STY: Mass ruff-ication

nibabies/__about__.py

@@ -5,15 +5,15 @@
 try:
     from ._version import __version__
 except ImportError:
-    __version__ = "0+unknown"
+    __version__ = '0+unknown'
 
-__org__ = "nipreps"
-__packagename__ = "nibabies"
-__copyright__ = "Copyright 2023, Center for Reproducible Neuroscience, Stanford University"
+__org__ = 'nipreps'
+__packagename__ = 'nibabies'
+__copyright__ = 'Copyright 2023, Center for Reproducible Neuroscience, Stanford University'
 __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__ = f"https://github.com/{__org__}/{__packagename__}"
+__url__ = f'https://github.com/{__org__}/{__packagename__}'
 
-DOWNLOAD_URL = f"https://github.com/{__org__}/{__packagename__}/archive/{__version__}.tar.gz"
+DOWNLOAD_URL = f'https://github.com/{__org__}/{__packagename__}/archive/{__version__}.tar.gz'

nibabies/__init__.py

@@ -1 +1 @@
-from .__about__ import __version__
+from .__about__ import __version__  # noqa: F401

nibabies/_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):

nibabies/cli/mcribs.py

@@ -8,7 +8,7 @@
 
 
 def _parser():
-    parser = ArgumentParser(description="Test script for MCRIBS surfaces")
+    parser = ArgumentParser(description='Test script for MCRIBS surfaces')
     parser.add_argument('subject', help='Subject ID')
     parser.add_argument('t2w', type=os.path.abspath, help='Input T2w (radioisotropic)')
     parser.add_argument(

nibabies/cli/parser.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Parser."""
+
 from __future__ import annotations
 
 import sys

nibabies/cli/run.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 """NiBabies runner."""
+
 from .. import config
 
 
@@ -85,7 +86,7 @@ def main():
 
         config.loggers.workflow.log(
             15,
-            '\n'.join(['nibabies config:'] + ['\t\t%s' % s for s in config.dumps().splitlines()]),
+            '\n'.join(['nibabies config:'] + [f'\t\t{s}' for s in config.dumps().splitlines()]),
         )
         config.loggers.workflow.log(25, 'nibabies started!')
 

nibabies/cli/version.py

@@ -2,15 +2,16 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Version CLI helpers."""
 
-from datetime import datetime
+from contextlib import suppress
+from datetime import datetime, timezone
 from pathlib import Path
 
 import requests
 
 from .. import __version__
 
 RELEASE_EXPIRY_DAYS = 14
-DATE_FMT = "%Y%m%d"
+DATE_FMT = '%Y%m%d'
 
 
 def check_latest():
@@ -20,65 +21,62 @@ def check_latest():
     latest = None
     date = None
     outdated = None
-    cachefile = Path.home() / ".cache" / "nibabies" / "latest"
+    now = datetime.now(tz=timezone.utc)
+    cachefile = Path.home() / '.cache' / 'nibabies' / 'latest'
     try:
         cachefile.parent.mkdir(parents=True, exist_ok=True)
     except OSError:
         cachefile = None
 
     if cachefile and cachefile.exists():
         try:
-            latest, date = cachefile.read_text().split("|")
-        except Exception:
+            latest, date = cachefile.read_text().split('|')
+        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/nibabies/json", timeout=1.0)
-        except Exception:
-            response = None
+        response = None
+        with suppress(Exception):
+            response = requests.get(url='https://pypi.org/pypi/nibabies/json', timeout=1.0)
 
         if response and response.status_code == 200:
-            versions = [Version(rel) for rel in response.json()["releases"].keys()]
+            versions = [Version(rel) for rel in response.json()['releases'].keys()]
             versions = [rel for rel in versions if not rel.is_prerelease]
             if versions:
                 latest = sorted(versions)[-1]
         else:
             latest = None
 
     if cachefile is not None and latest is not None:
-        try:
-            cachefile.write_text("|".join(("%s" % 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/nipreps/fmriprep/master/.versions.json
-    flagged = tuple()
-    try:
+    flagged = ()
+    response = None
+    with suppress(Exception):
         response = requests.get(
             url="""\
 https://raw.githubusercontent.com/nipreps/nibabies/master/.versions.json""",
             timeout=1.0,
         )
-    except Exception:
-        response = None
 
     if response and response.status_code == 200:
-        flagged = response.json().get("flagged", {}) or {}
+        flagged = response.json().get('flagged', {}) or {}
 
     if __version__ in flagged:
         return True, flagged[__version__]

nibabies/config.py

@@ -87,6 +87,7 @@
     :py:class:`~bids.layout.BIDSLayout`, etc.)
 
 """
+
 import os
 from multiprocessing import set_start_method
 

nibabies/conftest.py

@@ -8,22 +8,22 @@
 from nibabies.data import load as load_data
 
 FILES = (
-    "functional.nii",
-    "anatomical.nii",
-    "func.dlabel.nii",
-    "func.dtseries.nii",
-    "epi.nii",
-    "T1w.nii",
-    "func_to_struct.mat",
-    "atlas.nii",
-    "label_list.txt",
-    "sub-01_run-01_echo-1_bold.nii.gz",
-    "sub-01_run-01_echo-2_bold.nii.gz",
-    "sub-01_run-01_echo-3_bold.nii.gz",
+    'functional.nii',
+    'anatomical.nii',
+    'func.dlabel.nii',
+    'func.dtseries.nii',
+    'epi.nii',
+    'T1w.nii',
+    'func_to_struct.mat',
+    'atlas.nii',
+    'label_list.txt',
+    'sub-01_run-01_echo-1_bold.nii.gz',
+    'sub-01_run-01_echo-2_bold.nii.gz',
+    'sub-01_run-01_echo-3_bold.nii.gz',
 )
 
 
-@pytest.fixture(scope="package")
+@pytest.fixture(scope='package')
 def data_dir():
     with TemporaryDirectory() as tmpdir:
         tmp_path = Path(tmpdir)
@@ -33,7 +33,7 @@ def data_dir():
 
 
 @pytest.fixture(autouse=True)
-def set_namespace(doctest_namespace, data_dir):
-    doctest_namespace["data_dir"] = data_dir
-    doctest_namespace["test_data"] = load_data.cached('../tests/data')
-    doctest_namespace["Path"] = Path
+def _populate_namespace(doctest_namespace, data_dir):
+    doctest_namespace['data_dir'] = data_dir
+    doctest_namespace['test_data'] = load_data.cached('../tests/data')
+    doctest_namespace['Path'] = Path