build_executable_msi.yaml

name: Build windows executable (.msi)
on:
  push:
    branches: 
      - main
  pull_request:
    branches: [ "main" ]
  workflow_dispatch:
  
env:
  PYTHON_VERSION: 3.10.0
  # Define unique GUID for UpgradeCode
  APP_UpgradeCode: "c1c7c11f-b063-4100-9854-af555d1b26d1"
  # Define needed TOPP tools need in NuXLApp
  TOPP_TOOLS: "OpenNuXL FileConverter PercolatorAdapter TextExporter"
  # App name
  APP_NAME: OpenMS-NuXLApp
  
jobs: 
  build-executable:
    runs-on: windows-2022

    env:
      PYTHON_VERSION: 3.10.0
      APP_NAME: OpenMS-NuXLApp

    steps:
    - name: Checkout
      uses: actions/checkout@v4

    - name: Download OpenMS release asset
      env:
        GH_TOKEN: ${{ github.token }}
      shell: bash
      run: |
        gh release download OpenMS_3_5_windows \
          --repo Arslan-Siraj/nuxl_webapp_supporting_files \
          --pattern "*.zip"
          
    - name: Verify downloaded file
      shell: bash
      run: |
        ls -lh
        file *.zip
        unzip -t *.zip
        
    - name: Extract OpenMS package
      shell: bash
      run: |
        unzip *.zip -d openms-package
        ls -R openms-package
        
    - name: Extract inner OpenMS package
      shell: bash
      run: |
        unzip \
          openms-package/openms-package/OpenMS/bld/openms-package.zip \
          -d openms-inner
          
    - name: Promote OpenMS bin and share to root
      shell: bash
      run: |
        mkdir -p openms-bin openms-share
        cp -r openms-inner/openms-package/bin/* openms-bin/
        cp -r openms-inner/openms-package/share/* openms-share/
        
    - name: Set up Python (regular distribution)
      uses: actions/setup-python@v5
      with:
        python-version: ${{ env.PYTHON_VERSION }} # Use the same version as the embeddable version

    - name: Setup python embeddable version
      run: |
        # Create a directory for the embeddable Python version
        mkdir python-${{ env.PYTHON_VERSION }}
        
        # Download and unzip the embeddable 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
        # Define paths for the regular Python distribution and the embeddable distribution
        $PYTHON_DIR="${{ runner.tool_cache }}/Python/${{ env.PYTHON_VERSION }}/x64" # Path from actions/setup-python
        $EMBED_DIR="python-${{ env.PYTHON_VERSION }}"
        
        mkdir -p $EMBED_DIR/Lib/site-packages/tkinter
        mkdir -p $EMBED_DIR/tcl
        # Copy necessary Tkinter files from the regular Python distribution
        cp -r $PYTHON_DIR/Lib/tkinter/* $EMBED_DIR/Lib/site-packages/tkinter/
        cp -r $PYTHON_DIR/tcl/* $EMBED_DIR/tcl/
        cp $PYTHON_DIR/DLLs/_tkinter.pyd $EMBED_DIR/
        cp $PYTHON_DIR/DLLs/tcl86t.dll $EMBED_DIR/
        cp $PYTHON_DIR/DLLs/tk86t.dll $EMBED_DIR/

    - name: Bundle MSVC runtime DLLs
      shell: powershell
      run: |
        $embed = "python-${{ env.PYTHON_VERSION }}"
        $dlls = @(
          "vcomp140.dll",
          "vcruntime140.dll",
          "vcruntime140_1.dll",
          "msvcp140.dll"
        )

        foreach ($dll in $dlls) {
          Copy-Item "C:\Windows\System32\$dll" "$embed\$dll" -Force
        }
    
    - 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 python310._pth file
      run: |
        sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python310._pth

    #- name: Install Required Packages
    #  run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements_embd_py310_win.txt --no-warn-script-location
          
    - name: Set to offline deployment
      run: |
        $content = Get-Content -Raw settings.json | ConvertFrom-Json
        $content.online_deployment = $false
        $content | ConvertTo-Json -Depth 100 | Set-Content settings.json

    - name: Create launcher .bat file
      shell: pwsh
      run: |
        $batContent = @"
        @echo off
        set PYTHON=.\python-${{ env.PYTHON_VERSION }}\python
        set REQ=.\requirements_embd_py310_win.txt
        set MARKER=.\python-${{ env.PYTHON_VERSION }}\.deps_installed
        
        REM If marker exists, skip installation
        if exist "%MARKER%" goto RUN_APP
        
        echo Preparing Python environment for launching App...
        
        REM Ensure pip exists
        "%PYTHON%" -m ensurepip >nul 2>&1
        
        REM Attempt installation
        "%PYTHON%" -m pip install -r "%REQ%" --no-warn-script-location
        if errorlevel 1 (
            echo Dependency installation failed or was interrupted.
            exit /b 1
        )

        REM Copy NuXL share folder to pyopenms share
        xcopy /E /I /Y ".\NuXL" ".\python-3.10.0\Lib\site-packages\pyopenms\share\OpenMS\NuXL"

        REM Rename folder
        ren "streamlit" ".streamlit"

        REM Create marker only after full success
        echo OK>"%MARKER%"
        
        :RUN_APP
        start /min "" "%PYTHON%" -m streamlit run app.py
        "@
        
            $batContent | Set-Content -Encoding ASCII "${{ env.APP_NAME }}.bat"
            
    - name: Verify .streamlit folder exists
      shell: bash
      run: |
        echo "PWD:"
        pwd
        echo "Listing repo root:"
        ls -la
        echo "Listing .streamlit:"
        ls -la .streamlit

    - name: Create All-in-one executable folder
      shell: bash
      run: |       
        if [ -d "streamlit_exe" ]; then
          rm -rf streamlit_exe
        fi
        
        mkdir -p streamlit_exe
        mv python-${{ env.PYTHON_VERSION }} streamlit_exe
        cp -r src streamlit_exe
        cp -r content streamlit_exe
        cp -r assets streamlit_exe
        #cp -r example-data streamlit_exe
        cp app.py streamlit_exe
        cp settings.json streamlit_exe
        cp ${{ env.APP_NAME }}.bat streamlit_exe
        cp requirements_embd_py310_win.txt streamlit_exe
         
         mkdir -p streamlit_exe streamlit_exe/share
      
        # Copy all DLLs from openms-bin
        cp -r openms-bin/*.dll streamlit_exe/
    
        # Copy share folder
        cp -r openms-share/* streamlit_exe/share/
        cp -r openms-share/OpenMS/NuXL streamlit_exe/NuXL/
  
        # copy chemistry outside
        cp -r openms-share/OpenMS/CHEMISTRY streamlit_exe/
        
        # Copy only selected .exe files from openms-bin
        for tool in $TOPP_TOOLS; do
          if [ -f "openms-bin/$tool.exe" ]; then
            cp "openms-bin/$tool.exe" streamlit_exe/
          else
            echo "Warning: $tool.exe not found in openms-bin"
          fi
        done
  
        # copy thirdparty folder
        cp -r openms-package/openms-package/_thirdparty streamlit_exe/

    - name: Create Streamlit config
      shell: bash
      run: |
        mkdir -p streamlit_exe/streamlit
    
        cat <<'EOF' > streamlit_exe/streamlit/config.toml
        [global]
        developmentMode = false
        
        [server]
        maxUploadSize = 50000
        port = 8505 
    
        [theme]
        primaryColor = "#29379b"
        EOF
    
    - name: Generate Readme.txt
      shell: bash
      run: |
        cat <<EOF > streamlit_exe/Readme.txt
        Welcome to ${{ env.APP_NAME }} app!
        To launch the application:
        1. Navigate to the installation directory.
        2. Double-click on the file: ${{ env.APP_NAME }}.bat or ${{ env.APP_NAME }} shortcut.
        Additional Information:
        - If multiple Streamlit apps are running, you can change the port in the .streamlit/config.toml file.
          Example:
            [server]
            port = 8505
        Reach out to us:
        - Join our Discord server for support and community discussions: https://discord.com/invite/4TAGhqJ7s5
        - Contribute or stay updated with the latest OpenMS web app developments on GitHub: https://github.com/OpenMS/streamlit-template
        - Checkout the ${{ env.APP_NAME }} on Github: https://github.com/Arslan-Siraj/nuxl-app
        - Visit our website for more information: https://openms.de/
        
        Thanks for using ${{ env.APP_NAME }}!
        EOF

    - name: Install WiX Toolset
      run: |
        curl -LO https://github.com/wixtoolset/wix3/releases/download/wix3111rtm/wix311-binaries.zip
        unzip wix311-binaries.zip -d wix
        rm wix311-binaries.zip

    - name: Build .wxs for streamlit_exe folder
      run: |
        ./wix/heat.exe dir streamlit_exe -gg -sfrag -sreg -srd -template component -cg StreamlitExeFiles -dr AppSubFolder -out streamlit_exe_files.wxs

    - name: Generate VBScript file
      shell: bash
      run: |
        cat <<EOF > ShowSuccessMessage.vbs
        MsgBox "The ${{ env.APP_NAME }} application is successfully installed.", vbInformation, "Installation Complete"
        EOF

    - name: Prepare SourceDir
      run: |
        if (Test-Path -Path "SourceDir") {
            Remove-Item -Recurse -Force "SourceDir"
        }
        
        mkdir SourceDir
        mv streamlit_exe/* SourceDir
        cp ShowSuccessMessage.vbs SourceDir
        cp assets/openms_license.rtf SourceDir
        # Logo of app : from https://www.xiconeditor.com/
        cp assets/openNuXL.ico SourceDir

    - name: Generate WiX XML file
      shell: bash
      run: |
        cat <<EOF > streamlit_exe.wxs
        <?xml version="1.0"?>
        <Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">
          <Product Id="*" Name="${{ env.APP_NAME }}" Language="1033" Version="1.0.0.0" Codepage="1252" Manufacturer="OpenMS Developer Team" UpgradeCode="${{ env.APP_UpgradeCode }}">
            <Package Id="*" InstallerVersion="300" Compressed="yes" InstallPrivileges="elevated" Platform="x64" />
            <Media Id="1" Cabinet="streamlit.cab" EmbedCab="yes" />
        
            <!-- Folder structure -->
            <Property Id="WIXUI_INSTALLDIR" Value="INSTALLFOLDER" />
            <Directory Id="TARGETDIR" Name="SourceDir">
              <Directory Id="ProgramFilesFolder"> 
                <Directory Id="INSTALLFOLDER" Name="${{ env.APP_NAME }}">
                  <Directory Id="AppSubFolder" Name="${{ env.APP_NAME }}" /> 
                  <Component Id="CreateAppFolder" Guid="95dbfa06-d36a-427f-995c-e87769ac2e59">
                    <CreateFolder>
                      <Permission User="Everyone" GenericAll="yes" />
                    </CreateFolder>
                  </Component>
                </Directory>
              </Directory>
              <Directory Id="DesktopFolder" />
            </Directory>
        
            <!-- Add components -->
            <Feature Id="MainFeature" Title="Main Application" Level="1">
              <ComponentGroupRef Id="StreamlitExeFiles" />
              <ComponentRef Id="CreateAppFolder" />
              <ComponentRef Id="DesktopShortcutComponent" />
              <ComponentRef Id="InstallDirShortcutComponent" />
            </Feature>
        
            <!-- Create shortcut for running app on desktop -->
            <Component Id="DesktopShortcutComponent" Guid="3597b243-9180-4d0b-b105-30d8b0d1a334" Directory="DesktopFolder">
              <Shortcut Id="DesktopShortcut" Name="${{ env.APP_NAME }}" Description="Launch ${{ env.APP_NAME }}" Target="[AppSubFolder]${{ env.APP_NAME }}.bat" WorkingDirectory="AppSubFolder" Icon="AppIcon" />
              <RegistryValue Root="HKCU" Key="Software\\OpenMS\\${{ env.APP_NAME }}" Name="DesktopShortcut" Type="integer" Value="1" KeyPath="yes" />
            </Component>
        
            <!-- Create shortcut for running app in installer folder -->
            <Component Id="InstallDirShortcutComponent" Guid="c2df9472-3b45-4558-a56d-6034cf7c8b72" Directory="AppSubFolder">
              <Shortcut Id="InstallDirShortcut" Name="${{ env.APP_NAME }}" Description="Launch ${{ env.APP_NAME }}" Target="[AppSubFolder]${{ env.APP_NAME }}.bat" WorkingDirectory="AppSubFolder" Icon="AppIcon" />
              <RegistryValue Root="HKCU" Key="Software\\OpenMS\\${{ env.APP_NAME }}" Name="InstallFolderShortcut" Type="integer" Value="1" KeyPath="yes" />
            </Component>
        
            <!-- Provide icon here; it should exist in the SourceDir folder -->
            <Icon Id="AppIcon" SourceFile="SourceDir/openNuXL.ico" />
        
            <!-- Run app directly after installation -->
            <!-- <CustomAction Id="RunApp" Directory="AppSubFolder" Execute="deferred" Return="asyncNoWait" Impersonate="no"
                          ExeCommand="cmd.exe /c &quot;[AppSubFolder]${{ env.APP_NAME }}.bat&quot;" /> -->
            
            <!-- Custom Action to Show Success Message -->
            <Binary Id="ShowMessageScript" SourceFile="SourceDir/ShowSuccessMessage.vbs" />
            <CustomAction Id="ShowSuccessMessage" BinaryKey="ShowMessageScript" VBScriptCall="" Execute="immediate" Return="check" />
        
            <!-- Add all Custom Actions -->
            <InstallExecuteSequence>
              <!-- Custom action display success message -->
              <Custom Action="ShowSuccessMessage" After="InstallFinalize">NOT Installed</Custom>
              <!-- Run app directly after installation -->
              <!-- <Custom Action="RunApp" Before="InstallFinalize">NOT REMOVE</Custom> -->
            </InstallExecuteSequence>
        
            <!-- Interface options -->
            <UI>
                  <UIRef Id="WixUI_InstallDir" />
                  <UIRef Id="WixUI_ErrorProgressText" />
            </UI> 
        
            <!-- Provide license; it should exist in the SourceDir folder -->
            <WixVariable Id="WixUILicenseRtf" Value="SourceDir/openms_license.rtf" />
          </Product>
        </Wix>
        EOF
        
    - name: Build .wixobj file with candle.exe
      run: |
        ./wix/candle.exe streamlit_exe.wxs streamlit_exe_files.wxs
        
    - name: Link .wixobj file into .msi with light.exe
      run: |
        ./wix/light.exe -ext WixUIExtension -sice:ICE60 -o ${{ env.APP_NAME }}.msi streamlit_exe_files.wixobj streamlit_exe.wixobj
        
    #- name: Compress Installer
    #  run: |
    #    7z a ${{ env.APP_NAME }}.zip 
        
    - name: Archive build artifacts
      uses: actions/upload-artifact@v4
      with:
        name: ${{ env.APP_NAME }}
        path: |
          ${{ env.APP_NAME }}.msi