update rank_genes_groups #2729
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| name: GPU Tests | |
| on: | |
| workflow_dispatch: | |
| issue_comment: | |
| types: [created] | |
| push: | |
| branches: [main] | |
| pull_request: | |
| types: | |
| - 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.event.issue.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| set-pending: | |
| name: GPU Tests Pending | |
| if: github.event_name == 'pull_request' | |
| runs-on: ubuntu-latest | |
| permissions: | |
| statuses: write | |
| steps: | |
| - name: Set pending status on PR | |
| run: | | |
| for context in "CI-Pass" "All Tests Green"; do | |
| gh api repos/${{ github.repository }}/statuses/${{ github.event.pull_request.head.sha }} \ | |
| -f state=pending \ | |
| -f context="$context" \ | |
| -f description="Waiting for /test-gpu command..." | |
| done | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| check: | |
| runs-on: ubuntu-latest | |
| # Skip pull_request (handled by set-pending) and issue_comment unless /test-gpu | |
| if: >- | |
| github.event_name != 'pull_request' && ( | |
| github.event_name != 'issue_comment' || | |
| (github.event.issue.pull_request && startsWith(github.event.comment.body, '/test-gpu')) | |
| ) | |
| outputs: | |
| head-sha: ${{ steps.get-sha.outputs.sha }} | |
| permissions: | |
| pull-requests: write | |
| statuses: write | |
| steps: | |
| - name: Check permissions | |
| if: github.event_name == 'issue_comment' || github.event_name == 'workflow_dispatch' | |
| run: | | |
| PERMISSION=$(gh api repos/${{ github.repository }}/collaborators/${{ github.actor }}/permission --jq '.permission') | |
| if [[ "$PERMISSION" != "admin" && "$PERMISSION" != "maintain" ]]; then | |
| echo "::error::Only maintainers or admins can trigger this workflow. Your permission: $PERMISSION" | |
| exit 1 | |
| fi | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: React to comment | |
| if: github.event_name == 'issue_comment' | |
| run: | | |
| gh api repos/${{ github.repository }}/issues/comments/${{ github.event.comment.id }}/reactions -f content=rocket | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Get PR head SHA | |
| id: get-sha | |
| if: github.event_name == 'issue_comment' | |
| run: | | |
| SHA=$(gh pr view ${{ github.event.issue.number }} --repo ${{ github.repository }} --json headRefOid -q .headRefOid) | |
| echo "sha=$SHA" >> $GITHUB_OUTPUT | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set pending status on PR | |
| if: github.event_name == 'issue_comment' | |
| run: | | |
| for context in "CI-Pass" "All Tests Green"; do | |
| gh api repos/${{ github.repository }}/statuses/${{ steps.get-sha.outputs.sha }} \ | |
| -f state=pending \ | |
| -f context="$context" \ | |
| -f description="GPU tests running..." \ | |
| -f target_url="${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| done | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| get-envs: | |
| runs-on: ubuntu-latest | |
| needs: check | |
| outputs: | |
| stable-dev: ${{ steps.get-envs.outputs.stable-dev }} | |
| prerelease: ${{ steps.get-envs.outputs.prerelease }} | |
| steps: | |
| - uses: actions/checkout@v6 | |
| with: | |
| filter: blob:none | |
| fetch-depth: 0 | |
| ref: ${{ github.event_name == 'issue_comment' && format('refs/pull/{0}/head', github.event.issue.number) || '' }} | |
| - uses: astral-sh/setup-uv@v6 | |
| with: | |
| enable-cache: false | |
| - id: get-envs | |
| run: | | |
| # Stable and dev environments | |
| STABLE_DEV_JSON=$(uvx hatch env show --json | jq -c ' | |
| to_entries | |
| | map( | |
| select(.key | startswith("hatch-test") and endswith("12") and (contains("prerelease") | not)) | |
| | { | |
| name: .key, | |
| python: .value.python | sub("3[.]13"; "3.13.3"), | |
| } | |
| )') | |
| echo "stable-dev=${STABLE_DEV_JSON}" | tee -a $GITHUB_OUTPUT | |
| # Prerelease environments | |
| PRERELEASE_JSON=$(uvx hatch env show --json | jq -c ' | |
| to_entries | |
| | map( | |
| select(.key | startswith("hatch-test") and endswith("12") and contains("prerelease")) | |
| | { | |
| name: .key, | |
| python: .value.python | sub("3[.]13"; "3.13.3"), | |
| } | |
| )') | |
| echo "prerelease=${PRERELEASE_JSON}" | tee -a $GITHUB_OUTPUT | |
| test-stable-dev: | |
| name: Test (${{ matrix.env.name }}) | |
| needs: get-envs | |
| runs-on: cirun-aws-gpu | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| env: ${{ fromJson(needs.get-envs.outputs.stable-dev) }} | |
| env: | |
| ENV_NAME: ${{ matrix.env.name }} | |
| steps: | |
| - uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 0 | |
| filter: blob:none | |
| ref: ${{ github.event_name == 'issue_comment' && format('refs/pull/{0}/head', github.event.issue.number) || '' }} | |
| - uses: astral-sh/setup-uv@v6 | |
| with: | |
| python-version: ${{ matrix.env.python }} | |
| - name: Install dependencies | |
| run: uvx hatch -v env create ${{ matrix.env.name }} | |
| - name: Run tests | |
| run: | | |
| mkdir -p test-data | |
| if [[ "${{ matrix.env.name }}" == *"stable"* ]]; then | |
| uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes | |
| uvx hatch run ${{ matrix.env.name }}:coverage xml | |
| uvx hatch run ${{ matrix.env.name }}:cov-report | |
| else | |
| uvx hatch run ${{ matrix.env.name }}:run -v --color=yes | |
| fi | |
| - name: Upload test results | |
| if: ${{ !cancelled() && contains(matrix.env.name, 'stable') }} | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| report_type: test_results | |
| files: test-data/test-results.xml | |
| use_oidc: false | |
| fail_ci_if_error: false | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Upload coverage data | |
| if: contains(matrix.env.name, 'stable') | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| files: test-data/coverage.xml | |
| use_oidc: false | |
| fail_ci_if_error: false | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| test-prerelease: | |
| name: Test (${{ matrix.env.name }}) | |
| needs: get-envs | |
| runs-on: cirun-aws-gpu | |
| timeout-minutes: 30 | |
| continue-on-error: true # Prerelease failures don't fail the workflow | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| env: ${{ fromJson(needs.get-envs.outputs.prerelease) }} | |
| env: | |
| ENV_NAME: ${{ matrix.env.name }} | |
| steps: | |
| - uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 0 | |
| filter: blob:none | |
| ref: ${{ github.event_name == 'issue_comment' && format('refs/pull/{0}/head', github.event.issue.number) || '' }} | |
| - uses: astral-sh/setup-uv@v6 | |
| with: | |
| python-version: ${{ matrix.env.python }} | |
| - name: Install dependencies | |
| run: uvx hatch -v env create ${{ matrix.env.name }} | |
| - name: Run tests | |
| run: uvx hatch run ${{ matrix.env.name }}:run -v --color=yes | |
| stable-dev-green: | |
| name: CI-Pass | |
| if: always() && github.event_name != 'pull_request' | |
| needs: | |
| - check | |
| - get-envs | |
| - test-stable-dev | |
| runs-on: ubuntu-latest | |
| permissions: | |
| statuses: write | |
| steps: | |
| - uses: re-actors/alls-green@release/v1 | |
| with: | |
| jobs: ${{ toJSON(needs) }} | |
| - name: Set success status on PR | |
| if: success() && github.event_name == 'issue_comment' | |
| run: | | |
| gh api repos/${{ github.repository }}/statuses/${{ needs.check.outputs.head-sha }} \ | |
| -f state=success \ | |
| -f context="CI-Pass" \ | |
| -f description="GPU tests passed" \ | |
| -f target_url="${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set failure status on PR | |
| if: failure() && github.event_name == 'issue_comment' | |
| run: | | |
| gh api repos/${{ github.repository }}/statuses/${{ needs.check.outputs.head-sha }} \ | |
| -f state=failure \ | |
| -f context="CI-Pass" \ | |
| -f description="GPU tests failed" \ | |
| -f target_url="${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| all-green: | |
| name: All Tests Green | |
| if: always() && github.event_name != 'pull_request' | |
| needs: | |
| - check | |
| - get-envs | |
| - test-stable-dev | |
| - test-prerelease | |
| runs-on: ubuntu-latest | |
| permissions: | |
| statuses: write | |
| steps: | |
| - uses: re-actors/alls-green@release/v1 | |
| with: | |
| allowed-failures: test-prerelease | |
| jobs: ${{ toJSON(needs) }} | |
| - name: Set success status on PR | |
| if: success() && github.event_name == 'issue_comment' | |
| run: | | |
| gh api repos/${{ github.repository }}/statuses/${{ needs.check.outputs.head-sha }} \ | |
| -f state=success \ | |
| -f context="All Tests Green" \ | |
| -f description="All GPU tests passed" \ | |
| -f target_url="${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set failure status on PR | |
| if: failure() && github.event_name == 'issue_comment' | |
| run: | | |
| gh api repos/${{ github.repository }}/statuses/${{ needs.check.outputs.head-sha }} \ | |
| -f state=failure \ | |
| -f context="All Tests Green" \ | |
| -f description="GPU tests failed" \ | |
| -f target_url="${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}" | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} |