engine/__init__.py

"""Genetic-programming engine for OncoDSL — strict airgap, name-blind.

The engine sees only opaque feature IDs (`^g\\d+$`) and a binary outcome y.
It composes a small DSL (Select / Reduce / Fit) and evolves populations of
programs with tournament selection, crossover, mutation, and elitism, using
k-fold cross-validated AUROC on a TRAIN split as fitness. The held-out
TEST split is touched once per program, only for the final winner and the
internal baseline.

Public entry points:
- `run_gp_pipeline(M, y, *, objective=None, ...)` — batch path. Returns
  `(evolution_log, result)`, both safe to serialise (opaque IDs only).
- `run_gp_pipeline_streaming(M, y, *, on_generation, objective=None, ...)`
  — same pipeline with a per-generation callback for the Lab's SSE
  bridge. Returns `result` only.
- Objectives: `BinaryAUROCObjective` (MSI vs MSS), `CorrelationObjective`
  (continuous + direction), `objective_from_spec({target, metric, direction})`.
"""

from engine.objectives import (
    BinaryAUROCObjective,
    CorrelationObjective,
    Objective,
    objective_from_spec,
)
from engine.pipeline import run_gp_pipeline, run_gp_pipeline_streaming

__all__ = [
    "run_gp_pipeline",
    "run_gp_pipeline_streaming",
    "Objective",
    "BinaryAUROCObjective",
    "CorrelationObjective",
    "objective_from_spec",
]