docs: add citations

[njzjz]

Summary by CodeRabbit

Release Notes

• Documentation
  • Added DOI badge and credits section with formal citation information to README
  • Added bibliographic citation notice to the documentation landing page with research publication reference

[codspeed-hq]

CodSpeed Performance Report

Merging #908 will not alter performance

_{Comparing njzjz:citation (6fd7315) with devel (027453a)}

⚠️ Unknown Walltime execution environment detected

Using the Walltime instrument on standard Hosted Runners will lead to inconsistent data.

For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

Summary

✅ 2 untouched
⏩ 2 skipped¹

Footnotes

1. 2 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.06%. Comparing base (027453a) to head (6fd7315).
⚠️ Report is 15 commits behind head on devel.

Additional details and impacted files

@@           Coverage Diff           @@
##            devel     #908   +/-   ##
=======================================
  Coverage   86.06%   86.06%           
=======================================
  Files          83       83           
  Lines        7886     7886           
=======================================
  Hits         6787     6787           
  Misses       1099     1099           

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[coderabbitai]

📝 Walkthrough

Walkthrough

Added DOI badges and citation information to README and documentation landing page. These are presentation and attribution updates with no functional code modifications.

Changes

Cohort / File(s)	Summary
Documentation Citations README.md, docs/index.rst	Added DOI badge to README top and new Credits section with formal citation block and badge link. Added long-form bibliographic citation notice to documentation landing page referencing J. Chem. Inf. Model. paper.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

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 pull request title "docs: add citations" directly aligns with the primary changes in the changeset. Both modified files (README.md and docs/index.rst) focus on adding citation information—a Credits section with DOI and bibliographic details in the README, and a formal citation notice in the documentation index. The title is concise, specific, and uses standard commit message conventions with a clear scope ("docs:") and action ("add citations"). It effectively communicates the main objective without being vague or generic, and a teammate reviewing the history would immediately understand that this PR introduces citation functionality to the documentation.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

🧪 Generate unit tests (beta)

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

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📜 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 027453a and 6fd7315.

📒 Files selected for processing (2)

• README.md (1 hunks)
• docs/index.rst (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

**/*

📄 CodeRabbit inference engine (AGENTS.md)

**/*: Remove trailing whitespace in files (pre-commit trailing-whitespace hook)
Ensure files end with a newline at EOF (end-of-file-fixer)

Files:

• README.md
• docs/index.rst

🔇 Additional comments (5)

README.md (3)

3-3: DOI badge placement and formatting look good.

The badge is properly formatted with correct markdown syntax and positioned appropriately with other project badges.

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10-15: Credits section added with proper citation information.

The new Credits section provides clear citation guidance with complete author attribution, paper title, publication venue, and DOI. The citation badge link adds functionality for tracking citation metrics.

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1-56: File already complies with coding guidelines.

Verification confirms that README.md has no trailing whitespace and ends with a newline. No action required.

docs/index.rst (2)

11-22: Citation notice properly formatted for documentation.

The citation information is well-structured in reStructuredText format with proper indentation for the multi-line author list. Placement before the toctree is appropriate for the documentation landing page.

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1-44: No changes required — file already complies with coding guidelines.

Verification confirms docs/index.rst has no trailing whitespace and ends with a newline, satisfying all coding guideline requirements.

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