fix phanotate env #160
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| 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 }} |