chore: update to stable snakemake #45
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out the code | |
| uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - name: Install poetry | |
| run: pipx install poetry | |
| - name: Determine dependencies | |
| run: poetry lock | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| cache: poetry | |
| - name: Install Dependencies using Poetry | |
| run: poetry install | |
| - name: Check formatting | |
| run: poetry run black --check . | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out the code | |
| uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - name: Install poetry | |
| run: pipx install poetry | |
| - name: Determine dependencies | |
| run: poetry lock | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| cache: poetry | |
| - name: Install Dependencies using Poetry | |
| run: poetry install | |
| - name: Check code | |
| run: poetry run flake8 | |
| testing: | |
| runs-on: ubuntu-latest | |
| services: | |
| mysql: | |
| image: mysql:8.0 | |
| env: | |
| MYSQL_ROOT_PASSWORD: root | |
| ports: | |
| - "8888:3306" | |
| options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: koesterlab/setup-slurm-action@v1 | |
| - name: Setup drmaa | |
| run: | | |
| sudo add-apt-repository ppa:natefoo/slurm-drmaa | |
| sudo apt-get update | |
| sudo apt-get install -y slurm-drmaa1 gridengine-drmaa1.0 gridengine-drmaa-dev slurm-drmaa-dev | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| - name: Install poetry | |
| run: pip install poetry | |
| - name: Determine dependencies | |
| run: poetry lock | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| cache: poetry | |
| - name: Install Dependencies using Poetry | |
| run: poetry install | |
| - name: Run pytest | |
| run: poetry run coverage run -m pytest tests/tests.py | |
| - name: Run Coverage | |
| run: poetry run coverage report -m |