Updated Docs to use PeptideIdentificationList #480
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WalkthroughDocumentation 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
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Actionable comments posted: 0
🧹 Nitpick comments (7)
requirements.txt (1)
9-9: Add version pin or constraints for jupyter_bokeh (optional).Unpinned deps can drift and break the examples, especially with Bokeh/HoloViews stacks. Either pin jupyter_bokeh or add a constraints/lock file for the docs env to keep interactive plots stable.
docs/source/user_guide/interactive_plots.rst (1)
80-85: Nit: prefer standard axis label “m/z”.Minor terminology polish for consistency with MS literature.
Apply this diff:
-hd.dynspread(raster, threshold=0.7, how="add", shape="square").opts( - width=800, - height=800, - xlabel="Retention time (s)", - ylabel="mass/charge (Da)", -) +hd.dynspread(raster, threshold=0.7, how="add", shape="square").opts( + width=800, + height=800, + xlabel="Retention time (s)", + ylabel="m/z", +)docs/source/user_guide/other_ms_data_formats.rst (2)
20-22: Align prose with new container type.Since examples now use oms.PeptideIdentificationList, consider clarifying in the surrounding text that it’s a list-like container of PeptideIdentification.
51-53: Repeat the container note for pepXML.Same suggestion as above to avoid reader confusion about accepted types.
docs/source/user_guide/export_pandas_dataframe.rst (1)
113-117: Update parameter doc to accept Iterable[PeptideIdentification].peptide_identifications_to_df currently documents “list”; since the example passes PeptideIdentificationList, note that any iterable/list-like container is supported (if true). Otherwise, convert to list before calling.
docs/source/user_guide/peptide_search.rst (1)
146-149: Use of size() is consistent with the new container.Good update from len(peptide_ids) to peptide_ids.size(). Ensure other docs follow the same convention.
docs/source/user_guide/quality_control.rst (1)
45-49: Update the inline comment to match the new container.The code now uses a container, not a Python list.
- pep_ids = oms.PeptideIdentificationList() # list of PeptideIdentification() + pep_ids = oms.PeptideIdentificationList() # PeptideIdentificationList container
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📒 Files selected for processing (10)
docs/source/user_guide/PSM_to_features.rst(1 hunks)docs/source/user_guide/export_files_GNPS.rst(1 hunks)docs/source/user_guide/export_pandas_dataframe.rst(1 hunks)docs/source/user_guide/identification_data.rst(2 hunks)docs/source/user_guide/interactive_plots.rst(2 hunks)docs/source/user_guide/other_ms_data_formats.rst(3 hunks)docs/source/user_guide/peptide_search.rst(4 hunks)docs/source/user_guide/quality_control.rst(1 hunks)docs/source/user_guide/untargeted_metabolomics_preprocessing.rst(2 hunks)requirements.txt(1 hunks)
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🔇 Additional comments (9)
docs/source/user_guide/export_files_GNPS.rst (1)
50-51: Good: explicit size() check improves clarity with the new container.This avoids relying on truthiness and reads well with PeptideIdentificationList semantics.
docs/source/user_guide/interactive_plots.rst (1)
38-39: Document the 5th argument to get2DPeakDataLong.Please add a short note explaining what the “1” controls (e.g., MS level, binning, or threads) so readers know how to adjust it.
docs/source/user_guide/other_ms_data_formats.rst (1)
34-36: Consistency check: container works with load/store.Assuming IdXML/mzIdentML bindings accept PeptideIdentificationList seamlessly. If there are versions that still expect Python lists, add a brief note on the minimum pyOpenMS version here.
docs/source/user_guide/peptide_search.rst (1)
34-37: Switch to PeptideIdentificationList looks correct.Using oms.PeptideIdentificationList for SimpleSearchEngineAlgorithm.search is appropriate and iteration below remains compatible.
docs/source/user_guide/PSM_to_features.rst (1)
48-51: Loading into PeptideIdentificationList is correct.IdXMLFile.load accepts the new container; downstream IDMapper.annotate call matches this type.
docs/source/user_guide/untargeted_metabolomics_preprocessing.rst (2)
144-153: Correct container usage in IDMapper.annotate.Initializing peptide_ids as PeptideIdentificationList aligns with annotate’s expectations.
164-169: push_back usage is appropriate.Replacing append with push_back matches the new container API and Feature.setPeptideIdentifications accepts it.
docs/source/user_guide/identification_data.rst (2)
164-166: Good migration to PeptideIdentificationList.Creating the container and adding via push_back is correct and keeps iteration semantics unchanged.
197-199: Loading into PeptideIdentificationList is correct.IdXMLFile.load with pep_ids as the container is consistent with the earlier store example.
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AttributeError Traceback (most recent call last) |
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If you are hoping for 3.4.1: You never released it. https://pypi.org/project/pyopenms/#history |
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ah damn... forgot that we don't have a branching workflow. thanks for pointing this out |
Summary by CodeRabbit
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