feature/template maint 20250301 (#165)

cutoffthetop · RKIMetadataExchange · web-flow · commit 716a581e36bd · 2025-03-12T12:50:25.000+01:00
### Added

- add pre-commit hooks and linting CI workflow

### Changes

- update gitignores with `locked-requirements.txt` and invenio-specifics
- update versions in requirements.txt, pyproject.toml and pre-commit

### Fixed

- fix project page link on documentation pages
- use proper git tag for building containers in CI

---------

Signed-off-by: Nicolas Drebenstedt &lt;897972+cutoffthetop@users.noreply.github.com&gt;
Co-authored-by: RKI | Metadata Exchange &lt;121876825+RKIMetadataExchange@users.noreply.github.com&gt;
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -0,0 +1,54 @@
+name: Linting
+
+on:
+  push:
+    branches: ["main"]
+    tags: ["**"]
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
+  workflow_dispatch:
+
+env:
+  PDM_CHECK_UPDATE: False
+  PIP_DISABLE_PIP_VERSION_CHECK: on
+  PIP_NO_CLEAN: on
+  PIP_NO_INPUT: on
+  PIP_PREFER_BINARY: on
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Cache requirements
+        uses: actions/cache@v4
+        env:
+          cache-name: cache-requirements
+        with:
+          path: ~/.cache/pip
+          key: ${{ env.cache-name }}-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ env.cache-name }}-
+
+      - name: Setup python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install requirements
+        run: make install
+
+      - name: Run linters
+        run: make linter
diff --git a/.github/workflows/renovatebot.yml b/.github/workflows/renovatebot.yml
@@ -22,7 +22,7 @@ jobs:
           fetch-depth: 1
 
       - name: Run renovatebot
-        uses: renovatebot/github-action@v41.0.13
+        uses: renovatebot/github-action@v41.0.14
         env:
           RENOVATE_GIT_PRIVATE_KEY: ${{ secrets.GPG_SIGNING_KEY }}
           RENOVATE_REPOSITORIES: "robert-koch-institut/mex-template"
diff --git a/.gitignore b/.gitignore
@@ -22,6 +22,7 @@ downloads/
 eggs/
 lib/
 lib64/
+locked-requirements.txt
 MANIFEST
 parts/
 sdist/
@@ -49,7 +50,7 @@ coverage.xml
 test*.jpeg
 test*.png
 *.cover
-*.py,cover
+*,cover
 .hypothesis/
 .pytest_cache/
 cover/
@@ -84,7 +85,7 @@ ipython_config.py
 __pypackages__/
 
 # Celery stuff
-celerybeat-schedule
+celerybeat-schedule.*
 celerybeat.pid
 
 # Environments
@@ -126,10 +127,14 @@ dmypy.json
 assets/external/
 .web
 
-# Default exports
+# MEx specific
+.aws/
+.invenio.private
 *.ndjson
 data/
 identity.csv
+logs/
+payload
 schema.json
 tmp*/
 work/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,17 @@
+fail_fast: false
+default_language_version:
+  python: python3.11
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: pretty-format-json
+        name: json
+        args: [--autofix, --indent=4, --no-ensure-ascii]
+        exclude: cookiecutter.json
+      - id: end-of-file-fixer
+        name: eof
+      - id: trailing-whitespace
+        name: whitespaces
+      - id: fix-byte-order-marker
+        name: byte-order
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,14 +9,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- add pre-commit hooks and linting CI workflow
+
 ### Changes
 
+- update gitignores with `locked-requirements.txt` and invenio-specifics
+- update versions in requirements.txt, pyproject.toml and pre-commit
+
 ### Deprecated
 
 ### Removed
 
 ### Fixed
 
+- fix project page link on documentation pages
+- use proper git tag for building containers in CI
+
 ### Security
 
 ## [0.4.0] - 2025-02-18
diff --git a/Makefile b/Makefile
@@ -1,10 +1,23 @@
-.PHONY: all setup
-all: setup
-
-LATEST = $(shell git describe --tags $(shell git rev-list --tags --max-count=1))
-PWD = $(shell pwd)
+.PHONY: all setup hooks install linter
+all: install linter
 
 setup:
 	# install meta requirements system-wide
 	@ echo installing requirements; \
 	pip --disable-pip-version-check install --force-reinstall -r requirements.txt; \
+
+hooks:
+	# install pre-commit hooks when not in CI
+	@ if [ -z "$$CI" ]; then \
+		pre-commit install; \
+	fi; \
+
+install: setup hooks
+	# install packages from lock file in local virtual environment
+	@ echo installing package; \
+	pdm install; \
+
+linter:
+	# run the linter hooks from pre-commit on all files
+	@ echo linting all files; \
+	pre-commit run --all-files; \
diff --git a/README.md b/README.md
@@ -2,6 +2,9 @@
 
 Cookiecutter template for MEx python projects.
 
+[![cookiecutter](https://github.com/robert-koch-institut/mex-template/actions/workflows/cookiecutter.yml/badge.svg)](https://github.com/robert-koch-institut/mex-template)
+[![cve-scan](https://github.com/robert-koch-institut/mex-template/actions/workflows/cve-scan.yml/badge.svg)](https://github.com/robert-koch-institut/mex-template/actions/workflows/cve-scan.yml)
+[![linting](https://github.com/robert-koch-institut/mex-template/actions/workflows/linting.yml/badge.svg)](https://github.com/robert-koch-institut/mex-template/actions/workflows/linting.yml)
 [![open-code](https://github.com/robert-koch-institut/mex-template/actions/workflows/open-code.yml/badge.svg)](https://gitlab.opencode.de/robert-koch-institut/mex/mex-template)
 
 ## Project
diff --git a/mex-{{ cookiecutter.project_name }}/.dockerignore b/mex-{{ cookiecutter.project_name }}/.dockerignore
@@ -50,7 +50,7 @@ coverage.xml
 test*.jpeg
 test*.png
 *.cover
-*.py,cover
+*,cover
 .hypothesis/
 .pytest_cache/
 cover/
@@ -84,7 +84,7 @@ ipython_config.py
 __pypackages__/
 
 # Celery stuff
-celerybeat-schedule
+celerybeat-schedule.*
 celerybeat.pid
 
 # Environments
@@ -122,10 +122,14 @@ dmypy.json
 assets/external/
 .web
 
-# Default exports
+# MEx specific
+.aws/
+.invenio.private
 *.ndjson
 data/
 identity.csv
+logs/
+payload
 schema.json
 tmp*/
 work/
@@ -149,6 +153,7 @@ work/
 Makefile
 mex.bat
 *.lock
+Pipfile
 poetry.toml
 pytest.ini
 requirements.txt
diff --git a/mex-{{ cookiecutter.project_name }}/.github/workflows/release.yml b/mex-{{ cookiecutter.project_name }}/.github/workflows/release.yml
@@ -88,6 +88,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 1
+          {% raw %}ref: ${{ needs.release.outputs.tag }}{% endraw %}
 
       - name: Cache requirements
         uses: actions/cache@v4
diff --git a/mex-{{ cookiecutter.project_name }}/.github/workflows/renovatebot.yml b/mex-{{ cookiecutter.project_name }}/.github/workflows/renovatebot.yml
@@ -22,7 +22,7 @@ jobs:
           fetch-depth: 1
 
       - name: Run renovatebot
-        uses: renovatebot/github-action@v41.0.13
+        uses: renovatebot/github-action@v41.0.14
         env:
           RENOVATE_GIT_PRIVATE_KEY: {% raw %}${{ secrets.GPG_SIGNING_KEY }}{% endraw %}
           RENOVATE_REPOSITORIES: "robert-koch-institut/mex-{{ cookiecutter.project_name }}"
diff --git a/mex-{{ cookiecutter.project_name }}/.gitignore b/mex-{{ cookiecutter.project_name }}/.gitignore
@@ -22,6 +22,7 @@ downloads/
 eggs/
 lib/
 lib64/
+locked-requirements.txt
 MANIFEST
 parts/
 sdist/
@@ -49,7 +50,7 @@ coverage.xml
 test*.jpeg
 test*.png
 *.cover
-*.py,cover
+*,cover
 .hypothesis/
 .pytest_cache/
 cover/
@@ -84,7 +85,7 @@ ipython_config.py
 __pypackages__/
 
 # Celery stuff
-celerybeat-schedule
+celerybeat-schedule.*
 celerybeat.pid
 
 # Environments
@@ -126,10 +127,14 @@ dmypy.json
 assets/external/
 .web
 
-# Default exports
+# MEx specific
+.aws/
+.invenio.private
 *.ndjson
 data/
 identity.csv
+logs/
+payload
 schema.json
 tmp*/
 work/
diff --git a/mex-{{ cookiecutter.project_name }}/.pre-commit-config.yaml b/mex-{{ cookiecutter.project_name }}/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ default_language_version:
   python: python3.11
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.6
+    rev: v0.9.10
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -25,7 +25,7 @@ repos:
       - id: fix-byte-order-marker
         name: byte-order
   - repo: https://github.com/pdm-project/pdm
-    rev: 2.22.3
+    rev: 2.22.4
     hooks:
       - id: pdm-lock-check
         name: pdm
diff --git a/mex-{{ cookiecutter.project_name }}/docs/layout.html b/mex-{{ cookiecutter.project_name }}/docs/layout.html
@@ -3,7 +3,7 @@
 
 {% block footer %}
     <div class="footer">
-        <a href="https://www.rki.de/DE/Content/Forsch/MEx/MEx_inhalt.html" rel="nofollow">
+        <a href="https://www.rki.de/DE/Aktuelles/Publikationen/Forschungsdaten/MEx/metadata-exchange-plattform-mex-node.html" rel="nofollow">
             MEx Project
         </a> |
         <a href="https://www.rki.de/DE/Service/Impressum/impressum_node.html" rel="nofollow">
diff --git a/mex-{{ cookiecutter.project_name }}/pyproject.toml b/mex-{{ cookiecutter.project_name }}/pyproject.toml
@@ -11,7 +11,7 @@ dependencies = []
 optional-dependencies.dev = [
     "ipdb>=0.13,<1",
     "mypy>=1,<2",
-    "pytest-cov>=5,<6",
+    "pytest-cov>=6,<7",
     "pytest-random-order>=1,<2",
     "pytest-xdist>=3,<4",
     "pytest>=8,<9",
diff --git a/mex-{{ cookiecutter.project_name }}/requirements.txt b/mex-{{ cookiecutter.project_name }}/requirements.txt
@@ -1,4 +1,4 @@
 cruft==2.16.0
 mex-release==0.3.0
-pdm==2.22.3
+pdm==2.22.4
 pre-commit==4.1.0
diff --git a/mex.bat b/mex.bat
@@ -3,6 +3,7 @@
 set target=%1
 
 if "%target%"=="install" goto install
+if "%target%"=="test" goto test
 echo invalid argument %target%
 exit /b 1
 
@@ -12,3 +13,21 @@ exit /b 1
 echo installing requirements
 pip --disable-pip-version-check install --force-reinstall -r requirements.txt
 if %errorlevel% neq 0 exit /b %errorlevel%
+
+@REM install pre-commit hooks when not in CI
+if "%CI%"=="" (
+    pre-commit install
+    if %errorlevel% neq 0 exit /b %errorlevel%
+)
+
+@REM install packages from lock file in local virtual environment
+echo installing package
+pdm install
+exit /b %errorlevel%
+
+
+:test
+@REM run the linter hooks from pre-commit on all files
+echo linting all files
+pre-commit run --all-files
+exit /b %errorlevel%
diff --git a/pdm.lock b/pdm.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -9,4 +9,3 @@ urls = { Repository = "https://github.com/robert-koch-institut/mex-template" }
 requires-python = ">=3.11,<3.13"
 dependencies = []
 optional-dependencies.dev = []
-
diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
 cruft==2.16.0
 mex-release==0.3.0
-pdm==2.22.3
+pdm==2.22.4
 pre-commit==4.1.0
