Incorrect updating of parameters

An evil, sneaky bug that we introduced with the Cerberus refactoring. For the leap parameters, we are using the schema:

_LEAP_PARAMETERS_DEFAULT_SCHEMA = {'leap': {
    'required': False,
    'type': 'dict',
    'schema': _LEAP_PARAMETERS_SCHEMA,
    'default': {'parameters': []}}  # Default for if the parameter is missing
}

so we are assigning the same list object to every molecule by default. This means, for example, that after adding the antechamber frcmod file to the list of parameters of a molecule, we are effectively adding the same frcmod file to every molecule.

I’m thinking of switching to use a default_setter that creates a new list every time.

[Lnaden]

I think there are a couple other mutables in the schema, but they are wrapped in function calls so they get rebuilt per call anyways. This problem would also go away when we put in #824 i imagine, but there is no timeline for that so this should be fixed now

[andrrizzi]

Not a copy of the whole schema per se, but a copy of the default value {'parameters': []}} since it’s a mutable type. I think that’s the only instance in which we use a mutable type as a default value based on a quick scan anyway.