vivarium.core.process module

Process and Compartment Classes

class vivarium.core.process.Deriver(parameters=None)

Bases: vivarium.core.process.Process

is_deriver()

class vivarium.core.process.Generator(config)

Bases: object

Generator parent class

All compartment classes must inherit from this class.

defaults = {}

generate(config=None, path=())

Generate processes and topology dictionaries for the compartment

Parameters

• config (dict) – Updates values in the configuration declared in the constructor

• path (tuple) – Tuple with (‘path’, ‘to’, ‘level’) associates the processes and topology at this level

Returns

Dictionary with two keys: processes, which has a value of a processes dictionary, and topology, which has a value of a topology dictionary. Both are suitable to be passed to the constructor for vivarium.core.experiment.Experiment.

Return type

dict

generate_processes(config)

Generate processes dictionary

Every subclass must override this method.

Parameters

config (dict) – A dictionary of configuration options. All subclass implementation must accept this parameter, but some may ignore it.

Returns

Subclass implementations must return a dictionary mapping process names to instantiated and configured process objects.

Return type

dict

generate_topology(config)

Generate topology dictionary

Every subclass must override this method.

Parameters

config (dict) – A dictionary of configuration options. All subclass implementation must accept this parameter, but some may ignore it.

Returns

Subclass implementations must return a topology dictionary.

Return type

dict

get_parameters()

or_default(parameters, key)

class vivarium.core.process.ParallelProcess(process)

Bases: object

end()

get()

update(interval, states)

class vivarium.core.process.Process(parameters=None)

Bases: vivarium.core.process.Generator

default_state()

defaults = {}

derive_defaults(original_key, derived_key, f)

derivers()

generate_processes(config)

generate_topology(config)

get_schema(override=None)

is_deriver()

local_timestep()

Returns the favored timestep for this process. Meant to be overridden in subclasses, unless 1.0 is a happy value.

merge_overrides(override)

next_update(timestep, states)

Find the next update given the current states this process cares about. This is the main function a new process would override.

or_default(parameters, key)

ports()

ports_schema()

ports_schema returns a dictionary that declares which states are expected by the processes, and how each state will behave.

state keys can be assigned properties through schema_keys declared in Store:

‘_default’ ‘_updater’ ‘_divider’ ‘_value’ ‘_properties’ ‘_emit’ ‘_serializer’

pull_data()

vivarium.core.process.assoc_in(d, path, value)

vivarium.core.process.generate_derivers(processes, topology)

vivarium.core.process.override_schemas(overrides, processes)

vivarium.core.process.run_update(connection, process)

vivarium.core.process.serialize_dictionary(d)

vivarium.core.process.serialize_list(lst)

vivarium.core.process.serialize_value(value)