The Vivarium Framework

• Configuration Utilities
• build_model_specification()
• validate_model_specification_file()
• build_simulation_configuration()
• The Vivarium Engine
• SimulationContext
  • SimulationContext.name
  • SimulationContext.setup()
  • SimulationContext.initialize_simulants()
  • SimulationContext.step()
  • SimulationContext.run()
  • SimulationContext.finalize()
  • SimulationContext.report()
  • SimulationContext.get_performance_metrics()
  • SimulationContext.add_components()
  • SimulationContext.get_population()
• Builder
  • Builder.logging
  • Builder.lookup
  • Builder.value
  • Builder.event
  • Builder.population
  • Builder.resources
  • Builder.time
  • Builder.components
  • Builder.lifecycle
  • Builder.data
• run_simulation()
• The Vivarium Event Framework
• Event
  • Event.index
  • Event.user_data
  • Event.time
  • Event.step_size
  • Event.split()
• EventChannel
  • EventChannel.emit()
• EventManager
  • EventManager.name
  • EventManager.get_channel()
  • EventManager.setup()
  • EventManager.on_post_setup()
  • EventManager.get_emitter()
  • EventManager.register_listener()
  • EventManager.get_listeners()
  • EventManager.list_events()
• EventInterface
  • EventInterface.get_emitter()
  • EventInterface.register_listener()
• Life Cycle Management
• LifeCycleError
• InvalidTransitionError
• ConstraintError
• LifeCycleState
  • LifeCycleState.name
  • LifeCycleState.entrance_count
  • LifeCycleState.add_next()
  • LifeCycleState.valid_next_state()
  • LifeCycleState.enter()
  • LifeCycleState.add_handlers()
• LifeCyclePhase
  • LifeCyclePhase.name
  • LifeCyclePhase.states
  • LifeCyclePhase.add_next()
  • LifeCyclePhase.get_state()
• LifeCycle
  • LifeCycle.add_phase()
  • LifeCycle.get_state()
  • LifeCycle.get_state_names()
• ConstraintMaker
  • ConstraintMaker.check_valid_state()
  • ConstraintMaker.constrain_normal_method()
  • ConstraintMaker.to_guid()
• LifeCycleManager
  • LifeCycleManager.name
  • LifeCycleManager.current_state
  • LifeCycleManager.timings
  • LifeCycleManager.add_phase()
  • LifeCycleManager.set_state()
  • LifeCycleManager.get_state_names()
  • LifeCycleManager.add_handlers()
  • LifeCycleManager.add_constraint()
• LifeCycleInterface
  • LifeCycleInterface.add_handlers()
  • LifeCycleInterface.add_constraint()
  • LifeCycleInterface.current_state()
• Lookup Tables
• InterpolatedTable
  • InterpolatedTable.data
  • InterpolatedTable.population_view
  • InterpolatedTable.key_columns
  • InterpolatedTable.parameter_columns
  • InterpolatedTable.value_columns
  • InterpolatedTable.interpolation_order
  • InterpolatedTable.clock
  • InterpolatedTable.extrapolate
• ScalarTable
  • ScalarTable.values
  • ScalarTable.value_columns
• LookupTable
  • LookupTable.name
• validate_parameters()
• LookupTableManager
  • LookupTableManager.configuration_defaults
  • LookupTableManager.name
  • LookupTableManager.setup()
  • LookupTableManager.build_table()
• LookupTableInterface
  • LookupTableInterface.build_table()
• Output Metrics
• Metrics
  • Metrics.name
  • Metrics.setup()
• The Plugin Management System
• PluginConfigurationError
• PluginManager
  • PluginManager.get_plugin()
  • PluginManager.get_plugin_interface()
  • PluginManager.get_core_controllers()
  • PluginManager.get_core_interfaces()
  • PluginManager.get_optional_controllers()
  • PluginManager.get_optional_interfaces()
• Resource Management
• ResourceError
• ResourceGroup
  • ResourceGroup.type
  • ResourceGroup.names
  • ResourceGroup.producer
  • ResourceGroup.dependencies
• ResourceManager
  • ResourceManager.name
  • ResourceManager.graph
  • ResourceManager.sorted_nodes
  • ResourceManager.setup()
  • ResourceManager.add_resources()
• ResourceInterface
  • ResourceInterface.add_resources()
• State Machine
• Trigger
  • Trigger.NOT_TRIGGERED
  • Trigger.START_INACTIVE
  • Trigger.START_ACTIVE
• Transition
  • Transition.name
  • Transition.setup()
  • Transition.set_active()
  • Transition.set_inactive()
  • Transition.probability()
• State
  • State.state_id
  • State.transition_set
  • State.name
  • State.sub_components
  • State.setup()
  • State.next_state()
  • State.transition_effect()
  • State.cleanup_effect()
  • State.add_transition()
  • State.allow_self_transitions()
• Transient
• TransientState
• TransitionSet
  • TransitionSet.name
  • TransitionSet.sub_components
  • TransitionSet.setup()
  • TransitionSet.choose_new_state()
  • TransitionSet.append()
  • TransitionSet.extend()
• Machine
  • Machine.states
  • Machine.state_column
  • Machine.population_view
  • Machine.name
  • Machine.sub_components
  • Machine.setup()
  • Machine.add_states()
  • Machine.transition()
  • Machine.cleanup()
• The Simulation Clock
• SimulationClock
  • SimulationClock.name
  • SimulationClock.time
  • SimulationClock.stop_time
  • SimulationClock.step_size
  • SimulationClock.step_forward()
  • SimulationClock.step_backward()
• SimpleClock
  • SimpleClock.configuration_defaults
  • SimpleClock.name
  • SimpleClock.setup()
• get_time_stamp()
• DateTimeClock
  • DateTimeClock.configuration_defaults
  • DateTimeClock.name
  • DateTimeClock.setup()
• TimeInterface
  • TimeInterface.clock()
  • TimeInterface.step_size()
• Framework Utility Functions
• from_yearly()
• to_yearly()
• rate_to_probability()
• probability_to_rate()
• collapse_nested_dict()
• import_by_path()
• handle_exceptions()
• The Value Pipeline System
• DynamicValueError
• replace_combiner()
• list_combiner()
• rescale_post_processor()
• union_post_processor()
• Pipeline
  • Pipeline.name
  • Pipeline.source
  • Pipeline.mutators
  • Pipeline.combiner
  • Pipeline.post_processor
  • Pipeline.manager
• ValuesManager
  • ValuesManager.name
  • ValuesManager.setup()
  • ValuesManager.on_post_setup()
  • ValuesManager.register_value_producer()
  • ValuesManager.register_value_modifier()
  • ValuesManager.get_value()
  • ValuesManager.keys()
  • ValuesManager.items()
  • ValuesManager.values()
• ValuesInterface
  • ValuesInterface.register_value_producer()
  • ValuesInterface.register_rate_producer()
  • ValuesInterface.register_value_modifier()
  • ValuesInterface.get_value()
• Data Artifact Management
  • The Data Artifact
  • ArtifactException
  • Artifact
  • Keys
  • HDF Interface
  • touch()
  • write()
  • load()
  • remove()
  • get_keys()
  • EntityKey
  • The Artifact Manager
  • ArtifactManager
  • ArtifactInterface
  • filter_data()
  • validate_filter_term()
  • get_base_filter_terms()
  • parse_artifact_path_config()
• Component Management
  • The Component Manager System
  • ComponentConfigError
  • OrderedComponentSet
  • ComponentManager
  • ComponentInterface
  • The Component Configuration Parser
  • ParsingError
  • ComponentConfigurationParser
  • parse_component_config_to_list()
  • prep_components()
  • clean_args()
  • import_and_instantiate_components()
• Logging
• The Logging Subsystem
• LoggingManager
  • LoggingManager.configure_logging()
  • LoggingManager.name
  • LoggingManager.get_logger()
• LoggingInterface
  • LoggingInterface.get_logger()
• Logging Utilities
• configure_logging_to_terminal()
• configure_logging_to_file()
• list_loggers()
• Population Management
  • The Population Management System
  • Population Management Exceptions
  • PopulationError
  • The Population Manager
  • SimulantData
  • InitializerComponentSet
  • PopulationManager
  • PopulationInterface
  • The Population View
  • PopulationView
• Random Number Generation
  • Random Numbers in vivarium
  • Randomness System Exceptions
  • RandomnessError
  • Randomness IndexMap
  • IndexMap
  • Randomness System Manager
  • RandomnessManager
  • RandomnessInterface
  • Randomness Streams
  • get_hash()
  • RandomnessStream