Minor changes

[ypriverol]

Summary by CodeRabbit

• New Features

  • Added mzTab peptide section support for enhanced data parsing and conversion.
  • Implemented peptide-to-protein mapping to improve protein group resolution in quantitative analyses.

• Tests

  • Added comprehensive test coverage for peptide-protein resolution logic.

• Chores

  • Updated Pylint and Codacy configurations with additional linting rule suppressions.

[coderabbitai]

Caution

Review failed

Pull request was closed or merged during review

📝 Walkthrough

Walkthrough

Configuration updates disable line-too-long warnings in Pylint and Codacy. mzTab parser refactored to support peptide sections via section-driven architecture. QuantmsFeatureAdapter enhanced with peptide-to-protein mapping logic to resolve ambiguous protein groups using mzTab PEP section data.

Changes

Cohort / File(s)	Summary
Configuration .codacy.yml, .pylintrc	Added line-too-long to disabled Pylint warning codes; Codacy configuration excludes tests/** from top-level exclude_paths.
mzTab Parsing qpx/converters/mztab.py	Refactored parsing to section-driven architecture with prefix dispatch; added peptide section support via _MZTAB_SECTIONS and generic handlers; introduced _stream_mztab_to_files helper for fast loader; replaced manual temp-file cleanup with _cleanup_tmpdir; updated logging to include peptide counts.
Peptide-Protein Mapping qpx/converters/quantms/feature_adapter.py	Added __init__ method and _pep_protein_map instance attribute; introduced _build_peptide_protein_map() helper to detect peptides table and create sequence→accession mappings; modified _rows_to_feature_records() to resolve multi-accession protein groups using peptide mappings.
Tests tests/converters/test_pep_protein_resolution.py	New test module validating peptide→protein resolution logic with fixtures for DuckDB setup; test cases cover unambiguous/ambiguous mappings, missing tables, and protein group resolution in feature records.

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~50 minutes

Possibly related PRs

• major changes to update the schemas #166: Overlaps in qpx/converters/quantms/feature_adapter.py; both extend QuantmsFeatureAdapter with additional logic (peptide mapping vs. PSM/RT handling).
• Minor fix related with MSnet developments  #200: Also modifies qpx/converters/quantms/feature_adapter.py with ProForma and SQL changes within the same adapter class.

Poem

🐰 A section-driven hop, a peptide map so fine,
Proteins once ambiguous now cleanly align,
No more line-too-long warnings to dismay,
The adapter's grown wiser in every way! ✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'Minor changes' is vague and generic, failing to convey the actual scope of work which includes mzTab peptide section support, refactored parsing logic, new adapter initialization, and comprehensive test coverage.	Replace with a specific title describing the main changes, such as 'Add mzTab peptide section support and protein resolution logic' or 'Implement peptide parsing and peptide-protein mapping in converters'.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	Docstring coverage is 81.48% which is sufficient. The required threshold is 80.00%.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch dev

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[codacy-production]

Not up to standards ⛔

🔴 Issues 2 minor

Alerts:
⚠ 2 issues (≤ 0 issues of at least minor severity)

Results:
2 new issues

Category	Results
Documentation	2 minor

View in Codacy

🟢 Metrics 14 complexity · 2 duplication

Metric	Results
Complexity	14
Duplication	2

View in Codacy

_{TIP This summary will be updated as you push new changes. Give us feedback}