[pre-commit.ci] pre-commit autoupdate #259
Workflow file for this run
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: | |
| 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: ubuntu-latest | |
| if: "!contains(github.event.head_commit.message, 'ci skip')" | |
| env: | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - python: "3.12" | |
| r: release | |
| bioc: "3.19" | |
| - python: "3.9" | |
| r: oldrel | |
| 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 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.config.python }} | |
| cache: pip | |
| - id: setup-r | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| use-public-rspm: true # compiled packages from posit | |
| - name: Install python tools | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install --upgrade build | |
| - name: Set up rpy2 | |
| run: | | |
| pip install rpy2 | |
| echo "LD_LIBRARY_PATH=$(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 | |
| ${{ matrix.config.r == 'oldrel' && 'cran::[email protected]' || '' }} | |
| 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 |