run_tests.yml

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