alienbio¶

Topic: ABIO Topics Top-level module providing access to the alienbio runtime.

Public API¶

The alienbio module exports a curated set of symbols via __all__:

__all__ = [
    "bio", "Bio",
    "hydrate", "dehydrate",
    "Entity", "Scenario", "Chemistry", "Simulator", "State",
]

Main API¶

Export	Type	Description
`bio`	`Bio`	Module-level singleton for CLI and simple scripts
`Bio`	class	Environment class for sandboxes and testing

Module-level Functions¶

Export	Description
`hydrate(data)`	Convert dict with `_type` to typed object (advanced)
`dehydrate(obj)`	Convert typed object to dict with `_type` (advanced)

Core Protocols¶

Export	Description
`Entity`	Base class for all hydratable types
`Scenario`	Main runnable unit
`Chemistry`	Molecule and reaction definitions
`Simulator`	Simulation engine protocol
`State`	Simulation state protocol

Usage¶

Simple Usage (Singleton)¶

from alienbio import bio

# Fetch and run
scenario = bio.fetch("catalog/scenarios/mutualism")
result = bio.run("scenarios.baseline", seed=42)

# Build without running
built = bio.build("scenarios.test")

Sandbox Usage (Instance)¶

from alienbio import Bio

# Create isolated environment
sandbox = Bio()
scenario = sandbox.fetch("catalog/scenarios/test")
result = sandbox.run(scenario)

Type Hints¶

from alienbio import Entity, Scenario, Chemistry

class MyEntity(Entity):
    """Custom entity type."""
    ...

def process_scenario(s: Scenario) -> dict:
    """Type-hinted function."""
    ...

Advanced: Implementation Classes¶

Implementation classes are importable but NOT in __all__:

from alienbio import ReferenceSimulatorImpl  # works
from alienbio import *  # does NOT include ReferenceSimulatorImpl

Star Import¶

from alienbio import * imports only the curated public API — not implementation classes or internal utilities.