Fix Builds for OpenMS 3.5 (#299)

* remove temp fix

* add contrib libs the CMakeCache.txt

* switch to 3.5.0

* fix windows

* thirdparty is x86_64 now

* remove restrictions for cython and autowrap

* disable parquet support

* add contrib libraries to path

* remove deprecated pyinstaller

* set openms share path

Author: t0mdavid-m

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

@@ -13,7 +13,7 @@ permissions:
   contents: write
 
 env:
-  OPENMS_VERSION: 3.2.0 
+  OPENMS_VERSION: 3.5.0 
   PYTHON_VERSION: 3.11.0
   # Name of the installer
   APP_NAME: OpenMS-StreamlitTemplateApp
@@ -33,27 +33,14 @@ jobs:
         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
+
+    - name: Install Qt (Windows)
       uses: jurplel/install-qt-action@v4
       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'
+        version: '6.8.3'    ## Note this version is build with win64_msvc2022_64 and should always match what we use
+        arch: 'win64_msvc2022_64'
         cache: 'false'
-        aqtversion: '==3.1.*'
+        archives: 'qtsvg qtimageformats qtbase'
 
     # https://github.com/marketplace/actions/visual-studio-shell
     - name: Set up Visual Studio shell
@@ -101,6 +88,12 @@ jobs:
         rm contrib_build-Windows.tar.gz
         ls
 
+    - name: Add contrib to PATH
+      shell: bash
+      run: |
+        # Add contrib library path for runtime DLL resolution
+        echo "${{ github.workspace }}/OpenMS/contrib/lib" >> $GITHUB_PATH
+
     - name: Setup ccache cache
       uses: actions/cache@v4
       with:
@@ -122,7 +115,7 @@ jobs:
           # add third-party binaries to PATH
           # use flat THIRDPARTY structure
           mkdir -p _thirdparty
-          cp -R OpenMS/THIRDPARTY/Windows/64bit/* _thirdparty/
+          cp -R OpenMS/THIRDPARTY/Windows/x86_64/* _thirdparty/
           cp -R OpenMS/THIRDPARTY/All/* _thirdparty/
           # add third-party binaries to PATH
           for thirdpartytool in ${{ github.workspace }}/_thirdparty/*
@@ -134,9 +127,9 @@ jobs:
       shell: bash
       run: |
           mkdir $GITHUB_WORKSPACE/OpenMS/bld/
+          bash OpenMS/tools/ci/capture-env.sh -v $GITHUB_WORKSPACE/OpenMS/bld/CMakeCache.txt
           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"
@@ -146,6 +139,7 @@ jobs:
           ENABLE_TOPP_TESTING: "ON"
           ENABLE_CLASS_TESTING: "ON"
           WITH_GUI: "OFF"
+          WITH_PARQUET: "OFF"
           ADDRESS_SANITIZER: "Off"
           BUILD_TYPE: "Release"
           OPENMP: "Off"
@@ -264,6 +258,9 @@ jobs:
       run: |
         echo '@echo off' > ${{ env.APP_NAME }}.bat
         echo '' >> ${{ env.APP_NAME }}.bat
+        echo 'REM Set OpenMS data path for TOPP tools' >> ${{ env.APP_NAME }}.bat
+        echo 'set OPENMS_DATA_PATH=%~dp0share\OpenMS' >> ${{ env.APP_NAME }}.bat
+        echo '' >> ${{ env.APP_NAME }}.bat
         echo 'REM Create .streamlit directory in user''s home if it doesn''t exist' >> ${{ env.APP_NAME }}.bat
         echo 'if not exist "%USERPROFILE%\.streamlit" mkdir "%USERPROFILE%\.streamlit"' >> ${{ env.APP_NAME }}.bat
         echo '' >> ${{ env.APP_NAME }}.bat