Fix tests #167
Workflow file for this run
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| 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 |