build-windows-executable-app-with-pyinstaller.yaml

name: Build executable for Windows with pyinstaller
on:
  workflow_dispatch:
env:
  OPENMS_VERSION: 3.2.0 
  # Control whether to build pyOpenMS from source (true) or use pip (false). Default: false
  BUILD_PYOPENMS: false
  # Define needed TOPP tools here
  TOPP_TOOLS: "FeatureFinderMetabo MetaboliteAdductDecharger SiriusExport"

jobs:
  build-openms:
    runs-on: windows-latest
    env:
      PYTHON_VERSION: 3.11.0

    steps:
    - name: Checkout
      uses: actions/checkout@v3
      with:
        repository: OpenMS/OpenMS
        ref: release/${{ env.OPENMS_VERSION }}
        path: 'OpenMS'

    # Temporary fix - until seqan is back online or new OpenMS release (3.4)
    - name: Get latest cibuild.cmake
      working-directory: OpenMS
      run: |
        git config user.name "GitHub Actions"
        git config user.email "actions@github.com"
        git fetch origin develop
        git checkout origin/develop -- tools/ci/cibuild.cmake
        git checkout origin/develop -- tools/ci/citest.cmake
        git checkout origin/develop -- tools/ci/cipackage.cmake

    - 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: Set up Python for pyOpenMS build
      if: env.BUILD_PYOPENMS == 'true'
      uses: actions/setup-python@v5
      with:
        python-version: ${{ env.PYTHON_VERSION }}

    - name: Install Python dependencies for pyOpenMS build
      if: env.BUILD_PYOPENMS == 'true'
      shell: bash
      run: |
        python -m pip install --upgrade pip
        python -m pip install setuptools wheel nose 'cython<3.1' 'autowrap<0.23' numpy

    - 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
        7z x -so contrib_build-Windows.tar.gz | 7z x -si -ttar
        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;${{ env.Qt5_DIR }}"
          CONTRIB_BUILD_DIRECTORY: "${{ github.workspace }}/OpenMS/contrib"
          CI_PROVIDER: "GitHub-Actions"
          CMAKE_GENERATOR: "Ninja"
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          BUILD_NAME: "${{ env.RUN_NAME }}-Win64-class-topp-${{ github.run_number }}"
          ENABLE_STYLE_TESTING: "OFF"
          ENABLE_TOPP_TESTING: "ON"
          ENABLE_CLASS_TESTING: "ON"
          WITH_GUI: "ON"
          ADDRESS_SANITIZER: "Off"
          BUILD_TYPE: "Release"
          OPENMP: "Off"
          USE_STATIC_BOOST: "On"
          PYOPENMS: "${{ env.BUILD_PYOPENMS == 'true' && 'ON' || 'OFF' }}"
          #  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: Build pyOpenMS
      if: env.BUILD_PYOPENMS == 'true'
      shell: bash
      run: |
          cd $GITHUB_WORKSPACE/OpenMS/bld/
          ninja pyopenms
          
    - name: Package pyOpenMS wheel
      if: env.BUILD_PYOPENMS == 'true'
      shell: bash
      run: |
          cd $GITHUB_WORKSPACE/OpenMS/bld/pyOpenMS
          python -m pip install wheel
          python setup.py bdist_wheel
          
    - name: Upload pyOpenMS wheel as artifact
      if: env.BUILD_PYOPENMS == 'true'
      uses: actions/upload-artifact@v4
      with:
        name: pyopenms-wheel
        path: ${{ github.workspace }}/OpenMS/bld/pyOpenMS/dist/*.whl

    - name: Package
      shell: bash
      run: |
          ctest --output-on-failure -V -S $GITHUB_WORKSPACE/OpenMS/tools/ci/cipackage.cmake
      env:
          SOURCE_DIRECTORY: "${{ github.workspace }}/OpenMS"
          PACKAGE_TYPE: zip
          SEARCH_ENGINES_DIRECTORY: "${{ github.workspace }}/_thirdparty"
          CI_PROVIDER: "GitHub-Actions"
          CPACK_PACKAGE_FILE_NAME: "openms-package"

    - 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 package as artifact
      uses: actions/upload-artifact@v4
      with:
        name: openms-package
        path: ${{ github.workspace }}/OpenMS/bld/*.zip

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

    env:
      PYTHON_VERSION: 3.11.0

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

    - name: Download package as artifact
      uses: actions/download-artifact@v4
      with:
        name: openms-package
        path: openms-package

    - name: Extract bin and share from package
      run: |
        cd openms-package
        unzip "*.zip" -d .
        cp -r openms-package/bin ../openms-bin
        cp -r openms-package/share ../share

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

    - name: Download pyOpenMS wheel (if built from source)
      if: env.BUILD_PYOPENMS == 'true'
      uses: actions/download-artifact@v4
      with:
        name: pyopenms-wheel
        path: pyopenms-wheel

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

        call myenv\Scripts\activate.bat   

        if "${{ env.BUILD_PYOPENMS }}" == "true" (
          pip install pyopenms-wheel/*.whl
          findstr /v /r /c:"^pyopenms" requirements.txt > requirements_filtered.txt
          pip install -r requirements_filtered.txt
        ) else (
          pip install -r requirements.txt
        )

        pip install pyinstaller

    - name: Write function to cli.py
      shell: bash
      run: |
        head -n -2 D:/a/streamlit-template/streamlit-template/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/streamlit-template/streamlit-template/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: 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: Copy everything to dist directory
      run: |
        mkdir streamlit_exe

        mv python-${{ env.PYTHON_VERSION }} streamlit_exe
        mv run_app.bat streamlit_exe
        cp -r src streamlit_exe
        cp -r utils streamlit_exe
        cp -r content streamlit_exe
        cp -r docs streamlit_exe
        cp -r assets streamlit_exe
        cp -r example-data streamlit_exe
        cp openms-bin/*.dll streamlit_exe
        cp -r .streamlit streamlit_exe
        cp -r share streamlit_exe/share
        cp app.py streamlit_exe
        cp settings.json streamlit_exe
        cp default-parameters.json streamlit_exe

        $files = $env:TOPP_TOOLS -split ' '
        foreach ($file in $files) {
          Copy-Item "openms-bin/${file}.exe" -Destination "streamlit_exe/${file}.exe"
        }
    
    - 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 package artifact
      uses: geekyeggo/delete-artifact@v5
      with:
          name: openms-package

    - name: Upload artifact
      uses: actions/upload-artifact@v3
      with:
        name: OpenMS-App
        path: dist
  
    - name: Upload Artifact as Release Asset
      if: github.event_name == 'release'
      uses: softprops/action-gh-release@v2
      with:
        files: OpenMS-App.zip
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}