STY: Various manual fixes

Author: effigies

fmriprep/cli/parser.py

@@ -116,8 +116,8 @@ 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}>.')
 
@@ -130,8 +130,8 @@ def _slice_time_ref(value, parser):
             value = float(value)
         except ValueError:
             raise parser.error(
-                "Slice time reference must be number, 'start', or 'middle'. " f'Received {value}.'
-            )
+                f"Slice time reference must be number, 'start', or 'middle'. Received {value}."
+            ) from None
         if not 0 <= value <= 1:
             raise parser.error(f'Slice time reference must be in range 0-1. Received {value}.')
         return value
@@ -784,7 +784,7 @@ 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

fmriprep/cli/tests/test_parser.py

@@ -183,7 +183,7 @@ def test_bids_filter_file(tmp_path, capsys):
     _reset_config()
 
 
-@pytest.mark.parametrize('st_ref', (None, '0', '1', '0.5', 'start', 'middle'))
+@pytest.mark.parametrize('st_ref', (None, '0', '1', '0.5', 'start', 'middle'))  # noqa: PT007
 def test_slice_time_ref(tmp_path, st_ref):
     bids_path = tmp_path / 'data'
     out_path = tmp_path / 'out'
@@ -200,13 +200,13 @@ def test_slice_time_ref(tmp_path, st_ref):
 
 @pytest.mark.parametrize(
     ('args', 'expectation'),
-    (
+    [
         ([], False),
         (['--use-syn-sdc'], 'error'),
         (['--use-syn-sdc', 'error'], 'error'),
         (['--use-syn-sdc', 'warn'], 'warn'),
         (['--use-syn-sdc', 'other'], (SystemExit, ArgumentError)),
-    ),
+    ],
 )
 def test_use_syn_sdc(tmp_path, args, expectation):
     bids_path = tmp_path / 'data'

fmriprep/cli/tests/test_version.py

@@ -21,7 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Test version checks."""
-from datetime import datetime
+from datetime import datetime, timezone
 from os import getenv, geteuid
 from pathlib import Path
 
@@ -71,7 +71,7 @@ def mock_get(*args, **kwargs):
     assert v == Version('1.1.0')
     assert cachefile.read_text().split('|') == [
         str(v),
-        datetime.now().strftime(DATE_FMT),
+        datetime.now(tz=timezone.utc).strftime(DATE_FMT),
     ]
 
     # Second check - test the cache file is read
@@ -139,7 +139,7 @@ def mock_get(*args, **kwargs):
     [
         '3laj#r???d|3akajdf#',
         '2.0.0|3akajdf#',
-        '|'.join(('2.0.0', datetime.now().strftime(DATE_FMT), '')),
+        '|'.join(('2.0.0', datetime.now(tz=timezone.utc).strftime(DATE_FMT), '')),
         '',
     ],
 )
@@ -210,7 +210,7 @@ def test_readonly(tmp_path, monkeypatch):
         cachedir.mkdir(mode=0o555, exist_ok=True)
 
     # Make sure creating the folder will raise the exception.
-    with pytest.raises(OSError):
+    with pytest.raises(OSError, match=r'Read-only file system|Permission denied'):
         (cachedir / 'fmriprep').mkdir(parents=True)
 
     # Should not raise

fmriprep/cli/version.py

@@ -22,7 +22,8 @@
 #
 """Version CLI helpers."""
 
-from datetime import datetime
+from contextlib import suppress
+from datetime import datetime, timezone
 from pathlib import Path
 
 import requests
@@ -40,6 +41,7 @@ def check_latest():
     latest = None
     date = None
     outdated = None
+    now = datetime.now(tz=timezone.utc)
     cachefile = Path.home() / '.cache' / 'fmriprep' / 'latest'
     try:
         cachefile.parent.mkdir(parents=True, exist_ok=True)
@@ -49,23 +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 = None
+        with suppress(Exception):
             response = requests.get(url='https://pypi.org/pypi/fmriprep/json', timeout=1.0)
-        except Exception:
-            response = None
 
         if response and response.status_code == 200:
             versions = [Version(rel) for rel in response.json()['releases'].keys()]
@@ -76,10 +77,8 @@ def check_latest():
             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
 
@@ -88,14 +87,13 @@ def is_flagged():
     """Check whether current version is flagged."""
     # https://raw.githubusercontent.com/nipreps/fmriprep/master/.versions.json
     flagged = ()
-    try:
+    response = None
+    with suppress(Exception):
         response = requests.get(
             url="""\
 https://raw.githubusercontent.com/nipreps/fmriprep/master/.versions.json""",
             timeout=1.0,
         )
-    except Exception:
-        response = None
 
     if response and response.status_code == 200:
         flagged = response.json().get('flagged', {}) or {}

fmriprep/cli/workflow.py

@@ -215,7 +215,7 @@ def build_boilerplate(config_file, workflow):
 
         config.loggers.cli.info('Generating an HTML version of the citation boilerplate...')
         try:
-            check_call(cmd, timeout=10)
+            check_call(cmd, timeout=10)  # noqa: S603
         except (FileNotFoundError, CalledProcessError, TimeoutExpired):
             config.loggers.cli.warning('Could not generate CITATION.html file:\n%s', ' '.join(cmd))
 
@@ -232,6 +232,6 @@ def build_boilerplate(config_file, workflow):
         ]
         config.loggers.cli.info('Generating a LaTeX version of the citation boilerplate...')
         try:
-            check_call(cmd, timeout=10)
+            check_call(cmd, timeout=10)  # noqa: S603
         except (FileNotFoundError, CalledProcessError, TimeoutExpired):
             config.loggers.cli.warning('Could not generate CITATION.tex file:\n%s', ' '.join(cmd))

fmriprep/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 ImportError:
     _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 = '{}%'.format(Path('/proc/sys/vm/overcommit_ratio').read_text().strip())
-except Exception:
+except Exception:  # noqa: S110, BLE001
     pass
 
 

fmriprep/conftest.py

@@ -22,12 +22,12 @@ def copytree_or_skip(source, target):
 
     try:
         copytree(data_dir, target / data_dir.name)
-    except Exception:
+    except Exception:  # noqa: BLE001
         pytest.skip(f'Cannot copy {data_dir!r} into {target / data_dir.name}. Probably in a zip.')
 
 
 @pytest.fixture(autouse=True)
-def populate_namespace(doctest_namespace, tmp_path):
+def _populate_namespace(doctest_namespace, tmp_path):
     doctest_namespace['copytree_or_skip'] = copytree_or_skip
     doctest_namespace['testdir'] = tmp_path
 

fmriprep/data/__init__.py

@@ -163,7 +163,7 @@ def as_path(self, *segments) -> AbstractContextManager[Path]:
         """
         return as_file(self.files.joinpath(*segments))
 
-    @cache
+    @cache  # noqa: B019
     def cached(self, *segments) -> Path:
         """Ensure data is available as a :class:`~pathlib.Path`.
 

fmriprep/utils/bids.py

@@ -233,7 +233,7 @@ def validate_input_dir(exec_env, bids_dir, participant_label, need_T1w=True):
         temp.write(json.dumps(validator_config_dict))
         temp.flush()
         try:
-            subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name])
+            subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name])  # noqa: S603, S607
         except FileNotFoundError:
             print('bids-validator does not appear to be installed', file=sys.stderr)
 
@@ -263,10 +263,14 @@ def check_pipeline_version(pipeline_name, cvers, data_desc):
     Examples
     --------
     >>> check_pipeline_version('fMRIPrep', '23.2.0.dev0', 'sample_dataset_description.json')
-    >>> check_pipeline_version('fMRIPrep', '23.2.0.dev0+gb2e14d98', 'sample_dataset_description.json')
+    >>> check_pipeline_version(
+    ...     'fMRIPrep', '23.2.0.dev0+gb2e14d98', 'sample_dataset_description.json'
+    ... )
     >>> check_pipeline_version('fMRIPrep', '24.0.0', 'sample_dataset_description.json')
     'Previous output generated by version 23.2.0.dev0 found.'
-    >>> check_pipeline_version('fMRIPrep', '24.0.0', 'legacy_dataset_description.json')  # doctest: +ELLIPSIS
+    >>> check_pipeline_version(
+    ...     'fMRIPrep', '24.0.0', 'legacy_dataset_description.json'
+    ... )  # doctest: +ELLIPSIS
     'Previous output generated by version 1.1.1rc5 found.'
 
     Returns

fmriprep/workflows/base.py

@@ -237,6 +237,7 @@ def init_single_subject_wf(subject_id: str):
             "Future versions of fMRIPrep will use alternative conventions. "
             "Please refer to the documentation before upgrading.",
             FutureWarning,
+            stacklevel=1,
         )
 
     spaces = config.workflow.spaces