ENH: Optimise CLI Usage of ctree

[rmcar17]

Summary by Sourcery

Enhancements:

• Refactor the dvs_par_ctree class to use a mixin for shared functionality, improving code modularity and reusability.

[sourcery-ai]

Reviewer's Guide by Sourcery

This PR optimizes the CLI usage of the cluster tree functionality by introducing a new class dvs_cli_par_ctree that directly reads sequences from HDF5 storage, eliminating unnecessary sequence format conversions. It also includes performance improvements in the Mash sketch calculation by optimizing data structures and using NumPy arrays instead of Python lists.

Sequence diagram for optimized CLI usage of cluster tree

sequenceDiagram
    participant User
    participant CLI
    participant dvs_cli_par_ctree
    participant HDF5DataStore
    participant ClusterTree

    User->>CLI: Run ctree command
    CLI->>dvs_cli_par_ctree: Initialize with parameters
    dvs_cli_par_ctree->>HDF5DataStore: Read sequences from HDF5
    HDF5DataStore-->>dvs_cli_par_ctree: Return sequence data
    dvs_cli_par_ctree->>ClusterTree: Construct cluster tree
    ClusterTree-->>dvs_cli_par_ctree: Return PhyloNode
    dvs_cli_par_ctree-->>CLI: Return cluster tree
    CLI-->>User: Output tree to file

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Updated class diagram for cluster tree classes

classDiagram
    class ClusterTreeBase {
        <<abstract>>
    }

    class DvsParCtreeMixin {
        +_mash_dist(seq_arrays: Sequence[SeqArray])
    }

    class dvs_par_ctree {
        +__init__(k: int, sketch_size: int | None, moltype: str, distance_mode: Literal["mash", "euclidean"], mash_canonical_kmers: bool | None, show_progress: bool, max_workers: int | None, parallel: bool)
        +main(seqs: c3_types.SeqsCollectionType) : PhyloNode
    }

    class dvs_cli_par_ctree {
        +__init__(seq_store: str | Path, limit: int | None, k: int, sketch_size: int | None, moltype: str, distance_mode: Literal["mash", "euclidean"], mash_canonical_kmers: bool | None, show_progress: bool, max_workers: int | None, parallel: bool)
        +main(seq_names: list[str]) : PhyloNode
    }

    ClusterTreeBase <|-- dvs_par_ctree
    ClusterTreeBase <|-- dvs_cli_par_ctree
    DvsParCtreeMixin <|.. dvs_par_ctree
    DvsParCtreeMixin <|.. dvs_cli_par_ctree

    note for dvs_cli_par_ctree "New class introduced to optimize CLI usage by reading sequences directly from HDF5 storage."

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File-Level Changes

Change	Details	Files
Refactored cluster tree implementation by extracting common functionality into a mixin class	Created DvsParCtreeMixin class to share common functionality between cluster tree implementations Moved _mash_dist and related methods to the mixin class	src/diverse_seq/cluster.py
Added new CLI-optimized parallel cluster tree implementation	Created dvs_cli_par_ctree class that directly reads from HDF5 storage Implemented direct sequence array handling without intermediate conversions Added support for limiting the number of sequences processed	src/diverse_seq/cluster.py src/diverse_seq/cli.py
Optimized Mash sketch calculation performance	Replaced Python set with NumPy unique function for kmer hash deduplication Changed kmer hash storage from list to NumPy array Optimized heap initialization in mash_sketch function Added numba.njit decorator to mash_sketch for improved performance	src/diverse_seq/distance.py

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[sourcery-ai]

Hey @rmcar17 - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟡 General issues: 1 issue found
• 🟢 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 11734163625

Details

• 45 of 55 (81.82%) changed or added relevant lines in 3 files are covered.
• 6 unchanged lines in 2 files lost coverage.
• Overall coverage decreased (-1.0%) to 90.826%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/diverse_seq/cli.py	4	5	80.0%
src/diverse_seq/cluster.py	40	43	93.02%
src/diverse_seq/distance.py	1	7	14.29%

Files with Coverage Reduction	New Missed Lines	%
src/diverse_seq/data_store.py	2	87.82%
src/diverse_seq/distance.py	4	83.85%

Totals
Change from base Build 11720616749:	-1.0%
Covered Lines:	1188
Relevant Lines:	1308

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💛 - Coveralls

[GavinHuttley]

the issue caught by codacy should have been caught by a test, can you add one that executes that line of code