add docs for container #199
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: [push,pull_request] | |
| jobs: | |
| tests: | |
| name: "Python ${{ matrix.python-version }}" | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| matrix: | |
| os: [macos-latest, ubuntu-latest] | |
| python-version: ["3.9"] | |
| steps: | |
| - uses: "actions/checkout@v3" | |
| with: | |
| fetch-depth: 0 | |
| # Setup env | |
| - uses: "conda-incubator/setup-miniconda@v2" | |
| with: | |
| activate-environment: pharokka_env | |
| environment-file: environment.yml | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: strict | |
| auto-update-conda: true | |
| - name: Install pharokka | |
| shell: bash -l {0} | |
| run: | | |
| mamba install python=${{ matrix.python-version }} | |
| python -m pip install --upgrade pip | |
| pip install -e . | |
| - name: Run tests and collect coverage | |
| run: pytest --cov=./ --cov-report=xml | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |