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[ypriverol]

Pull Request

Description

Brief description of the changes made in this PR.

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Performance improvement
• Code refactoring
• Test addition/update
• Updates to the dependencies has been done.

Summary by CodeRabbit

• Refactor
  • Optimized peptide length calculations using vectorized operations for improved processing performance across data analysis modules.

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Caution

Review failed

The pull request is closed.

📝 Walkthrough

Walkthrough

This pull request optimizes peptide length computations in DIA and MS/mztab modules by replacing per-row lambda operations with vectorized str.len() calls, and removes the draw_dia_heatmap wrapper function in favor of direct function calls.

Changes

Cohort / File(s)	Summary
DIA Utilities Optimization & Cleanup pmultiqc/modules/common/dia_utils.py	Vectorized peptide length computation using str.len() for improved performance; flipped column membership check style; removed draw_dia_heatmap wrapper function requiring direct calls to cal_dia_heatmap and dia_plots.draw_heatmap
MSTab Vectorization pmultiqc/modules/common/ms/mztab.py	Optimized pep_length computation from per-row apply(lambda) to vectorized str.len() operation

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Major improvements in DIA #358 — Converts per-row sequence operations to vectorized approaches and modifies heatmap-related logic in DIA code, mirroring the optimization pattern in this PR.
• Fix bugs and add heatmap in DIA #324 — Introduces draw_dia_heatmap wrapper and related heatmap functions that this PR removes in favor of direct function calls.

Suggested labels

Review effort 2/5

Suggested reviewers

• daichengxin

Poem

🐰 Peptides lined up, row by row,
Now vectorized—much faster flow!
Wrapper gone, direct calls remain,
Performance gains, efficiency's gain! ⚡

✨ Finishing touches

• 📝 Generate docstrings

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