[pre-commit.ci] pre-commit autoupdate (#157) #192
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: Unit Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - "*" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -e {0} # -e to fail on error | |
| jobs: | |
| run_tester: | |
| runs-on: ${{ matrix.config.os }} | |
| if: "!contains(github.event.head_commit.message, 'ci skip')" | |
| env: | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { | |
| name: "3.11", | |
| os: ubuntu-latest, | |
| python: "3.11", | |
| r: release, | |
| bioc: "3.18", | |
| } | |
| - { | |
| name: "3.10", | |
| os: ubuntu-latest, | |
| python: "3.10", | |
| r: release, | |
| bioc: "3.18", | |
| } | |
| - { | |
| name: "3.9", | |
| os: ubuntu-latest, | |
| python: "3.9", | |
| r: release, | |
| bioc: "3.18", | |
| } | |
| # Cannot test | |
| # - Python 3.12 because of numba | |
| # - R oldrel because of a bug in BiocFileCache that only got released to BioC 3.18+ | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| filter: blob:none | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| uses: awalsh128/cache-apt-pkgs-action@latest | |
| with: | |
| packages: pandoc gfortran libblas-dev liblapack-dev libedit-dev llvm-dev libcurl4-openssl-dev ffmpeg libhdf5-dev | |
| version: 1.0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.config.python }} | |
| cache: pip | |
| - name: Set up R | |
| id: setup-r | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - name: Install python tools | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install --upgrade build | |
| - name: Set up rpy2 | |
| run: | | |
| pip install rpy2 | |
| echo "LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):${LD_LIBRARY_PATH}" >> $GITHUB_ENV | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 1 # increment to bust cache | |
| packages: | | |
| bioc::SingleCellExperiment | |
| bioc::scRNAseq | |
| env: | |
| R_BIOC_VERSION: ${{ matrix.config.bioc }} | |
| - name: Install anndata2ri | |
| run: | | |
| python -m build --wheel | |
| pip install $(ls -1 dist/anndata2ri*.whl)[test] | |
| python -c "import anndata2ri" | |
| - name: Run tests | |
| run: pytest --verbose --color=yes |