A fix for annotating theoretical mz values miscellaneous

[acquayefrank]

Describe your changes

Removed seemingly redundant function that splits comments in .msp files by semicolon.
This function causes an error in other files but is actually redundant in most cases.

Checklist before requesting a review

• I have performed a self-review of my code

[Copilot]

Pull Request Overview

This PR removes a redundant function get_peak_tuples that was splitting peak lines by semicolon in MSP file processing. The change simplifies the peak parsing logic by directly reading peak lines instead of unnecessarily splitting them.

• Removed the get_peak_tuples function that was causing errors in other files
• Simplified the peak reading loop to directly process individual peak lines
• Cleaned up unused import and formatting

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
tools/misc/use_theoretical_mz_annotations.py	Removed redundant get_peak_tuples function and simplified peak processing logic
tools/misc/test-data/output_plus_no_annotated.msp	Removed trailing empty line
tools/misc/test-data/output_only_annotated.msp	Removed trailing empty line
tools/misc/test-data/input.msp	Removed trailing empty line

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[Copilot]

The removal of the for loop over peak_pairs creates a logic error. The original code processed multiple peaks per line (split by semicolon), but now only the first peak from file.readline() is processed once per iteration. This will skip peaks if multiple peaks exist on a single line, or process incomplete data if peaks span multiple lines differently than expected.