fix: update markdown images #1055
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| name: Compatibility Tests | |
| on: | |
| schedule: | |
| - cron: "0 8 7 * 2" | |
| push: | |
| branches: | |
| - main | |
| # For debug - uncomment below to run on all PRs | |
| pull_request: | |
| branches: "*" | |
| env: | |
| JEST_ENV: prod | |
| jobs: | |
| docker-build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| 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-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: 3.11 | |
| 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@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| 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@v4 | |
| with: | |
| path: ${{ env.PIP_CACHE }} | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Node cache | |
| uses: actions/cache@v4 | |
| 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@v4 | |
| 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: 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 |