main.yml

name: MetaGraph CI

on:
  push:
    branches:
      - master
    tags:
      - 'v*'
  pull_request:
    branches:
      - master

env:
  REGISTRY: ghcr.io
  IMAGE_NAME: ${{ github.repository }}


jobs:

  Linux:
    runs-on: ubuntu-20.04

    strategy:
      matrix:
        alphabet: [DNA, Protein]
        build_type: [Debug, Release]
        compiler: [g++-8, g++-9, g++-10, g++-11]
        build_static: [OFF, ON]
        with_avx: [OFF, ON]
        include:
          - compiler: g++-8
            cxx: g++-8
            cc: gcc-8

          - compiler: g++-9
            cxx: g++-9
            cc: gcc-9

          - compiler: g++-10
            cxx: g++-10
            cc: gcc-10

          - compiler: g++-11
            cxx: g++-11
            cc: gcc-11

        exclude:
          - alphabet: Protein
            compiler: g++-9
          - compiler: g++-8
            build_static: ON
          - compiler: g++-9
            build_static: ON
          - compiler: g++-10
            build_static: ON
          - build_type: Debug
            build_static: ON
          - with_avx: OFF
            build_static: OFF

    name: Linux (${{ matrix.alphabet }}, ${{ matrix.build_type }}, ${{ matrix.compiler }}${{ matrix.build_static == 'ON' && ', static' || '' }}${{ matrix.with_avx == 'OFF' && ', noAVX' || '' }})

    steps:
    - uses: actions/checkout@v1

    - name: checkout submodules
      run: git submodule update --init --recursive

    - name: install dependencies
      run: |
        sudo apt-get update

        # If clang, use the default version. Otherwise the compiler install with apt-get.
        if [[ "${{ matrix.compiler }}" != "clang" ]]; then
            sudo apt-get install ${{ matrix.compiler }}
        fi

        sudo apt-get install libbz2-dev libjemalloc-dev libboost-all-dev libdeflate-dev

        if [ "${{ matrix.build_static }}" = "ON" ]; then
          # for static builds, compile curl ourselves
          git clone https://github.com/curl/curl.git
          mkdir curl/_build
          cd curl/_build
          cmake -DBUILD_SHARED_LIBS=off ..
          make -j 2
          sudo make install
          cd ..
        fi

        echo "CC=$(which ${{ matrix.cc }})" >> $GITHUB_ENV
        echo "CXX=$(which ${{ matrix.cxx }})" >> $GITHUB_ENV

    - name: install dependencies for integration tests
      run: |
        pip3 install parameterized
        sudo apt-get install python3-venv

    - name: install sdsl-lite
      run: |
        cd metagraph/external-libraries/sdsl-lite
        ./install.sh $(pwd)

    - name: configure
      run: |
        mkdir metagraph/build
        cd metagraph/build
        cmake -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
              -DBUILD_STATIC=${{ matrix.build_static }} \
              -DWITH_AVX=${{ matrix.with_avx }} -DWITH_MSSE42=${{ matrix.with_avx }} \
              -DCMAKE_DBG_ALPHABET=${{ matrix.alphabet }} ..

    - name: build metagraph
      run: cd metagraph/build && make -j 2 metagraph

    - name: build unit tests
      if: matrix.build_static == 'OFF'
      run: cd metagraph/build && make -j 2 unit_tests

    - name: build other
      if: matrix.build_static == 'OFF'
      run: cd metagraph/build && make -j 2

    # for potential release
    - name: rename binary
      if: matrix.with_avx == 'OFF'
      run: mv metagraph/build/metagraph_${{ matrix.alphabet }} metagraph/build/metagraph_${{ matrix.alphabet }}_noAVX
    - name: upload static binary
      if: ${{ matrix.build_static == 'ON' && matrix.compiler == 'g++-11' }}
      uses: actions/upload-artifact@v4
      with:
        name: metagraph_${{ matrix.alphabet }}${{ matrix.with_avx == 'OFF' && '_noAVX' || '' }}_linux_x86
        path: metagraph/build/metagraph_${{ matrix.alphabet }}${{ matrix.with_avx == 'OFF' && '_noAVX' || '' }}
        
    - name: run unit tests
      if: matrix.build_static == 'OFF'
      run: |
        export LD_LIBRARY_PATH="/usr/local/lib/:$LD_LIBRARY_PATH"
        cd metagraph/build && ./unit_tests

    - name: run integration tests
      uses: nick-fields/retry@v2
      with:
        timeout_minutes: 1000
        max_attempts: 5
        retry_on: error
        command: |
          export LD_LIBRARY_PATH="/usr/local/lib/:$LD_LIBRARY_PATH"
          cd metagraph/build && make check

  MacOS:
    runs-on: macos-latest

    strategy:
      matrix:
        alphabet: [DNA]
        build_type: [Debug, Release]
        platform: [x64, arm64]

    steps:
    - uses: actions/checkout@v1

    - name: checkout submodules
      run: git submodule update --init --recursive

    - name: install dependencies
      run: brew install bzip2 libomp boost jemalloc autoconf automake libtool libdeflate

    - name: install dependencies for integration tests
      run: pip3 install parameterized --break-system-packages --user

    - name: install sdsl-lite
      run: |
        cd metagraph/external-libraries/sdsl-lite
        ./install.sh $(pwd)

    - name: configure
      run: |
        mkdir metagraph/build
        cd metagraph/build

        cmake -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
              -DCMAKE_DBG_ALPHABET=${{ matrix.alphabet }} \
              -DWITH_AVX=OFF -DWITH_MSSE42=OFF ..

    - name: build metagraph
      run: cd metagraph/build && make -j 2 metagraph

    - name: build unit tests
      run: cd metagraph/build && make -j 2 unit_tests

    - name: build other
      run: cd metagraph/build && make -j 2

    - name: run unit tests
      run: cd metagraph/build && ./unit_tests

    - name: run integration tests
      run: cd metagraph/build && make check


  Metagraph-Workflows:
    name: Test metagraph workflows
    runs-on: ubuntu-20.04
    needs: [Linux]

    steps:
        - uses: actions/checkout@v2

        - name: Set up Python 3.8
          uses: actions/setup-python@v1
          with:
              python-version: 3.8

        - name: fetch static binary
          uses: actions/download-artifact@v4
          with:
              path: artifacts

        - name: setup metagraph binary
          run: |
            sudo ln -s $(pwd)/artifacts/metagraph_DNA_linux_x86/metagraph_DNA /usr/local/bin/metagraph
            sudo chmod +rx /usr/local/bin/metagraph
            /usr/local/bin/metagraph --help
            metagraph --help

        - name: Install python dependencies
          run: |
              python -m pip install --upgrade pip
              pip install pytest
              pip install -r metagraph/workflows/requirements.txt
        - name: Test metagraph-workflows pytest
          run: |
              cd metagraph/workflows
              pytest


  Build-and-Push-Docker:
    # adapted from https://docs.github.com/en/actions/guides/publishing-docker-images#publishing-images-to-github-packages
    if: github.event_name != 'pull_request'
    needs: [Linux, Metagraph-Workflows]
    runs-on: ubuntu-20.04
    permissions:
      contents: read
      packages: write

    steps:
    - name: Checkout repository
      uses: actions/checkout@v2

    - name: checkout submodules
      run: git submodule update --init --recursive

    - name: Log in to the Container registry
      uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
      with:
          registry: ${{ env.REGISTRY }}
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}

    - name: Extract metadata (tags, labels) for Docker
      id: meta
      uses: docker/metadata-action@v3
      with:
          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}

    - name: Build and push Docker image
      uses: docker/build-push-action@v2
      with:
          context: .
          push: true
          tags: ${{ steps.meta.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}


  Release:
    name: Create Release
    if: startsWith(github.ref, 'refs/tags/v')
    runs-on: ubuntu-latest
    needs: [Linux, Metagraph-Workflows]
    steps:
      - uses: actions/checkout@v1

      - name: checkout submodules
        run: git submodule update --init --recursive

      - name: fetch static binary
        uses: actions/download-artifact@v4
        with:
          path: artifacts

      - name: Tag name
        id: tag_name
        run: |
          echo ::set-output name=TAG::${GITHUB_REF#refs/tags/}
          echo ::set-output name=VER::${GITHUB_REF#refs/tags/v}

      # from https://stackoverflow.com/a/61919791/6869319
      - name: read current version
        id: read_version
        run: |
          content=`cat package.json`
          # the following lines are only required for multi line json
          content="${content//'%'/'%25'}"
          content="${content//$'\n'/'%0A'}"
          content="${content//$'\r'/'%0D'}"
          # end of optional handling for multi line json
          echo "::set-output name=packageJson::$content"

      - name: build source archive including submodules
        run: |
          [[ v${{fromJson(steps.read_version.outputs.packageJson).version}} == ${{ steps.tag_name.outputs.TAG }} ]] \
            || (echo "::error file=package.json::Version in package.json (v${{fromJson(steps.read_version.outputs.packageJson).version}}) does not match tag ${{ steps.tag_name.outputs.TAG }}. Update package.json and set the tag again."; \
                exit 1)
          mkdir -p artifacts/sources
          tag=${{ steps.tag_name.outputs.TAG }}
          bash .github/workflows/git-archive-all.sh --format tar.gz artifacts/sources/${tag}-sources-with-submodules.tar.gz
          bash .github/workflows/git-archive-all.sh --format zip artifacts/sources/${tag}-sources-with-submodules.zip

      - name: create release with static binaries
        uses: svenstaro/upload-release-action@v2
        with:
          release_name: Version ${{ steps.tag_name.outputs.VER }}
          body: |
            The pre-compiled binaries (only for Linux) are statically linked and hence don't require additional libraries to be installed.
            The *_noAVX binaries are compiled without the modern AVX2 and MSSE4.2 instructions and should be used when the processor does not support these instructions.
          file: 'artifacts/*/*'
          file_glob: true
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          tag: ${{ github.ref }}
          prerelease: true