refactor(umi): use binary search for count_index and deduplicate MoleculeId formatting

[nh13]

Summary

• Replace O(n) linear .find() scan on count_index with O(log n) partition_point binary search in both build_adjacency_graph_bitenc and build_adjacency_graph — the array is sorted descending by count, making binary search straightforward
• Simplify MoleculeId::to_string_with_offset to delegate to write_with_offset, removing duplicated format logic

Test plan

• cargo nextest run -p fgumi-umi — all tests pass
• cargo ci-fmt — clean
• cargo ci-lint — clean

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 3a460ea and fb4d570.

📒 Files selected for processing (2)

• crates/fgumi-umi/src/assigner.rs
• crates/fgumi-umi/src/lib.rs

---

📝 Walkthrough

Walkthrough

The changes optimize and refactor two modules in the fgumi-umi crate. In assigner.rs, a linear search for count constraints is replaced with a binary-search-based approach using partition_point, applied consistently across two mirrored code paths. A clippy expectation attribute is added for a complex section. In lib.rs, to_string_with_offset is refactored to reuse the existing write_with_offset function via a mutable buffer, eliminating inlined branching while preserving the public API and output behavior.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately summarizes the two main changes: binary search optimization for count_index and deduplication of MoleculeId formatting logic.
Description check	✅ Passed	The description clearly explains both refactoring objectives, includes complexity improvements (O(n) to O(log n)), and documents the test plan covering all verification steps.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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

✨ Finishing Touches

• 📝 Generate docstrings (stacked PR)
• 📝 Generate docstrings (commit on current branch)

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch refactor/nh/simplify-fgumi-umi

---

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.}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.61%. Comparing base (3a460ea) to head (fb4d570).
⚠️ Report is 9 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #146   +/-   ##
=======================================
  Coverage   83.61%   83.61%           
=======================================
  Files         126      126           
  Lines       51510    51510           
=======================================
  Hits        43069    43069           
  Misses       8441     8441           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[nh13]

@coderabbitai review

[coderabbitai]

✅ Actions performed

Review triggered.

Note: CodeRabbit is an incremental review system and does not re-review already reviewed commits. This command is applicable only when automatic reviews are paused.

[nh13]

@coderabbitai review

[coderabbitai]

✅ Actions performed

Review triggered.

Note: CodeRabbit is an incremental review system and does not re-review already reviewed commits. This command is applicable only when automatic reviews are paused.