Add sphinx.ext.napoleon for NumPy-style docstrings

[timosachsenberg]

Summary

Enable proper rendering of NumPy and Google-style docstrings in the pyOpenMS documentation.

This is needed to support docstrings like those in the new statistical functions (OpenMS/OpenMS#8524) which use the standard scientific Python docstring format with Parameters, Returns, Examples sections.

Changes

• Added sphinx.ext.napoleon to the extensions list
• Added napoleon configuration settings with sensible defaults

Why napoleon?

• Built into Sphinx - no extra dependency required (available since Sphinx 1.3)
• Used by pydata-sphinx-theme - the theme we use includes napoleon in their own documentation
• Scientific Python standard - NumPy-style docstrings are the convention for scientific Python packages

Docstring rendering

Environment	Before	After
Jupyter / IPython	✅ Works	✅ Works
ReadTheDocs	❌ Raw text with ---- underlines	✅ Properly formatted sections

Example

NumPy-style docstrings like this:

def qvalue(p_values, pi0=1.0, pfdr=False):
    """
    Compute q-values from p-values.

    Parameters
    ----------
    p_values : array-like
        Vector of p-values from hypothesis tests

    Returns
    -------
    ndarray
        Vector of q-values
    """

Will now render with proper "Parameters" and "Returns" sections in the documentation.

Test plan

• Build docs locally and verify docstrings render correctly
• Check that existing documentation still renders properly

🤖 Generated with Claude Code

Summary by CodeRabbit

• Documentation
  • Enhanced documentation system to support NumPy and Google-style docstrings for improved API documentation clarity and formatting.

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

[coderabbitai]

📝 Walkthrough

Walkthrough

Added Sphinx Napoleon extension to docs/source/conf.py to support NumPy and Google style docstring parsing. Configuration includes settings for docstring parsing, parameter/return type handling, and attribute annotation.

Changes

Cohort / File(s)	Change Summary
Documentation Configuration docs/source/conf.py	Added sphinx.ext.napoleon extension to the extensions list with comprehensive Napoleon configuration: enabled NumPy and Google docstring parsing, configured init/private/special member inclusion, parameter/return type annotation settings, and attribute annotation handling. Total: 17 lines added.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Poem

Whiskers twitch with docstring delight,
Napoleon brings NumPy and Google insight,
Configuration crafted with careful care,
Documentation flourishes everywhere! 📚✨🐰

🚥 Pre-merge checks | ✅ 3

✅ 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 clearly and specifically describes the main change: adding the sphinx.ext.napoleon extension to enable NumPy-style docstring support in the documentation.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing touches

• 📝 Generate docstrings

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