(fix): add compatibility for anndata with sparse_dataset #326
Workflow file for this run
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| name: AWS GPU | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| types: | |
| - labeled | |
| - opened | |
| - synchronize | |
| # Cancel the job if new commits are pushed | |
| # https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| # There are two jobs: | |
| # 1. `check` determines if the second job (`test`) will be run (through a job dependency). | |
| # 2. `test` runs on an AWS runner and executes the GPU tests. | |
| jobs: | |
| # If the `skip-gpu-ci` label is set, this job is skipped, and consequently the `test` job too. | |
| # If the `run-gpu-ci` label is set or we reacted to a `push` event, this job succeeds (and `test` is run). | |
| # If neither is set, this job fails, `test` is skipped, and the whole workflow fails. | |
| check: | |
| name: "Triage: Check if GPU tests are allowed to run" | |
| if: (!contains(github.event.pull_request.labels.*.name, 'skip-gpu-ci')) | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: flying-sheep/check@v1 | |
| with: | |
| success: ${{ github.event_name == 'push' || contains(github.event.pull_request.labels.*.name, 'run-gpu-ci') }} | |
| # If `check` wasn’t skipped or failed, start an AWS runner and run the GPU tests on it. | |
| test: | |
| name: GPU Tests | |
| needs: check | |
| runs-on: "cirun-aws-gpu--${{ github.run_id }}" | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Nvidia SMI sanity check | |
| run: nvidia-smi | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| micromamba-version: "1.3.1-0" | |
| environment-name: anndata-gpu-ci | |
| create-args: >- | |
| python=3.11 | |
| cupy | |
| numba | |
| pytest | |
| pytest-cov | |
| pytest-xdist | |
| init-shell: >- | |
| bash | |
| generate-run-shell: false | |
| - name: Install AnnData | |
| run: pip install .[dev,test,gpu] | |
| - name: Mamba list | |
| run: micromamba list | |
| - name: Run test | |
| run: pytest -m gpu --cov --cov-report=xml --cov-context=test -n 4 | |
| - uses: codecov/codecov-action@v3 | |
| with: | |
| flags: gpu-tests |