[pre-commit.ci] pre-commit autoupdate (#135) #143
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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 } | |
- { name: "3.10", os: ubuntu-latest, python: "3.10", r: release } | |
- { name: "3.9", os: ubuntu-latest, python: "3.9", r: release } | |
- { name: "3.8", os: ubuntu-latest, python: "3.8", r: oldrel } | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- 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 | |
- 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 |