Add mzIdentML converter with multi-mzML and pyopenms 3.5.0+ support

[Shen-YuFei]

Enhance mzIdentML Converter with Multi-mzML Support

Summary

Add comprehensive mzIdentML converter with support for multiple mzML file integration and upgrade pyopenms compatibility.

Changes

New Features

• Add mzIdentML to PSM parquet converter (qpxc convert mzidentml)
• Support --mzml-folder option for multi-file mzML spectral data integration
• Auto-detect native ID formats (scan=, cycle=, index=, spectrum=)
• Case-insensitive mzML file matching with .mzML and .mzML.gz support

Improvements

• Upgrade pyopenms dependency to 3.5.0+
• Add backward compatibility for pyopenms < 3.5.0 API changes
• Update IdXML loading to use new PeptideIdentificationList API

Tests

• Add unit tests for scan number extraction formats
• Add tests for multi-mzML folder support

Documentation

• Add mzIdentML converter documentation to CLI reference

Testing

• Validated on PXD000923 dataset (117,891 PSMs with spectral data)

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[Copilot]

Pull request overview

This PR adds a comprehensive mzIdentML converter to QPX with support for multiple mzML file integration and upgrades pyopenms compatibility to version 3.5.0+.

Changes:

• New mzIdentML to PSM parquet converter with multi-mzML folder support
• pyopenms API compatibility layer for 3.5.0+ with backward compatibility
• Auto-detection of native ID formats for various instrument vendors
• SQL query formatting cleanup and whitespace normalization across test files

Reviewed changes

Copilot reviewed 20 out of 24 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
qpx/core/mzidentml.py	New mzIdentML parser with multi-mzML support and native ID format detection
qpx/core/openms.py	Enhanced OpenMSHandler with native ID pattern auto-detection and multi-pattern support
qpx/core/idxml.py	Updated IdXML loader with pyopenms 3.5.0+ PeptideIdentificationList API support
qpx/core/idxml_utils/idxml.py	Added backward compatibility for pyopenms < 3.5.0
qpx/commands/convert/mzidentml.py	CLI command for mzIdentML conversion with validation
qpx/qpxc.py	Registered mzidentml command in CLI
docs/cli-convert.md	Comprehensive documentation for mzIdentML converter
tests/core/mzidentml/test_mzidentml.py	Test suite covering parser, scan extraction, and multi-mzML features
tests/examples/mzidentml/test_sample.mzid	Test fixture with valid mzIdentML structure
Multiple test files	SQL query formatting and whitespace cleanup

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[Copilot]

Variable residues is not used.

Suggested change

residues = mod_elem.get("residues", "")

[Copilot]

Variable rank is not used.

Suggested change

rank = int(sii.get("rank", 1))