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Ran 21 Apr 2026 04:32PM UTC

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Build # 24733984187

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github

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web-flow

Commit Message

Genotype → DataclassSerializable + drop biopython (closes #293; partial #272) (#347)

* Genotype → DataclassSerializable, drop biopython dep (#272 part, #293)

Two narrowly scoped cleanups that fit together:

Genotype (#272 part):
- Add DataclassSerializable as a base. Genotype was already a
  frozen dataclass, so this is a one-line inheritance addition —
  gains to_dict / from_dict / to_json / from_json without any
  hand-rolled code.
- New test asserts JSON round-trip preserves all fields (alleles,
  allele_depths, phase_set, depth, quality).

Biopython (#293):
- Replace the two `from Bio.Seq import reverse_complement` imports
  (util.py, effects/effect_prediction.py) with a local
  str.translate-based helper in varcode/nucleotides.py.
- Drop `biopython>=1.64` from requirements.txt.
- Handles IUPAC ambiguity codes + case preservation to match
  biopython's behavior.

Deferred from #272 (Variant, effect classes): Variant carries a
large custom __init__ with ref/alt normalization and contig-name
cleanup; the effect-class hierarchy is polymorphic with per-class
init signatures. Neither fits the dataclass shape without a much
larger refactor, and the existing Serializable path round-trips
correctly. File a scoped follow-up if/when we want to migrate them
explicitly.

* Fix version.py conflict-marker leftover from rebase

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