Add plots for DE analysis and unify plotting API #799
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| name: Test | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -e {0} # -e to fail on error | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: ubuntu-latest | |
| python: "3.10" | |
| run_mode: "slow" | |
| - os: ubuntu-latest | |
| python: "3.12" | |
| run_mode: "slow" | |
| # - os: ubuntu-latest | |
| # python: "3.12" | |
| # run_mode: "fast" | |
| # - os: ubuntu-latest | |
| # python: "3.12" | |
| # run_mode: slow | |
| # pip-flags: "--pre" | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - uses: actions/checkout@v4 | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "4" | |
| - name: Install edgeR | |
| run: Rscript --vanilla -e "install.packages(c('BiocManager', 'statmod'), repos='https://cran.r-project.org'); library('BiocManager'); BiocManager::install('edgeR')" | |
| - name: Install test dependencies | |
| run: python -m pip install --upgrade uv wheel | |
| - name: Install dependencies | |
| run: | | |
| uv pip install --system rpy2 | |
| uv pip install --system ${{ matrix.pip-flags }} ".[dev,test,coda,de]" | |
| - name: Test | |
| env: | |
| MPLBACKEND: agg | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| run: | | |
| pytest_args="-m pytest -v --color=yes" | |
| if [ "${{ matrix.run_mode }}" = "slow" ]; then | |
| pytest_args="$pytest_args --runslow" | |
| fi | |
| coverage run $pytest_args | |
| - name: Show coverage report | |
| run: coverage report -m | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| verbose: true |