ReferencesSupported Python API

Supported Python API surface

This is the list of supported public imports from the biosimulant package. Names not listed here are implementation details and may change without notice. The compatibility biosim import path exposes the same runtime APIs for existing projects.

Core composition

from biosimulant import (
    BioWorld, WorldEvent,
    BioModule, ExecutionContext, ExecutionPolicy,
    SignalEmitterBioModule, StatefulBioModule,
    WiringBuilder, build_from_spec, load_wiring, load_wiring_toml,
    load_wiring_yaml,
)

Use BioWorld, BioModule, and WiringBuilder for their contracts.

Signals and visuals

from biosimulant import (
    BioSignal, AcceptedSignalProfile, ScalarSignal, ArraySignal,
    RecordSignal, EventSignal, InputValueType, SignalSpec,
    unwrap_payload, coerce_float, scalar_or_record_input, make_signal,
    validate_connection_specs, validate_port_spec_direction,
    VisualSpec, validate_visual_spec, normalize_visuals,
)

See BioSignal & Metadata and the Visualization Contract.

Lab packaging

from biosimulant import (
    build_package, export_lab_package, fetch_package, publish_package,
    run_package, unpack_package, validate_package,
)

For supported CLI workflows and archive layout, see the lab manifest reference and CLI reference.

Hub-backed local composition

from biosimulant.hub import (
    HubComposition, LOCK_FILE_NAME, dependency_directory,
    materialize_vendored_lab,
)

HubComposition is intentionally in biosimulant.hub, rather than the root namespace, to make dependency resolution an explicit choice. See the HubComposition API.

Runtime helpers (provisional)

from biosimulant.runtime import (
    FlattenedLab, LabTree, LabTreeChild, LabTreeIO, LabTreeModel,
    LabTreePort, LabTreeWire,
    coerce_typed_inputs, extract_communication_step, extract_settle_steps,
    flatten_lab_tree, flush_package_cache, lab_io_from_mapping,
    load_entrypoint,
)

biosimulant.runtime holds the package interpretation helpers the CLI uses: entrypoint loading, typed input coercion, communication-step resolution, and lab flattening. It is public but provisional, so these names may still change between minor releases.

Optional simulator bases

from biosimulant.contrib.sbml import TelluriumSBMLBioModule
from biosimulant.contrib.cellml import LibCellMLBioModule

Import the contrib module you need directly. Both bases import their simulator lazily. The CellML base needs pip install "biosimulant[cellml]". No extra installs Tellurium, so add it to the model’s own dependencies. See Wrap an External Simulator.

Managed Developer API

from biosimulant import (
    Client, AsyncClient, Run, RunResult, Artifact,
    ApiError, AuthenticationError, ValidationError, RateLimitError,
    InsufficientCreditsError, RunFailed, RunTimeout,
    verify_webhook_signature,
)

Client and AsyncClient submit accessible versioned Hub Labs to managed infrastructure; they do not change local BioWorld.run() behavior. See the Developer API, runs and results, and errors reference.

Optional machine-learning helper

from biosimulant import OnnxClassifierModule

This helper is imported lazily and requires the optional ML dependencies:

pip install "biosimulant[ml]"

Version

from biosimulant import __version__
HubComposition APIBioSignal & Metadata