Updated Docs to use PeptideIdentificationList

[matteopilz]

Summary by CodeRabbit

• New Features

  • Introduced PeptideIdentificationList as a standard container for managing peptide identifications in the public API.

• Documentation

  • Updated user guides across multiple topics to reflect the new peptide identification container usage patterns.

• Chores

  • Added jupyter_bokeh dependency to requirements.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

[coderabbitai]

Walkthrough

This PR updates documentation examples across multiple user guide files to replace Python list initialization ([]) with the new oms.PeptideIdentificationList() container for holding peptide identifications. Additionally, corresponding API calls are updated from .append() and .len() to .push_back() and .size() respectively. A jupyter_bokeh dependency is added to requirements.txt.

Changes

Cohort / File(s)	Summary
Documentation: PeptideIdentificationList container adoption docs/source/user_guide/PSM_to_features.rst, docs/source/user_guide/export_pandas_dataframe.rst, docs/source/user_guide/other_ms_data_formats.rst, docs/source/user_guide/quality_control.rst	Replace peptide_ids = [] or pep_ids = [] with oms.PeptideIdentificationList() in example code blocks.
Documentation: PeptideIdentificationList with method updates docs/source/user_guide/identification_data.rst, docs/source/user_guide/untargeted_metabolomics_preprocessing.rst	Replace list initialization with oms.PeptideIdentificationList() and update method calls from .append() to .push_back().
Documentation: Size check updates docs/source/user_guide/export_files_GNPS.rst	Replace truthiness check if feature.getPeptideIdentifications(): with explicit size check if feature.getPeptideIdentifications().size() > 0:.
Documentation: Length method updates docs/source/user_guide/peptide_search.rst	Replace peptide_ids = [] with oms.PeptideIdentificationList() and update result counting from len(peptide_ids) to peptide_ids.size().
Dependencies requirements.txt	Add jupyter_bokeh dependency after bokeh.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

These are straightforward, repetitive pattern replacements across documentation examples. The changes consistently replace Python lists with the new container type and update corresponding method calls in a uniform manner. The requirements.txt change is trivial. No complex logic or architectural decisions are involved.

Possibly related issues

• Update doc to use new PeptideIdentificationList #474: This PR directly addresses the objective of updating documentation examples to use the new oms.PeptideIdentificationList container instead of plain Python lists across multiple user guide files.

Poem

🐰 A list becomes a box so fine,
With push_back() in place of line,
PyOpenMS shows a better way,
Containers dance where lists once lay! 📦

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately summarizes the main change across all files: updating documentation examples to use oms.PeptideIdentificationList instead of Python lists for peptide identification containers.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing touches

🧪 Generate unit tests (beta)

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

---

📜 Recent review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 132f3f7 and c720b85.

📒 Files selected for processing (1)

• requirements.txt (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (2)

• GitHub Check: build-test
• GitHub Check: build-test

🔇 Additional comments (1)

requirements.txt (1)

9-9: Confirm jupyter_bokeh necessity and version compatibility

Adding jupyter_bokeh alongside bokeh makes sense if the docs/notebooks actually rely on the Jupyter extension, but it does add another runtime dependency. Please double‑check that:

• The examples (or the docs build/binder image) really require jupyter_bokeh, and
• Its version is compatible with the Bokeh and Jupyter stack used for rendering the docs.

If both hold, this addition looks good to ship.

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[coderabbitai]

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

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

💡 Knowledge Base configuration:

• MCP integration is disabled by default for public repositories
• Jira integration is disabled by default for public repositories
• Linear integration is disabled by default for public repositories

You can enable these sources in your CodeRabbit configuration.

📥 Commits

Reviewing files that changed from the base of the PR and between 2332706 and 132f3f7.

📒 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)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (2)

• GitHub Check: build-test
• GitHub Check: build-test

🔇 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.

[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