Merge pull request OpenMS#57 from Arslan-Siraj/main

window executable available with embeddable python

.github/workflows/build-windows-executable-app-with-pyinstaller.yaml

@@ -0,0 +1,253 @@
+name: Build executable for Windows with pyinstaller
+on:
+  workflow_dispatch:
+
+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: release/${{ env.OPENMS_VERSION }}
+        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
+        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"
+          #  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: 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
+
+    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: 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: |
+        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: 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 dist/bin
+        cp -r share dist/share
+        cp app.py dist/
+    
+    - 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

.github/workflows/build-windows-executable-app.yaml

@@ -63,6 +63,7 @@ jobs:
         key: ${{ runner.os }}-contrib3
 
     - name: Load contrib build
+      if: steps.cache-contrib-win.outputs.cache-hit != 'true'
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       run: |
@@ -176,67 +177,44 @@ jobs:
         name: OpenMS-share
         path: share
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ env.PYTHON_VERSION }}
-
-    - name: Setup virtual environment
-      shell: cmd
+    - name: Setup python embeddable version
       run: |
-        python -m venv myenv
-
-        call myenv\Scripts\activate.bat   
-
-        pip install -r requirements.txt
+        mkdir python-${{ 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
 
-        pip install pyinstaller
-
-    - name: Write function to cli.py
-      shell: bash
+    - name: Install pip
       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)
-
+        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
 
-        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
+    - name: Uncomment 'import site' in python311._pth file
       run: |
-        call myenv\Scripts\activate.bat 
-        pyinstaller --onefile --additional-hooks-dir ./hooks run_app.py --clean
+        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: Copy everything to dist directory
+    - name: Create run_app.bat file
       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 dist/bin
-        cp -r share dist/share
-        cp app.py dist/
-    
-    - name: Modify .spec file
-      shell: bash
+        echo '@echo off' > run_app.bat
+        echo '.\\python-${{ env.PYTHON_VERSION }}\\python -m streamlit run app.py local' >> run_app.bat
+      
+    - name: Create All-in-one executable folder
       run: |
-        cp run_app_temp.spec run_app.spec
-
-    - name: Make executable
-      shell: cmd
-      run: |
-        call myenv\Scripts\activate.bat
-        pyinstaller run_app.spec --clean
+        mkdir streamlit_exe
+        mv python-${{ env.PYTHON_VERSION }} streamlit_exe
+        mv run_app.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 -r openms-bin streamlit_exe/bin
+        cp -r share streamlit_exe/share
+        cp app.py streamlit_exe
 
     - name: Delete OpenMS bin artifact
       uses: geekyeggo/delete-artifact@v2
@@ -247,9 +225,14 @@ jobs:
       uses: geekyeggo/delete-artifact@v2
       with:
           name: OpenMS-share
+
+    - name: Compress streamlit_exe folder to OpenMS-App.zip
+      run: |
+        7z a OpenMS-App.zip ./streamlit_exe/* -r
 
     - name: Upload artifact
       uses: actions/upload-artifact@v3
       with:
         name: OpenMS-App
-        path: dist
+        path: OpenMS-App.zip
+