Python dependency checks #310
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| name: Python dependency checks | |
| # This workflow is intended to check that the latest release of the `cellxgene-census` package | |
| # continues to function correctly using the latest upstream dependencies. | |
| # | |
| # Method: | |
| # 1. Check out the repo at the latest release tag | |
| # 2. Install latest cellxgene-census package from pypi | |
| # 3. Verify versions match | |
| # 4. Run tests from the repo | |
| on: | |
| schedule: | |
| - cron: "30 1 * * *" | |
| workflow_dispatch: # used for debugging or manual validation | |
| jobs: | |
| python-dependency-check: | |
| name: python-dependency-check | |
| strategy: | |
| fail-fast: false # don't fail-fast, as errors are often specific to a single cell in the matrix | |
| matrix: | |
| os: [single-cell-8c64g-runner, macos-latest] | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| exclude: | |
| - os: macos-latest | |
| python-version: "3.8" | |
| runs-on: ${{matrix.os}} | |
| steps: | |
| - name: install tooling | |
| if: matrix.os == 'single-cell-8c64g-runner' | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y jq | |
| - name: get latest release with tag | |
| id: latestrelease | |
| run: | | |
| echo "releasetag=$(curl --header 'authorization: Bearer ${{ secrets.GITHUB_TOKEN }}' --silent https://api.github.com/repos/chanzuckerberg/cellxgene-census/releases/latest | jq '.tag_name' | sed 's/\"//g')" >> "$GITHUB_OUTPUT" | |
| - name: confirm release tag | |
| run: | | |
| # REST api sometimes returns a release tag of "null" | |
| if [ -z "${{ steps.latestrelease.outputs.releasetag }}" ] || [ "${{ steps.latestrelease.outputs.releasetag }}" = "null" ]; then | |
| echo Unable to fetch latest release tag! | |
| exit 1 | |
| fi | |
| echo Latest GH release tag ${{ steps.latestrelease.outputs.releasetag }} | |
| - name: checkout latest release of repo | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ steps.latestrelease.outputs.releasetag }} | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies (including experimental) | |
| run: | | |
| python -m pip install -U pip setuptools wheel | |
| pip install --use-pep517 accumulation-tree # Geneformer dependency needs --use-pep517 for Cython | |
| GIT_CLONE_PROTECTION_ACTIVE=false pip install -U -r ./api/python/cellxgene_census/scripts/requirements-dev.txt | |
| pip install -U cellxgene-census[experimental] | |
| # dump pip config for logs | |
| pip freeze | |
| LATEST_RELEASE_TAG=$(echo "${{ steps.latestrelease.outputs.releasetag }}" | sed 's/^.//') | |
| echo LATEST_RELEASE_TAG="$LATEST_RELEASE_TAG" | |
| LATEST_PYPI_RELEASE=$(pip freeze | grep cellxgene-census | sed 's/^.*\=\=//') | |
| echo LATEST_PYPI_RELEASE="$LATEST_PYPI_RELEASE" | |
| if [ "$LATEST_PYPI_RELEASE" != "$LATEST_RELEASE_TAG" ]; then | |
| echo Github and PyPi latest release tags do not match. | |
| echo Latest PyPi release: "$LATEST_PYPY_RELEASE" | |
| echo Latest GH release: "$LATEST_RELEASE_TAG" | |
| exit 1 | |
| else | |
| echo Release tags match | |
| fi | |
| - name: Test with pytest | |
| run: | | |
| PYTHONPATH=. pytest -v -rP --experimental ./api/python/cellxgene_census/tests/ |