Use self-hosted azure runners for bionemo unit tests #31
Workflow file for this run
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| name: BioNemo Image Build and Unit Tests | |
| on: | |
| pull_request: | |
| branches: [main] | |
| push: | |
| branches: [main] | |
| merge_group: | |
| types: [checks_requested] | |
| defaults: | |
| run: | |
| shell: bash -x -e -u -o pipefail {0} | |
| 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 | |
| - uses: trufflesecurity/trufflehog@main | |
| with: | |
| extra_args: --only-verified | |
| build-bionemo-image: | |
| needs: pre-commit | |
| runs-on: self-hosted-nemo-gpus-1 # TODO: make this a CPU-only builder runner. | |
| steps: | |
| - name: Clean runner cache | |
| env: | |
| LABEL: bionemo | |
| run: | | |
| docker system prune $([[ "$LABEL" != "" ]] && echo --filter "label=nemo.library=$LABEL" || echo '') --filter "until=168h" --force | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: ${{ github.run_id }} | |
| submodules: 'recursive' | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Docker Metadata | |
| id: metadata | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: nemoci.azurecr.io/bionemo | |
| labels: nemo.library=bionemo | |
| tags: | | |
| type=schedule | |
| type=ref,event=branch | |
| type=ref,event=tag | |
| type=ref,event=pr | |
| type=raw,value=${{ github.run_id }} | |
| - name: Build and push | |
| uses: docker/build-push-action@v5 | |
| with: | |
| file: ${{ github.run_id }}/Dockerfile | |
| context: ${{ github.run_id }}/ | |
| push: true | |
| tags: ${{ steps.metadata.outputs.tags }} | |
| labels: ${{ steps.metadata.outputs.labels }} | |
| cache-from: | | |
| type=registry,ref=nemoci.azurecr.io/bionemo:buildcache | |
| cache-to: | | |
| type=registry,ref=nemoci.azurecr.io/bionemo:buildcache,mode=max | |
| # ${{ github.ref == 'refs/heads/main' && 'type=registry,ref=nemoci.azurecr.io/bionemo:buildcache,mode=max' || '' }} | |
| # TODO: Add persistent volume for cache | |
| # https://confluence.nvidia.com/display/NLLMS/NeMo+Framework+-+Github+Actions+CICD%3A+User+Guide | |
| run-tests: | |
| needs: build-bionemo-image | |
| runs-on: self-hosted-nemo-gpus-1 | |
| defaults: | |
| run: | |
| working-directory: ./${{ github.run_id }} | |
| container: | |
| image: nemoci.azurecr.io/bionemo:${{ github.run_id }} | |
| options: --gpus all | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: ${{ github.run_id }} | |
| - name: Run tests | |
| run: | | |
| echo "Inside container at $PWD" | |
| echo $(ls) | |
| python -m coverage erase | |
| error=false | |
| for dir in docs/ ./sub-packages/bionemo-*/; do | |
| echo "Running pytest in $dir" | |
| python -m coverage run --parallel-mode --source=bionemo \ | |
| -m pytest -v --nbval-lax --durations=0 --durations-min=60.0 "$dir" || error=true | |
| done | |
| python -m coverage combine | |
| python -m coverage report --show-missing | |
| if [ "$error" = true ]; then | |
| exit 1 | |
| fi | |
| # TODO: exclude tests from base image; run tests from github workspace mounted in the image. | |
| # TODO: upload coverage report to codecov.io |