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
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