unit-tests.yml

name: "BioNemo Image Build and Unit Tests"

on:
  pull_request:
    branches: [main]
    types: [opened, synchronize, reopened, ready_for_review]
  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
      # For pull requests and merge_group events, trufflehog only runs on the diff between the base and head branches.
      # For `push` events, (i.e., post-merge tests), we run trufflehog on the entire main branch by setting the base to
      # ''. For some reason, the default behavior doesn't work well with the merge_group event, so we need to set these
      # manually.
      - uses: trufflesecurity/trufflehog@main
        with:
          path: ./
          base: ${{ github.event_name != 'push' && github.event.repository.default_branch || '' }}
          head: HEAD
          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:
          # This working directory / path business is because our self-hosted runners are not ephemeral VMs, so we
          # isolate each build into their own folder. Note that these are not currently cleaned up, so that will need to
          # be automated in the future.
          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 }}

      # 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: 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 }}
            ${{ github.event_name == 'merge_group' && 'nemoci.azurecr.io/bionemo/build-cache:main' || '' }}
          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
      # We mount the cache directory to avoid downloading the test data every run. Note that this only works because our
      # VMs are not ephemeral, otherwise we'd need to cache the data somewhere that persists between runs.
      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
        # 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: Run slow tests
        if: |
          github.event_name == 'merge_group' ||
          (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'INCLUDE_SLOW_TESTS'))
        env:
          BIONEMO_DATA_SOURCE: ngc
        run: pytest -v -m "slow" sub-packages/

      - name: Run notebook tests
        if: |
          github.event_name == 'merge_group' ||
          (github.event_name == 'pull_request' &&
            contains(github.event.pull_request.labels.*.name, 'INCLUDE_NOTEBOOKS_TESTS'))
        env:
          BIONEMO_DATA_SOURCE: ngc
        run: pytest -v --nbval-lax -p no:python docs/ sub-packages/

      - name: Upload coverage to Codecov
        # Don't run coverage on merge queue CI to avoid duplicating reports
        # to codecov. See https://github.com/matplotlib/napari-matplotlib/issues/155
        if: github.event_name != 'merge_group'
        uses: codecov/codecov-action@v5
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          working-directory: ${{ github.run_id }}

      - name: Upload test results to Codecov
        # Don't run coverage on merge queue CI to avoid duplicating reports
        # to codecov. See https://github.com/matplotlib/napari-matplotlib/issues/155
        if: ${{ !cancelled() && github.event_name != 'merge_group' }}
        uses: codecov/test-results-action@v1
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          working-directory: ${{ github.run_id }}

  # Again, because our VMs are not ephemeral, we need to clean up the image after the tests are done. Otherwise `docker
  # images list` will get very cluttered and we'll run out of disk space on these runners.
  clean-up:
    needs: run-tests
    runs-on: self-hosted-nemo-gpus-1
    if: ${{ success() || failure() }}
    steps:
      - name: clean up image
        run: docker rmi nemoci.azurecr.io/bionemo:${{ 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)