fix(results): support pyOpenMS 3.5.0 IdXMLFile.load signature

[t0mdavid-m]

Problem

Every workflow run on the cluster dies as soon as it tries to read a Comet result:

ERROR: can not handle type of ('/workspaces-streamlit-template/.../B000248_..._comet.idXML', [], [])
  File "/app/./src/WorkflowTest.py", line 758, in execution
    id_df, spectra_data = parse_idxml(idxml_path)
  File "/app/./src/common/results_helpers.py", line 104, in parse_idxml
    IdXMLFile().load(str(idxml_path), proteins, peptides)
Exception: can not handle type of (...)

Root cause

pyOpenMS 3.5.0 changed the signature of IdXMLFile.load()/store(). The third
parameter went from a libcpp_vector[PeptideIdentification], which accepted an ordinary
Python list, to a dedicated PeptideIdentificationList container:

# 3.4.0
def load(self, filename, protein_ids: List[ProteinIdentification], peptide_ids: List[PeptideIdentification]) -> None

# 3.5.0
def load(self, filename, protein_ids: List[ProteinIdentification], peptide_ids: PeptideIdentificationList) -> None

Passing [] matches no overload, so autowrap's dispatcher raises before any file I/O —
which is why the message names the file but never touches it. protein_ids is unchanged
and still takes a plain list.

Bisected across locally installed releases:

pyopenms	IdXMLFile().load(path, [], [])
3.1.0, 3.2.0, 3.3.0, 3.4.0, 3.4.1	works
3.5.0	can not handle type of

requirements.txt pins pyopenms==3.5.0 and Dockerfile builds OpenMS release/3.5.0,
so deployed images always hit this, while dev environments still on 3.3.x never do.
That's the version mismatch — the deployment is ahead of the code, not behind it.

Other pyOpenMS loaders in the repo (MzMLFile, ConsensusXMLFile, ParamXMLFile) pass
properly wrapped objects rather than plain lists, and were verified unaffected on 3.5.0.

Fix

Add load_idxml() to results_helpers, which feature-detects the new container and
normalises the result back to a plain list so every caller is unchanged:

proteins = []
peptides = PeptideIdentificationList() if PeptideIdentificationList else []
IdXMLFile().load(str(idxml_file), proteins, peptides)
return proteins, list(peptides)

Feature detection rather than a version check keeps the app working on 3.4.x and earlier,
so local dev environments don't have to be upgraded in lockstep. The three call sites
(idxml_to_df, parse_idxml, and the inline copy in WorkflowTest) now route through it;
IdXMLFile is no longer referenced in WorkflowTest, so that import is dropped.

Note PeptideIdentificationList exposes push_back, not append — worth remembering for
any future code that builds one to hand to store().

Verification

• End-to-end against a generated idXML on 3.1.0, 3.3.0, 3.4.0 (legacy list path) and
  3.5.0 (new container) — all four produce identical parsed output through
  load_idxml, idxml_to_df and parse_idxml.
• Two regression tests added to tests/test_results_helpers.py. Reverting the fix makes
  them fail with the exact production error message,
  Exception: can not handle type of ('...', [], []).
• Full suite in a CI-faithful venv (streamlit 1.49.1 + requirements.txt, i.e. pyopenms
  3.5.0): 102 passed.
• Pylint, run as CI invokes it: no new findings — the change removes one pre-existing
  E0611 by dropping the now-unused import.

🤖 Generated with Claude Code

https://claude.ai/code/session_016Qn3mLqr7zBr7rgCokx6ku

[coderabbitai]

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