Mixscape reproducibility #842
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |