Custom dataloader registry support #37
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| name: test (custom dataloaders) | |
| on: | |
| push: | |
| branches: [main, "[0-9]+.[0-9]+.x"] | |
| pull_request: | |
| branches: [main, "[0-9]+.[0-9]+.x"] | |
| types: [labeled, synchronize, opened] | |
| schedule: | |
| - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| # if PR has label "custom_dataloader" or "all tests" or if scheduled or manually triggered | |
| if: >- | |
| ( | |
| contains(github.event.pull_request.labels.*.name, 'custom_dataloader') || | |
| contains(github.event.pull_request.labels.*.name, 'all tests') || | |
| contains(github.event_name, 'schedule') || | |
| contains(github.event_name, 'workflow_dispatch') | |
| ) | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -e {0} # -e to fail on error | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python: ["3.11"] | |
| name: integration | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: "pip" | |
| cache-dependency-path: "**/pyproject.toml" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel uv | |
| python -m uv pip install --system "scvi-tools[tests] @ ." | |
| python -m pip install tiledbsoma | |
| python -m pip install s3fs | |
| python -m pip install torchdata | |
| python -m pip install psutil | |
| python -m pip install cellxgene-census | |
| python -m pip install lamindb | |
| python -m pip install bionty | |
| - name: Install Specific Branch of Repository | |
| env: | |
| GH_TOKEN: ${{ secrets.GH_TOKEN }} | |
| run: | | |
| git config --global url."https://${GH_TOKEN}:[email protected]/".insteadOf "https://github.com/" | |
| git clone --single-branch --branch ebezzi/census-scvi-datamodule https://github.com/ori-kron-wis/cellxgene-census.git | |
| git clone --single-branch --branch main https://github.com/jkobject/scDataLoader.git | |
| - name: Run specific custom dataloader pytest | |
| env: | |
| MPLBACKEND: agg | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| COLUMNS: 120 | |
| run: | | |
| coverage run -m pytest tests/dataloaders/test_custom_dataloader.py -v --color=yes --custom-dataloader-tests | |
| coverage report | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |