update GitHub Actions workflow to test Wipertools and collect coverage #149
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| name: Test code | |
| on: [pull_request, push] | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] # , macos-latest, windows-latest | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: "3.10" | |
| name: Test Wipertools | |
| steps: | |
| - uses: actions/checkout@v4 | |
| name: Clone repository | |
| - name: Install Miniconda (Mambaforge) | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: true | |
| show-channel-urls: true | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ env.PYTHON }} | |
| environment-file: .devcontainer/environment.yml | |
| - name: Run tests and collect coverage | |
| shell: bash -el {0} | |
| run: pytest --pyargs ./tests --cov-config=.coveragerc --cov=./wipertools --cov-report=xml | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| env_vars: OS,PYTHON | |
| files: ./coverage.xml # optional | |
| flags: pytest # optional | |
| name: codecov-umbrella # optional | |
| fail_ci_if_error: true # optional (default = false) | |
| verbose: true # optional (default = false) |