Misc

[GavinHuttley]

Summary by Sourcery

Enhancements:

• Refactor distance calculation logic to use a unified function call for both mash and euclidean distances, reducing code duplication.

[sourcery-ai]

Reviewer's Guide by Sourcery

This PR refactors the sequence distance calculation implementation to improve code organization and sets new default parameters. The main changes include restructuring the distance calculation logic in the __init__ method to use a function mapping approach, updating default parameters for k-mer size and sketch size, and adding code coverage pragmas.

Updated class diagram for distance calculation

classDiagram
    class DistanceCalculator {
        -int k
        -int|None sketch_size
        -str moltype
        -bool|None mash_canonical_kmers
        -bool show_progress
        -function _s2a
        -function _func
        -dict _func_kwargs
        +main(seqs: c3_types.SeqsCollectionType) c3_types.PairwiseDistanceType
    }
    note for DistanceCalculator "Refactored to use function mapping for distance calculation"
    class mash_distances
    class euclidean_distances
    DistanceCalculator --> mash_distances : uses
    DistanceCalculator --> euclidean_distances : uses

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File-Level Changes

Change	Details	Files
Refactored distance calculation implementation for better organization	Moved distance calculation logic setup to init method Created function mapping and kwargs dictionary for different distance modes Simplified main() method by using stored function and kwargs Added sequence moltype conversion at the start of main() Removed redundant distance mode validation	src/diverse_seq/distance.py
Updated default parameters for sequence analysis	Changed default k-mer size from 16 to 12 Set default sketch size to 3000 instead of None Removed redundant default value descriptions from docstrings	src/diverse_seq/distance.py
Added code coverage pragmas and removed validation	Added 'pragma: no cover' to several low-level hash functions Removed validation for sketch size when distance mode is not mash	src/diverse_seq/distance.py

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[sourcery-ai]

Hey @GavinHuttley - I've reviewed your changes - here's some feedback:

Overall Comments:

• Please explain the rationale for changing the default k-mer size from 16 to 12 and sketch_size from None to 3000. These changes could impact performance and accuracy.

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 11623855545

Details

• 9 of 9 (100.0%) changed or added relevant lines in 1 file are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+3.1%) to 91.947%

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Totals
Change from base Build 11512015058:	3.1%
Covered Lines:	1176
Relevant Lines:	1279

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💛 - Coveralls