feat: remove pysam and bwa warmup hack #170
Workflow file for this run
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| name: tests | |
| on: | |
| push: | |
| branches: | |
| - "**" | |
| tags: | |
| - "!**" | |
| workflow_call: | |
| env: | |
| POETRY_VERSION: 1.8.2 | |
| jobs: | |
| Tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| PYTHON_VERSION: ["3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Checkout fulcrumgenomics/bwa | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: fulcrumgenomics/bwa | |
| ref: interactive_aln | |
| path: bwa | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.PYTHON_VERSION }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.PYTHON_VERSION }} | |
| - name: Set up miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| channels: conda-forge,bioconda | |
| activate-environment: prymer | |
| environment-file: prymer.yml | |
| channel-priority: true | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| python-version: ${{ matrix.PYTHON_VERSION }} | |
| - name: Install fulcrumgenomics/bwa | |
| shell: bash -l {0} | |
| run: | | |
| conda activate prymer | |
| pushd bwa | |
| make -j $(nproc) | |
| cp bwa ${CONDA_PREFIX}/bin | |
| popd | |
| - name: Configure poetry and check lock file | |
| shell: bash -l {0} | |
| run: | | |
| conda activate prymer | |
| poetry config virtualenvs.in-project false | |
| poetry check --lock | |
| - name: Poetry install | |
| shell: bash -l {0} | |
| run: | | |
| conda activate prymer | |
| poetry lock --no-update | |
| poetry install --with dev | |
| - name: Unit tests (with doctest and coverage) | |
| shell: bash -l {0} | |
| run: | | |
| conda activate prymer | |
| poetry run pytest --cov=prymer --cov-report=xml --cov-branch --doctest-plus --doctest-modules prymer tests | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/[email protected] | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Style checking | |
| shell: bash -l {0} | |
| run: | | |
| conda activate prymer | |
| poetry run ruff format --check | |
| - name: Run lint | |
| shell: bash -l {0} | |
| run: | | |
| conda activate prymer | |
| poetry run ruff check | |
| - name: Run mypy | |
| shell: bash -l {0} | |
| run: | | |
| conda activate prymer | |
| poetry run mypy | |
| - name: Run docs | |
| shell: bash -l {0} | |
| run: | | |
| conda activate prymer | |
| set -euo pipefail | |
| poetry run mkdocs build --strict |