Operating System and Hardware

Any

OpenMS Version

pyOpenMS 3.5

Installation Method

Python: pip

Bug Description

As a note to other users; feel free to close immediately.

In pyOpenMS 3.5, the signature for IdXMLFile.load() and IdXMLFile.store() changed in a breaking way. The peptide_ids parameter now requires a PeptideIdentificationList object instead of a regular Python list.

Before (pyOpenMS <3.5):

protein_ids = []
peptide_ids = []
oms.IdXMLFile().load(filename, protein_ids, peptide_ids)

After (pyOpenMS 3.5+):

protein_ids = []
peptide_ids = oms.PeptideIdentificationList()  # Changed!
oms.IdXMLFile().load(filename, protein_ids, peptide_ids)

Additionally, PeptideIdentificationList uses .push_back() instead of .append():

peptide_ids.push_back(peptide_id)  # Instead of .append()

Backward compatible solution:

if hasattr(oms, "PeptideIdentificationList"):
    peptide_ids = oms.PeptideIdentificationList()
    # Use .push_back() to add items
else:
    peptide_ids = []
    # Use .append() to add items

This change affects any code that reads or writes idXML files.