cellxgene/.github/workflows/compatibility_tests.yml

name: Compatibility Tests

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

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 .

  matrix-compatibility-test:
    name: cxg:${{ matrix.cellxgene_build }} os:${{ matrix.os }} py:${{ matrix.python-version }} anndata:${{ matrix.anndata_version || 'latest' }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        # note: The `macos-latest` is latest Catalina version, and not Big Sur. So we explicitly ask for Big Sur (`macos-11`)
        os: [ubuntu-latest, macos-latest, macos-11]
        python-version: [3.6, 3.7, 3.8, 3.9]
        cellxgene_build: [main, latest]
        exclude:
          # 3.6 no longer avail on Big Sur (`macos-11`)
          - os: macos-11
            python-version: 3.6
          # no pypi build exists for macos+py3.9 and source install fails to
          # install `tables` py pkg (a `scanpy` dependency), so we test py3.9
          # only on ubuntu
          - os: macos-11
            python-version: 3.9
          - os: macos-latest
            python-version: 3.9
        # add anndata pinned version test for subset of matrix configurations,
        # in order to reduce matrix cross-product explosion
        include:
          - python-version: 3.8
            cellxgene_build: latest
            # TODO: dynamically use the literal version in requirements.txt,
            # to avoid having to update this in manually in the future
            # TODO: Do not bother running this if anndata latest version
            # matches this pinned version, to avoid a redundant test
            anndata_version: '==0.7.6'
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Cache env vars
      run: echo "PIP_CACHE=`python -m pip cache dir`" >> $GITHUB_ENV
    - name: Cache env vars (MacOS)
      if: startsWith(matrix.os, 'macos')
      run: echo "BREW_CACHE=`brew --cache`" >> $GITHUB_ENV
    # FIXME: Only working for Linux
    - name: Python cache
      uses: actions/cache@v1
      with:
        path: ${{ env.PIP_CACHE }}
        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
        restore-keys: |
          ${{ runner.os }}-pip-
    - name: Node cache
      uses: actions/cache@v1
      with:
        path: ~/.npm
        key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
        restore-keys: |
          ${{ runner.os }}-node-
    - name: Brew cache (MacOS)
      if: startsWith(matrix.os, 'macos')
      uses: actions/cache@v1
      with:
        path: ${{ env.BREW_CACHE }}
        key: ${{ runner.os }}-brew-
    - name: Install dependencies (Ubuntu Linux)
      if: startsWith(matrix.os, 'ubuntu')
      run: |
        sudo apt-get update
        sudo apt-get install -y libhdf5-serial-dev
    - name: Install dependencies (MacOS)
      if: startsWith(matrix.os, 'macos')
      run: brew install hdf5
    - name: Install cellxgene from `main` branch
      if: matrix.cellxgene_build == 'main'
      run: |
        pip install -r server/requirements-dev.txt
        make pydist install-dist
    - name: Install cellxgene from latest release (pypi.org)
      if: matrix.cellxgene_build == 'latest'
      run: |
        pip install --upgrade cellxgene
        # install the additional dev requirements on top of what is in the
        # cellxgene pip package, which are needed for testing, but otherwise
        # keep same pip pkg versions as in the cxg release
        sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
        pip install -r server/requirements-dev.txt
    - name: Install anndata version per matrix variable
      run: pip install anndata${{ matrix.anndata_version }}
    - name: Install node
      run: make dev-env-client
    # Run different types of test separately, to facilitate troubleshooting
    - name: Unit Tests - client
      run: make unit-test-client
    - name: Unit Tests - server
      run: make unit-test-server
    - name: Smoke Tests
      run: make smoke-test
    # FIXME: Fails intermittently. See https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/chanzuckerberg/cellxgene/2415
    # - name: Smoke Tests with Annotations
    #   run: make smoke-test-annotations