cellxgene/.github/workflows/compatibility_tests.yml

name: Compatibility Tests

on:
  schedule:
    - cron: '0 8 7 * 2'
  push:
    branches:
      - master

env:
  JEST_ENV: prod

jobs:
  docker-build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v1
        with:
          python-version: ${{ matrix.python-version }}
      - name: Build docker image
        run: docker build .

  cellxgene-master-with-python-and-anndata-versions:
    name: python versions x anndata versions
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.6, 3.7, 3.8]
        anndata-version: [0.6.22.post1, 0.7.1]
        test-suite: [smoke-test, smoke-test-annotations]
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        # 1. only install the dev requirements on top of what is in the cellxgene pip package
        sudo apt-get update && sudo apt-get install -y libhdf5-serial-dev
        sed -i 's/-r requirements.txt//' server/requirements-dev.txt
        pip install -r server/requirements-dev.txt
        # 2. install cellxgene
        make pydist install-dist
        # 3. install anndata
        pip install anndata==${{ matrix.anndata-version }}
        # workaround for anndata 0.6.22.post1 bug
        [[ "0.6.22.post1" = "${{ matrix.anndata-version }}" ]] && pip install h5py==2.9.0 || true
    - name: Tests
      run: make unit-test ${{ matrix.test-suite }}

  cellxgene-release-with-anndata-master:
    name: cellxgene release with anndata master
    runs-on: ubuntu-latest
    strategy:
      matrix:
        test-suite: [smoke-test, smoke-test-annotations]
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python 3.7
        uses: actions/setup-python@v1
        with:
          python-version: 3.7
      - name: Checkout
        uses: actions/checkout@v2
        with:
          path: cellxgene
      - name: Checkout tools repo
        uses: actions/checkout@v2
        with:
          repository: theislab/anndata
          path: anndata
      - name: Install dependencies
        run: |
          cd cellxgene
          # 1. only install the dev requirements on top of what is in the cellxgene pip package
          make dev-env-client
          sed -i 's/-r requirements.txt//' server/requirements-dev.txt
          pip install -r server/requirements-dev.txt
          # 2. install cellxgene
          pip install --upgrade cellxgene
          # 3. install anndata
          cd ../anndata && pip install -e .
      - name: Tests
        run: cd cellxgene && make unit-test ${{ matrix.test-suite }}

  cellxgene-master-with-anndata-master:
    name: cellxgene master with anndata master
    runs-on: ubuntu-latest
    strategy:
      matrix:
        test-suite: [smoke-test, smoke-test-annotations]
    steps:
      - uses: actions/checkout@v2
      - name: Set up Python 3.7
        uses: actions/setup-python@v1
        with:
          python-version: 3.7
      - name: Checkout
        uses: actions/checkout@v2
        with:
          path: cellxgene
      - name: Checkout tools repo
        uses: actions/checkout@v2
        with:
          repository: theislab/anndata
          path: anndata
      - name: Install dependencies
        run: |
          cd cellxgene
          sed -i -E 's/^anndata[>=]=[0-9]+.[0-9]+.[0-9]+$/anndata/g' server/requirements.txt
          make pydist install-dist dev-env
          cd ../anndata
          pip install -e .
      - name: Tests
        run: cd cellxgene && make unit-test ${{ matrix.test-suite }}