Updated Docs to use PeptideIdentificationList

[matteopilz]

Summary by CodeRabbit

• New Features

  • Introduced a dedicated PeptideIdentificationList container in the Python API for handling peptide identifications.
  • Enhanced 2D peak data retrieval to accept an additional parameter in get2DPeakDataLong.

• Documentation

  • Updated multiple user guides to use PeptideIdentificationList instead of Python lists, including counting via .size() and item insertion via push_back.
  • Clarified feature filtering by using explicit size checks.
  • Refreshed interactive plotting examples with updated options and calls.

• Chores

  • Added jupyter_bokeh to requirements for improved notebook visualization support.

[coderabbitai[bot]]

Walkthrough

Documentation examples were updated to use oms.PeptideIdentificationList instead of Python lists, with corresponding size/count and push_back adjustments. One GNPS example now uses an explicit size check. Interactive plotting code adds a fifth argument to get2DPeakDataLong and simplifies opts usage. requirements.txt adds jupyter_bokeh.

Changes

Cohort / File(s)	Summary
Adopt PeptideIdentificationList in docs docs/source/user_guide/PSM_to_features.rst, docs/source/user_guide/export_pandas_dataframe.rst, docs/source/user_guide/identification_data.rst, docs/source/user_guide/other_ms_data_formats.rst, docs/source/user_guide/peptide_search.rst, docs/source/user_guide/quality_control.rst, docs/source/user_guide/untargeted_metabolomics_preprocessing.rst	Replace Python lists with oms.PeptideIdentificationList() in examples; update additions to push_back; adjust counting to .size() where shown; iteration and IdXML load/store use the new container.
GNPS export explicit check docs/source/user_guide/export_files_GNPS.rst	Change truthiness check to feature.getPeptideIdentifications().size() > 0 before pushing to filtered_map.
Interactive plots example update docs/source/user_guide/interactive_plots.rst	Add fifth argument (1) to exp.get2DPeakDataLong(...); simplify plotting by applying .opts(...) directly to the raster/dynspread pipeline and remove nested plot dict.
Dependency update requirements.txt	Add jupyter_bokeh after bokeh.

Sequence Diagram(s)

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Suggested reviewers

• timosachsenberg

Poem

A nibble of docs, a hop through the code,
I swap my lists for containers bestowed.
With size I check, with push_back I cheer,
Plots gain a tweak, the picture is clear.
jupyter_bokeh joins the show—
Thump-thump! Onward the features grow. 🐇✨

✨ Finishing Touches

🧪 Generate unit tests

• [ ] Create PR with unit tests
• [ ] Post copyable unit tests in a comment

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[timosachsenberg]

AttributeError Traceback (most recent call last) Cell In[5], line 12 8 for i, feature_map in enumerate(feature_maps): 9 if feature_map.getMetaValue("spectra_data")[ 10 0 11 ].decode() == exp.getMetaValue("mzML_path"): ---> 12 peptide_ids = oms.PeptideIdentificationList() 13 protein_ids = [] 14 mapper.annotate( 15 feature_map, 16 peptide_ids, (...) 20 exp, 21 )

[jpfeuffer]

If you are hoping for 3.4.1: You never released it. https://pypi.org/project/pyopenms/#history If you are hoping for nightly. We have still not adapted a branching workflow here, so we only support docs for latest stable.

[timosachsenberg]

ah damn... forgot that we don't have a branching workflow. thanks for pointing this out