Fix Windows builds: use system Python to compile packages into embeddable target

The embeddable Python lacks development headers (Python.h) needed to
compile native extensions like pyprophet. Use actions/setup-python to
get a full Python installation for compiling, then install packages
with --target pointing to the embeddable Python's site-packages.

Author: t0mdavid-m

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

@@ -245,11 +245,9 @@ jobs:
       run: |
         sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python311._pth
 
-    - name: Install build dependencies (required for pyprophet build)
-      run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install cython numpy --no-warn-script-location
-
-    - name: Install Required Packages
-      run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements.txt --no-warn-script-location
+    - name: Install Required Packages (using system Python to compile, targeting embeddable)
+      run: |
+        python -m pip install -r requirements.txt --target python-${{ env.PYTHON_VERSION }}/Lib/site-packages --upgrade
 
     - name: Set to offline deployment
       run: |

.github/workflows/test-win-exe-w-embed-py.yaml

@@ -1,5 +1,5 @@
 name: Test streamlit executable for Windows with embeddable python
-on: 
+on:
   push:
     branches: [ "main" ]
   workflow_dispatch:
@@ -17,37 +17,40 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
 
+      - name: Set up Python (for building packages with native extensions)
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
       - name: Download python embeddable version
         run: |
           mkdir python-${{ 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
 
-      - name: Install pip
+      - name: Install pip in embeddable Python
         run: |
           curl -O https://bootstrap.pypa.io/get-pip.py
           ./python-${{ env.PYTHON_VERSION }}/python get-pip.py --no-warn-script-location
           rm get-pip.py
-          
+
       - name: Uncomment 'import site' in python311._pth file
         run: |
           sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python311._pth
-          
+
       - name: Print content of python311._pth file
         run: |
           cat python-${{ env.PYTHON_VERSION }}/python311._pth
 
-      - name: Install build dependencies (required for pyprophet build)
-        run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install cython numpy --no-warn-script-location
+      - name: Install Required Packages (using system Python to compile, targeting embeddable)
+        run: |
+          python -m pip install -r requirements.txt --target python-${{ env.PYTHON_VERSION }}/Lib/site-packages --upgrade
 
-      - name: Install Required Packages
-        run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install -r requirements.txt --no-warn-script-location
-      
       - name: Create .bat file
         run: |
           echo " start /min .\python-${{ env.PYTHON_VERSION }}\python -m streamlit run app.py local" > ${{ env.APP_NAME }}.bat
-          
+
       - name: Create All-in-one executable folder
         run: |
           mkdir streamlit_exe
@@ -62,7 +65,7 @@ jobs:
           cp settings.json streamlit_exe
           cp default-parameters.json streamlit_exe
           cp ${{ env.APP_NAME }}.bat streamlit_exe
-          
+
       - name: Generate Readme.txt
         shell: bash
         run: |
@@ -83,20 +86,20 @@ jobs:
           - 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
           - Visit our website for more information: https://openms.de/
-          
+
           Thank you for using ${{ env.APP_NAME }}!
           EOF
-          
+
       - name: Install WiX Toolset
         run: |
           curl -LO https://github.com/wixtoolset/wix3/releases/download/wix3111rtm/wix311-binaries.zip
           unzip wix311-binaries.zip -d wix
           rm wix311-binaries.zip
-      
+
       - name: Build .wxs for streamlit_exe folder
         run: |
           ./wix/heat.exe dir streamlit_exe -gg -sfrag -sreg -srd -template component -cg StreamlitExeFiles -dr AppSubFolder -out streamlit_exe_files.wxs
-      
+
       - name: Generate VBScript file
         shell: bash
         run: |
@@ -112,7 +115,7 @@ jobs:
           cp assets/openms_license.rtf SourceDir
           # Logo of app
           cp assets/openms.ico SourceDir
-          
+
       - name: Generate WiX XML file
         shell: bash
         run: |
@@ -122,13 +125,13 @@ jobs:
             <Product Id="*" Name="${{ env.APP_NAME }}" Language="1033" Version="1.0.0.0" Codepage="1252" Manufacturer="OpenMS Developer Team" UpgradeCode="${{ env.APP_UpgradeCode }}">
               <Package Id="*" InstallerVersion="300" Compressed="yes" InstallPrivileges="elevated" Platform="x64" />
               <Media Id="1" Cabinet="streamlit.cab" EmbedCab="yes" />
-          
+
               <!-- Folder structure -->
               <Property Id="WIXUI_INSTALLDIR" Value="INSTALLFOLDER" />
               <Directory Id="TARGETDIR" Name="SourceDir">
-                <Directory Id="ProgramFilesFolder"> 
+                <Directory Id="ProgramFilesFolder">
                   <Directory Id="INSTALLFOLDER" Name="${{ env.APP_NAME }}">
-                    <Directory Id="AppSubFolder" 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" />
@@ -138,52 +141,52 @@ jobs:
                 </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/openms.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> 
-          
+              </UI>
+
               <!-- Provide license; it should exist in the SourceDir folder -->
               <WixVariable Id="WixUILicenseRtf" Value="SourceDir/openms_license.rtf" />
             </Product>
@@ -193,7 +196,7 @@ jobs:
       - 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
@@ -203,4 +206,4 @@ jobs:
         with:
           name: OpenMS-App-Test
           path: |
-            ${{ env.APP_NAME }}.msi
+            ${{ env.APP_NAME }}.msi