modify_dependencies does not recursively deserialize gufetokenizables

[IAlibay]

The use case

I have a subclass of a SolventComponent that has a SmallMoleculeComponent as one of its attributes.

The problem

Roundtripping on keyed dict fails because (in part) modify_dependencies does not deserialize the SmallMoleculeComponent in the dict.

[dotsdl]

@IAlibay can you point us to where this class is implemented? Or provide it here as a snippet and show what it is you are trying that produces the failure?

[IAlibay]

@dotsdl of course, here is the code, including my current short time fix (had to reimplement the shallow/keyed dict method) https://github.com/IAlibay/pontibus/blob/develop/src%2Fpontibus%2Fcomponents%2Fextended_solvent_component.py

[dotsdl]

@atravitz this will require some initial investigation. From @IAlibay's description, this shouldn't be the behavior of gufe.