(fix): cache arrays in BaseCompressedSparseDataset
#3198
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| name: AWS GPU | |
| on: | |
| push: | |
| branches: [main, "[0-9]+.[0-9]+.x"] | |
| 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 }}" | |
| # Setting a timeout of 30 minutes, as the AWS costs money | |
| # At time of writing, a typical run takes about 5 minutes | |
| timeout-minutes: 30 | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Nvidia SMI sanity check | |
| run: nvidia-smi | |
| - name: Install yq | |
| run: | | |
| sudo snap install yq | |
| - name: Extract max Python version from classifiers | |
| run: | | |
| classifiers=$(yq .project.classifiers pyproject.toml -oy | grep --only-matching --perl-regexp '(?<=Python :: )(\d\.\d+)') | |
| max_version=$(echo "$classifiers" | sort -V | tail -1) | |
| echo "max_python_version=$max_version" >> $GITHUB_ENV | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.max_python_version }} | |
| - name: Install UV | |
| uses: hynek/setup-cached-uv@v2 | |
| with: | |
| cache-dependency-path: pyproject.toml | |
| - name: Install AnnData | |
| run: uv pip install --system -e ".[dev,test,cu12]" llvmlite>=0.43 | |
| - name: Env list | |
| run: pip list | |
| - name: Run test | |
| run: pytest -m gpu --cov --cov-report=xml --cov-context=test | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| verbose: true | |
| - name: Remove 'run-gpu-ci' Label | |
| if: always() | |
| uses: actions-ecosystem/action-remove-labels@v1 | |
| with: | |
| labels: "run-gpu-ci" | |
| github_token: ${{ secrets.GITHUB_TOKEN }} |