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enable thirdparty tools for template #300

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Merged
t0mdavid-m merged 4 commits into from
Dec 22, 2025
Merged

enable thirdparty tools for template #300

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2c0fb31
enable thirdparty tools for template
t0mdavid-m Dec 22, 2025
03db427
Merge branch 'main' into thirdparty_tools
t0mdavid-m Dec 22, 2025
6725013
add delayed expansion local
t0mdavid-m Dec 22, 2025
d4f0204
Merge remote-tracking branch 'openms/thirdparty_tools' into thirdpart…
t0mdavid-m Dec 22, 2025
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6 changes: 6 additions & 0 deletions .github/workflows/build-windows-executable-app.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -257,10 +257,16 @@ jobs:
- name: Create .bat file
run: |
echo '@echo off' > ${{ env.APP_NAME }}.bat
echo 'setlocal EnableDelayedExpansion' > ${{ 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 Add each subfolder in share\OpenMS\THIRDPARTY to PATH' >> ${{ env.APP_NAME }}.bat
echo 'for /D %%D in ("%OPENMS_DATA_PATH%\THIRDPARTY\*") do (' >> ${{ env.APP_NAME }}.bat
echo ' set "PATH=!PATH!;%%D"' >> ${{ env.APP_NAME }}.bat
echo ')' >> ${{ env.APP_NAME }}.bat
echo '' >> ${{ env.APP_NAME }}.bat
Comment on lines +265 to +269
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@coderabbitai coderabbitai bot Dec 22, 2025

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⚠️ Potential issue | 🔴 Critical

Critical: Delayed expansion not enabled for PATH variable update.

Line 266 uses the !PATH! syntax which requires delayed expansion to be enabled in the batch file. Without setlocal enabledelayedexpansion at the beginning of the batch file, !PATH! will be treated as a literal string rather than expanding the PATH variable, breaking the intended functionality.

Additionally, verify that the share\OpenMS\THIRDPARTY directory structure with subdirectories actually exists in the packaged files, as the build process (lines 108-124) flattens the THIRDPARTY structure during the build.

🔎 Proposed fix for delayed expansion 
 echo '@echo off' > ${{ env.APP_NAME }}.bat
+echo 'setlocal enabledelayedexpansion' >> ${{ 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

Run the following script to verify the THIRDPARTY directory structure in the packaging process:

#!/bin/bash
# Description: Verify if THIRDPARTY subdirectories are preserved in the package
# Expected: Find evidence that THIRDPARTY structure is maintained in share/OpenMS

# Check packaging configuration
rg -n "THIRDPARTY" --type yaml -C3

# Look for any CMake or packaging scripts that handle THIRDPARTY
fd -e cmake -e txt | xargs rg -l "THIRDPARTY" | head -10

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
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