Merge pull request #1375 from DimitriPapadopoulos/ruff_0.9.1

MAINT: Upgrade to ruff 0.9.1

Author: oesteban

.maint/update_authors.py

@@ -120,7 +120,7 @@ def get_git_lines(fname='line-contributors.txt'):
 
     git_line_summary_path = shutil.which('git-line-summary')
     if not git_line_summary_path:
-        git_line_summary_path = "git summary --dedup-by-email".split(" ")
+        git_line_summary_path = 'git summary --dedup-by-email'.split(' ')
     else:
         git_line_summary_path = [git_line_summary_path]
 
@@ -233,7 +233,7 @@ def zenodo(
             creator['affiliation'] = creator['affiliation'][0]
 
     Path(zenodo_file).write_text(
-        '%s\n' % json.dumps(zenodo, indent=2)
+        f'{json.dumps(zenodo, indent=2)}\n'
     )
 
 
@@ -301,20 +301,18 @@ def _aslist(value):
 
     print('Authors (%d):' % len(hits))
     print(
-        '%s.'
-        % '; '.join(
+        '{}.'.format('; '.join(
             [
                 '{} \\ :sup:`{}`\\ '.format(i['name'], idx)
                 for i, idx in zip(hits, aff_indexes)
             ]
-        )
+        ))
     )
 
     print(
-        '\n\nAffiliations:\n%s'
-        % '\n'.join(
+        '\n\nAffiliations:\n{}'.format('\n'.join(
             [f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)]
-        )
+        ))
     )
 
 

mriqc/bin/abide2bids.py

@@ -127,7 +127,7 @@ def fetch(args: (str, str, str, str)) -> (str, str):
         out_dir = op.abspath(out_dir)
 
     pkg_id = [u[9:] for u in url.split('/') if u.startswith('NITRC_IR_')][0]
-    sub_file = op.join(tmpdir, '%s.zip' % pkg_id)
+    sub_file = op.join(tmpdir, f'{pkg_id}.zip')
 
     cmd = [_curl_cmd, '-s', '-u', f'{user}:{password}', '-o', sub_file, url]
     sp.check_call(cmd)

mriqc/bin/fs2gif.py

@@ -114,14 +114,14 @@ def main():
         center = np.average([bbox_min, bbox_max], axis=0)
 
         if opts.hist_eq:
-            ref_file = op.join(tmp_sub, '%s.mgz' % subid)
+            ref_file = op.join(tmp_sub, f'{subid}.mgz')
             img = nb.load(op.join(sub_path, 'mri', 'norm.mgz'))
             data = exposure.equalize_adapthist(img.get_fdata(), clip_limit=0.03)
             nb.MGHImage(data, img.affine, img.header).to_filename(ref_file)
 
         if not opts.zoom:
             # Export tiffs for left hemisphere
-            tcl_file = op.join(tmp_sub, '%s.tcl' % subid)
+            tcl_file = op.join(tmp_sub, f'{subid}.tcl')
             with open(tcl_file, 'w') as tclfp:
                 tclfp.write(tcl_contents)
                 tclfp.write(
@@ -147,7 +147,7 @@ def main():
             if opts.use_xvfb:
                 cmd = _xvfb_run() + cmd
 
-            print('Running tkmedit: %s' % ' '.join(cmd))
+            print('Running tkmedit: {}'.format(' '.join(cmd)))
             sp.call(cmd, env=environ)
             # Convert to animated gif
             print('Stacking coronal slices')
@@ -165,7 +165,7 @@ def main():
 
         else:
             # Export tiffs for left hemisphere
-            tcl_file = op.join(tmp_sub, 'lh-%s.tcl' % subid)
+            tcl_file = op.join(tmp_sub, f'lh-{subid}.tcl')
             with open(tcl_file, 'w') as tclfp:
                 tclfp.write(tcl_contents)
                 tclfp.write('SetZoomLevel 2')
@@ -184,13 +184,13 @@ def main():
             if opts.use_xvfb:
                 cmd = _xvfb_run() + cmd
 
-            print('Running tkmedit: %s' % ' '.join(cmd))
+            print('Running tkmedit: {}'.format(' '.join(cmd)))
             sp.call(cmd, env=environ)
             # Convert to animated gif
             print('Stacking coronal slices')
 
             # Export tiffs for right hemisphere
-            tcl_file = op.join(tmp_sub, 'rh-%s.tcl' % subid)
+            tcl_file = op.join(tmp_sub, f'rh-{subid}.tcl')
             with open(tcl_file, 'w') as tclfp:
                 tclfp.write(tcl_contents)
                 tclfp.write('SetZoomLevel 2')
@@ -209,7 +209,7 @@ def main():
             if opts.use_xvfb:
                 cmd = _xvfb_run() + cmd
 
-            print('Running tkmedit: %s' % ' '.join(cmd))
+            print('Running tkmedit: {}'.format(' '.join(cmd)))
             sp.call(cmd, env=environ)
             # Convert to animated gif
             print('Stacking coronal slices')
@@ -260,7 +260,7 @@ def _xvfb_run(wait=5, server_args='-screen 0, 1600x1200x24', logs=None):
 
 
 def _myerror(msg):
-    print('WARNING: Error deleting temporal files: %s' % msg)
+    print(f'WARNING: Error deleting temporal files: {msg}')
 
 
 if __name__ == '__main__':

mriqc/bin/labeler.py

@@ -54,7 +54,7 @@ def main():
                 finished[j - 1] = finished[j - 1] + 1
                 hold[j - 1, i - 1] = int(file[i][j])
     finished = np.divide(np.round(np.divide(finished, total) * 1000), 10)
-    print(f'Completed: {" ".join(["%g%%" % f for f in finished])}')
+    print(f'Completed: {" ".join([f"{f:g}%" for f in finished])}')
     print(f'Total: {np.round(np.divide(np.sum(finished), 3))}%')
     input('Waiting: [enter]')
 

mriqc/cli/version.py

@@ -77,9 +77,7 @@ def check_latest():
 
     if cachefile is not None and latest is not None:
         with suppress(Exception):
-            cachefile.write_text(
-                '|'.join(('%s' % latest, datetime.now(tz=UTC).strftime(DATE_FMT)))
-            )
+            cachefile.write_text('|'.join((f'{latest}', datetime.now(tz=UTC).strftime(DATE_FMT))))
 
     return latest
 

mriqc/config.py

@@ -618,7 +618,7 @@ def init(cls) -> None:
 
         if cls.inputs_path.exists():
             with open(cls.inputs_path, 'rb') as handle:
-                _inputs = pickle.load(handle)
+                _inputs = pickle.load(handle)  # noqa: S301
 
                 cls.inputs = _inputs['paths']
                 cls.inputs_metadata = _inputs['metadata']

mriqc/interfaces/webapi.py

@@ -290,7 +290,7 @@ def upload_qc_metrics(
             timeout=15,
         )
     except requests.ConnectionError as err:
-        errmsg = (f'Error uploading IQMs: Connection error:', f'{err}')
+        errmsg = ('Error uploading IQMs: Connection error:', f'{err}')
     except requests.exceptions.ReadTimeout as err:
         errmsg = (f'Error uploading IQMs: Server {endpoint} is down.', f'{err}')
 

mriqc/reports/group.py

@@ -23,7 +23,6 @@
 """Encapsulates report generation functions."""
 
 from itertools import product
-from sys import version_info
 
 import pandas as pd
 
@@ -34,18 +33,14 @@
 def gen_html(csv_file, mod, csv_failed=None, out_file=None):
     import os.path as op
     from datetime import datetime, timezone
+    from io import StringIO as TextIO
 
     from niworkflows.data import Loader
 
     from mriqc.data.config import GroupTemplate
 
     from .. import __version__ as ver
 
-    if version_info[0] > 2:
-        from io import StringIO as TextIO
-    else:
-        from io import BytesIO as TextIO
-
     UTC = timezone.utc
     load_data = Loader('mriqc')
 
@@ -185,7 +180,7 @@ def gen_html(csv_file, mod, csv_failed=None, out_file=None):
             (['efc'], None),
             (['fber'], None),
             (['fwhm', 'fwhm_x', 'fwhm_y', 'fwhm_z'], 'mm'),
-            (['gsr_%s' % a for a in ('x', 'y')], None),
+            ([f'gsr_{a}' for a in ('x', 'y')], None),
             (['snr'], None),
             (['dvars_std', 'dvars_vstd'], None),
             (['dvars_nstd'], None),

mriqc/tests/test_parser.py

@@ -23,9 +23,10 @@
 
 """Test parser."""
 
-import pytest
 from pathlib import Path
 
+import pytest
+
 from mriqc.cli.parser import _build_parser
 
 MIN_ARGS = ['bids_dir', 'out', 'participant']

mriqc/workflows/diffusion/output.py

@@ -45,8 +45,7 @@ def init_dwi_report_wf(name='dwi_report_wf'):
             wf = init_dwi_report_wf()
 
     """
-    from nireports.interfaces import FMRISummary, PlotMosaic, PlotSpikes
-    from niworkflows.interfaces.morphology import BinaryDilation, BinarySubtraction
+    from nireports.interfaces import PlotMosaic
 
     # from mriqc.interfaces.reports import IndividualReport