make diann2mztab optional for large-scale datasets

[daichengxin]

PR Type

Enhancement

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Description

• Added new optional flag --enable-diann2mztab (-e) to control mzTab file generation
• Made mzTab conversion optional to improve performance for large-scale datasets
• MSstats and Triqler output formats remain enabled by default
• Updated package version to 0.0.18

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Changes walkthrough 📝

	Relevant files
Configuration changes	__init__.py Version bump to 0.0.18                                                                      quantmsutils/init.py Bumped version from 0.0.17 to 0.0.18 +1/-1
Enhancement	diann2mztab.py Make mzTab conversion optional in DIA-NN processing            quantmsutils/diann/diann2mztab.py Added new enable_diann2mztab flag parameter to make mzTab conversion optional Modified diann2mztab function to only convert to mzTab format when flag is enabled Kept MSstats and Triqler conversions as mandatory +13/-10

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[qodo-merge-pro]

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PR Reviewer Guide 🔍

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⏱️ Estimated effort to review: 1 🔵⚪⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Missing Logging The mzTab conversion is now optional but there's no logging to indicate whether it was enabled/disabled or when the conversion is complete

[qodo-merge-pro]

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
General	Add logging for skipped operations to improve system observability and debugging Add logging statement to indicate when mzTab conversion is skipped to improve observability quantmsutils/diann/diann2mztab.py [182-192] if enable_diann2mztab: mztab_out = f"{Path(exp_design).stem}_out.mzTab" # Convert to mzTab diann_directory.convert_to_mztab( report=report, f_table=f_table, charge=charge, missed_cleavages=missed_cleavages, dia_params=dia_params, out=mztab_out, ) +else: + logger.info("Skipping mzTab conversion as enable_diann2mztab is False") Apply this suggestion Suggestion importance[1-10]: 5 Why: Adding a log message when mzTab conversion is skipped is a good practice for observability and debugging, though it's a minor enhancement that doesn't affect core functionality.	5