openms-ci.yml

# This is a basic workflow to help you get started with Actions

name: openms-ci

# Controls when the action will run. Triggers the workflow on push or pull request
# events
on: [push]

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:

  build-win:
    runs-on: windows-2022
    outputs:
      job-status: ${{ job.status }}
    steps:
    - uses: actions/checkout@v3
      with:
        path: OpenMS

    - name: Reduce PATH
      run: echo "PATH=C:\hostedtoolcache\windows\Python\3.7.9\x64\Scripts;C:\hostedtoolcache\windows\Python\3.7.9\x64;C:\hostedtoolcache\windows\Ruby\2.5.8\x64\bin;C:\Program Files\Java\jdk8u265-b01\bin;C:\ProgramData\kind;C:\vcpkg;C:\cf-cli;C:\Program Files (x86)\NSIS;C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0;C:\windows\System32\OpenSSH;C:\ProgramData\Chocolatey\bin;C:\Program Files\Docker;C:\Program Files\PowerShell\7;C:\Program Files\OpenSSL\bin;C:\Strawberry\c\bin;C:\Strawberry\perl\site\bin;C:\Strawberry\perl\bin;C:\Program Files\Git\cmd;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\bin;C:\Program Files (x86)\Microsoft Visual Studio\2022\\Enterprise\Common7\IDE\CommonExtensions\Microsoft\CMake\CMake\bin" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append

    - name: Install Qt
      uses: jurplel/install-qt-action@v3
      with:
        version: '5.15.2' # 5.12.7 is broken https://bugreports.qt.io/browse/QTBUG-81715, > 5.15.2 is not available on official archives (https://github.com/miurahr/aqtinstall/issues/636)
        host: 'windows' # default: win64_msvc2017_64
        target: 'desktop'
        install-deps: 'true'
        cache: 'false'
        aqtversion: '==3.1.*'

    # https://github.com/marketplace/actions/visual-studio-shell
    - name: Set up Visual Studio shell
      uses: egor-tensin/vs-shell@v2
      with:
        arch: x64

    - name: Setup build tools
      shell: bash
      run: |
        choco install ccache ninja cmake
        ## GH CLI "SHOULD BE" installed. Sometimes I had to manually install nonetheless. Super weird.
        # https://github.com/actions/runner-images/blob/main/images/win/scripts/Installers/Install-GitHub-CLI.ps1
        echo "C:\Program Files (x86)\GitHub CLI" >> $GITHUB_PATH

    - name: Extract branch/PR infos
      shell: bash
      run: |
        cd OpenMS
        RUN_NAME_LOCAL=$(echo ${GITHUB_REF#refs/heads/} | tr / -)
        echo "RUN_NAME=${RUN_NAME_LOCAL}" >> $GITHUB_ENV
        echo "BASE_REF=$(gh pr view --json baseRefName -q .baseRefName || echo ${RUN_NAME_LOCAL})" >> $GITHUB_ENV
      id: extract_branch
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

    - name: Cache contrib
      id: cache-contrib-win
      uses: actions/cache@v3
      with:
        path: ${{ github.workspace }}/OpenMS/contrib
        key: ${{ runner.os }}-contrib3

    - name: Load contrib build
      if: steps.cache-contrib-win.outputs.cache-hit != 'true'
      run: |
          cd OpenMS/contrib
          curl -o contribbld.tar.gz https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/windows/x64/msvc-14.2/contrib_build.tar.gz
          tar -xzf contribbld.tar.gz
          rm contribbld.tar.gz

    - name: Setup ccache cache
      uses: actions/cache@v3
      with:
        path: .ccache
        key: ${{ runner.os }}-ccache-${{ env.RUN_NAME }}-${{ github.run_number }}
        # Restoring: From current branch, otherwise from base branch, otherwise from any branch.
        restore-keys: |
          ${{ runner.os }}-ccache-${{ env.RUN_NAME }}
          ${{ runner.os }}-ccache-${{ env.BASE_REF }}
          ${{ runner.os }}-ccache-

    - name: Add THIRDPARTY
      shell: bash
      run: |
          # initialize THIRDPARTY
          cd OpenMS
          git submodule update --init THIRDPARTY
          cd ..
          # add third-party binaries to PATH
          # use flat THIRDPARTY structure
          mkdir -p _thirdparty
          cp -R OpenMS/THIRDPARTY/Windows/64bit/* _thirdparty/
          cp -R OpenMS/THIRDPARTY/All/* _thirdparty/
          # add third-party binaries to PATH
          for thirdpartytool in ${{ github.workspace }}/_thirdparty/*
          do
            echo $thirdpartytool >> $GITHUB_PATH
          done

    - name: Build Windows
      shell: bash
      run: |
          mkdir $GITHUB_WORKSPACE/OpenMS/bld/
          ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/ci/cibuild.cmake
      env:
          #OS_PREFIX_PATH: "${{ env.Qt5_DIR }}/lib/cmake;${{ env.Qt5_DIR }}"
          CONTRIB_BUILD_DIRECTORY: "${{ github.workspace }}/OpenMS/contrib"
          CI_PROVIDER: "GitHub-Actions"
          CMAKE_GENERATOR: "Ninja"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}"
          ENABLE_STYLE_TESTING: "OFF"
          ENABLE_TOPP_TESTING: "ON"
          ENABLE_CLASS_TESTING: "ON"
          WITH_GUI: "ON"
          ADDRESS_SANITIZER: "Off"
          BUILD_TYPE: "Release"
          OPENMP: "Off"
          USE_STATIC_BOOST: "On"
          #  BUILD_FLAGS: "-p:CL_MPCount=2" # For VS Generator and MSBuild
          BUILD_FLAGS: "-j2" # Ninja will otherwise use all cores (doesn't go well in GHA)
          CMAKE_CCACHE_EXE: "ccache"
          CCACHE_BASEDIR: ${{ github.workspace }}
          CCACHE_DIR: ${{ github.workspace }}/.ccache
          CCACHE_COMPRESS: true
          CCACHE_COMPRESSLEVEL: 12
          CCACHE_MAXSIZE: 400M

    - name: Test Windows
      shell: bash
      run: $LAUNCHER ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
      env:
          LAUNCHER: ""
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CI_PROVIDER: "GitHub-Actions"
          BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}"

  build-macos:
    runs-on: macos-latest
    outputs:
      job-status: ${{ job.status }}
    steps:
    - uses: actions/checkout@v3
      with:
        path: OpenMS

    - name: Extract branch/PR infos
      shell: bash
      run: |
        cd OpenMS
        RUN_NAME_LOCAL=$(echo ${GITHUB_REF#refs/heads/} | tr / -)
        echo "RUN_NAME=${RUN_NAME_LOCAL}" >> $GITHUB_ENV
        echo "BASE_REF=$(gh pr view --json baseRefName -q .baseRefName || echo ${RUN_NAME_LOCAL})" >> $GITHUB_ENV
      id: extract_branch
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

    - name: Install ccache
      run: |
        brew install ccache && brew link --overwrite ccache

    - name: Setup ccache cache
      uses: actions/cache@v3
      with:
        path: .ccache
        key: ${{ runner.os }}-ccache-${{ env.RUN_NAME }}-${{ github.run_number }}
        # Restoring: From current branch, otherwise from base branch, otherwise from any branch
        #   (probably only access to default branch "develop" is allowed).
        # TODO: Check if this is even necessary. This should be the default lookup order by GH.
        #  So maybe ${{ runner.os }}-ccache- is enough.
        restore-keys: |
          ${{ runner.os }}-ccache-${{ env.RUN_NAME }}
          ${{ runner.os }}-ccache-${{ env.BASE_REF }}
          ${{ runner.os }}-ccache-

    - name: Install Qt
      uses: jurplel/install-qt-action@v3
      with:
        version: '5.15.2' # 5.12.7 is broken https://bugreports.qt.io/browse/QTBUG-81715, > 5.15.2 is not available on official archives (https://github.com/miurahr/aqtinstall/issues/636)
        host: 'mac'
        target: 'desktop'
        install-deps: 'true'
        cache: 'false'
        setup-python: 'false' # see https://github.com/jurplel/install-qt-action/issues/130
        aqtversion: '==3.1.*'

    - name: Install build tools
      run: brew install autoconf automake libtool ninja

    - name: Cache contrib
      id: cache-contrib-os
      uses: actions/cache@v3
      with:
        path: ${{ github.workspace }}/OpenMS/contrib
        key: ${{ runner.os }}-contrib3

    - name: Load contrib build
      if: steps.cache-contrib-os.outputs.cache-hit != 'true'
      run: |
          cd OpenMS/contrib
          curl -o contribbld.tar.gz https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/macOS/10.15.5/x64/appleclang-11.0.0/contrib_build.tar.gz
          tar -xzf contribbld.tar.gz
          rm contribbld.tar.gz

    - name: Fix contrib install names
      shell: bash
      run: |
          shopt -s nullglob # ensure that for loop is only executated if there is at least one .dylib file
          for lib in $GITHUB_WORKSPACE/OpenMS/contrib/lib/*.dylib
          do
            install_name_tool -id $lib $lib
          done

          # create symlinks like brew https://github.com/Homebrew/homebrew-core/blob/master/Formula/qt.rb#L61
          # Warning: Qt5_DIR will change meaning in the new jurplel/install-qt-action. Use QT_ROOT_DIR instead
          # https://github.com/jurplel/install-qt-action/blob/master/README_upgrade_guide.md
          pushd $Qt5_DIR/include
            for f in $Qt5_DIR/lib/*.framework/Headers
            do
              lnknm=$(basename "${f%/*}" ".framework")
              ln -s $f $lnknm
            done
            for f in $Qt5_DIR/lib/*.framework/Versions/5/Qt*
            do
              install_name_tool -id $f $f
            done
          popd

    - name: Add THIRDPARTY
      shell: bash
      run: |
          # initialize THIRDPARTY
          cd OpenMS
          git submodule update --init THIRDPARTY
          cd ..
          # add third-party binaries to PATH
          # use flat THIRDPARTY structure
          mkdir -p _thirdparty
          cp -R OpenMS/THIRDPARTY/MacOS/64bit/* _thirdparty/
          cp -R OpenMS/THIRDPARTY/All/* _thirdparty/
          # add third-party binaries to PATH
          for thirdpartytool in ${{ github.workspace }}/_thirdparty/*
          do
            echo $thirdpartytool >> $GITHUB_PATH
          done

    - name: Build macOS
      run: |
            mkdir $GITHUB_WORKSPACE/OpenMS/bld/
            ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
            # For debugging full logs: find $GITHUB_WORKSPACE/OpenMS/bld/ -name "LastBuild*" -type f -exec cat {} \;
      env:
          OS_PREFIX_PATH: "${{ env.Qt5_Dir }}/lib/cmake;${{ env.Qt5_Dir }}"
          CONTRIB_BUILD_DIRECTORY: "${{ github.workspace }}/OpenMS/contrib"
          CI_PROVIDER: "GitHub-Actions"
          CMAKE_GENERATOR: "Ninja"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          BUILD_NAME: "${{ env.RUN_NAME }}-macOS-class-topp-${{ github.run_number }}"
          OPENMS_CONTRIB_LIBS: "${{ github.workspace }}/OpenMS/contrib"
          ENABLE_STYLE_TESTING: "OFF"
          ENABLE_TOPP_TESTING: "ON"
          ENABLE_CLASS_TESTING: "ON"
          WITH_GUI: "ON"
          ADDRESS_SANITIZER: "Off"
          BUILD_TYPE: "Release"
          OPENMP: "On"
          USE_STATIC_BOOST: "On"
          BUILD_FLAGS: "-j3"
          CMAKE_CCACHE_EXE: "ccache"
          CCACHE_BASEDIR: ${{ github.workspace }}
          CCACHE_DIR: ${{ github.workspace }}/.ccache
          CCACHE_COMPRESS: true
          CCACHE_COMPRESSLEVEL: 12
          CCACHE_MAXSIZE: 400M

    - name: Test macOS
      run: $LAUNCHER ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
      env:
          LAUNCHER: ""
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CI_PROVIDER: "GitHub-Actions"
          BUILD_NAME: "${{ env.RUN_NAME }}-macOS-clang-class-topp-${{ github.run_number }}"

  build-lnx:
    runs-on: ubuntu-latest
    outputs:
      job-status: ${{ job.status }}

    steps:
    # Cancels older builds if still running
    - uses: rokroskar/workflow-run-cleanup-action@master
      env:
        GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
      if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/develop'"

    - uses: actions/checkout@v3
      name: Checkout sources
      with:
        path: OpenMS

    - name: Extract branch/PR infos
      shell: bash
      run: |
        cd OpenMS
        RUN_NAME_LOCAL=$(echo ${GITHUB_REF#refs/heads/} | tr / -)
        echo "RUN_NAME=${RUN_NAME_LOCAL}" >> $GITHUB_ENV
        echo "BASE_REF=$(gh pr view --json baseRefName -q .baseRefName || echo ${RUN_NAME_LOCAL})" >> $GITHUB_ENV
      id: extract_branch
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        
    - name: Install dev tools, xvfb, ...
      run: |
           sudo add-apt-repository universe
           sudo apt update   
           sudo apt-get install -y build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache
           sudo apt-get install -y qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
           sudo apt-get install -y libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev

    - name: Setup ccache cache
      uses: actions/cache@v3
      with:
        path: .ccache
        key: ${{ runner.os }}-ccache-${{ env.RUN_NAME }}-${{ github.run_number }}
        # Restoring: From current branch, otherwise from base branch, otherwise from any branch.
        restore-keys: |
          ${{ runner.os }}-ccache-${{ env.RUN_NAME }}
          ${{ runner.os }}-ccache-${{ env.BASE_REF }}
          ${{ runner.os }}-ccache-

    - name: Add THIRDPARTY
      shell: bash
      run: |
          # initialize THIRDPARTY
          cd OpenMS
          git submodule update --init THIRDPARTY
          cd ..
          # add third-party binaries to PATH
          # use flat THIRDPARTY structure
          mkdir -p _thirdparty
          cp -R OpenMS/THIRDPARTY/Linux/64bit/* _thirdparty/
          cp -R OpenMS/THIRDPARTY/All/* _thirdparty/
          # add third-party binaries to PATH
          for thirdpartytool in ${{ github.workspace }}/_thirdparty/*
          do
            echo $thirdpartytool >> $GITHUB_PATH
          done

    - name: Build lnx
      run: |
            mkdir $GITHUB_WORKSPACE/OpenMS/bld/
            ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
            # For debugging full logs: find $GITHUB_WORKSPACE/OpenMS/bld/ -name "LastBuild*" -type f -exec cat {} \;
      env:
          OS_PREFIX_PATH: "${{ env.Qt5_Dir }}/lib/cmake;${{ env.Qt5_Dir }}"
          CONTRIB_BUILD_DIRECTORY: "/contrib-build"
          CI_PROVIDER: "GitHub-Actions"
          CMAKE_GENERATOR: "Ninja"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          BUILD_NAME: "${{ env.RUN_NAME }}-Ubuntu-gcc-class-topp-${{ github.run_number }}"
          ENABLE_STYLE_TESTING: "OFF"
          ENABLE_TOPP_TESTING: "ON"
          ENABLE_CLASS_TESTING: "ON"
          WITH_GUI: "ON"
          ADDRESS_SANITIZER: "Off"
          BUILD_TYPE: "Release"
          OPENMP: "On"
          USE_STATIC_BOOST: "Off"
          BUILD_FLAGS: "-j2"
          CMAKE_CCACHE_EXE: "ccache"
          CCACHE_BASEDIR: "${{ github.workspace }}"
          CCACHE_DIR: "${{ github.workspace }}/.ccache"
          CCACHE_COMPRESS: true
          CCACHE_COMPRESSLEVEL: 12
          CCACHE_MAXSIZE: 400M
          CCACHE_SLOPPINESS: time_macros,include_file_ctime,include_file_mtime
          CCACHE_COMPILERCHECK: content

    - name: Test lnx
      run: $LAUNCHER ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
      env:
          LAUNCHER: "xvfb-run"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CI_PROVIDER: "GitHub-Actions"
          BUILD_NAME: "${{ env.RUN_NAME }}-Ubuntu-gcc-class-topp-${{ github.run_number }}"

  build-lnx-clang:
    runs-on: ubuntu-22.04
    outputs:
      job-status: ${{ job.status }}
    steps:
    # Cancels older builds if still running
    - uses: rokroskar/workflow-run-cleanup-action@master
      env:
        GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
      if: "!startsWith(github.ref, 'refs/tags/') && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/develop'"

    - uses: actions/checkout@v3
      name: Checkout sources
      with:
        path: OpenMS

    - name: Extract branch/PR infos
      shell: bash
      run: |
        cd OpenMS
        RUN_NAME_LOCAL=$(echo ${GITHUB_REF#refs/heads/} | tr / -)
        echo "RUN_NAME=${RUN_NAME_LOCAL}" >> $GITHUB_ENV
        echo "BASE_REF=$(gh pr view --json baseRefName -q .baseRefName || echo ${RUN_NAME_LOCAL})" >> $GITHUB_ENV
      id: extract_branch
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

    - name: Install dev tools, xvfb, ...
      run: |
           sudo add-apt-repository universe
           sudo apt update    
           sudo apt-get install build-essential cmake autoconf patch libtool git automake ninja-build xvfb ccache
           sudo apt-get install qtbase5-dev libqt5svg5-dev libqt5opengl5-dev
           sudo apt-get install libeigen3-dev libboost-random-dev libboost-regex-dev libboost-iostreams-dev libboost-date-time-dev libboost-math-dev libxerces-c-dev zlib1g-dev libsvm-dev libbz2-dev coinor-libcoinmp-dev libhdf5-dev

    - name: Setup ccache cache
      uses: actions/cache@v3
      with:
        path: .ccache
        key: ${{ runner.os }}-clng-ccache-${{ env.RUN_NAME }}-${{ github.run_number }}
        # Restoring: From current branch, otherwise from base branch, otherwise from any branch.
        restore-keys: |
          ${{ runner.os }}-clng-ccache-${{ env.RUN_NAME }}
          ${{ runner.os }}-clng-ccache-${{ env.BASE_REF }}
          ${{ runner.os }}-clng-ccache-

    - name: Add THIRDPARTY
      shell: bash
      run: |
          # initialize THIRDPARTY
          cd OpenMS
          git submodule update --init THIRDPARTY
          cd ..
          # add third-party binaries to PATH
          # use flat THIRDPARTY structure
          mkdir -p _thirdparty
          cp -R OpenMS/THIRDPARTY/Linux/64bit/* _thirdparty/
          cp -R OpenMS/THIRDPARTY/All/* _thirdparty/
          # add third-party binaries to PATH
          for thirdpartytool in ${{ github.workspace }}/_thirdparty/*
          do
            echo $thirdpartytool >> $GITHUB_PATH
          done

    - name: Set up Clang
      uses: egor-tensin/setup-clang@v1
      with:
        version: 15
        platform: x64   
  
    - name: Build lnx-clang
      run: |
            mkdir $GITHUB_WORKSPACE/OpenMS/bld/
            ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
      env:
          OS_PREFIX_PATH: "${{ env.Qt5_DIR }}/lib/cmake;${{ env.Qt5_DIR }}"
          CONTRIB_BUILD_DIRECTORY: "/contrib-build"
          CI_PROVIDER: "GitHub-Actions"
          CMAKE_GENERATOR: "Ninja"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          BUILD_NAME: "${{ env.RUN_NAME }}-Ubuntu-clang-class-topp-${{ github.run_number }}"
          ENABLE_STYLE_TESTING: "OFF"
          ENABLE_TOPP_TESTING: "ON"
          ENABLE_CLASS_TESTING: "ON"
          WITH_GUI: "ON"
          ADDRESS_SANITIZER: "Off"
          BUILD_TYPE: "Release"
          OPENMP: "On"
          USE_STATIC_BOOST: "Off"
          BUILD_FLAGS: "-j2"
          CMAKE_CCACHE_EXE: "ccache"
          CCACHE_BASEDIR: "${{ github.workspace }}"
          CCACHE_DIR: "${{ github.workspace }}/.ccache"
          CCACHE_COMPRESS: true
          CCACHE_COMPRESSLEVEL: 12
          CCACHE_MAXSIZE: 400M
          CCACHE_SLOPPINESS: time_macros,include_file_ctime,include_file_mtime
          CCACHE_COMPILERCHECK: content

    - name: Test lnx-clang
      run: $LAUNCHER ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/citest.cmake
      env:
          LAUNCHER: "xvfb-run"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          CI_PROVIDER: "GitHub-Actions"
          BUILD_NAME: "${{ env.RUN_NAME }}-Ubuntu-clang-class-topp-${{ github.run_number }}"

  overall-status:
    runs-on: ubuntu-latest
    needs: [build-win, build-lnx, build-lnx-clang, build-macos]
    if: ${{ always() }}
    steps:
    - name: Check on failures
      if: ${{ needs.build-win.outputs.job-status != 'Success' || needs.build-lnx.outputs.job-status != 'Success' || needs.build-lnx-clang.outputs.job-status != 'Success' || needs.build-macos.outputs.job-status != 'Success' }} 
      run: exit 1