Merge main

[GavinHuttley]

Summary by Sourcery

Update BRCA1 test data and improve sequence selection stability.

Enhancements:

• Preserve input sequence collection type when selecting sequences.

CI:

• Update CI to use latest version of uv.

Tests:

• Add tests for serialisability and return type consistency in sequence selection.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request updates the paper.bib file by adding DOIs and other metadata to existing entries, and adds several new article citations. It also modifies tests/test_records.py to include new tests for serializability and return types, and updates src/diverse_seq/records.py to improve type hinting and ensure consistent return types. Finally, it updates package metadata, including version and dependencies.

Class diagram showing updated type hints in records.py

classDiagram
    class AppOutType {
        <<Union>>
        SeqsCollectionType
        SerialisableType
    }

    class DiverseSeqBase {
        +__init__(moltype, k, seed, include)
        +main(seqs: SeqsCollectionType) AppOutType
    }

    note for AppOutType "New type alias for improved
return type specification"

    note for DiverseSeqBase "Updated return type
to be more flexible"

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File-Level Changes

Change	Details	Files
Updated paper.bib with DOIs and metadata	Added DOIs and URLs to existing entries. Added metadata such as language, editor, and issue number. Standardized formatting of entries.	paper/paper.bib
Added new citations to paper.bib	Added citations for relevant articles. Ensured new entries conform to the existing formatting standards.	paper/paper.bib
Improved tests for sequence records	Added tests for serializability of nmost and max functions. Added tests to check return types of select functions. Parameterized tests to cover different cases.	tests/test_records.py
Improved type hinting and return types	Added AppOutType to handle union of sequence collection and serializable types. Updated main functions to return consistent types. Improved documentation for return types.	src/diverse_seq/records.py
Updated package metadata	Updated package version. Updated dependencies, including ruff and piqtree. Updated CI workflow to use latest setup-uv action.	pyproject.toml __init__.py .github/workflows/ci-cogent3-dev.yml
Added aligned BRCA1 sequences for testing	Added aligned sequences to the brca1.fasta file. This provides a consistent dataset for testing alignment-related functions.	tests/data/brca1.fasta

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[sourcery-ai]

Hey @GavinHuttley - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[coveralls]

Pull Request Test Coverage Report for Build 12737805197

Details

• 8 of 8 (100.0%) changed or added relevant lines in 2 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.006%) to 91.898%

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Totals
Change from base Build 11785964138:	0.006%
Covered Lines:	1191
Relevant Lines:	1296

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💛 - Coveralls