Bump GitHub Actions and pre-commit Hooks

.github/dependabot.yml

@@ -17,8 +17,6 @@ updates:
     insecure-external-code-execution: "deny"
     pull-request-branch-name:
       separator: "/"
-    reviewers:
-      - "andthum"
     labels:
       - "dependencies"
       - "patch"
@@ -33,8 +31,6 @@ updates:
     insecure-external-code-execution: "deny"
     pull-request-branch-name:
       separator: "/"
-    reviewers:
-      - "andthum"
     labels:
       - "dependencies"
       - "skip-changelog"
@@ -49,8 +45,6 @@ updates:
     insecure-external-code-execution: "deny"
     pull-request-branch-name:
       separator: "/"
-    reviewers:
-      - "andthum"
     labels:
       - "dependencies"
       - "skip-changelog"
@@ -62,8 +56,6 @@ updates:
       interval: "weekly"
     pull-request-branch-name:
       separator: "/"
-    reviewers:
-      - "andthum"
     labels:
       - "dependencies"
       - "skip-changelog"

.github/workflows/codeql-analysis.yml

@@ -21,14 +21,14 @@ jobs:
       security-events: "write"
     steps:
       - name: "Checkout repository"
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
       - name: "Initialize CodeQL"
-        uses: "github/codeql-action/init@v3"
+        uses: "github/codeql-action/init@v4"
         with:
           languages: "python"
           # Override the default behavior so that the action doesn't
           # attempt to auto-install Python dependencies. See:
           # https://docs.github.com/en/code-security/secure-coding/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#analyzing-python-dependencies
           setup-python-dependencies: false
       - name: "Perform CodeQL Analysis"
-        uses: "github/codeql-action/analyze@v3"
+        uses: "github/codeql-action/analyze@v4"

.github/workflows/tests.yml

@@ -40,9 +40,9 @@ jobs:
     runs-on: "${{ matrix.os }}"
     steps:
       - name: "Checkout repository"
-        uses: "actions/checkout@v4"
+        uses: "actions/checkout@v6"
       - name: "Set up Python ${{ matrix.python-version }}"
-        uses: "actions/setup-python@v5"
+        uses: "actions/setup-python@v6"
         with:
           python-version: "${{ matrix.python-version }}"
       - name: "Add directories where pip installs scripts to PATH"
@@ -59,7 +59,7 @@ jobs:
           python -m pip install --user --upgrade pip
           echo "dir=$(pip cache dir)" >> ${GITHUB_OUTPUT}
       - name: "Create/Restore cache"
-        uses: "actions/cache@v4"
+        uses: "actions/cache@v5"
         with:
           path: |
             ${{ steps.pip-cache.outputs.dir }}/**

.pre-commit-config.yaml

@@ -11,7 +11,7 @@
 # Bypass pre-commit and commit-msg hook with `git commit --no-verify`
 # or bypass individual hooks with `SKIP=<hook_id> git commit`.
 
-minimum_pre_commit_version: "3.0"
+minimum_pre_commit_version: "4.0"
 
 default_language_version:
   python: "python3"
@@ -30,7 +30,7 @@ ci:
 
 repos:
   - repo: "https://github.com/pre-commit/pre-commit-hooks"
-    rev: "v5.0.0"
+    rev: "v6.0.0"
     hooks:
       ### Git ###
       # Protect specific branches from direct check-ins.
@@ -108,7 +108,7 @@ repos:
       - id: "check-pre-commit-ci-config"
 
   - repo: "https://github.com/python-jsonschema/check-jsonschema"
-    rev: "0.31.2"
+    rev: "0.37.0"
     hooks:
       # Validate Dependabot Config (v2) against the schema provided by
       # SchemaStore.
@@ -145,7 +145,7 @@ repos:
       - id: "rst-inline-touching-normal"
 
   - repo: "https://github.com/PyCQA/isort"
-    rev: "6.0.0"
+    rev: "8.0.1"
     hooks:
       # Sort import statements with isort
       - id: "isort"
@@ -176,7 +176,7 @@ repos:
           - "--color"
 
   - repo: "https://github.com/PyCQA/flake8"
-    rev: "7.1.2"
+    rev: "7.3.0"
     hooks:
       # Lint Python code with Flake8.
       - id: "flake8"
@@ -185,17 +185,17 @@ repos:
           # Keep in sync with `requirements-dev.txt` and `.flake8`!
           - "flake8-bandit >=4.0, <5.0"
           - "flake8-bugbear >=24.0, <25.0"
-          - "flake8-builtins >=2.0, <3.0"
+          - "flake8-builtins >=3.0, <4.0"
           - "flake8-comprehensions >=3.0, <4.0"
           - "flake8-docstrings >=1.0, <2.0"
-          - "flake8-isort >=6.0, <7.0"
+          - "flake8-isort >=7.0, <8.0"
           - "flake8-logging-format >=0.1, <1.0"
           - "flake8-pytest-style >=2.0, <3.0"
           - "flake8-rst-docstrings >=0.2.6, <1.0"
           - "pep8-naming >=0.1, <1.0"
 
   - repo: "https://github.com/PyCQA/bandit"
-    rev: "1.8.3"
+    rev: "1.9.4"
     hooks:
       # Check code security with bandit.
       - id: "bandit"
@@ -217,7 +217,7 @@ repos:
   ######################################################################
 
   - repo: "https://github.com/maxwinterstein/shfmt-py"
-    rev: "v3.7.0.1"
+    rev: "v3.12.0.1"
     hooks:
       # Format shell scripts with shfmt.
       # NOTE: The official shfmt hook from
@@ -238,7 +238,7 @@ repos:
           - "-l"
 
   - repo: "https://github.com/shellcheck-py/shellcheck-py"
-    rev: "v0.10.0.1"
+    rev: "v0.11.0.1"
     hooks:
       # Lint shell scripts with shellcheck.
       # NOTE: The official shellcheck hook from

docs/requirements-docs.txt

@@ -1,5 +1,5 @@
 # Requirements to build hpcss' documentation.
 
-sphinx >=5.0, <9.0
+sphinx >=5.0, <10.0
 sphinx-rtd-theme >=3.0, <4.0
 tomlkit >=0.1, < 1.0

docs/source/conf.py

@@ -447,6 +447,10 @@
 linkcheck_ignore = [
     # Errno 110 Connection timed out.
     r"https://confluence\.uni-muenster\.de.",
+    # Errno 403 Client Error: Forbidden for url.
+    r"https://docutils\.sourceforge\.io/docs/ref/rst/restructuredtext\.html#bullet-lists",  # noqa: E501
+    r"https://zenodo\.org/badge/447523192\.svg",
+    r"https://zenodo\.org/doi/10\.5281/zenodo\.10154885",
 ]
 linkcheck_retries = 2
 

requirements-dev.txt

@@ -10,14 +10,14 @@ black >=23.0, <24.0
 flake8 >=7.0, <8.0
 flake8-bandit >=4.0, <5.0
 flake8-bugbear >=24.0, <25.0
-flake8-builtins >=2.0, <3.0
+flake8-builtins >=3.0, <4.0
 flake8-comprehensions >=3.0, <4.0
 flake8-docstrings >=1.0, <2.0
-flake8-isort >=6.0, <7.0
+flake8-isort >=7.0, <8.0
 flake8-logging-format >=0.1, <1.0
 flake8-pytest-style >=2.0, <3.0
 flake8-rst-docstrings >=0.2.6, <1.0
-isort >=6.0, <7.0
+isort >=8.0, <9.0
 pep8-naming >=0.1, <1.0
 pre-commit >=4.0, <5.0
 pytest >=8.0, <9.0