Assigning reference values in the config throws a warning

[MatthewPaskin]

When assigning the reference values in the config using a dictionary, pydantic throws a serialization warning when assigning the data:

PydanticSerializationUnexpectedValue(Expected Reference - serialized value may not be as expected [field_name='ref', input_value={'DOI': 'example'}, input_type=dict])

A solution with an alternative to explicitly assigning a Reference object is needed to assign data through code, rather than in the YAML directly. The most intuitive way I see this happening is through a dictionary.

[MatthewPaskin]

Similarly this happens when assigning other data types e.g. surface fraction:

PydanticSerializationUnexpectedValue(Expected float - serialized value may not be as expected [field_name='sfr', input_value=0.1, input_type=RefValue[float]])