From 2e249aa373a7c9c98a62075cfcbf1940571288dd Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 4 Aug 2026 15:40:55 -0400 Subject: [PATCH 1/4] chore: pin ruff --- tox.ini | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tox.ini b/tox.ini index 9166636a1e6..ad9255bac75 100644 --- a/tox.ini +++ b/tox.ini @@ -73,7 +73,7 @@ commands = description = Check our style guide labels = check deps = - ruff + ruff ==0.16.1 skip_install = true commands = python tools/check_python_headers.py @@ -84,7 +84,7 @@ commands = description = Auto-apply style guide to the extent possible labels = pre-release deps = - ruff + ruff ==0.16.1 skip_install = true commands = ruff check --fix From c23d484e8ca35598bd94a177086f8191f5eeb68c Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 4 Aug 2026 15:42:17 -0400 Subject: [PATCH 2/4] sty: ruff checks --- docs/conf.py | 4 ++-- src/smriprep/cli/run.py | 4 ++-- src/smriprep/interfaces/templateflow.py | 5 ++--- src/smriprep/utils/misc.py | 2 +- src/smriprep/workflows/base.py | 2 +- 5 files changed, 8 insertions(+), 9 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 262ec9f09c8..62ef3e6e3bb 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -27,7 +27,7 @@ sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), 'sphinxext'))) -from github_link import make_linkcode_resolve # noqa: E402 +from github_link import make_linkcode_resolve os.environ['NO_ET'] = '1' @@ -35,7 +35,7 @@ # -- Project information ----------------------------------------------------- project = _package -copyright = _copyright # noqa: A001 +copyright = _copyright author = 'The sMRIPrep Developers' # The short X.Y version diff --git a/src/smriprep/cli/run.py b/src/smriprep/cli/run.py index eac21e8b835..2afde0ae45b 100644 --- a/src/smriprep/cli/run.py +++ b/src/smriprep/cli/run.py @@ -744,7 +744,7 @@ def build_workflow(opts, retval): str(log_dir / 'CITATION.html'), ] try: - check_call(cmd, timeout=10) # noqa: S603 + check_call(cmd, timeout=10) except (FileNotFoundError, CalledProcessError, TimeoutExpired): logger.warning('Could not generate CITATION.html file:\n%s', ' '.join(cmd)) @@ -760,7 +760,7 @@ def build_workflow(opts, retval): str(log_dir / 'CITATION.tex'), ] try: - check_call(cmd, timeout=10) # noqa: S603 + check_call(cmd, timeout=10) except (FileNotFoundError, CalledProcessError, TimeoutExpired): logger.warning('Could not generate CITATION.tex file:\n%s', ' '.join(cmd)) else: diff --git a/src/smriprep/interfaces/templateflow.py b/src/smriprep/interfaces/templateflow.py index 840664f8850..8fe07688c3b 100644 --- a/src/smriprep/interfaces/templateflow.py +++ b/src/smriprep/interfaces/templateflow.py @@ -191,9 +191,8 @@ def fetch_template_files( } ) - if res := specs.pop('res', None): - if res != 'native': - specs['resolution'] = res + if (res := specs.pop('res', None)) and res != 'native': + specs['resolution'] = res if not specs.get('resolution'): specs['resolution'] = 2 if sloppy else 1 diff --git a/src/smriprep/utils/misc.py b/src/smriprep/utils/misc.py index 2d109be8877..8e219fadafd 100644 --- a/src/smriprep/utils/misc.py +++ b/src/smriprep/utils/misc.py @@ -93,7 +93,7 @@ def fs_isRunning(subjects_dir, subject_id, mtime_tol=86400, logger=None): for fl in isrunning: fl.unlink() if logger: - logger.warn(f'Removed "IsRunning*" files found under {subj_dir}') + logger.warning(f'Removed "IsRunning*" files found under {subj_dir}') return subjects_dir diff --git a/src/smriprep/workflows/base.py b/src/smriprep/workflows/base.py index 123650ba1b4..ef1cb95166d 100644 --- a/src/smriprep/workflows/base.py +++ b/src/smriprep/workflows/base.py @@ -366,7 +366,7 @@ def init_single_subject_wf( )[0] if not subject_data['t1w']: - raise Exception( + raise FileNotFoundError( f'No T1w images found for participant {subject_id}. All workflows require T1w images.' ) From 5645ebe60894dc0650704ea66c2e891127e00a8f Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 4 Aug 2026 16:46:20 -0400 Subject: [PATCH 3/4] maint: bump pre-commit yaml --- .pre-commit-config.yaml | 2 +- tox.ini | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 67b8d1b6b82..ac2a83f1f1d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -18,7 +18,7 @@ repos: - id: rst-directive-colons - id: rst-inline-touching-normal - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.15.4 + rev: v0.16.1 hooks: - id: ruff-check args: [ --fix, --show-fixes ] diff --git a/tox.ini b/tox.ini index ad9255bac75..b41853ed4de 100644 --- a/tox.ini +++ b/tox.ini @@ -73,7 +73,7 @@ commands = description = Check our style guide labels = check deps = - ruff ==0.16.1 + ruff ==0.16.1 # keep in sync with .pre-commit-config.yaml skip_install = true commands = python tools/check_python_headers.py @@ -84,7 +84,7 @@ commands = description = Auto-apply style guide to the extent possible labels = pre-release deps = - ruff ==0.16.1 + ruff ==0.16.1 # keep in sync with .pre-commit-config.yaml skip_install = true commands = ruff check --fix From 7e2845c504baa1f4632d317c59e7f676825a0bec Mon Sep 17 00:00:00 2001 From: mathiasg Date: Wed, 5 Aug 2026 10:29:16 -0400 Subject: [PATCH 4/4] tst: update mock function name --- test/utils/test_misc.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/utils/test_misc.py b/test/utils/test_misc.py index 90231a18a91..c8a36649f87 100644 --- a/test/utils/test_misc.py +++ b/test/utils/test_misc.py @@ -65,7 +65,7 @@ class _Logger: def __init__(self): self.msg = None - def warn(self, msg): + def warning(self, msg): self.msg = msg logger = _Logger()