openvax / varcode / 24700072067
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Migrate dataclass serialization to DataclassSerializable (closes #343) (#344)

* Migrate dataclass serialization to DataclassSerializable (#343)

serializable 1.1.0 ships a DataclassSerializable mixin that
contributes to_dict / from_dict / to_json / from_json without
overriding the dunder methods @dataclass generates, and is
wire-compatible with Serializable outputs (same __class__ +
__module__ stamping, same polymorphic dispatch via _lookup_value).

- Bump requirements.txt: serializable>=1.1.0.
- Add DataclassSerializable to Outcome, TranscriptEdit,
  ReferenceSegment, MutantTranscript, SpliceCandidate.
- Delete SpliceCandidate.to_dict/from_dict tagging (the
  __effect_class__ registry dance). Keep a minimal to_dict/from_dict
  override on SpliceCandidate just to stringify the SpliceOutcome
  enum (python-serializable has no built-in enum branch).
- Delete SpliceOutcomeSet.to_dict + _reconstruct_nested_objects —
  Serializable's default picks up the right shape and
  to_serializable_repr handles the disrupted_signal_class type
  object via the standard class-path stamp.
- Delete _CODING_EFFECT_CLASS_REGISTRY, _SPLICE_SIGNAL_CLASS_REGISTRY,
  _coding_effect_class_registry, _rehydrate_coding_effect — all
  subsumed by serializable.helpers._lookup_value.
- New test: Outcome(effect=<real MutationEffect>) round-trips via
  JSON with polymorphic class preservation.

Net: ~85 lines removed from splice_outcomes.py. Existing
round-trip regression tests still pass without modification.

* #344 review fixes

- Replace DataclassSerializable.from_dict.__func__(cls, state_dict)
  with super().from_dict(state_dict); same for to_dict. Idiomatic
  Python classmethod dispatch.
- Add JSON round-trip tests for TranscriptEdit, ReferenceSegment,
  and MutantTranscript (point-variant shape) exercising the new
  DataclassSerializable inheritance.
- Document in the module-level enum-handling comment that future
  Enum-typed dataclass fields need the same stringify override
 ... (continued)
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