tests(converters): fix spectronaut and metamorpheus tests

[tonywu1999]

Motivation and Context

https://bioconductor.org/checkResults/3.22/bioc-LATEST/MSstatsPTM/nebbiolo2-checksrc.html

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules

Summary by CodeRabbit

• Documentation

  • Updated package documentation metadata and maintainership information.
  • Revised function documentation to reorder parameters and clarify deprecation of an argument.
  • Enhanced internal function documentation for improved clarity on terminus location adjustments.

• Refactor

  • Improved code clarity by using explicit named arguments in several function calls.

• New Features

  • No new features were introduced.

• Bug Fixes

  • No user-facing bugs were addressed.

[coderabbitai]

Walkthrough

The changes update documentation metadata for the MSstatsPTM package and its maintainer, clarify function argument passing in converter functions by switching to explicit named arguments, reorder parameters in the documentation for groupComparisonPTM to reflect upcoming deprecation of data.type, and improve internal function .fixTerminus documentation. No functional code logic was altered.

Changes

Cohort / File(s)	Change Summary
Package Documentation Metadata R/MSstatsPTM.R, man/MSstatsPTM.Rd	Updated documentation metadata: removed @docType package, replaced NULL with "_PACKAGE", added @keywords internal, changed maintainer from Devon Kohler to Anthony Wu, adjusted author roles, and added the "internal" keyword.
Converter Function Argument Clarity R/converters.R	Updated function calls within SpectronauttoMSstatsPTMFormat and MetamorpheusToMSstatsPTMFormat to use explicit named arguments instead of positional arguments. No functional changes.
Function Documentation Parameter Order man/groupComparisonPTM.Rd	Reordered ptm_label_type and protein_label_type parameters in the documentation for groupComparisonPTM, moving them to the end and updating descriptions to reflect planned deprecation of data.type.
Internal Function Documentation Enhancement R/utils_converters.R, man/dot-fixTerminus.Rd	Added detailed roxygen-style documentation for internal function .fixTerminus, clarifying parameters, purpose, and return value; updated Rd documentation accordingly. No code logic changes.

Sequence Diagram(s)

Not applicable: all changes are documentation or argument naming updates with no new or modified control flow.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Suggested reviewers

• devonjkohler

Poem

A bunny hopped through docs and code,
Tidying names on every road.
Maintainers swapped, parameters moved—
Explicit calls, all doubts removed.
With metadata neat and clear,
This patch brings order, far and near!
🐇✨

Note

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 154a72b and 2935a93.

📒 Files selected for processing (2)

• R/utils_converters.R (1 hunks)
• man/dot-fixTerminus.Rd (1 hunks)

✅ Files skipped from review due to trivial changes (2)

• R/utils_converters.R
• man/dot-fixTerminus.Rd

✨ Finishing Touches

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