fix PSM_to_features tutorial

[cbielow]

fixes OpenMS/OpenMS#8139

Summary by CodeRabbit

• Documentation
  • Updated the user guide to clarify the creation and usage of an empty MSExperiment object in code examples, and revised method arguments for improved clarity.

[coderabbitai]

Walkthrough

A code snippet in the user guide was updated to explicitly create an empty MSExperiment object named spectra and pass it as a positional argument to the IDMapper.annotate method, replacing the previous use of spectra=None and keyword arguments.

Changes

Cohort / File(s)	Change Summary
User Guide Example Update docs/source/user_guide/PSM_to_features.rst	Modified code example to instantiate an empty MSExperiment object and pass it positionally to IDMapper.annotate, replacing keyword arguments and spectra=None.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant MSExperiment
    participant IDMapper

    User->>MSExperiment: Create empty instance (spectra)
    User->>IDMapper: annotate(feature_map, peptide_ids, protein_ids, True, True, spectra)
    IDMapper->>MSExperiment: Uses spectra for annotation

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Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

Assessment against linked issues

Objective	Addressed	Explanation
Update tutorial code to avoid error in IDMapper.annotate by passing a valid MSExperiment instance instead of None (#8139)	✅

Suggested reviewers

• timosachsenberg

Poem

The guide now shines with code anew,
An empty spectra joins the crew!
No more errors, just smooth delight,
As features map and peptides write.
A hop, a skip, a doc improved—
This bunny’s whiskers are quite moved! 🐇✨

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• docs/source/user_guide/PSM_to_features.rst (1 hunks)

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• docs/source/user_guide/PSM_to_features.rst

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Actionable comments posted: 0

🧹 Nitpick comments (2)

docs/source/user_guide/PSM_to_features.rst (2)

72-73: Add a brief explanation for creating an empty MSExperiment

The snippet now instantiates spectra = oms.MSExperiment() solely to satisfy the type requirement of IDMapper.annotate. A short inline comment (e.g., # empty experiment required by annotate) or a one-sentence note above the cell would help readers understand why this seemingly unused object is necessary.

---

73-73: Positional flags reduce readability; leave a reminder to revert to keywords

Switching to positional arguments (True, True, spectra) works around the current binding issue but obscures the meaning of each flag and ties the example to the exact parameter order. Consider adding a TODO comment indicating that, once the pyOpenMS binding accepts keyword arguments again, the call should be restored to a clearer form:

# TODO: switch back once fixed upstream
# id_mapper.annotate(feature_map, peptide_ids, protein_ids,
#                    use_centroid_rt=True, use_centroid_mz=True, spectra=spectra)

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[blacken-docs] _{reported by reviewdog 🐶}

pyopenms-docs/docs/source/user_guide/PSM_to_features.rst

Lines 1 to 91 in 33c7a02

	Feature Map Annotation with Peptide Identifications
	===================================================
	A :term:`feature map` is usually obtained from running a :term:`feature finder`, e.g. :py:class:`~.FeatureFinderAlgorithmPicked` (see `Feature Detection <feature_detection.html>`_).
	A logical next step is to compare features across runs using `Map Alignment <map_alignment.html>`_ and `Feature Linking <feature_linking.html>`_.
	However, most map aligners in pyOpenMS require features which are annotated with PSMs (see `Identication Data <identification_data.html>`_).
	To link features to their respective PSMs (as obtained from a search engine, such as Comet), we can use the :py:class:`~.IDMapper`.
	Step 0: Download Example data
	-----------------------------
	.. code-block:: python
	:linenos:
	import pyopenms as oms
	from urllib.request import urlretrieve
	base_url = (
	"https://raw.githubusercontent.com/OpenMS/pyopenms-docs/master/src/data/"
	)
	feature_file = "BSA1_F1.featureXML"
	urlretrieve(base_url + feature_file, feature_file)
	idxml_file = "BSA1_F1.idXML"
	urlretrieve(base_url + idxml_file, idxml_file)
	Step 1: Load the Feature Map
	----------------------------
	First, load the FeatureMap from a `.featureXML` file:
	.. code-block:: python
	import pyopenms as oms
	feature_map = oms.FeatureMap()
	oms.FeatureXMLFile().load(feature_file, feature_map)
	Step 2: Load Peptide Identifications
	------------------------------------
	Next, load the PeptideIdentifications from an `.idXML` file:
	.. code-block:: python
	peptide_ids = []
	protein_ids = []
	oms.IdXMLFile().load(idxml_file, protein_ids, peptide_ids)
	Step 3: Initialize and Configure `IDMapper`
	-------------------------------------------
	Now, configure `IDMapper` to apply **retention time (RT) and m/z tolerance settings**:
	.. code-block:: python
	id_mapper = oms.IDMapper()
	params = id_mapper.getParameters()
	params.setValue("rt_tolerance", 5.0) # RT tolerance in seconds
	params.setValue("mz_tolerance", 10.0) # m/z tolerance in ppm
	id_mapper.setParameters(params)
	Step 4: Annotate the FeatureMap
	-------------------------------
	Use the configured `IDMapper` to link peptide IDs to the FeatureMap:
	.. code-block:: python
	# annotate() can optionally use the underlying raw MS data (spectra) to annotate unidentified MS/MS scans to features in the FeatureMap
	# We don't need this here, so we provide an empty default.
	spectra = oms.MSExperiment()
	id_mapper.annotate(feature_map, peptide_ids, protein_ids, True, True, spectra)
	Step 5: Save the Annotated FeatureMap
	--------------------------------------
	Finally, store the modified FeatureMap back to a file:
	.. code-block:: python
	oms.FeatureXMLFile().store("BSA1_F1_annotated.featureXML", feature_map)
	.. tip::
	You can visualize the annotated FeatureMap using OpenMS visualization tools like `TOPPView`.
	You have successfully **annotated a FeatureMap** with PeptideIdentifications using `IDMapper`. This allows further downstream analysis in (py)OpenMS workflows.