Patch 5 22 2026

[Jpickard1]

Bug fix for hypergaph constructor

Summary by CodeRabbit

• Bug Fixes

  • Resolved a potential undefined variable issue in hypergraph initialization logic

• Documentation

  • Redesigned README with improved structure and enhanced navigation
  • Added comprehensive installation instructions for Python and MATLAB environments
  • Included quick start code examples and expanded feature descriptions
  • Enhanced with PyPI badge, documentation links, related publications, and BibTeX citation format

[coderabbitai]

Caution

Review failed

Pull request was closed or merged during review

📝 Walkthrough

Walkthrough

This PR applies a bug fix to the Hypergraph constructor initialization logic, updates corresponding test weight expectations, and comprehensively restructures the README with improved documentation layout, badges, installation instructions, quick-start examples, and a tabular publications list.

Changes

Hypergraph Module Fix and Validation

Layer / File(s)	Summary
Hypergraph constructor variable initialization Python/HAT/hypergraph.py	name_to_int is initialized to None before the edge_list-dependent branch, ensuring the variable is always defined when later conditional logic checks if name_to_int is not None.
Test weight value expectations update Tests/hypergraph_constructors.py	Expected weight values in test_add_edge_2 and test_add_edge_3 are changed from pd.NA to np.nan for edge rows added without an explicit weight, aligning test expectations with numeric handling behavior.
README documentation restructure README.md	Previous narrative intro and embedded logo are replaced with a new sectioned layout including badges, feature highlights, installation instructions (Python/MATLAB), quick-start example, consolidated documentation link, tabular publications list with links and preprints, BibTeX citation block, and contributing/GitHub Issues link.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Possibly related PRs

• Jpickard1/Hypergraph-Analysis-Toolbox#23: Both PRs modify Hypergraph.__init__ initialization logic around edge_list handling, making the constructor undefined-variable fix directly related to prior refactoring.

Poem

🐰 A rabbit hops through initialization's gate,
Where None now guards what once was fate,
Tests hop along with np.nan in stride,
While docs bloom fresh with README pride—
bounces ✨

🚥 Pre-merge checks | ✅ 3 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.
Title check	❓ Inconclusive	The title 'Patch 5 22 2026' is vague and generic, providing no meaningful information about the changeset and does not convey what the patch addresses.	Replace with a descriptive title that clarifies the main change, such as 'Fix undefined variable in Hypergraph.init' or 'Initialize name_to_int to prevent undefined variable error'.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch patch_5_22_2026

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