:>> ABIO → ABIO Architecture → ABIO-Infra

ABIO-Infra

Two mutually independent packages: infra is what the entities are made of, protocols is what they promise and, since T057, what pyright src/ checks (protocols/_conformance.py; the viz leftover went with T056).

Entity is the base class of every chemistry object: a local name, a bidirectional parent/child tree, a _top slot that is either a DAT anchor (root) or the root entity (so root() and dat() are O(1)), a head registered by __init_subclass__ for serialization round-trips, and to_dict/hydrate/save. The pegboard erases the anchoring boilerplate: families register a one-letter maker (bio/makers.py registers M/R/C with prefixes mol/rxn/chem), mk.M("A") resolves its anchor from a with mk.anchor(target) block or mints a MockDat outside one, so a bare unit test and a production catalog share call sites. protocols/bio.py states the substrate's surface as runtime_checkable Protocols and bio/__init__.py re-exports each beside its *Impl. bio.io is a declared attachment point: entity.py reads it lazily through _bio_io() and raises rather than inventing one, and no production path assigns it. The vendored src/dvc_dat is reached from infra/io.py alone; everywhere else the anchor is duck-typed.

Modules

MODULE	LOC	Role
infra/entity.py	478	Entity, MockDat, the head registry, DatLike, _bio_io().
infra/io.py	592	IO: prefix binding, ref rendering and parsing, DAT load/save; the D: virtual root.
infra/mk.py	124	Pegboard, the mk singleton, mk.anchor, Maker.
infra/graph_ops.py	174	GraphView, neighbors, paths, subgraph_selection, match (backtracking subgraph isomorphism) for ChemistryImpl.
protocols/bio.py	415	Atom, Molecule, Reaction, Flow, GeneralFlow, Chemistry, CompartmentTree, WorldState, Simulator — stated on the substrate's one state class and one tree class.
protocols/_conformance.py	62	Under TYPE_CHECKING, every *Impl assigned to its Protocol, so a drift in either is a red pyright src/ (T057).

Inbound: infra has 24 import sites (12 in bio, 9 in suite, none in expr/commands), led by mk (11), Entity (7), MockDat (6). protocols has three (bio/__init__, two TYPE_CHECKING uses of WorldState in suite/) plus the conformance file.

Where the declared surface and the code could drift

Box 4 hypotheses (2026-09-10), each now answered: the Flow shadow, the __all__ ghosts and the Protocol drift are fixed (T056/T057 — bio/__init__ exports the ABC only, _conformance.py makes the contracts live), the pegboard and bio.io rows were confirmed as designed (T054 discarded them), and the viz branch went with viz/ (T056).

Hypotheses for the latent-bug pass (T051 box 4).

HYPOTHESIS	Why it would be quiet	Where
A Protocol shadowed by its implementation	bio/__init__.py imports Flow from protocols then rebinds it from .flow; isinstance(x, bio.Flow) tests the ABC, and __all__ exports the winners	bio/__init__.py ~42, ~63, ~172
__all__ names three symbols that do not exist	Scenario, Region, Organism; from alienbio.protocols import * raises	protocols/__init__.py ~46
Simulator drift	the Protocol's run(state, steps, sample_every) vs ReferenceSimulatorImpl.run(state, steps); MembraneFlow.stoichiometry keyed by str in the Protocol, by int in TransportFlux	protocols/bio.py ~220, ~489; bio/simulator.py ~64; bio/flow.py ~482
Pegboard re-registration is identity-based	importlib.reload of makers.py raises on M; a different prefix under the same build is accepted; the key space is flat and single-letter	infra/mk.py ~60
bio.io is attached only by tests	Entity.detach() and ref rendering raise outside tests; __str__ swallows it and falls back to full_name	infra/entity.py ~59, ~445
A dead branch in viz	the isinstance(snapshot, dict) arm and its else are identical; demos/_core.py imports agent_comparison_chart, which does not exist	viz/helpers.py ~34