build: update actions to perform linting and minimal dry-run testing #19
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| name: Tests | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.11 | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| conda install -c conda-forge mamba | |
| - name: Lint with flake8 | |
| run: | | |
| mamba install flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Setup snakemake | |
| run: | | |
| mamba install -c conda-forge -c bioconda pytest snakemake singularity snakefmt | |
| - name: Lint with snakemake and snakefmt | |
| run: | | |
| snakemake --lint | |
| snakefmt workflow | |
| - name: Unit tests | |
| run: | | |
| pytest .tests/unit | |
| - name: Integration test | |
| run: | | |
| pytest .tests/integration | |