Bump actions/checkout from 6 to 7 (#285) #501
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| name: Unit Tests | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| run_tester: | |
| runs-on: ubuntu-24.04 | |
| if: "!contains(github.event.head_commit.message, 'ci skip')" | |
| env: | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - python: "3.14" | |
| r: release | |
| - python: "3.11" | |
| r: oldrel | |
| steps: | |
| - uses: actions/checkout@v7 | |
| with: | |
| fetch-depth: 0 | |
| filter: blob:none | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| uses: awalsh128/cache-apt-pkgs-action@v1 | |
| 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@v6 | |
| with: | |
| python-version: ${{ matrix.config.python }} | |
| - uses: astral-sh/setup-uv@v7 | |
| - name: Install python tools | |
| run: uv tool install build | |
| - id: setup-r | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| use-public-rspm: true # compiled packages from posit | |
| - name: Set up rpy2 | |
| run: | | |
| uv pip install --system rpy2 | |
| echo "LD_LIBRARY_PATH=$(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 | |
| - name: Install anndata2ri | |
| run: | | |
| pyproject-build --installer=uv --wheel | |
| uv pip install --system --group=test $(ls -1 dist/anndata2ri*.whl) | |
| python -c "import anndata2ri" | |
| - name: Run tests | |
| run: pytest --verbose --color=yes | |
| check: | |
| if: always() | |
| needs: [run_tester] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: re-actors/alls-green@release/v1 | |
| with: | |
| jobs: ${{ toJSON(needs) }} |