HubComposition API

HubComposition explicitly resolves version-pinned Hub Labs into one caller-owned BioWorld. It is the local-runtime API for mixing a Hub Lab with your own BioModule instances.

from biosimulant import BioWorld
from biosimulant.hub import HubComposition
 
world = BioWorld(communication_step=0.1)
world.add_biomodule("controller", DoseController())
 
composition = HubComposition(world, lab_root="./lab")
composition.add("medium", "acme/nutrient-medium@1.1.0")
composition.apply()
composition.setup()
world.run(duration=24.0)

Constructor

HubComposition(world, lab_root, registry_url=None, dependency_root=None)

By default, dependency state belongs only to the parent Lab:

<lab_root>/.biosimulant/dependencies/

It is disposable operational state, excluded from ordinary package payloads. Each package-backed child must use an exact package@version and have a matching SHA-256 entry in the sibling biosimulant.lock.

Methods

.add(alias, reference)

Adds a Hub Lab beneath alias and resolves reference, which must be exactly namespace/name@version.

composition.add("medium", "acme/nutrient-medium@1.1.0")

The parent lockfile must pin that same package and version. The downloaded archive is checksum-verified before its Lab tree is added. An alias can be added only once. Returns the composition so calls can be chained.

.connect(source, targets)

Adds wiring between aliases in the caller’s composed Lab. targets is a list of destination references.

composition.connect("controller.dose", ["medium.inflow"])

Only connect ports exposed by the referenced Lab’s root io; signal types must remain compatible. Returns the composition so calls can be chained.

.apply(install_deps=True)

Flattens the resolved Lab tree into the supplied BioWorld, instantiates its models, and applies the declared wiring. Set install_deps=False only when the model dependencies have already been installed by your environment.

.setup()

Calls world.setup(...) with the resolved Labs’ setup declarations. Call it after .apply() and before world.run(...).

.dependency_root

Read-only Path property for the effective Lab-local dependency directory. Pass dependency_root= to the constructor when the default Lab location is not writable.

Packaging and standalone archives

Normal .bsilab releases retain package references and lockfile provenance. Use biosimulant labs package --vendor-dependencies to build a fully self-contained archival package. When running a standalone archive in a read-only directory, use the CLI --dependency-root option to choose writable state.

For the end-to-end manifest, lockfile, cache, and vendoring workflow, follow the Compose Hub Labs Locally guide.