Refresh lock and linter dependencies

.devcontainer/devcontainer.json

@@ -17,7 +17,7 @@
   // cache pip installs
   "mounts": ["type=volume,source=dev-pip-cache,target=/root/.cache/uv"],
 
-  "postCreateCommand": "uv sync && uv run pre-commit install || true && npm ci",
+  "postCreateCommand": "uv sync --frozen && uv run pre-commit install || true && npm ci",
 
   "customizations": {
     "vscode": {
@@ -35,7 +35,6 @@
         "ms-vscode.test-adapter-converter",
         "njpwerner.autodocstring",
         "cschlosser.doxdocgen",
-        "davidanson.vscode-markdownlint",
         // version pinned (for now) since an old version (1.6.2) is installed otherwise
         "biomejs.biome@3.3.0"
       ],

.github/dependabot.yml

@@ -7,4 +7,23 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "cron"
+      cronjob: "0 8 * * 1" # Every Monday at 8:00 UTC
+    groups:
+      all-dependencies:
+        patterns:
+          - "*"
+    cooldown:
+      default-days: 7
+
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "cron"
+      cronjob: "0 8 * * 1" # Every Monday at 8:00 UTC
+    groups:
+      all-dependencies:
+        patterns:
+          - "*"
+    cooldown:
+      default-days: 7

.github/workflows/check-code-quality.yml

@@ -32,34 +32,34 @@ jobs:
 
       - name: Install most linters from uv
         run: |
-          CC=gcc-14 CXX=g++-14 uv sync --group lint
+          CC=gcc-14 CXX=g++-14 uv sync --locked --group lint
 
       - name: Run mypy
         run: |
-          uv run mypy .
+          uv run --frozen mypy .
 
       - name: Run ruff
         run: |
-          uv run ruff check .
-          uv run ruff format .
+          uv run --frozen ruff check .
+          uv run --frozen ruff format .
           git restore README.md
 
       - name: Run clang-format
         run: |
-          git ls-files -z -- '*.h' '*.c' '*.cpp' '*.hpp' '*.cc' '*.cxx' | xargs -0 -r uv run clang-format -style=file -i
+          git ls-files -z -- '*.h' '*.c' '*.cpp' '*.hpp' '*.cc' '*.cxx' | xargs -0 -r uv run --frozen clang-format -style=file -i
 
       - name: Run cmake-linter
         run: |
-          uv run gersemi -i --warnings-as-errors src/ tests/ cmake/
+          uv run --frozen gersemi -i --warnings-as-errors src/ tests/ cmake/
 
-      - name: Install npm packages
+      - name: Run pymarkdown
         run: |
-          npm ci
+          echo "Running pymarkdown"
+          git ls-files -z -- '*.md' | xargs -0 -r uv run --frozen pymarkdown fix
 
-      - name: Run markdownlint
+      - name: Install npm packages
         run: |
-          echo "Running markdownlint"
-          npx markdownlint --fix .
+          npm ci
 
       - name: Run Biome
         run: |
@@ -77,8 +77,8 @@ jobs:
       - name: Check generated code
         if: success()
         run: |
-          uv sync --group code-generation
-          uv run code_generation/code_gen.py
+          uv sync --locked --group code-generation
+          uv run --frozen code_generation/code_gen.py
           if [ -n "$(git status --porcelain)" ]; then
             echo
             echo "The following files are outdated or were manually updated:"

.github/workflows/refresh-lock-and-linter-dependencies.yml

@@ -41,11 +41,11 @@ jobs:
         uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
 
       - name: upgrade uv lock
-        run: uv lock --upgrade  
+        run: uv lock --upgrade
 
       - name: Install linters from uv
         run: |
-          uv sync --only-group lint
+          uv sync --locked --only-group lint
 
       - name: retrieve uv package versions
         id: versions_uv
@@ -78,7 +78,6 @@ jobs:
             echo "${nospecialchars_pkg}=$version" >> "$GITHUB_OUTPUT"
           }
           grab_installed_version_npm "@biomejs/biome"
-          grab_installed_version_npm "markdownlint-cli"
 
       - name: Update .pre-commit-config.yaml
         uses: cuchi/jinja2-action@8bd801365a8d36a0b20f45ee969161685de7785a # v1.3.0
@@ -91,7 +90,6 @@ jobs:
             mypy=${{ steps.versions_uv.outputs.mypy }}
             gersemi=${{ steps.versions_uv.outputs.gersemi }}
             biome=${{ steps.versions_npm.outputs.biomejsbiome }}
-            markdownlint_cli=${{ steps.versions_npm.outputs.markdownlint-cli }}
 
       - name: show changed files
         run: |

.github/workflows/sonar.yml

@@ -48,8 +48,8 @@ jobs:
 
       - name: Python test and coverage
         run: |
-          CC=clang CXX=clang++ uv sync --no-default-groups --group test
-          uv run pytest
+          CC=clang CXX=clang++ uv sync --locked --no-default-groups --group test
+          uv run --frozen pytest
 
       - name: Run build-wrapper for C++
         run: |

.pre-commit-config.yaml

@@ -3,54 +3,70 @@
 # SPDX-License-Identifier: MPL-2.0
 
 repos:
-  - repo: https://github.com/fsfe/reuse-tool  # outside pypi
-    rev: v6.2.0
+  - repo: local
     hooks:
       - id: reuse
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.15.22
-    hooks:
-      # Run the linter.
-      - id: ruff-check
-        name: ruff-check
-        args: [ --fix ]
-      # Run the formatter.
+        name: reuse
+        entry: uv run --frozen reuse lint
+        language: system
+        pass_filenames: false
+      - id: pytest
+        name: pytest
+        entry: uv run --frozen pytest
+        language: system
+        pass_filenames: false
+        types_or: [ python, c++, c ]
       - id: ruff-format
         name: ruff-format
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v2.3.0
-    hooks:
+        entry: uv run --frozen ruff format
+        language: system
+        pass_filenames: false
+        types: [ python ]
+      - id: ruff-check
+        name: ruff-check
+        entry: uv run --frozen ruff check
+        language: system
+        pass_filenames: false
+        types: [ python ]
       - id: mypy
-        additional_dependencies:
-          - numpy
-  - repo: local
-    hooks:
-      - id: pytest
-        name: pytest
-        entry: uv run pytest
+        name: mypy
+        entry: uv run --frozen mypy .
         language: system
         pass_filenames: false
-        always_run: true
-  - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v18.1.8
-    hooks:
+        types: [ python ]
       - id: clang-format
+        name: clang-format
+        entry: uv run --frozen clang-format -style=file -i
+        language: system
+        pass_filenames: true
         types_or: [ c++, c ]
-  - repo: https://github.com/BlankSpruce/gersemi-pre-commit
-    rev: 0.27.7
-    hooks:
       - id: gersemi
         name: cmake-linter
         alias: cmake-linter
-  - repo: https://github.com/igorshubovych/markdownlint-cli  # outside pypi 
-    rev: v0.49.1
-    hooks:
-      - id: markdownlint
-        args: ["--fix"]
+        entry: uv run --frozen gersemi -i --warnings-as-errors
+        language: system
+        pass_filenames: true
+        types: [ cmake ]
+      - id: pymarkdown-fix
+        name: pymarkdown-fix
+        alias: markdown-fix
+        entry: uv run --frozen pymarkdown fix
+        language: system
+        pass_filenames: true
+        types: [ markdown ]
+        require_serial: true
+      - id: pymarkdown-scan
+        name: pymarkdown-scan
+        alias: markdown-check
+        entry: uv run --frozen pymarkdown scan
+        language: system
+        pass_filenames: true
+        types: [ markdown ]
+        require_serial: true
+        # format .json and .jsonc files
   # format .json and .jsonc files
   - repo: https://github.com/biomejs/pre-commit  # outside pypi 
-    rev: v2.5.4
+    rev: v2.5.6
     hooks:
       # configuration is located in biome.jsonc
       - id: biome-format

.pre-commit-config.yaml.jinja

@@ -3,51 +3,67 @@
 # SPDX-License-Identifier: MPL-2.0
 
 repos:
-  - repo: https://github.com/fsfe/reuse-tool  # outside pypi
-    rev: v6.2.0
+  - repo: local
     hooks:
       - id: reuse
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v{{ ruff }}
-    hooks:
-      # Run the linter.
-      - id: ruff-check
-        name: ruff-check
-        args: [ --fix ]
-      # Run the formatter.
+        name: reuse
+        entry: uv run --frozen reuse lint
+        language: system
+        pass_filenames: false
+      - id: pytest
+        name: pytest
+        entry: uv run --frozen pytest
+        language: system
+        pass_filenames: false
+        types_or: [ python, c++, c ]
       - id: ruff-format
         name: ruff-format
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v{{ mypy }}
-    hooks:
+        entry: uv run --frozen ruff format
+        language: system
+        pass_filenames: false
+        types: [ python ]
+      - id: ruff-check
+        name: ruff-check
+        entry: uv run --frozen ruff check
+        language: system
+        pass_filenames: false
+        types: [ python ]
       - id: mypy
-        additional_dependencies:
-          - numpy
-  - repo: local
-    hooks:
-      - id: pytest
-        name: pytest
-        entry: uv run pytest
+        name: mypy
+        entry: uv run --frozen mypy .
         language: system
         pass_filenames: false
-        always_run: true
-  - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v{{ clang_format }}
-    hooks:
+        types: [ python ]
       - id: clang-format
+        name: clang-format
+        entry: uv run --frozen clang-format -style=file -i
+        language: system
+        pass_filenames: true
         types_or: [ c++, c ]
-  - repo: https://github.com/BlankSpruce/gersemi-pre-commit
-    rev: {{ gersemi }}
-    hooks:
       - id: gersemi
         name: cmake-linter
         alias: cmake-linter
-  - repo: https://github.com/igorshubovych/markdownlint-cli  # outside pypi 
-    rev: v{{ markdownlint_cli }}
-    hooks:
-      - id: markdownlint
-        args: ["--fix"]
+        entry: uv run --frozen gersemi -i --warnings-as-errors
+        language: system
+        pass_filenames: true
+        types: [ cmake ]
+      - id: pymarkdown-fix
+        name: pymarkdown-fix
+        alias: markdown-fix
+        entry: uv run --frozen pymarkdown fix
+        language: system
+        pass_filenames: true
+        types: [ markdown ]
+        require_serial: true
+      - id: pymarkdown-scan
+        name: pymarkdown-scan
+        alias: markdown-check
+        entry: uv run --frozen pymarkdown scan
+        language: system
+        pass_filenames: true
+        types: [ markdown ]
+        require_serial: true
+        # format .json and .jsonc files
   # format .json and .jsonc files
   - repo: https://github.com/biomejs/pre-commit  # outside pypi 
     rev: v{{ biome }}

.readthedocs.yaml

@@ -24,7 +24,7 @@ build:
     create_environment:
       - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
     install:
-      - CC=gcc-14 CXX=g++-14 UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group doc
+      - CC=gcc-14 CXX=g++-14 UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --locked --group doc
     post_install:
       # remove API DLL define in header
       - find power_grid_model_c/power_grid_model_c/include -name *.h -exec sed -i -r "s/#define PGM.*//g" {} \;