Various fixes in io modules

[RalfG]

Fixed

• io.idxml: Fix compatibility with pyOpenMS 3.5+ for PeptideIdentificationList handling (also see Note: Breaking API change in pyOpenMS 3.5: IdXMLFile.load() and store() now require PeptideIdentificationList OpenMS/OpenMS#8552).
• io.percolator: Fix missing ScanNr values when using write_file (fixes ms2pip feature generator file identification ms2rescore#235).
• io.percolator: Fix missing style argument when checking whether PercolatorTabWriter supports write_psm.
• io.pepxml: Fix robustness of PepXMLReader against missing params in file.

[Copilot]

Pull request overview

This PR addresses three specific issues in the io modules for percolator and pepxml file handling, improving robustness and fixing missing functionality.

• Fixed missing ScanNr values when using write_file in PercolatorTabWriter
• Fixed missing style argument when checking PercolatorTabWriter's write_psm support
• Enhanced PepXMLReader robustness to handle optional/missing parameters in pepXML files

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
psm_utils/io/percolator.py	Added ScanNr assignment in write_file method to ensure each PSM gets a sequential scan number
psm_utils/io/pepxml.py	Added KNOWN_METADATA_KEYS constant and refactored _parse_psm to safely handle missing optional fields (metadata, provenance data, proteins, rank, score) using .get() methods and dictionary comprehensions
psm_utils/io/init.py	Added writer-specific kwargs to provide required 'style' parameter when testing PercolatorTabWriter's write_psm support

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[codecov]

Codecov Report

❌ Patch coverage is 44.11765% with 19 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.01%. Comparing base (19a657d) to head (07e6544).
⚠️ Report is 8 commits behind head on main.

Files with missing lines	Patch %	Lines
psm_utils/io/idxml.py	65.00%	7 Missing ⚠️
psm_utils/io/__init__.py	0.00%	4 Missing ⚠️
psm_utils/io/percolator.py	0.00%	4 Missing ⚠️
psm_utils/io/peptide_record.py	0.00%	2 Missing ⚠️
psm_utils/io/pepxml.py	33.33%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #140      +/-   ##
==========================================
- Coverage   72.23%   72.01%   -0.23%     
==========================================
  Files          32       32              
  Lines        3224     3245      +21     
==========================================
+ Hits         2329     2337       +8     
- Misses        895      908      +13     

Flag	Coverage Δ
unittests	72.01% <44.11%> (-0.23%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.