unit-tests.yml

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"

        error=false
        for dir in ./sub-packages/bionemo-*/; do
          pytest -v --cov=bionemo --cov-append --junitxml=$(basename $dir).junit.xml -o junit_family=legacy $dir || error=true
        done

        if [ "$error" = true ]; then
            exit 1
        fi

    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v5
      with:
        token: ${{ secrets.CODECOV_TOKEN }}

    - name: Upload test results to Codecov
      if: ${{ !cancelled() }}
      uses: codecov/test-results-action@v1
      with:
        token: ${{ secrets.CODECOV_TOKEN }}

# TODO: exclude tests from base image; run tests from github workspace mounted in the image.
# TODO: upload coverage report to codecov.io