Merge branch 'main' into 430_minimal_profile

Author: fdiblen

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: ".github/workflows"
+    schedule:
+      interval: "daily"

.github/workflows/markdown-link-check.yml

@@ -7,15 +7,27 @@ on:
   pull_request:
     branches:
     - main
+  schedule:
+    - cron: '0 0 * * 0' # every Sunday at 00:00
 
 jobs:
-
-  markdown-link-check:
-    name: Check markdown links
+  linkChecker:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-    - uses: gaurav-nelson/github-action-markdown-link-check@v1
-      with:
-        use-quiet-mode: 'yes'
-        config-file: '.mlc-config.json'
+      - uses: actions/checkout@v4
+
+      - name: Link Checker
+        id: lychee
+        uses: lycheeverse/lychee-action@v1
+        with:
+          # fail action if there are broken links
+          fail: true
+
+      - name: Create Issue From File
+        # create issues only when triggered by schedule
+        if: github.event_name == 'schedule' && env.lychee_exit_code != 0
+        uses: peter-evans/create-issue-from-file@v5
+        with:
+          title: Link Checker Report
+          content-filepath: ./lychee/out.md
+          labels: report, automated issue

.mlc-config.json

@@ -5,23 +5,23 @@ Spend less time setting up and configuring your new Python packages and comply w
 Use this [Copier](https://copier.readthedocs.io) template to generate an empty Python package. Features include:
 
 - Boilerplate unit tests and documentation,
-- [Python static setup configuration](template/pyproject.toml),
+- [Python static setup configuration](template/pyproject.toml.jinja),
 - Open source software license,
 - Continuous integration with [GitHub action workflows](template/.github/workflows) for building, testing, link checking and linting,
 - Code style checking with [ruff](https://beta.ruff.rs/),
 - [Editorconfig](template/.editorconfig),
 - Usage and contribution documents:
-  - [README.md](template/README.md) for package users,
-  - [README.dev.md](template/README.dev.md) for package developer,
-  - [project_setup.md](template/project_setup.md) with extensive documentation about project setup,
+  - [README.md](template/README.md.jinja) for package users,
+  - [README.dev.md](template/README.dev.md.jinja) for package developer,
+  - [project_setup.md](template/project_setup.md.jinja) with extensive documentation about project setup,
   - [Change log](template/CHANGELOG.md),
-  - [Code of Conduct](template/CODE_OF_CONDUCT.md),
-  - [Contributing guidelines](template/CONTRIBUTING.md),
+  - [Code of Conduct](template/CODE_OF_CONDUCT.md.jinja),
+  - [Contributing guidelines](template/CONTRIBUTING.md.jinja),
 - Continuous code quality and code coverage reporting using [Sonarcloud](https://sonarcloud.io/),
 - Automatic creation of [issues](template/.github/next_steps) with instructions how to pass all GitHub action workflows and integrate with services like Zenodo and Read the Docs,
-- Instructions how to make package [citable](template/.github/next_steps/02_citation.md)
+- Instructions how to make package [citable](template/.github/next_steps/02_citation.md.jinja)
 - FAIR software recommendation badge,
-- Optional [pre commit hook](template/README.dev.md#running-linters-locally) to catch lint errors early
+- Optional [pre commit hook](template/README.dev.md.jinja#running-linters-locally) to catch lint errors early
 
 ## Badges
 
@@ -92,7 +92,7 @@ copier copy https://github.com/nlesc/python-template.git path/to/destination
 | code_of_conduct_email     | [email protected] | Email address of the person who should be contacted in case of violations of the Code of Conduct. |
 
 Once the project files have been generated, follow the steps outlined in
-[next_steps.md](template/next_steps.md).
+[next_steps.md](template/next_steps.md.jinja).
 
 #### Step 2/2: Read about what was just generated
 
@@ -152,7 +152,7 @@ Good job! You have now generated the skeleton for your package:
 └── .zenodo.json
 ```
 
-For an explanation of what's there, read on in the [project_setup.md](template/project_setup.md) file.
+For an explanation of what's there, read on in the [project_setup.md](template/project_setup.md.jinja) file.
 
 ### Scenario 2: Apply to pre-existing code
 

README.md

@@ -102,6 +102,7 @@ extras = dev
 [tool.ruff]
 line-length = 120
 output-format = "concise"
+extend-exclude = ["docs"]
 
 [tool.ruff.lint]
 # Allow unused variables when underscore-prefixed.
@@ -126,7 +127,15 @@ ignore = [
 ]
 pydocstyle.convention = "google"
 
-[tool.ruff.isort]
+[tool.ruff.lint.per-file-ignores]
+# Tests can ignore a few extra rules
+"tests/**.py" = [
+    "ANN201", # Missing return type annotation for public function
+    "PT011",  # Missing `match` parameter in `pytest.raises()`
+    "S101",   # Use of assert is detected
+]
+
+[tool.ruff.lint.isort]
 known-first-party = ["{{ package_name }}"]
 force-single-line = true
 no-lines-before = ["future","standard-library","third-party","first-party","local-folder"]

template/pyproject.toml.jinja

@@ -25,5 +25,6 @@ def hello(name: str) -> str:
 
     """
     if name == 'nobody':
-        raise ValueError('Can not say hello to nobody')
+        msg = 'Can not say hello to nobody'
+        raise ValueError(msg)
     return f'Hello {name}!'

template/src/{{package_name}}/my_module.py.jinja

@@ -21,6 +21,6 @@ def some_name():
     return 'Jane Smith'
 
 
-def test_hello_with_fixture(some_name):
+def test_hello_with_fixture(some_name: str):
     """Example using a fixture."""
     assert hello(some_name) == 'Hello Jane Smith!'