CI.yml

name: CI
on: [push, pull_request]

jobs:

  target:
    strategy:
      matrix:
        ci_target:
          - ci_housekeeping
          - ci_unit_tests
          - integration_tests
          - viral_refbased
          - viral_assemble
          # disabled due to test data bitrot (Apr 2023)
          # - skylab_bulk_rna
    runs-on: ubuntu-20.04
    steps:
    - name: Login to GitHub Packages Docker Registry
      uses: docker/login-action@v1
      with:
        registry: docker.pkg.github.com
        username: ${{ github.repository_owner }}
        password: ${{ secrets.GITHUB_TOKEN }}
    - uses: actions/checkout@v2
      with:
        fetch-depth: 0
        submodules: recursive
    - name: docker build
      run: |
        # Cache the dependency-installation image layer on GitHub Packages to speed up CI. Use a
        # year/month tag to ensure we do refresh them occasionally.
        DOCKER_TAG="docker.pkg.github.com/${GITHUB_REPOSITORY}/miniwdl_ci:$(date +%Y%m)"
        echo "DOCKER_TAG=${DOCKER_TAG}" >> $GITHUB_ENV
        if docker pull "$DOCKER_TAG"; then
          docker build -t "$DOCKER_TAG" --cache-from "$DOCKER_TAG" .
        else
          docker build -t "$DOCKER_TAG" .
        fi
        if [ "${{ matrix.ci_target }}" == "ci_housekeeping" ]; then
          docker push "$DOCKER_TAG" || true  # allow failure for third-party PRs
        fi
    - name: make ${{ matrix.ci_target }}
      run: |
        chmod -R ugo+rw .
        # AWS_EC2_METADATA_DISABLED needed on Azure: https://github.com/aws/aws-cli/issues/5623
        docker run \
          --group-add $(stat -c %g /var/run/docker.sock) -v /var/run/docker.sock:/var/run/docker.sock \
          -v $(pwd):/home/wdler/miniwdl -v /tmp:/tmp \
          -e AWS_EC2_METADATA_DISABLED=true -e CI=true \
          "$DOCKER_TAG" make -C miniwdl ${{ matrix.ci_target }}
    - name: Coveralls
      if: ${{ matrix.ci_target == 'ci_unit_tests' }}
      # https://github.com/coverallsapp/github-action/issues/30
      # https://github.com/marketplace/actions/coveralls-python
      uses: AndreMiras/coveralls-python-action@develop

  bionic_self_test:
    # run_self_test in a ubuntu:18.04 image with only the minimal runtime dependencies installed
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - name: docker build
      run: |
        mkdir bionic_self_test
        cp requirements.txt bionic_self_test

        cat << 'EOF' > bionic_self_test/Dockerfile
          FROM ubuntu:18.04
          ENV LC_ALL C.UTF-8
          ENV LANG C.UTF-8
          RUN apt-get -qq update && DEBIAN_FRONTEND=noninteractive apt-get -qq install -y python3-pip

          RUN useradd -ms /bin/bash -u 1337 wdler
          USER wdler
          WORKDIR /home/wdler
          RUN mkdir miniwdl

          COPY requirements.txt /home/wdler/
          RUN pip3 install --user -r requirements.txt

          ENV PYTHONPATH $PYTHONPATH:/home/wdler/.local/lib/python3.6
          ENV PATH $PATH:/home/wdler/.local/bin

          # expectation -- mount miniwdl source tree at /home/wdler/miniwdl
          CMD env -C miniwdl python3 -m WDL run_self_test
        EOF
        docker build -t miniwdl_bionic_self_test bionic_self_test
    - name: miniwdl run_self_test
      run: |
        docker run \
          --group-add $(stat -c %g /var/run/docker.sock) -v /var/run/docker.sock:/var/run/docker.sock \
          -v $(pwd):/home/wdler/miniwdl -v /tmp:/tmp \
          -e AWS_EC2_METADATA_DISABLED=true \
          miniwdl_bionic_self_test