Run ruff --fix.

.circleci/get_data.py

@@ -4,7 +4,7 @@
 
 from aslprep.tests.utils import download_test_data
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     data_dir = sys.argv[1]
     dset = sys.argv[2]
     download_test_data(dset, data_dir)

.maint/update_authors.py

@@ -36,30 +36,30 @@ def read_md_table(md_text):
     keys = None
     retval = []
     for line in md_text.splitlines():
-        if line.strip().startswith("| --- |"):
-            keys = (k.replace("*", "").strip() for k in prev.split("|"))
+        if line.strip().startswith('| --- |'):
+            keys = (k.replace('*', '').strip() for k in prev.split('|'))
             keys = [k.lower() for k in keys if k]
             continue
         elif not keys:
             prev = line
             continue
 
-        if not line or not line.strip().startswith("|"):
+        if not line or not line.strip().startswith('|'):
             break
 
-        values = [v.strip() or None for v in line.split("|")][1:-1]
-        retval.append({k: v for k, v in zip(keys, values) if v})
+        values = [v.strip() or None for v in line.split('|')][1:-1]
+        retval.append({k: v for k, v in zip(keys, values, strict=False) if v})
 
     return retval
 
 
 def sort_contributors(entries, git_lines, exclude=None, last=None):
     """Return a list of author dictionaries, ordered by contribution."""
     last = last or []
-    sorted_authors = sorted(entries, key=lambda i: i["name"])
+    sorted_authors = sorted(entries, key=lambda i: i['name'])
 
-    first_last = [" ".join(val["name"].split(",")[::-1]).strip() for val in sorted_authors]
-    first_last_excl = [" ".join(val["name"].split(",")[::-1]).strip() for val in exclude or []]
+    first_last = [' '.join(val['name'].split(',')[::-1]).strip() for val in sorted_authors]
+    first_last_excl = [' '.join(val['name'].split(',')[::-1]).strip() for val in exclude or []]
 
     unmatched = []
     author_matches = []
@@ -77,15 +77,15 @@ def sort_contributors(entries, git_lines, exclude=None, last=None):
         if val not in author_matches:
             author_matches.append(val)
 
-    names = {" ".join(val["name"].split(",")[::-1]).strip() for val in author_matches}
+    names = {' '.join(val['name'].split(',')[::-1]).strip() for val in author_matches}
     for missing_name in first_last:
         if missing_name not in names:
             missing = sorted_authors[first_last.index(missing_name)]
             author_matches.append(missing)
 
     position_matches = []
     for i, item in enumerate(author_matches):
-        pos = item.pop("position", None)
+        pos = item.pop('position', None)
         if pos is not None:
             position_matches.append((i, int(pos)))
 
@@ -97,7 +97,7 @@ def sort_contributors(entries, git_lines, exclude=None, last=None):
     return author_matches, unmatched
 
 
-def get_git_lines(fname="line-contributors.txt"):
+def get_git_lines(fname='line-contributors.txt'):
     """Run git-line-summary."""
     import shutil
     import subprocess as sp
@@ -106,15 +106,15 @@ def get_git_lines(fname="line-contributors.txt"):
 
     lines = []
     if contrib_file.exists():
-        print("WARNING: Reusing existing line-contributors.txt file.", file=sys.stderr)
+        print('WARNING: Reusing existing line-contributors.txt file.', file=sys.stderr)
         lines = contrib_file.read_text().splitlines()
 
-    git_line_summary_path = shutil.which("git-line-summary")
+    git_line_summary_path = shutil.which('git-line-summary')
     if not lines and git_line_summary_path:
-        print("Running git-line-summary on repo")
+        print('Running git-line-summary on repo')
         lines = sp.check_output([git_line_summary_path]).decode().splitlines()
-        lines = [l for l in lines if "Not Committed Yet" not in l]
-        contrib_file.write_text("\n".join(lines))
+        lines = [l for l in lines if 'Not Committed Yet' not in l]
+        contrib_file.write_text('\n'.join(lines))
 
     if not lines:
         raise RuntimeError(
@@ -124,13 +124,13 @@ def get_git_lines(fname="line-contributors.txt"):
 git-line-summary not found, please install git-extras. """
             * (git_line_summary_path is None)
         )
-    return [" ".join(line.strip().split()[1:-1]) for line in lines if "%" in line]
+    return [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]
 
 
 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
 
@@ -142,13 +142,13 @@ def cli():
 
 
 @cli.command()
-@click.option("-z", "--zenodo-file", type=click.Path(exists=True), default=".zenodo.json")
-@click.option("-m", "--maintainers", type=click.Path(exists=True), default=".maint/MAINTAINERS.md")
+@click.option('-z', '--zenodo-file', type=click.Path(exists=True), default='.zenodo.json')
+@click.option('-m', '--maintainers', type=click.Path(exists=True), default='.maint/MAINTAINERS.md')
 @click.option(
-    "-c", "--contributors", type=click.Path(exists=True), default=".maint/CONTRIBUTORS.md"
+    '-c', '--contributors', type=click.Path(exists=True), default='.maint/CONTRIBUTORS.md'
 )
-@click.option("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
-@click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
+@click.option('--pi', type=click.Path(exists=True), default='.maint/PIs.md')
+@click.option('-f', '--former-file', type=click.Path(exists=True), default='.maint/FORMER.md')
 def zenodo(
     zenodo_file,
     maintainers,
@@ -175,12 +175,12 @@ def zenodo(
     zen_pi = _namelast(
         sorted(
             read_md_table(Path(pi).read_text()),
-            key=lambda v: (int(v.get("position", -1)), v.get("lastname")),
+            key=lambda v: (int(v.get('position', -1)), v.get('lastname')),
         )
     )
 
-    zenodo["creators"] = zen_creators
-    zenodo["contributors"] = zen_contributors + zen_pi
+    zenodo['creators'] = zen_creators
+    zenodo['contributors'] = zen_contributors + zen_pi
 
     misses = set(miss_creators).intersection(miss_contributors)
     if misses:
@@ -190,30 +190,30 @@ def zenodo(
         )
 
     # Remove position
-    for creator in zenodo["creators"]:
-        creator.pop("position", None)
-        creator.pop("handle", None)
-        if isinstance(creator["affiliation"], list):
-            creator["affiliation"] = creator["affiliation"][0]
+    for creator in zenodo['creators']:
+        creator.pop('position', None)
+        creator.pop('handle', None)
+        if isinstance(creator['affiliation'], list):
+            creator['affiliation'] = creator['affiliation'][0]
 
-    for creator in zenodo["contributors"]:
-        creator.pop("handle", None)
-        creator["type"] = "Researcher"
-        creator.pop("position", None)
+    for creator in zenodo['contributors']:
+        creator.pop('handle', None)
+        creator['type'] = 'Researcher'
+        creator.pop('position', None)
 
-        if isinstance(creator["affiliation"], list):
-            creator["affiliation"] = creator["affiliation"][0]
+        if isinstance(creator['affiliation'], list):
+            creator['affiliation'] = creator['affiliation'][0]
 
-    Path(zenodo_file).write_text("%s\n" % json.dumps(zenodo, indent=2))
+    Path(zenodo_file).write_text('%s\n' % json.dumps(zenodo, indent=2))
 
 
 @cli.command()
-@click.option("-m", "--maintainers", type=click.Path(exists=True), default=".maint/MAINTAINERS.md")
+@click.option('-m', '--maintainers', type=click.Path(exists=True), default='.maint/MAINTAINERS.md')
 @click.option(
-    "-c", "--contributors", type=click.Path(exists=True), default=".maint/CONTRIBUTORS.md"
+    '-c', '--contributors', type=click.Path(exists=True), default='.maint/CONTRIBUTORS.md'
 )
-@click.option("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
-@click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
+@click.option('--pi', type=click.Path(exists=True), default='.maint/PIs.md')
+@click.option('-f', '--former-file', type=click.Path(exists=True), default='.maint/FORMER.md')
 def publication(
     maintainers,
     contributors,
@@ -234,12 +234,12 @@ def publication(
     pi_hits = _namelast(
         sorted(
             read_md_table(Path(pi).read_text()),
-            key=lambda v: (int(v.get("position", -1)), v.get("lastname")),
+            key=lambda v: (int(v.get('position', -1)), v.get('lastname')),
         )
     )
 
-    pi_names = [pi["name"] for pi in pi_hits]
-    hits = [hit for hit in hits if hit["name"] not in pi_names] + pi_hits
+    pi_names = [pi['name'] for pi in pi_hits]
+    hits = [hit for hit in hits if hit['name'] not in pi_names] + pi_hits
 
     def _aslist(value):
         if isinstance(value, (list, tuple)):
@@ -249,16 +249,16 @@ def _aslist(value):
     # Remove position
     affiliations = []
     for item in hits:
-        item.pop("position", None)
-        for a in _aslist(item.get("affiliation", "Unaffiliated")):
+        item.pop('position', None)
+        for a in _aslist(item.get('affiliation', 'Unaffiliated')):
             if a not in affiliations:
                 affiliations.append(a)
 
     aff_indexes = [
-        ", ".join(
+        ', '.join(
             [
-                "%d" % (affiliations.index(a) + 1)
-                for a in _aslist(author.get("affiliation", "Unaffiliated"))
+                '%d' % (affiliations.index(a) + 1)
+                for a in _aslist(author.get('affiliation', 'Unaffiliated'))
             ]
         )
         for author in hits
@@ -270,18 +270,18 @@ def _aslist(value):
             file=sys.stderr,
         )
 
-    print("Authors (%d):" % len(hits))
+    print('Authors (%d):' % len(hits))
     print(
-        "%s."
-        % "; ".join(["%s \\ :sup:`%s`\\ " % (i["name"], idx) for i, idx in zip(hits, aff_indexes)])
+        '%s.'
+        % '; '.join(['%s \\ :sup:`%s`\\ ' % (i['name'], idx) for i, idx in zip(hits, aff_indexes, strict=False)])
     )
 
     print(
-        "\n\nAffiliations:\n%s"
-        % "\n".join(["{0: >2}. {1}".format(i + 1, a) for i, a in enumerate(affiliations)])
+        '\n\nAffiliations:\n%s'
+        % '\n'.join([f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)])
     )
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     """Install entry-point"""
     cli()

aslprep/__about__.py

@@ -4,14 +4,14 @@
 try:
     from aslprep._version import __version__
 except ImportError:
-    __version__ = "0+unknown"
+    __version__ = '0+unknown'
 
-__packagename__ = "aslprep"
-__copyright__ = "Copyright 2023, The ASLPrep Developers"
+__packagename__ = 'aslprep'
+__copyright__ = 'Copyright 2023, The ASLPrep Developers'
 __credits__ = (
-    "Contributors: please check the ``.zenodo.json`` file at the top-level folder "
-    "of the repository."
+    'Contributors: please check the ``.zenodo.json`` file at the top-level folder '
+    'of the repository.'
 )
-__url__ = "https://github.com/PennLINC/aslprep"
+__url__ = 'https://github.com/PennLINC/aslprep'
 
-DOWNLOAD_URL = f"https://github.com/PennLINC/{__packagename__}/archive/{__version__}.tar.gz"
+DOWNLOAD_URL = f'https://github.com/PennLINC/{__packagename__}/archive/{__version__}.tar.gz'

aslprep/__init__.py

@@ -5,8 +5,8 @@
 from aslprep.__about__ import __copyright__, __credits__, __packagename__, __version__
 
 __all__ = [
-    "__copyright__",
-    "__credits__",
-    "__packagename__",
-    "__version__",
+    '__copyright__',
+    '__credits__',
+    '__packagename__',
+    '__version__',
 ]

aslprep/__main__.py

@@ -2,12 +2,12 @@
 
 from aslprep.cli.run import main
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     import sys
 
     from aslprep import __name__ as module
 
     # `python -m <module>` typically displays the command as __main__.py
-    if "__main__.py" in sys.argv[0]:
-        sys.argv[0] = f"{sys.executable} -m {module}"
+    if '__main__.py' in sys.argv[0]:
+        sys.argv[0] = f'{sys.executable} -m {module}'
     main()

aslprep/_warnings.py

@@ -3,17 +3,17 @@
 import logging
 import warnings
 
-_wlog = logging.getLogger("py.warnings")
+_wlog = logging.getLogger('py.warnings')
 _wlog.addHandler(logging.NullHandler())
 
 
 def _warn(message, category=None, stacklevel=1, source=None):
     """Redefine the warning function."""
     if category is not None:
         category = type(category).__name__
-        category = category.replace("type", "WARNING")
+        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/aggregate_qc.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Aggregate QC measures across all subjects in dataset."""
@@ -14,9 +13,9 @@ def get_parser():
 
     parser = ArgumentParser(description=__doc__, formatter_class=RawTextHelpFormatter)
 
-    parser.add_argument("aslprep_dir", action="store", type=Path, help="aslprep output dir")
+    parser.add_argument('aslprep_dir', action='store', type=Path, help='aslprep output dir')
 
-    parser.add_argument("output_prefix", action="store", type=str, help="output prefix for group")
+    parser.add_argument('output_prefix', action='store', type=str, help='output prefix for group')
     return parser
 
 
@@ -25,23 +24,23 @@ def main():
     opts = get_parser().parse_args()
 
     allsubj_dir = os.path.abspath(opts.aslprep_dir)
-    outputfile = os.getcwd() + "/" + str(opts.output_prefix) + "_allsubjects_qc.tsv"
+    outputfile = os.getcwd() + '/' + str(opts.output_prefix) + '_allsubjects_qc.tsv'
 
     qclist = []
     for r, d, f in os.walk(allsubj_dir):
         for filex in f:
-            if filex.endswith("desc-qualitycontrol_cbf.tsv"):
-                qclist.append(r + "/" + filex)
+            if filex.endswith('desc-qualitycontrol_cbf.tsv'):
+                qclist.append(r + '/' + filex)
 
     datax = pd.read_table(qclist[0])
     for i in range(1, len(qclist)):
         dy = pd.read_table(qclist[i])
         datax = pd.concat([datax, dy])
 
-    datax.to_csv(outputfile, index=None, sep="\t")
+    datax.to_csv(outputfile, index=None, sep='\t')
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     raise RuntimeError(
-        "this should be run after running aslprep;\nit required installation of  aslprep"
+        'this should be run after running aslprep;\nit required installation of  aslprep'
     )