:>> ABIO → ABIO Architecture → ABIO alienbio

alienbio

Topic: ~~[[ABIO Topics]]~~ The top-level package: what import alienbio gives you.

Public API

from alienbio import (
    Dat, Entity, IO, mk, Pegboard,
    biotype, get_biotype,
    Atom, Molecule, Reaction, Chemistry, Simulator,
    AtomImpl, MoleculeImpl, ReactionImpl, ChemistryImpl,
    WorldStateImpl, WorldSimulatorImpl,
    COMMON_ATOMS, get_atom, config,
)

The first line is infrastructure, the second the @biotype registry, the third the Protocols, then the substrate. The instrument lives in alienbio.suite (load_spec, run_experiment, DRAFTERS, AGENTS, render_report) and the language in alienbio.expr (Env, X, evaluate, fn, expander, guard). The bio CLI fronts both — see ABIO Commands.

Entities and the anchor

Every chemistry object is an Entity with a local name and a parent; mk.M("A") / mk.R(...) / mk.C(...) build them, minting a MockDat anchor outside a with mk.anchor(target): block. alienbio.bio.io is the IO attachment point: None until one is attached, and an entity that needs it before then raises rather than inventing one.

What is not here

The M1 scenario runtime (bio.fetch / run / build over catalog/scenarios, Scenario, the single-compartment StateImpl / ReferenceSimulatorImpl) was deleted in M47.7 and T056. There is one runtime — run_experiment over catalog/experiments — and one physics, the world simulator.