Add topp tool selection

[t0mdavid-m]

User description

This PR adds the selection of TOPP tools to the github workflows. Copying only required TOPP tools has two advantages:

1. Reduction of package size
2. Quicker extraction as on the first install Windows Defender scans all binaries, causing significant extraction times (I observed up to 20 minutes).

This should improve the situation with #65.

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PR Type

enhancement, configuration changes

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Description

• Added environment variables OPENMS_VERSION and TOPP_TOOLS to specify the OpenMS version and required TOPP tools.
• Updated the GitHub Actions workflows to copy only the specified TOPP tools instead of the entire openms-bin directory.
• This change reduces package size and speeds up extraction times, especially on Windows where antivirus scans can significantly delay the process.

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Changes walkthrough 📝

Relevant files

Configuration changes

build-windows-executable-app-with-pyinstaller.yaml Selective copying of TOPP tools in PyInstaller workflow    .github/workflows/build-windows-executable-app-with-pyinstaller.yaml Added environment variables for OpenMS version and TOPP tools. Modified the script to copy only specified TOPP tools instead of the entire openms-bin directory. +9/-4      build-windows-executable-app.yaml Selective copying of TOPP tools in build workflow                .github/workflows/build-windows-executable-app.yaml Added environment variables for OpenMS version and TOPP tools. Modified the script to copy only specified TOPP tools instead of the entire openms-bin directory. +9/-4

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PR Reviewer Guide 🔍

⏱️ Estimated effort to review [1-5]	2
🧪 Relevant tests	No
🔒 Security concerns	No
⚡ Key issues to review	Possible Bug: The PR introduces a change where only specified TOPP tools are copied to the distribution directories. Ensure that all necessary dependencies of these tools are also copied, as missing dependencies could cause runtime failures.

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PR Code Suggestions ✨

Category	Suggestion	Score
Enhancement	Add error handling to the file copying process to manage missing files gracefully To ensure that the script fails gracefully if the specified .exe files do not exist, consider adding error handling around the Copy-Item command. This could involve checking if the file exists before attempting to copy it, and logging an error or skipping the copy if it does not. .github/workflows/build-windows-executable-app-with-pyinstaller.yaml [230] -Copy-Item "openms-bin/${file}.exe" -Destination "dist/bin/${file}.exe" +if (Test-Path "openms-bin/${file}.exe") { + Copy-Item "openms-bin/${file}.exe" -Destination "dist/bin/${file}.exe" +} else { + Write-Output "Warning: File ${file}.exe does not exist." +} Apply this suggestion Suggestion importance[1-10]: 9 Why: Adding error handling ensures that the script fails gracefully if the specified .exe files do not exist, which enhances the reliability and robustness of the deployment process.	9
	Implement error handling for file copying to ensure the workflow does not fail silently To enhance the reliability of the deployment script, add error handling for the Copy-Item command in the workflow. This ensures that any issues during the file copying are caught and handled, preventing the workflow from failing silently if an expected file is missing. .github/workflows/build-windows-executable-app.yaml [222] -Copy-Item "openms-bin/${file}.exe" -Destination "streamlit_exe/bin/${file}.exe" +if (Test-Path "openms-bin/${file}.exe") { + Copy-Item "openms-bin/${file}.exe" -Destination "streamlit_exe/bin/${file}.exe" +} else { + Write-Output "Warning: File ${file}.exe does not exist." +} Apply this suggestion Suggestion importance[1-10]: 9 Why: This suggestion enhances the reliability of the deployment script by adding error handling for the Copy-Item command, ensuring that any issues during file copying are caught and managed appropriately.	9
Possible issue	Improve the robustness of the script by handling potential spaces in tool names more safely Consider using a more robust method to handle potential spaces in the TOPP_TOOLS environment variable values. Using -split ' ' assumes that the tool names do not contain spaces. If they do, this could lead to incorrect paths or filenames. A safer approach might be to use a character that is less likely to be part of a filename, such as a comma, and adjust the split accordingly. .github/workflows/build-windows-executable-app-with-pyinstaller.yaml [228] -$files = $env:TOPP_TOOLS -split ' ' +$files = $env:TOPP_TOOLS -split ',' Apply this suggestion Suggestion importance[1-10]: 8 Why: This suggestion addresses a potential issue with spaces in tool names, which could lead to incorrect paths or filenames. Using a comma as a delimiter is a safer approach and improves the robustness of the script.	8
	Use a comma as a delimiter in TOPP_TOOLS to better handle tool names with spaces Similar to the previous suggestion, consider changing the delimiter used in the TOPP_TOOLS environment variable to handle potential spaces in tool names. Using a comma as a delimiter can help avoid issues if tool names include spaces. .github/workflows/build-windows-executable-app.yaml [220] -$files = $env:TOPP_TOOLS -split ' ' +$files = $env:TOPP_TOOLS -split ',' Apply this suggestion Suggestion importance[1-10]: 8 Why: Similar to the first suggestion, this addresses the potential issue of spaces in tool names, improving the robustness of the script by using a safer delimiter.	8

[t0mdavid-m]

Maybe this PR should wait until the next release as well as there seems to be no release yet where SiriusExport.exe is available.

[Arslan-Siraj]

Thanks @t0mdavid-m