compatibility_tests.yml

name: Compatibility Tests

on:
  schedule:
    - cron: "0 8 7 * 2"
  push:
    branches:
      - main
  # DEBUG
  # DEBUG
  # DEBUG
  pull_request:
    branches: "*"

env:
  JEST_ENV: prod

jobs:
  docker-build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        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:${{ matrix.python-version }} anndata:${{ '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-13]
        python-version: ["3.10", "3.11"]
        cellxgene_build: [main, latest]
        # add anndata pinned version test for subset of matrix configurations,
        # in order to reduce matrix cross-product explosion
        include:
          - python-version: 3.10
            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: "==0.10.9"
    steps:
      - uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        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@v2
        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: ${{ runner.os }}-brew-
      - name: Install dependencies (Ubuntu Linux)
        if: startsWith(matrix.os, 'ubuntu')
        run: |
          sudo apt-get update
          sudo apt-get install -y libhdf5-serial-dev
      - name: Install dependencies (MacOS)
        if: startsWith(matrix.os, 'macos')
        run: brew install hdf5
      - name: Install cellxgene from `main` branch
        if: matrix.cellxgene_build == 'main'
        run: |
          pip install -r server/requirements-dev.txt
          make pydist install-dist
      - name: Install cellxgene from latest release (pypi.org)
        if: matrix.cellxgene_build == 'latest'
        run: |
          pip install --upgrade cellxgene
          # install the additional dev requirements on top of what is in the
          # cellxgene pip package, which are needed for testing, but otherwise
          # keep same pip pkg versions as in the cxg release
          sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
          pip install -r server/requirements-dev.txt
          pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas
      # - name: Install anndata version per matrix variable
      #   run: pip install anndata${{ matrix.anndata_version }}
      # - name: Update Flatbuffers
      #   if: matrix.python-version == '3.12'
      #   run: pip install --upgrade flatbuffers
      - name: Install node
        run: make dev-env-client
      - name: Install Chromium
        run: |
          sudo apt-get update
          sudo apt-get install -y wget
          wget https://commondatastorage.googleapis.com/chromium-browser-snapshots/Linux_x64/901912/chrome-linux.zip
          unzip chrome-linux.zip
          sudo mv chrome-linux/chrome /usr/bin/chrome
        env:
          PUPPETEER_EXECUTABLE_PATH: /usr/bin/chrome
      # 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