Modules¶

Code organization for alienbio (src/alienbio/, ~35k LOC), module by module.

As of T056 (2026-09-10). The design-level view is ABIO Architecture; this page is the tree.

Source Tree¶

Top level — the public surface (__init__.py), the bio front door (cli.py, whose command list is COMMANDS), config.py (API keys and the default agent/model), capabilities.py (the 35 capability dimensions behind bio test-matrix) and report.py (bio report).

src/alienbio/
├── bio/         the chemistry substrate
├── suite/       the instrument
├── expr/        the Expr language: loader, evaluator, sandbox
├── spec_lang/   the AST allowlist, Scope, @biotype
├── infra/       Entity, IO, the mk pegboard, graph_ops
├── protocols/   the Protocols the substrate implements
└── commands/    bio suite | config | test-matrix | report

bio/ — atom molecule reaction chemistry (the entities, plus Modulation); compartment compartment_tree world_state; world (WorldImpl, the declarative world and its one resolution point); rate_expr (the compiled rate grammar; ROUNDING_FLOOR, RATE_CAP); world_simulator (the reference stepper: reactions, flows, populations); jax_core jax_simulator (the JAX stepper, parity to 1e-9); flow (TransportFlux, GeneralFlow); population (PerCapitaGrowth / PerCapitaDeath / CountFlow and the shared summed-demand ration); conservation energy (the canaries); makers (mk.M / mk.R / mk.C).

suite/ — experiment (the spec, preflight, the drafter heads, the record store, run_experiment, render_report); expr_experiment (!experiment and its heads); registration (catalog/registrations.yaml, the no-peeking licence); the runtime runner agent llm_agent brief naming trial mass_trial; composition skeleton blocks; the drafters pressure_gen phase1_gen conflict_gen delta_gen arch_diagnose arch_predict arch_intervene hazard; analysis dose delta caution degradation faking tradeoff census realism plots and the score_* primitives; expr_heads rate_law verify dist. See ABIO Suite Runtime.

expr/ — yaml_tags parse env interp registry heads include x. See ABIO Expr Spec.

catalog/ holds the experiments (experiments/*.yaml, golden-pinned), the examples (examples/*/) and registrations.yaml; runs/ the record stores. The M1 layout this page used to list (spec_lang/bio.py, run.py, bio/state.py, bio/simulator.py, the bio build|run|expand verbs) was deleted in M47.7 and T056.