Serialize¶

Serializer for Numpy arrays. Numpy array serialization is lossy–we serialize to Python lists, so deserialization will produce a Python list instead of a Numpy array.

class Codec[source]¶: Bases: bson.codec_options.TypeEncoder

get_codecs() → List [source]¶

class vivarium.core.serialize.ProcessSerializer[source]¶

Bases: vivarium.core.registry.Serializer

Serializer for processes if emit_process is enabled.

serialize(data: vivarium.core.process.Process) → str [source]¶

class vivarium.core.serialize.SequenceDeserializer(name='')[source]¶

Bases: vivarium.core.registry.Serializer

Iterates through lists and applies deserializers.

can_deserialize(data: Any) → bool [source]¶

deserialize(data: Any) → List[Any][source]¶

class vivarium.core.serialize.SetSerializer(name='')[source]¶

Bases: vivarium.core.registry.Serializer

Serializer for set objects.

class Codec[source]¶: Bases: bson.codec_options.TypeEncoder

get_codecs() → List [source]¶

class vivarium.core.serialize.UnitsSerializer[source]¶

Bases: vivarium.core.registry.Serializer

Serializes data with units into strings of the form !units[...], where ... is the result of calling str(data). Deserializes strings of this form back into data with units.

class QuantityCodec[source]¶: Bases: vivarium.core.serialize.UnitsSerializer.UnitCodec

class UnitCodec[source]¶: Bases: bson.codec_options.TypeEncoder

can_deserialize(data: Any) → bool [source]¶

deserialize(data: str, unit: Optional[pint.unit.Unit] = None) → pint.quantity.Quantity [source]¶

Deserialize data with units from a human-readable string.

Parameters

data – The data to deserialize. Providing a list here is deprecated. You should use deserialize_value instead, which uses a separate list deserializer.
unit – The units to convert data to after deserializing. If omitted, no conversion occurs. This option is deprecated.

Returns

A single deserialized object or, if data is a list, a list of deserialized objects.

get_codecs() → List [source]¶

serialize(data: Any) → str [source]¶

vivarium.core.serialize.deserialize_value(value: Any) → Any[source]¶

Find and apply the correct serializer for a value by calling each registered serializer’s vivarium.core.registry.Serializer.can_deserialize() method. Returns the value as is if no compatible serializer is found.

Parameters: value (Any) – Data to be deserialized
Raises: ValueError – Only one serializer should apply for any given value
Returns: Deserialized data
Return type: Any

vivarium.core.serialize.get_codec_options() → bson.codec_options.CodecOptions [source]¶: Returns a set of options used for serializing and deserializing BSON by collecting codecs from all registered serializers.

vivarium.core.serialize.serialize_value(value: Any, codec_options: Optional[bson.codec_options.CodecOptions] = None) → Any[source]¶

Apply PyMongo’s TypeCodec-based serialization routine on value.

Parameters

value (Any) – Data to be serialized
codec_options (bson.codec_options.CodecOptions) – Options used when encoding / decoding BSON. Defaults to None, in which case options are generated from the currently registered serializer codecs.

Returns

Serialized data

Return type

Any