagneticFieldStrength'])
     if not t1tissue:
         raise ValueError(
-            f"T1tissue cannot be inferred for {metadata['MagneticFieldStrength']}T data."
+            f'T1tissue cannot be inferred for {metadata["MagneticFieldStrength"]}T data.'
         )
 
     return t1blood, t1tissue

aslprep/workflows/asl/cbf.py

@@ -140,7 +140,7 @@ def init_cbf_wf(
         )
     elif m0type == 'Estimate':
         m0_str = (
-            f"A single M0 estimate of {metadata['M0Estimate']} was used to produce a calibration "
+            f'A single M0 estimate of {metadata["M0Estimate"]} was used to produce a calibration '
             f"'image' and was scaled by {m0_scale}."
         )
     else:

aslprep/workflows/base.py

@@ -58,7 +58,7 @@ def init_aslprep_wf():
                 spaces=config.workflow.spaces.get_fs_spaces(),
                 minimum_fs_version='7.0.0',
             ),
-            name=f"fsdir_run_{config.execution.run_uuid.replace('-', '_')}",
+            name=f'fsdir_run_{config.execution.run_uuid.replace("-", "_")}',
             run_without_submitting=True,
         )
         if config.execution.fs_subjects_dir is not None:
@@ -190,9 +190,9 @@ def init_single_subject_wf(subject_id: str):
 
     if subject_data['roi']:
         warnings.warn(
-            f"Lesion mask {subject_data['roi']} found. "
-            "Future versions of fMRIPrep will use alternative conventions. "
-            "Please refer to the documentation before upgrading.",
+            f'Lesion mask {subject_data["roi"]} found. '
+            'Future versions of fMRIPrep will use alternative conventions. '
+            'Please refer to the documentation before upgrading.',
             FutureWarning,
             stacklevel=1,
         )
@@ -802,7 +802,7 @@ def map_fieldmap_estimation(
     for bold_file, estimator_key in all_estimators.items():
         if len(estimator_key) > 1:
             config.loggers.workflow.warning(
-                f"Several fieldmaps <{', '.join(estimator_key)}> are "
+                f'Several fieldmaps <{", ".join(estimator_key)}> are '
                 f"'IntendedFor' <{bold_file}>, using {estimator_key[0]}"
             )
             estimator_key[1:] = []