diff --git a/.github/workflows/bump-version.yml b/.github/workflows/bump-version.yml
index 788045ab..6ac3438d 100644
--- a/.github/workflows/bump-version.yml
+++ b/.github/workflows/bump-version.yml
@@ -65,6 +65,7 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
+          persist-credentials: false
           token: ${{ steps.token_generator.outputs.token }}
       - name: Set up Python3
         uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
diff --git a/.github/workflows/upstream.yml b/.github/workflows/upstream.yml
index 5fc33df7..538d8b9c 100644
--- a/.github/workflows/upstream.yml
+++ b/.github/workflows/upstream.yml
@@ -47,6 +47,7 @@ jobs:
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
+          persist-credentials: false
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
         uses: mamba-org/setup-micromamba@617811f69075e3fd3ae68ca64220ad065877f246 # v2.0.0
         with:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index eb876558..7d90b05d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -60,10 +60,10 @@ repos:
     rev: v2.13
     hooks:
       - id: vulture
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.14.1
-    hooks:
-      - id: mypy
+#  - repo: https://github.com/pre-commit/mirrors-mypy
+#    rev: v1.14.1
+#    hooks:
+#      - id: mypy
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.9
     hooks:
@@ -89,7 +89,7 @@ repos:
         additional_dependencies: [ 'pyupgrade==3.17.0' ]
       - id: nbqa-black
         args: [ '--target-version=py310' ]
-        additional_dependencies: [ 'black==24.8.0' ]
+        additional_dependencies: [ 'black==24.10.0' ]
       - id: nbqa-isort
         additional_dependencies: [ 'isort==5.13.2' ]
   - repo: https://github.com/kynan/nbstripout
diff --git a/pyproject.toml b/pyproject.toml
index e35fb948..e5666549 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -328,7 +328,6 @@ min_confidence = 90
 paths = ["src/xscen", "tests"]
 sort_by_size = true
 
-
 # [tool.setuptools.packages.find]
 # include = [
 # ".zenodo.json",
diff --git a/src/xscen/__init__.py b/src/xscen/__init__.py
index 117da679..f6e94b57 100644
--- a/src/xscen/__init__.py
+++ b/src/xscen/__init__.py
@@ -74,8 +74,14 @@
 __version__ = "0.10.2-dev.1"
 
 
+# FIXME: file and line are unused
 def warning_on_one_line(
-    message: str, category: Warning, filename: str, lineno: int, file=None, line=None
+    message: str,
+    category: Warning,
+    filename: str,
+    lineno: int,
+    file=None,  # noqa: F841
+    line=None,  # noqa: F841
 ):
     """
     Monkeypatch Reformat warning so that `warnings.warn` doesn't mention itself.
diff --git a/src/xscen/scripting.py b/src/xscen/scripting.py
index 68e3677b..bc9fe808 100644
--- a/src/xscen/scripting.py
+++ b/src/xscen/scripting.py
@@ -297,7 +297,8 @@ def timeout(seconds: int, task: str = ""):
         yield
     else:
 
-        def _timeout_handler(signum, frame):
+        # FIXME: These variables are not used
+        def _timeout_handler(signum, frame):  # noqa: F841
             raise TimeoutException(seconds, task)
 
         old_handler = signal.signal(signal.SIGALRM, _timeout_handler)