Migrate gene_cnv() to AnophelesCnvData

[kunal-10-cloud]

Fixes: #1208
Move gene_cnv() data access method from AnophelesCnvFrequencyAnalysis to AnophelesCnvData class to achieve architectural consistency with the modular CNV data-layer mixin pattern used throughout the codebase.

Changes Made

Core Migration

• Moved gene_cnv() method from cnv_frq.py to cnv_data.py

  • Public API method for computing modal copy number per gene
  • Decorator: @_check_types, @doc(...)
  • Return type: xr.Dataset

• Moved _gene_cnv() implementation from cnv_frq.py to cnv_data.py

  • Private implementation method with bitwise mode computation
  • Accesses genome features, HMM data, and region parsing
  • Uses bisect, dask, and numba helpers

• Moved numba helpers to cnv_data.py

  • _cn_mode_1d(): 1D modal copy number computation
  • _cn_mode(): 2D modal copy number computation (calls 1D per column)

Cleanup

• Removed unused imports from cnv_frq.py (bisect, dask, numba)
• Cleaned TODO block from dipclust.py
• Removed type:ignore comment from dipclust.py (type checking now passes)

Architecture

Before: Analysis layer method → Data access mixed with frequency analysis
After: Data layer method → Frequency analysis inherits from data layer

Inheritance Chain:

AnophelesDipClustAnalysis
  ↓ inherits from
AnophelesCnvFrequencyAnalysis
  ↓ inherits from
AnophelesCnvData (now includes gene_cnv)

Testing & Validation

• Unit Tests: 96/96 passed (68 cnv_frq + 28 dipclust)
• Linting: ruff check passed (0 issues)
• Formatting: ruff format validated
• Pre-commit Hooks: All 5 hooks passed
  • trim-trailing-whitespace
  • fix-end-of-files
  • ruff (lint)
  • ruff-format
• Type Checking: mypy validation (0 errors)

Breaking Changes

None. The method signature, return type, and public API remain unchanged. All existing code continues to work through inheritance.

Code Quality

• Lines Added: 198 (gene_cnv, _gene_cnv, helpers in cnv_data.py)
• Lines Removed: 202 (moved functions from cnv_frq.py)
• Net Change: -4 LOC (improved organization)
• Files Modified: 3 (cnv_data.py, cnv_frq.py, dipclust.py)

[Copilot]

Pull request overview

This PR migrates the gene_cnv() CNV gene-level data access method from the CNV frequency analysis layer into the AnophelesCnvData data-layer mixin, aligning CNV access patterns with the existing modular architecture and unblocking cleaner inheritance usage in dipclust.

Changes:

• Moved gene_cnv() and _gene_cnv() from cnv_frq.py into cnv_data.py (including required helpers/imports).
• Removed now-unneeded imports and numba helper definitions from cnv_frq.py.
• Cleaned up dipclust.py by removing the migration TODO and the # type: ignore on self.gene_cnv(...).

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
malariagen_data/anoph/cnv_data.py	Adds gene_cnv() implementation to the CNV data-layer mixin and relocates numba mode helpers.
malariagen_data/anoph/cnv_frq.py	Removes the migrated gene_cnv() implementation and associated unused imports/helpers.
malariagen_data/anoph/dipclust.py	Removes TODO and type ignore now that gene_cnv() exists in the inherited data layer.

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[kunal-10-cloud]

Hi @jonbrenas can you please take a look at this PR i have also stated my approach in the issue(#1208)
please let me know if any changes are required
Also i have made the changes you requrested to in the PR(#1212, #1199), whenever you are available please take a look at them as well