build-windows-executable-app.yaml

name: Build executable for Windows
on:
  push:
    branches: [ "main" , "TaggerViewerDeploy"]
  pull_request:
    branches: [ "main" , "TaggerViewerDeploy"]

jobs:
  build-vue-js-component:
    runs-on: ubuntu-latest

    steps:

    # Step to set up Node.js environment
    - name: Set up Node.js
      uses: actions/setup-node@v4
      with:
        node-version: '21'

    # Step to clone the Vue.js repository
    - name: Checkout Vue.js repository
      uses: actions/checkout@v4
      with:
        repository: 't0mdavid-m/openms-streamlit-vue-component'
        ref: 'TaggerViewer'
        path: 'openms-streamlit-vue-component'

    - name: Install and build Vue.js component
      run: |
        cd openms-streamlit-vue-component
        npm install
        npm run build

    - name: Upload dist as artifact
      uses: actions/upload-artifact@v4
      with:
        name: vue-js-dist
        path: openms-streamlit-vue-component/dist

  build-openms:
    runs-on: windows-latest

    env:
      OPENMS_VERSION: 3.0.0 

    steps:

    - name: Checkout
      uses: actions/checkout@v3
      with:
        repository: t0mdavid-m/OpenMS
        ref: TaggerViewerDeployment
        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'
      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 $GITHUB_WORKSPACE/OpenMS/tools/ci/cibuild.cmake
      env:
          #OS_PREFIX_PATH: "${{ 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: ${{ github.workspace }}/.ccache
          CCACHE_COMPRESS: true
          CCACHE_COMPRESSLEVEL: 12
          CCACHE_MAXSIZE: 400M
          Eigen3_DIR: "${{ steps.tools-prefix.outputs.eigen_choco }}"

    - 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 }}"

    - 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, build-vue-js-component]

    env:
      PYTHON_VERSION: 3.11.0

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

    - name: Download vue js as artifact
      uses: actions/download-artifact@v4
      with:
        name: vue-js-dist
        path: js-dist

    - 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: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: ${{ env.PYTHON_VERSION }}

    - name: Setup virtual environment
      shell: cmd
      run: |
        python -m venv myenv

        call myenv\Scripts\activate.bat   

        pip install -r requirements.txt

        pip install pyinstaller

    - name: Write function to cli.py
      shell: bash
      run: |
        echo "{ls {D:/a/FlashViewer/FlashViewer/myenv/Lib/site-packages/streamlit/web/}}"
        head -n -2 D:/a/FlashViewer/FlashViewer/myenv/Lib/site-packages/streamlit/web/cli.py > temp_cli.py

        cat << EOF >> temp_cli.py
        def _main_run_clExplicit(file, command_line, args=[], flag_options=[]):
            main._is_running_with_streamlit = True
            bootstrap.run(file, command_line, args, flag_options)


        if __name__ == "__main__":
            main()
        EOF

        mv temp_cli.py D:/a/FlashViewer/FlashViewer/myenv/Lib/site-packages/streamlit/web/cli.py  

    - name: Compile app with pyinstaller
      shell: cmd
      run: |
        call myenv\Scripts\activate.bat 
        pyinstaller --onefile --additional-hooks-dir ./hooks run_app.py --clean


    - name: Copy everything to dist directory
      run: |
        cp -r .streamlit dist/.streamlit
        cp -r pages dist/pages
        cp -r src dist/src
        cp -r assets dist/assets
        cp -r example-data dist/example-data
        cp -r openms-bin/*.dll dist/
        cp -r openms-bin/FLASHDeconv.exe dist/
        cp -r openms-bin/FLASHTagger.exe dist/
        cp -r openms-bin/DecoyDatabase.exe dist/
        cp -r share dist/share
        cp -r js-dist dist/js-component/dist
        cp example_database.fasta dist/
        cp example_spectrum_1.mzML dist/
        cp example_spectrum_2.mzML dist/
        cp app.py dist/

    - name: Patch WorkflowManager.py for windows
      run: |
        cp dist/src/workflow/WorkflowManagerWindows.py dist/src/workflow/WorkflowManager.py
    
    - name: Modify .spec file
      shell: bash
      run: |
        cp run_app_temp.spec run_app.spec

    - name: Make executable
      shell: cmd
      run: |
        call myenv\Scripts\activate.bat
        pyinstaller run_app.spec --clean

    - 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: OpenMS-App
        path: dist