MAINT: update to latest cogent3

[GavinHuttley]

[CHANGED] and bump version to 2025.7.17

Summary by Sourcery

Migrate the codebase to the latest cogent3 API, update imports and function calls accordingly, adjust tests for removed parameters, and bump the package version and dependency requirement.

Bug Fixes:

• Fix DNA.make_seq call signature in complement.py
• Ensure correct dtype casting in array_to_str

Enhancements:

• Replace custom FASTA loader with cogent3.load_aligned_seqs and update various imports to match the new cogent3 structure
• Refactor motif_count, complement, util, and log_lin modules to use updated cogent3 functions and tables

Build:

• Bump package version to 2025.7.17
• Update cogent3 dependency to >=2025.7.10a3 in pyproject.toml

Tests:

• Remove deprecated array_align parameter in tests and switch to using the .array_seqs attribute
• Update make_aligned_seqs usage in tests to match new API signature

Chores:

• Remove deprecated load_from_fasta utility function

[sourcery-ai]

Reviewer's Guide

This PR modernizes the codebase for the latest cogent3 API by replacing custom loading utilities with cogent3 loaders, updating imports and API calls across production code and tests, and bumping the package version and dependency spec

Class diagram for updated sequence loading in aln_to_counts.py

classDiagram
    class align_to_counts {
        +direction
        +chosen_base
        +orig_seqs
        +seqs
        +just_nucs(seqs)
    }
    class cogent3 {
        +load_aligned_seqs(path, moltype)
    }
    align_to_counts --> cogent3 : uses load_aligned_seqs

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Class diagram for removal of load_from_fasta utility

classDiagram
    class util {
        -load_from_fasta(filename)
        +array_to_str(data)
    }
    class cogent3 {
        +load_aligned_seqs(path, moltype)
    }
    util ..> cogent3 : replaced by load_aligned_seqs

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Class diagram for motif_count.py cogent3 API update

classDiagram
    class motif_count {
        +profile_to_seq_counts(data, flank_size)
        +dna_alpha
    }
    class cogent3 {
        +get_moltype(type)
        +make_table(...)
    }
    motif_count --> cogent3 : uses get_moltype, make_table

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Class diagram for log_lin.py Table import update

classDiagram
    class log_lin {
        +Table
    }
    class cogent3_core_table {
        +Table
    }
    log_lin ..> cogent3_core_table : imports Table

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File-Level Changes

Change	Details	Files
Test suite fixtures and helpers updated to the new loader API	Removed array_align argument from load_aligned_seqs calls Replaced seq_data references with array_seqs Swapped ArrayAlignment constructions for make_aligned_seqs invocations Aligned test helper signatures with updated cogent3 loader	tests/test_entropy.py tests/test_control.py tests/test_motif_count.py tests/test_util.py
Replaced custom FASTA loader with cogent3.load_aligned_seqs	Imported cogent3 and removed load_from_fasta import and definition Changed sequence loading in align_to_counts to use cogent3.load_aligned_seqs Adjusted data extraction to use array_seqs Added dtype cast in array_to_str to ensure uint8 indices	src/mutation_motif/aln_to_counts.py src/mutation_motif/util.py
Updated cogent3-based imports and API usages in core modules	Imported get_moltype alongside make_table in motif_count Introduced dna_alpha via get_moltype Changed Table import path from util.table to core.table in log_lin Adjusted DNA.make_seq call signature in complement	src/mutation_motif/motif_count.py src/mutation_motif/log_lin.py src/mutation_motif/complement.py
Bumped package version and cogent3 dependency	Raised cogent3 requirement in pyproject.toml to >=2025.7.10a3 Updated version in init.py to 2025.7.17	pyproject.toml src/mutation_motif/__init__.py

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[sourcery-ai]

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

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