Fix remaining ruff issues.

.maint/update_authors.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 """Update and sort the creators list of the zenodo record."""
+
 import json
 import sys
 from pathlib import Path
@@ -113,16 +114,17 @@ def get_git_lines(fname='line-contributors.txt'):
     if not lines and git_line_summary_path:
         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]
+        lines = [line for line in lines if 'Not Committed Yet' not in line]
         contrib_file.write_text('\n'.join(lines))
 
     if not lines:
         raise RuntimeError(
             """\
-Could not find line-contributors from git repository.%s"""
-            % """ \
+Could not find line-contributors from git repository.{}""".format(
+                """ \
 git-line-summary not found, please install git-extras. """
-            * (git_line_summary_path is None)
+                * (git_line_summary_path is None)
+            )
         )
     return [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]
 
@@ -185,7 +187,7 @@ def zenodo(
     misses = set(miss_creators).intersection(miss_contributors)
     if misses:
         print(
-            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
+            f"Some people made commits, but are missing in .maint/ files: {', '.join(misses)}",
             file=sys.stderr,
         )
 
@@ -204,7 +206,7 @@ def zenodo(
         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(f'{json.dumps(zenodo, indent=2)}\n')
 
 
 @cli.command()
@@ -242,7 +244,7 @@ def publication(
     hits = [hit for hit in hits if hit['name'] not in pi_names] + pi_hits
 
     def _aslist(value):
-        if isinstance(value, (list, tuple)):
+        if isinstance(value, list | tuple):
             return value
         return [value]
 
@@ -266,22 +268,29 @@ def _aslist(value):
 
     if misses:
         print(
-            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
+            f"Some people made commits, but are missing in .maint/ files: {', '.join(misses)}",
             file=sys.stderr,
         )
 
     print('Authors (%d):' % len(hits))
     print(
-        '%s.'
-        % '; '.join(['%s \\ :sup:`%s`\\ ' % (i['name'], idx) for i, idx in zip(hits, aff_indexes, strict=False)])
+        '{}.'.format(
+            '; '.join(
+                [
+                    rf'{i["name"]} \ :sup:`{idx}`\ '
+                    for i, idx in zip(hits, aff_indexes, strict=False)
+                ]
+            )
+        )
     )
 
     print(
-        '\n\nAffiliations:\n%s'
-        % '\n'.join([f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)])
+        '\n\nAffiliations:\n{}'.format(
+            '\n'.join([f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)])
+        )
     )
 
 
 if __name__ == '__main__':
-    """Install entry-point"""
+    """ Install entry-point """
     cli()

aslprep/cli/aggregate_qc.py

@@ -27,7 +27,7 @@ def main():
     outputfile = os.getcwd() + '/' + str(opts.output_prefix) + '_allsubjects_qc.tsv'
 
     qclist = []
-    for r, d, f in os.walk(allsubj_dir):
+    for r, _, f in os.walk(allsubj_dir):
         for filex in f:
             if filex.endswith('desc-qualitycontrol_cbf.tsv'):
                 qclist.append(r + '/' + filex)

aslprep/cli/parser.py

@@ -72,8 +72,8 @@ def _bids_filter(value, parser):
             if Path(value).exists():
                 try:
                     return loads(Path(value).read_text(), object_hook=_filter_pybids_none_any)
-                except JSONDecodeError:
-                    raise parser.error(f'JSON syntax error in: <{value}>.')
+                except JSONDecodeError as e:
+                    raise parser.error(f'JSON syntax error in: <{value}>.') from e
             else:
                 raise parser.error(f'Path does not exist: <{value}>.')
 
@@ -671,7 +671,7 @@ def parse_args(args=None, namespace=None):
         import yaml
 
         with open(opts.use_plugin) as f:
-            plugin_settings = yaml.load(f, Loader=yaml.FullLoader)
+            plugin_settings = yaml.safe_load(f)
         _plugin = plugin_settings.get('plugin')
         if _plugin:
             config.nipype.plugin = _plugin

aslprep/cli/version.py

@@ -1,13 +1,34 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
 """Version CLI helpers."""
 
-from datetime import datetime
+from contextlib import suppress
+from datetime import datetime, timezone
 from pathlib import Path
 
 import requests
 
-from aslprep import __version__
+from .. import __version__
 
 RELEASE_EXPIRY_DAYS = 14
 DATE_FMT = '%Y%m%d'
@@ -20,6 +41,7 @@ def check_latest():
     latest = None
     date = None
     outdated = None
+    now = datetime.now(tz=timezone.utc)
     cachefile = Path.home() / '.cache' / 'aslprep' / 'latest'
     try:
         cachefile.parent.mkdir(parents=True, exist_ok=True)
@@ -29,23 +51,22 @@ def check_latest():
     if cachefile and cachefile.exists():
         try:
             latest, date = cachefile.read_text().split('|')
-        except Exception:
+        except Exception:  # noqa: S110, BLE001
             pass
         else:
             try:
                 latest = Version(latest)
-                date = datetime.strptime(date, DATE_FMT)
+                date = datetime.strptime(date, DATE_FMT).astimezone(timezone.utc)
             except (InvalidVersion, ValueError):
                 latest = None
             else:
-                if abs((datetime.now() - date).days) > RELEASE_EXPIRY_DAYS:
+                if abs((now - date).days) > RELEASE_EXPIRY_DAYS:
                     outdated = True
 
     if latest is None or outdated is True:
-        try:
-            response = requests.get(url='https://pypi.org/pypi/alprep/json', timeout=1.0)
-        except Exception:
-            response = None
+        response = None
+        with suppress(Exception):
+            response = requests.get(url='https://pypi.org/pypi/aslprep/json', timeout=1.0)
 
         if response and response.status_code == 200:
             versions = [Version(rel) for rel in response.json()['releases'].keys()]
@@ -56,26 +77,23 @@ def check_latest():
             latest = None
 
     if cachefile is not None and latest is not None:
-        try:
-            cachefile.write_text('|'.join((latest, datetime.now().strftime(DATE_FMT))))
-        except Exception:
-            pass
+        with suppress(OSError):
+            cachefile.write_text(f'{latest}|{now.strftime(DATE_FMT)}')
 
     return latest
 
 
 def is_flagged():
     """Check whether current version is flagged."""
-    # https://raw.githubusercontent.com/pennlinc/aslprep/master/.versions.json
-    flagged = tuple()
-    try:
+    # https://raw.githubusercontent.com/pennlinc/aslprep/main/.versions.json
+    flagged = ()
+    response = None
+    with suppress(Exception):
         response = requests.get(
             url="""\
-https://raw.githubusercontent.com/pennlinc/aslprep/master/.versions.json""",
+https://raw.githubusercontent.com/pennlinc/aslprep/main/.versions.json""",
             timeout=1.0,
         )
-    except Exception:
-        response = None
 
     if response and response.status_code == 200:
         flagged = response.json().get('flagged', {}) or {}

aslprep/config.py

@@ -179,7 +179,7 @@
     from psutil import virtual_memory
 
     _free_mem_at_start = round(virtual_memory().available / 1024**3, 1)
-except Exception:
+except Exception:  # noqa: BLE001
     _free_mem_at_start = None
 
 _oc_limit = 'n/a'
@@ -197,7 +197,7 @@
                 _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()}%"
-except Exception:
+except Exception:  # noqa: S110, BLE001
     pass
 
 
@@ -209,7 +209,7 @@
 class _Config:
     """An abstract class forbidding instantiation."""
 
-    _paths = tuple()
+    _paths = ()
 
     def __init__(self):
         """Avert instantiation."""
@@ -223,7 +223,7 @@ def load(cls, settings, init=True, ignore=None):
             if k in ignore or v is None:
                 continue
             if k in cls._paths:
-                if isinstance(v, (list, tuple)):
+                if isinstance(v, list | tuple):
                     setattr(cls, k, [Path(val).absolute() for val in v])
                 else:
                     setattr(cls, k, Path(v).absolute())
@@ -248,7 +248,7 @@ def get(cls):
             if callable(getattr(cls, k)):
                 continue
             if k in cls._paths:
-                if isinstance(v, (list, tuple)):
+                if isinstance(v, list | tuple):
                     v = [str(val) for val in v]
                 else:
                     v = str(v)