From 4fe5faede077f1cb734279b44baca0b5c805eba2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 3 Aug 2026 22:08:34 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.15.4 → v0.16.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.4...v0.16.1)
- [github.com/woodruffw/zizmor-pre-commit: v1.22.0 → v1.29.0](https://github.com/woodruffw/zizmor-pre-commit/compare/v1.22.0...v1.29.0)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 67b8d1b6b82..28178b893e8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -18,13 +18,13 @@ 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 ]
       - id: ruff-format
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.22.0
+    rev: v1.29.0
     hooks:
       - id: zizmor
   - repo: local

From 6d7b6f0ae7d7ebbcecfc107404cd1485ca3bce1f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 3 Aug 2026 22:10:55 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 docs/conf.py               | 4 ++--
 src/smriprep/cli/run.py    | 4 ++--
 src/smriprep/utils/misc.py | 2 +-
 3 files changed, 5 insertions(+), 5 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/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