Repro spurious DoesNotExistError #55
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| name: Test cellxgene_census_builder/tests/test_builder.py | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| runs-on: | |
| description: 'Select a runner ("macos-latest" = Intel, "macos-latest-xlarge" = M1)' | |
| default: ubuntu-latest | |
| type: choice | |
| options: | |
| - macos-latest | |
| - macos-latest-xlarge | |
| - ubuntu-latest | |
| # - windows-latest | |
| ref: | |
| description: 'TileDB-SOMA branch or tag clone/install/test (leave blank to install latest version from PyPI)' | |
| default: 'main' | |
| checkout: | |
| description: 'Checkout TileDB-SOMA at this commit or ref' | |
| jobs: | |
| build: | |
| name: Test ${{ inputs.checkout || inputs.ref || 'main' }} | |
| runs-on: ${{ inputs.runs-on || 'ubuntu-latest' }} | |
| steps: | |
| - name: 'Debug: `github` context' | |
| run: echo "${{ toJSON(github.event) }}" | |
| - name: Clone census | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: chanzuckerberg/cellxgene-census | |
| ref: main | |
| path: census | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11.8 | |
| - name: Install cellxgene_census_builder | |
| run: | | |
| pip install -e census/tools/cellxgene_census_builder | |
| pip list | |
| python -c 'import cellxgene_census_builder' | |
| - name: Clone TileDB-SOMA@${{ inputs.ref || 'main' }} | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: single-cell-data/TileDB-SOMA | |
| ref: ${{ inputs.ref || 'main' }} | |
| fetch-depth: ${{ inputs.checkout == '' && 1 || 0 }} | |
| path: tiledbsoma | |
| - name: Checkout ${{ inputs.checkout }} | |
| if: inputs.checkout != '' | |
| working-directory: tiledbsoma | |
| run: | | |
| git checkout ${{ inputs.checkout }} | |
| git log -1 | |
| - name: Install TileDB-SOMA | |
| run: pip install -e tiledbsoma/apis/python pytest | |
| - name: Show package versions | |
| run: | | |
| uname -a | |
| pip list | |
| python -c 'import tiledbsoma; tiledbsoma.show_package_versions()' | |
| python tiledbsoma/scripts/show-versions.py | |
| - name: Run census test | |
| working-directory: census/tools/cellxgene_census_builder | |
| run: pytest tests/test_builder.py |