ESM2 Finetuning refactor #88
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| name: "[Optional] 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} | |
| 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 | |
| - uses: trufflesecurity/trufflehog@main | |
| with: | |
| extra_args: --only-verified | |
| build-bionemo-image: | |
| needs: pre-commit | |
| runs-on: self-hosted-azure-cpu | |
| if: ${{ !contains(github.event.pull_request.labels.*.name, 'SKIP_CI') }} | |
| steps: | |
| - 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 }} | |
| - uses: int128/docker-build-cache-config-action@v1 | |
| id: cache | |
| with: | |
| image: nemoci.azurecr.io/bionemo/build-cache | |
| pull-request-cache: true | |
| - 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: ${{ steps.cache.outputs.cache-from }} | |
| cache-to: ${{ steps.cache.outputs.cache-to }} | |
| run-tests: | |
| needs: build-bionemo-image | |
| runs-on: self-hosted-nemo-gpus-1 | |
| defaults: | |
| run: | |
| working-directory: ./${{ github.run_id }} | |
| container: | |
| image: nemoci.azurecr.io/bionemo:${{ github.run_id }} | |
| options: --gpus all | |
| volumes: | |
| - /home/azureuser/actions-runner-bionemo/cache:/github/home/.cache | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| path: ${{ github.run_id }} | |
| - name: Run tests | |
| env: | |
| BIONEMO_DATA_SOURCE: ngc | |
| run: ./ci/scripts/run_pytest.sh --no-nbval --skip-slow | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| working-directory: ${{ github.run_id }} | |
| - name: Upload test results to Codecov | |
| if: ${{ !cancelled() }} | |
| uses: codecov/test-results-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| working-directory: ${{ github.run_id }} | |
| clean-up: | |
| needs: run-tests | |
| runs-on: self-hosted-nemo-gpus-1 | |
| if: ${{ always() }} | |
| steps: | |
| - name: clean up image | |
| run: docker rmi nemoci.azurecr.io/bionemo:${{ github.run_id }} | |
| # TODO: exclude tests from base image; run tests from github workspace mounted in the image. | |
| # TODO: figure out way of cleaning up working directory (requires sudo or for us to fix file ownership from release container) |