build-windows-executable-app.yaml

name: Build executable for Windows

on:
  push:
    branches: [ "main"]
  pull_request:
    branches: [ "main"]

jobs:
  build-openms:
    runs-on: windows-latest

    env:
      OPENMS_VERSION: 3.0.0 

    steps:
    - name: Checkout
      uses: actions/checkout@v3
      with:
        repository: OpenMS/OpenMS
        ref: develop
        path: 'OpenMS'

    - 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'
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      run: |
        cd OpenMS/contrib
        # Download the file using the URL fetched from GitHub
        gh release download -R OpenMS/contrib --pattern 'contrib_build-Windows.tar.gz'
        # Extract the archive
        tar -xzf contrib_build-Windows.tar.gz
        rm contrib_build-Windows.tar.gz
        ls

    - 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 $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
      env:
          #OS_PREFIX_PATH: "${{ env.Qt5_DIR }}/lib/cmake;${{ env.Qt5_DIR }}"
          OPENMS_CONTRIB_LIBS: "${{ 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: Upload TOPP tools as artifact
      uses: actions/upload-artifact@v3
      with:
        name: OpenMS-bin
        path: OpenMS/bld/bin

    - name: Upload share as artifact
      uses: actions/upload-artifact@v3
      with:
        name: OpenMS-share
        path: OpenMS/share

  build-executable:
    runs-on: windows-latest
    needs: [build-openms]

    env:
      PYTHON_VERSION: 3.11.0

    steps:
    - name: Checkout
      uses: actions/checkout@v3

    - name: Download TOPP tools as artifact
      uses: actions/download-artifact@v3
      with:
        name: OpenMS-bin
        path: openms-bin

    - name: Download share as artifact
      uses: actions/download-artifact@v3
      with:
        name: OpenMS-share
        path: share

    - name: Setup python embeddable version
      run: |
        mkdir python-${{ env.PYTHON_VERSION }}
        curl -O https://www.python.org/ftp/python/${{ env.PYTHON_VERSION }}/python-${{ env.PYTHON_VERSION }}-embed-amd64.zip
        unzip python-${{ env.PYTHON_VERSION }}-embed-amd64.zip -d python-${{ env.PYTHON_VERSION }}
        rm python-${{ env.PYTHON_VERSION }}-embed-amd64.zip

    - name: Install pip
      run: |
        curl -O https://bootstrap.pypa.io/get-pip.py
        ./python-${{ env.PYTHON_VERSION }}/python get-pip.py --no-warn-script-location
        rm get-pip.py

    - name: Uncomment 'import site' in python311._pth file
      run: |
        sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python311._pth

    - name: Install Required Packages
      run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements.txt --no-warn-script-location

    - name: Create UmetaFlow.bat file
      run: |
        echo '@echo off' > UmetaFlow.bat
        echo '.\\python-${{ env.PYTHON_VERSION }}\\python -m streamlit run Home.py local' >> UmetaFlow.bat
      
    - name: Create All-in-one executable folder
      run: |
        mkdir streamlit_exe
        mv python-${{ env.PYTHON_VERSION }} streamlit_exe
        mv UmetaFlow.bat streamlit_exe
        cp -r src streamlit_exe
        cp -r pages streamlit_exe
        cp -r assets streamlit_exe
        cp -r example-data streamlit_exe
        cp -r .streamlit streamlit_exe
        cp openms-bin/*.dll streamlit_exe
        cp openms-bin/FileFilter.exe streamlit_exe
        cp openms-bin/HighResPrecursorMassCorrector.exe streamlit_exe
        cp openms-bin/FeatureFinderMetabo.exe streamlit_exe
        cp openms-bin/FeatureFinderMetaboIdent.exe streamlit_exe
        cp openms-bin/MetaboliteAdductDecharger.exe streamlit_exe
        cp openms-bin/MapAlignerPoseClustering.exe streamlit_exe
        cp openms-bin/MapRTTransformer.exe streamlit_exe
        cp openms-bin/FeatureLinkerUnlabeledKD.exe streamlit_exe
        cp openms-bin/IDMapper.exe streamlit_exe
        cp openms-bin/GNPSExport.exe streamlit_exe
        cp openms-bin/SiriusExport.exe streamlit_exe
        cp openms-bin/MetaboliteSpectralMatcher.exe streamlit_exe
        cp -r share streamlit_exe/share
        cp Home.py streamlit_exe

    - name: Delete OpenMS bin artifact
      uses: geekyeggo/delete-artifact@v2
      with:
          name: OpenMS-bin

    - name: Delete OpenMS share artifact
      uses: geekyeggo/delete-artifact@v2
      with:
          name: OpenMS-share

    - name: Upload artifact
      uses: actions/upload-artifact@v3
      with:
        name: UmetaFlow-App
        path: streamlit_exe