working with bcr checkpoint #1744
Workflow file for this run
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| name: "BioNemo Image Build and Unit Tests" | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - "pull-request/[0-9]+" | |
| - "dependabot/**" | |
| merge_group: | |
| types: [checks_requested] | |
| schedule: | |
| - cron: "0 7 * * *" # Runs at 7 AM UTC daily (12 AM MST) | |
| defaults: | |
| run: | |
| shell: bash -x -e -u -o pipefail {0} | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| submodules: "recursive" | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: "pip" | |
| - run: pip install -r requirements-dev.txt | |
| - run: ./ci/scripts/static_checks.sh | |
| # With copy-pr-bot, we need to get the PR labels from the PR API rather than from the event metadata. | |
| get-pr-labels: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| labels: ${{ steps.get-labels.outputs.labels }} | |
| steps: | |
| - name: Get PR number from branch | |
| if: startsWith(github.ref, 'refs/heads/pull-request/') | |
| id: get-pr-num | |
| run: | | |
| PR_NUM=$(echo ${{ github.ref_name }} | grep -oE '[0-9]+$') | |
| echo "pr_num=$PR_NUM" >> $GITHUB_OUTPUT | |
| - name: Get PR labels | |
| id: get-labels | |
| if: startsWith(github.ref, 'refs/heads/pull-request/') | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| LABELS=$(gh api repos/${{ github.repository }}/pulls/${{ steps.get-pr-num.outputs.pr_num }} --jq '[.labels[].name]' || echo "[]") | |
| echo "labels=$LABELS" >> $GITHUB_OUTPUT | |
| - name: Set empty labels for non-PR branches | |
| if: ${{ !startsWith(github.ref, 'refs/heads/pull-request/') }} | |
| id: get-labels-empty | |
| run: echo "labels=[]" >> $GITHUB_OUTPUT | |
| build-bionemo-image: | |
| needs: | |
| - pre-commit | |
| - get-pr-labels | |
| runs-on: linux-amd64-cpu16 | |
| if: ${{ !contains(fromJSON(needs.get-pr-labels.outputs.labels || '[]'), 'SKIP_CI') }} | |
| steps: | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ vars.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: "recursive" | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Docker Metadata | |
| id: metadata | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: svcbionemo023/bionemo-framework | |
| tags: | | |
| type=schedule | |
| type=ref,event=branch | |
| type=ref,event=tag | |
| type=ref,event=pr | |
| type=raw,value=${{ github.run_id }} | |
| # This action sets up our cache-from and cache-to flags appropriately; see the README of this action for more | |
| # info. It doesn't seem to cache correctly for merge_group events, so we need to add that as an extra argument in | |
| # the step below. There's probably a slight optimization to be had here by caching from the pr- caches for | |
| # merge_group events. See https://github.com/int128/docker-build-cache-config-action/issues/1005 for more info. | |
| - uses: int128/docker-build-cache-config-action@v1 | |
| id: cache | |
| with: | |
| image: svcbionemo023/bionemo-build-cache | |
| - name: Build and push | |
| uses: docker/build-push-action@v5 | |
| with: | |
| push: true | |
| tags: ${{ steps.metadata.outputs.tags }} | |
| labels: ${{ steps.metadata.outputs.labels }} | |
| cache-from: | | |
| ${{ steps.cache.outputs.cache-from }} | |
| type=registry,ref=svcbionemo023/bionemo-build-cache:main | |
| cache-to: ${{ steps.cache.outputs.cache-to }} | |
| run-tests: | |
| needs: | |
| - build-bionemo-image | |
| - get-pr-labels | |
| runs-on: linux-amd64-gpu-l4-latest-1 | |
| container: | |
| image: svcbionemo023/bionemo-framework:${{ github.run_id }} | |
| credentials: | |
| username: ${{ vars.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Run tests | |
| # Tests in this stage generate code coverage metrics for the repository | |
| # Coverage data is uploaded to Codecov in subsequent stages | |
| env: | |
| BIONEMO_DATA_SOURCE: ngc | |
| run: ./ci/scripts/run_pytest.sh --no-nbval --skip-slow | |
| - name: Upload coverage to Codecov | |
| # Don't run coverage on merge queue or nightly CI to avoid duplicating reports | |
| # to codecov. See https://github.com/matplotlib/napari-matplotlib/issues/155 | |
| if: github.event_name != 'merge_group' && github.event_name != 'schedule' | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Upload test results to Codecov | |
| # Don't run coverage on merge queue or nightly CI to avoid duplicating reports | |
| # to codecov. See https://github.com/matplotlib/napari-matplotlib/issues/155 | |
| if: ${{ !cancelled() && github.event_name != 'merge_group' && github.event_name != 'schedule' }} | |
| uses: codecov/test-results-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| run-slow-tests: | |
| needs: | |
| - build-bionemo-image | |
| - get-pr-labels | |
| runs-on: linux-amd64-gpu-l4-latest-1 | |
| container: | |
| image: svcbionemo023/bionemo-framework:${{ github.run_id }} | |
| credentials: | |
| username: ${{ vars.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| if: | | |
| github.event_name == 'schedule' || github.event_name == 'merge_group' || | |
| contains(fromJSON(needs.get-pr-labels.outputs.labels || '[]'), 'INCLUDE_SLOW_TESTS') | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Run slow tests | |
| env: | |
| BIONEMO_DATA_SOURCE: ngc | |
| # Not every sub-package has slow tests, and since some sub-packages have tests under the same name we need | |
| # to run package by package like we do with the fast tests. | |
| run: ./ci/scripts/run_pytest.sh --no-nbval --only-slow --allow-no-tests | |
| run-notebooks-docs: | |
| needs: | |
| - build-bionemo-image | |
| - get-pr-labels | |
| runs-on: linux-amd64-gpu-l4-latest-1 | |
| if: | | |
| github.event_name == 'schedule' || github.event_name == 'merge_group' || | |
| contains(fromJSON(needs.get-pr-labels.outputs.labels || '[]'), 'INCLUDE_NOTEBOOKS_TESTS') | |
| container: | |
| image: svcbionemo023/bionemo-framework:${{ github.run_id }} | |
| credentials: | |
| username: ${{ vars.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Run notebook tests | |
| env: | |
| BIONEMO_DATA_SOURCE: ngc | |
| # this variable should be used in the notebooks to run a subset of the model layers or a smaller model/dataset | |
| FAST_CI_MODE: true | |
| run: | | |
| pytest -v --nbval-lax -p no:python docs/ sub-packages/ | |
| verify-tests-status: | |
| # Base on the status of this job, the unit-tests workflow succeeds or fails | |
| # This steps checks the status of all test jobs and fails if any of them failed or were cancelled. | |
| # It is a workaround for the lack of a built-in feature to finalize a pipeline by checking the status of multiple jobs | |
| needs: # List all your run-*-test jobs | |
| - pre-commit | |
| - get-pr-labels | |
| - build-bionemo-image | |
| - run-tests | |
| - run-slow-tests | |
| - run-notebooks-docs | |
| # Add all other run-*-test jobs | |
| runs-on: ubuntu-latest | |
| if: always() # This ensures the job runs even if previous jobs fail | |
| steps: | |
| - name: Check test job statuses | |
| run: | | |
| if [[ "${{ contains(needs.*.result, 'failure') || contains(needs.*.result, 'cancelled') }}" == "true" ]]; then | |
| echo "Some test jobs have failed or been cancelled!" | |
| exit 1 | |
| else | |
| echo "All test jobs have completed successfully or been skipped!" | |
| exit 0 | |
| fi |