Fix merge conflicts

lyashevska · lyashevska · commit 83c590d12add · 2024-08-20T11:46:46.000+02:00
diff --git a/.github/workflows/cffconvert.yml b/.github/workflows/cffconvert.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out a copy of the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Check whether the citation metadata from CITATION.cff is valid
         uses: citation-file-format/cffconvert-github-action@2.0.0
diff --git a/.github/workflows/markdown-link-check.yml b/.github/workflows/markdown-link-check.yml
@@ -14,7 +14,8 @@ jobs:
     name: Check markdown links
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: gaurav-nelson/github-action-markdown-link-check@v1
       with:
+        use-quiet-mode: 'yes'
         config-file: '.mlc-config.json'
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -18,9 +18,9 @@ jobs:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Python info
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -28,6 +28,7 @@
 * Regenerated docs/conf.py with sphinx-quickstart v3.5.4 + enabled built-in extensions [#44](https://github.com/NLeSC/python-template/issues/44)
 * Generate api rst files with extension instead of custom function [#95](https://github.com/NLeSC/python-template/issues/95)
 * Change from bump2version (unmaintained) to bump-my-version.
+* Set markdown link checker to quiet mode: only report broken links [#262](https://github.com/NLeSC/python-template/issues/262)
 
 ### Removed
 
diff --git a/template/.githooks/pre-commit b/template/.githooks/pre-commit
@@ -6,7 +6,8 @@ echo "Script $0 triggered ..."
 echo "Starting ruff analysis..."
 
 # quietly run ruff
-ruff . --fix
+ruff check --fix
+ruff format
 
 # use return code to abort commit if necessary
 if [ $? != "0" ]; then
diff --git a/template/.github/workflows/build.yml b/template/.github/workflows/build.yml
@@ -19,9 +19,9 @@ jobs:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ '{{ ' -}} matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ '{{ ' -}} matrix.python-version }}
       - name: Python info
@@ -44,9 +44,9 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.9
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
       - name: Python info
@@ -59,4 +59,6 @@ jobs:
           python -m pip install --upgrade pip setuptools
           python -m pip install .[dev,publishing]
       - name: Check style against standards using ruff
-        run: ruff .
+        run: |
+          ruff check
+          ruff format --check
diff --git a/template/.github/workflows/cffconvert.yml b/template/.github/workflows/cffconvert.yml
@@ -14,7 +14,7 @@ jobs:
     name: "cffconvert"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out a copy of the repository
 
       - name: Check whether the citation metadata from CITATION.cff is valid
diff --git a/template/.github/workflows/documentation.yml b/template/.github/workflows/documentation.yml
@@ -15,9 +15,9 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python 3.9
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
       - name: Python info
@@ -33,4 +33,4 @@ jobs:
         run: sudo apt install pandoc        
       - name: Build documentation
         run: make coverage doctest html
-        working-directory: docs
+        working-directory: docs
diff --git a/template/.github/workflows/markdown-link-check.yml b/template/.github/workflows/markdown-link-check.yml
@@ -14,7 +14,8 @@ jobs:
     name: Check markdown links
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: gaurav-nelson/github-action-markdown-link-check@v1
       with:
+        use-quiet-mode: 'yes'
         config-file: '.mlc-config.json'
diff --git a/template/.github/workflows/next_steps.yml b/template/.github/workflows/next_steps.yml
@@ -7,7 +7,7 @@ jobs:
   next_steps:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Create Sonarcloud integration issue
         uses: JasonEtco/create-an-issue@v2
         env:
diff --git a/template/.github/workflows/sonarcloud.yml b/template/.github/workflows/sonarcloud.yml
@@ -15,11 +15,11 @@ jobs:
     name: SonarCloud
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
       - name: Python info
diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
@@ -100,74 +100,31 @@ extras = dev
 """
 
 [tool.ruff]
-# Enable Pyflakes `E` and `F` codes by default.
-select = [
-    "F",  # Pyflakes
-    "E",  # pycodestyle (error)
-    "W",    # pycodestyle (warning)
-    # "C90",  # mccabe
-    "I",    # isort
-    "D",    # pydocstyle
-    # "PL",   # Pylint
-    # "PLC",  # Convention
-    # "PLE",  # Error
-    # "PLR",  # Refactor
-    # "PLW",  # Warning
-
-]
-ignore = [
-    'D100',  # Missing module docstring
-    'D104',  # Missing public package docstring
-    # The following list excludes rules irrelevant to the Google style
-    'D203',
-    'D204',
-    'D213',
-    'D215',
-    'D400',
-    'D401',
-    'D404',
-    'D406',
-    'D407',
-    'D408',
-    'D409',
-    'D413',
-]
-
-# Allow autofix for all enabled rules (when `--fix`) is provided.
-fixable = ["A", "B", "C", "D", "E", "F", "I"]
-unfixable = []
-
-exclude = [
-    ".bzr",
-    ".direnv",
-    ".eggs",
-    ".git",
-    ".hg",
-    ".mypy_cache",
-    ".nox",
-    ".pants.d",
-    ".ruff_cache",
-    ".svn",
-    ".tox",
-    ".venv",
-    "__pypackages__",
-    "_build",
-    "buck-out",
-    "build",
-    "dist",
-    "node_modules",
-    "venv",
-    ".venv",
-    "scripts",
-]
-per-file-ignores = {}
-
+line-length = 120
+output-format = "concise"
 
+[tool.ruff.lint]
 # Allow unused variables when underscore-prefixed.
 dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 
-target-version = "py39"
-line-length = 120
+# Enable Pyflakes `E` and `F` codes by default.
+select = ["ALL"]
+ignore = [
+    "ANN101", # Missing type annotation for `self` in method
+    "ANN102", # Missing type annotation for `cls` in classmethod
+    "ANN204", # Missing return type annotation for special (dunder) method
+    "FBT",    # Using boolean function arguments
+    "TD",     # TODOs
+    "FIX001", # Resolve FIXMEs
+    "FIX002", # Resolve TODOs
+    "B028",   # No explicit `stacklevel` keyword argument found in warning
+    # No docstrings required in the following cases
+    "D100", # Missing module docstring
+    "D104", # Missing public package docstring
+    "D105", # Missing docstring in magic method
+    "D107", # Missing docstring in `__init__`
+]
+pydocstyle.convention = "google"
 
 [tool.ruff.isort]
 known-first-party = ["{{ package_name }}"]
diff --git a/template/src/{{package_name}}/my_module.py.jinja b/template/src/{{package_name}}/my_module.py.jinja
@@ -2,7 +2,7 @@
 
 
 # FIXME: put actual code here
-def hello(name):
+def hello(name: str) -> str:
     """Say hello.
 
     Function docstring using Google docstring style.
diff --git a/tests/test_project.py b/tests/test_project.py
@@ -169,7 +169,7 @@ def test_ruff_check(baked_with_development_dependencies, project_env_bin_dir):
     project_dir = baked_with_development_dependencies
     bin_dir = project_env_bin_dir
 
-    result = run([f'{bin_dir}ruff', 'check', '.'], project_dir)
+    result = run([f'{bin_dir}ruff', 'check', '--fix'], project_dir)
     assert result.returncode == 0
     assert '' in result.stdout
 
