fasta output for list #166
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| name: Testing and Coverage | |
| on: [ push ] | |
| jobs: | |
| test: | |
| name: Test | |
| runs-on: ${{ matrix.os }}-latest | |
| strategy: | |
| max-parallel: 6 | |
| fail-fast: false | |
| matrix: | |
| # os: [ "ubuntu", "macos" ] | |
| # python-version: [ "3.10", "3.11", "3.12" ] | |
| os: [ "ubuntu" ] | |
| python-version: [ "3.10" ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| mamba-version: '*' | |
| use-mamba: true | |
| channels: conda-forge, defaults, bioconda | |
| channel-priority: true | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Install conda dependencies | |
| run: mamba install -c bioconda -y mafft | |
| - name: Install self with pip | |
| run: pip install . | |
| - name: Install test dependencies | |
| run: mamba install -c conda-forge -y pytest pytest-cov | |
| - name: Run tests | |
| run: pytest --cov=lXtractor --cov-branch --cov-report=xml:coverage-report-${{ matrix.python-version }}.xml | |
| - name: List files in the directory | |
| run: ls -l | |
| - name: Upload coverage data | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage-report-${{ matrix.python-version }} | |
| path: coverage-report-${{ matrix.python-version }}.xml | |
| publish-coverage: | |
| name: Publish Coverage | |
| needs: test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Download coverage data for Python 3.10 | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: coverage-report-3.10 | |
| path: . | |
| - name: Coveralls GitHub Action | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| file: ./coverage-report-3.10.xml |