Integrating Snakemake Unittests & CI / CD #115
Workflow file for this run
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| # This pipeline checks whether the package | |
| # installs properly, passes unit tests and whether | |
| # the code formatting is right. | |
| name: build | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ["3.11.2"] | |
| poetry-version: ["1.8.3"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Run black formatting check | |
| uses: psf/black@stable | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| - name: Install Poetry | |
| uses: snok/install-poetry@v1 | |
| with: | |
| virtualenvs-create: true | |
| virtualenvs-in-project: true | |
| version: ${{ matrix.poetry-version }} | |
| - name: Cache dependencies | |
| id: cache-deps | |
| uses: actions/cache@v2 | |
| with: | |
| path: .venv | |
| key: pydeps-${{ hashFiles('**/poetry.lock') }} | |
| - name: Install the dependencies | |
| run: poetry install --no-interaction --no-root --with dev | |
| if: steps.cache-deps.outputs.cache-hit != 'true' | |
| - name: Install the module | |
| run: poetry install --with dev --no-interaction | |
| - name: Run unit tests | |
| run: poetry run pytest | |
| - name: Run Ruff | |
| run: poetry run ruff check . | |
| - name: Run interrogate | |
| run: poetry run interrogate src | |
| - name: Run Pyright (type checking) | |
| run: poetry run pyright | |
| - name: Linting | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: '.test' | |
| snakefile: 'workflow/Snakefile' | |
| args: '--lint' | |
| - name: Testing | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: '.test' | |
| snakefile: 'workflows/Snakefile' | |
| args: '--cores 1 --use-conda --conda-cleanup-pkgs cache' | |
| stagein: '' # additional preliminary commands to run (can be multiline) | |
| show-disk-usage-on-error: true |