Added error free BAMs, optimized read processing and functions #58
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - ".github/workflows/unit-tests.yml" | |
| - "tests/**" | |
| - "mess/**" | |
| - "setup.py" | |
| - "!.github/workflows/build-docs.yml" | |
| - "!docs/**" | |
| - "!mkdocs.yml" | |
| - "!README.md" | |
| pull_request: | |
| paths: | |
| - ".github/workflows/unit-tests.yml" | |
| - "tests/**" | |
| - "mess/**" | |
| - "setup.py" | |
| - "!.github/workflows/build-docs.yml" | |
| - "!docs/**" | |
| - "!mkdocs.yml" | |
| - "!README.md" | |
| permissions: | |
| contents: read | |
| jobs: | |
| tests: | |
| name: "Python ${{ matrix.python-version }} on ${{ matrix.os }}" | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup apptainer | |
| uses: eWaterCycle/[email protected] | |
| - name: Setup MeSS environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: mess | |
| python-version: ${{ matrix.python-version }} | |
| auto-update-conda: true | |
| - name: Install MeSS and pytest-cov | |
| run: | | |
| pip install -e . | |
| pip install pytest coverage | |
| - name: Run tests on ${{ matrix.os }} for python ${{ matrix.python-version }} | |
| run: | | |
| coverage run -m pytest |