Composite, Composer, and MetaComposer Classes

class vivarium.core.composer.Composer(config: Optional[dict] = None)

Bases: object

Base class for composer classes.

Composers generate composites.

All composer classes must inherit from this class.

Parameters

config – Dictionary of configuration options that can override the class defaults.

defaults: Dict[str, Any] = {}

generate(config: Optional[dict] = None, path: Tuple[str, …] = ()) → vivarium.core.composer.Composite

Generate processes and topology dictionaries.

Parameters

• config – Updates values in the configuration declared in the constructor.

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

Returns

Dictionary with the following keys

• processes: Generated by generate_processes().

• steps: Generated by generate_steps().

• flow: Generated by generate_flow().

• topology: Generated by generate_topology().

The values of these keys are all dictionaries suitable to be passed to the constructor for vivarium.core.engine.Engine.

generate_flow(config: Optional[dict]) → Dict[str, Sequence[Tuple[str, …]]]

Generate the flow of step dependencies.

Parameters

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

Returns

Subclass implementations should return a dictionary mapping step names to sequences (e.g. lists or tuples) of paths. Steps with no dependencies must be included, but they should be mapped to an empty sequence. Any steps returned by generate_steps() or generate_processes() that are not included in the flow will be treated as if they depend on every step previously added to the engine.

abstract generate_processes(config: Optional[dict]) → Dict[str, Any]

Generate processes dictionary.

Every subclass must override this method. For backwards compatibility, vivarium.core.process.Step objects may be included in the returned dictionary, but this practice is discouraged and may be disallowed in a future release.

Parameters

config – 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 vivarium.core.process.Process objects.

generate_steps(config: Optional[dict]) → Dict[str, Any]

Generate the steps dictionary.

Subclasses that want to include steps should override this method. This method is the preferred way to specify steps, though they may also be returned by generate_processes().

Parameters

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

Returns

Subclass implementations should return a dictionary mapping step names to instantiated and configured vivarium.core.process.Step objects.

generate_store(config: Optional[dict] = None) → vivarium.core.store.Store

abstract generate_topology(config: Optional[dict]) → Dict[str, Union[Tuple[str, …], dict, object]]

Generate topology dictionary.

Every subclass must override this method.

Parameters

config – 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.

get_parameters() → dict

Get the parameters for all processes.

Returns

A map from process names to dictionaries of those processes’ parameters.

initial_state(config: Optional[dict] = None) → Optional[Dict[str, Any]]

Merge all processes’ initial states

Every subclass may 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 state paths to initial values.

Return type

dict

class vivarium.core.composer.Composite(config: Optional[Dict[str, Any]] = None, store: Optional[vivarium.core.store.Store] = None, processes: Optional[Dict[str, Any]] = None, steps: Optional[Dict[str, Any]] = None, flow: Optional[Dict[str, Sequence[Tuple[str, …]]]] = None, topology: Optional[Dict[str, Union[Tuple[str, …], dict, object]]] = None, state: Optional[Dict[str, Any]] = None)

Bases: vivarium.library.datum.Datum

Composite parent class.

Contains keys for processes and topology

default_state(config: Optional[dict] = None) → Optional[Dict[str, Any]]

Merge all processes’ default states :param config: A dictionary of configuration options. All :type config: dict :param subclass implementation must accept this parameter: :param but: :param some may ignore it.:

Returns

Subclass implementations must return a dictionary mapping state paths to default values.

Return type

(dict)

defaults: Dict[str, Any] = {'flow': {}, 'processes': {}, 'state': {}, 'steps': {}, 'topology': {}}

flow: Dict[str, Sequence[Tuple[str, …]]] = {}

generate_store(config: Optional[dict] = None) → vivarium.core.store.Store

get_parameters() → Dict

Get the parameters for all processes. :returns: A map from process names to parameters.

initial_state(config: Optional[dict] = None) → Optional[Dict[str, Any]]

Merge all processes’ initial states :param config: A dictionary of configuration options. All :type config: dict :param subclass implementation must accept this parameter: :param but: :param some may ignore it.:

Returns

Subclass implementations must return a dictionary mapping state paths to initial values.

Return type

(dict)

merge(composite: Optional[vivarium.core.composer.Composite] = None, processes: Optional[Dict[str, vivarium.core.process.Process]] = None, topology: Optional[Dict[str, Union[Tuple[str, …], dict, object]]] = None, steps: Optional[Dict[str, Any]] = None, flow: Optional[Dict[str, Sequence[Tuple[str, …]]]] = None, state: Optional[Dict[str, Any]] = None, path: Optional[Tuple[str, …]] = None, schema_override: Optional[Dict[str, Any]] = None) → None

processes: Dict[str, Any] = {}

state: Dict[str, Any] = {}

steps: Dict[str, Any] = {}

topology: Dict[str, Union[Tuple[str, …], dict, object]] = {}

class vivarium.core.composer.MetaComposer(composers: Iterable[Any] = (), config: Optional[dict] = None)

Bases: vivarium.core.composer.Composer

A collection of Composer objects.

The MetaComposer can be used to create composites that combine all the composers in the collection.

Parameters

• composers – Initial collection of composers.

• config – Initial configuration.

add_composer(composer: vivarium.core.composer.Composer, config: Optional[Dict] = None) → None

Add a composer to the collection of stored composers.

Parameters

• composer – The composer to add.

• config – The composer’s configuration, which will be merged with the stored config.

add_composers(composers: List, config: Optional[Dict] = None) → None

Add multiple composers to the collection of stored composers.

Parameters

• composers – The composers to add.

• config – Configuration for the composers, which will be merged with the stored config.

generate_flow(config: Optional[dict] = None) → Dict[str, Any]

generate_processes(config: Optional[dict] = None) → Dict[str, Any]

generate_steps(config: Optional[dict] = None) → Dict[str, Any]

generate_topology(config: Optional[dict] = None) → Dict[str, Union[Tuple[str, …], dict, object]]

vivarium.core.composer.get_composite_from_store(store: vivarium.core.store.Store) → vivarium.core.composer.Composite

Make a Composite from a Store