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 but only for the master branch
on:
  push:
    branches: [ develop, add/openms_ci_thirdparty_tests ]

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

  build-win:
    runs-on: windows-latest
    continue-on-error: true
    steps:
    - uses: actions/checkout@v2
      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\2019\\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@v2
      with:
        version: '5.12.6' # 5.12.7 is broken https://bugreports.qt.io/browse/QTBUG-81715
        host: 'windows' # default: win64_msvc2017_64
        target: 'desktop'
        install-deps: 'true'
        modules: 'qtsvg'
        cached: 'false'

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

    - name: Cache contrib
      id: cache-contrib-win
      uses: actions/cache@v2
      with:
        path: ${{ github.workspace }}/OpenMS/contrib
        key: ${{ runner.os }}-contrib

    - name: Load contrib build
      if: steps.cache-contrib-win.outputs.cache-hit != 'true'
      run: |
          cd OpenMS/contrib
          curl -o contribbld.tar.gz https://abibuilder.informatik.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: Extract branch name
      if: github.event_name == 'push'
      shell: bash
      run: |
        ref=`jq --raw-output .ref "$GITHUB_EVENT_PATH"`
        ref=${ref#"refs/heads/"}
        ref=${ref#"refs/"}
        ref=${ref//\//-}
        echo "RUN_NAME=$ref" >> $GITHUB_ENV
      id: extract_branch

    - name: Extract PR number
      if: github.event_name == 'pull_request'
      shell: bash
      run: echo "RUN_NAME=pr$(jq --raw-output .pull_request.number $GITHUB_EVENT_PATH)" >> $GITHUB_ENV
      id: extract_pr

    - name: Setup cmake
      uses: jwlawson/actions-setup-cmake@v1.8
      with:
        cmake-version: '3.20.x'

    - 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: Tests windows
      shell: bash
      run: |
          cmake --version
          
          #run openms tests
          mkdir $GITHUB_WORKSPACE/OpenMS/bld/
          ctest --output-on-failure -V -S ../OpenMS/OpenMS/tools/travis/cibuild.cmake

          FAILED_TEST=$(find $GITHUB_WORKSPACE/OpenMS/bld/ -name "Test.xml" -type f -exec grep "<Test Status=\"failed\">" -c {} \; )
          if [ "$FAILED_TEST" -gt "0" ] ; then
            echo "$FAILED_TEST tests failed"
            exit -1
          fi

      env:
          CMAKE_GENERATOR: "Visual Studio 16 2019"
          CONTRIB_BUILD_DIRECTORY: "${{ github.workspace }}/OpenMS/contrib"
          CI_PROVIDER: "GitHub-Actions"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          BUILD_NAME: "${{ env.RUN_NAME }}-Windows-testClass-testTOPP"
          OPENMS_CONTRIB_LIBS: "${{ 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: "Off"
          USE_STATIC_BOOST: "On"
          BUILD_FLAGS: "-p:CL_MPCount=2"

  build-macos:
    runs-on: macos-latest
    continue-on-error: true
    steps:
    - uses: actions/checkout@v2
      with:
        path: OpenMS

    - name: Install Qt
      uses: jurplel/install-qt-action@v2
      with:
        version: '5.12.7'
        host: 'mac'
        target: 'desktop'
        install-deps: 'true'
        modules: 'qtsvg'
        cached: 'false'

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

    - name: Cache contrib
      id: cache-contrib-os
      uses: actions/cache@v2
      with:
        path: ${{ github.workspace }}/OpenMS/contrib
        key: ${{ runner.os }}-contrib

    - name: Load contrib build
      if: steps.cache-contrib-os.outputs.cache-hit != 'true'
      run: |
          cd OpenMS/contrib
          curl -o contribbld.tar.gz https://abibuilder.informatik.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: |
          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
          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
            otool -L /Users/runner/work/OpenMS/Qt/5.12.7/clang_64/lib/QtCore.framework/Versions/5/QtCore
          popd

    - name: Extract branch name
      if: github.event_name == 'push'
      shell: bash
      run: |
        ref=`jq --raw-output .ref "$GITHUB_EVENT_PATH"`
        ref=${ref#"refs/heads/"}
        ref=${ref#"refs/"}
        ref=${ref//\//-}
        echo "RUN_NAME=$ref" >> $GITHUB_ENV
      id: extract_branch

    - name: Extract PR number
      if: github.event_name == 'pull_request'
      shell: bash
      run: echo "RUN_NAME=pr$(jq --raw-output .pull_request.number $GITHUB_EVENT_PATH)" >> $GITHUB_ENV
      id: extract_pr

    - 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 and test osx
      run: |
          export OS_PREFIX_PATH="${Qt5_Dir}/lib/cmake;${Qt5_Dir}"
          mkdir $GITHUB_WORKSPACE/OpenMS/bld/
          ## TODO allow changing of ctest build site in cmake
          ## TODO potentially parse some OS infos and add to build name
          ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/travis/cibuild.cmake

          FAILED_TEST=$(find $GITHUB_WORKSPACE/OpenMS/bld/ -name "Test.xml" -type f -exec grep "<Test Status=\"failed\">" -c {} \; )
          if [ "$FAILED_TEST" -gt "0" ] ; then
            echo "$FAILED_TEST tests failed"
            exit -1
          fi
      env:
          CONTRIB_BUILD_DIRECTORY: "${{ github.workspace }}/OpenMS/contrib"
          CI_PROVIDER: "GitHub-Actions"
          CMAKE_GENERATOR: "Unix Makefiles"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          BUILD_NAME: "${{ env.RUN_NAME }}-macOS-testClass-testTOPP"
          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: "Off"
          BUILD_FLAGS: "-j3"

  build-lnx:
    runs-on: ubuntu-latest
    continue-on-error: true
    container: openms/manylinux:latest

    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@v2
      name: Checkout sources
      with:
        path: OpenMS

    - name: Extract branch name
      if: github.event_name == 'push'
      shell: bash
      run: |
        yum -y install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
        yum -y install jq
        ref=`jq --raw-output .ref "$GITHUB_EVENT_PATH"`
        ref=${ref#"refs/heads/"}
        ref=${ref#"refs/"}
        ref=${ref//\//-}
        echo "RUN_NAME=$ref" >> $GITHUB_ENV
      id: extract_branch

    - name: Extract PR number
      if: github.event_name == 'pull_request'
      shell: bash
      run: |
        yum -y install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
        yum -y install jq
        echo "RUN_NAME=pr$(jq --raw-output .pull_request.number $GITHUB_EVENT_PATH)" >> $GITHUB_ENV
      id: extract_pr
      
      #  open step log to get ssh access
      #  If the CI has failed and the branch is ci-debug then start a tmate
      #  session. SSH rendezvous point is emited continuously in the job output.
      #  hack needed to fix apt dependency
#    - name: "Debug: Package dependancies for tmate"
#      run: |
#        yum install -y xz
#        ln -s /bin/true /bin/apt-get      
#      
#    - name: "Debug: Start tmate"
#      uses: mxschmitt/action-tmate@v3.3
#      with:
#        limit-access-to-actor: true
#        sudo: false

    - name: Install Xvfb package
      run: |
            yum -y install xorg-x11-server-Xvfb

    - 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 and test lnx
      run: |
            export OS_PREFIX_PATH="${Qt5_Dir}/lib/cmake;${Qt5_Dir}"
            mkdir $GITHUB_WORKSPACE/OpenMS/bld/
            ## TODO allow changing of ctest build site in cmake
            ## TODO potentially parse some OS infos and add to build name
            ## TODO allow changing Contrib path to get rid of the extra cmake file!
            dbus-uuidgen > /var/lib/dbus/machine-id
            xvfb-run ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/travis/cibuild.cmake

            FAILED_TEST=$(find $GITHUB_WORKSPACE/OpenMS/bld/ -name "Test.xml" -type f -exec grep "<Test Status=\"failed\">" -c {} \; )
            if [ "$FAILED_TEST" -gt "0" ] ; then
              echo "$FAILED_TEST tests failed"
              exit -1
            fi

      env:
          CONTRIB_BUILD_DIRECTORY: "/contrib-build"
          CI_PROVIDER: "GitHub-Actions"
          CMAKE_GENERATOR: "Unix Makefiles"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          BUILD_NAME: "${{ env.RUN_NAME }}-Ubuntu-testClass-testTOPP"
          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: "Off"
          BUILD_FLAGS: "-j2"