Update GMSO to work with pydantic 2.0

[daico007]

Pydantic v2 just recently comes out and seem to offer a lot of benefits, but also bring along many breaking changes to our current API. This PR will attempt to update GMSO classes to work with the latest version of pydantic.

[github-advanced-security]

CodeQL found more than 10 potential problems in the proposed changes. Check the Files changed tab for more details.

[codecov]

Codecov Report

Attention: 6 lines in your changes are missing coverage. Please review.

Comparison is base (c014a44) 92.81% compared to head (e69f03b) 92.36%.

Files	Patch %	Lines
gmso/core/atom.py	92.00%	2 Missing ⚠️
gmso/core/atom_type.py	91.66%	2 Missing ⚠️
gmso/core/element.py	88.88%	1 Missing ⚠️
gmso/formats/json.py	87.50%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #745      +/-   ##
==========================================
- Coverage   92.81%   92.36%   -0.46%     
==========================================
  Files          66       66              
  Lines        6862     6860       -2     
==========================================
- Hits         6369     6336      -33     
- Misses        493      524      +31     

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[CalCraven]

So what is the result of removing the JSONHandler class in gmso.abc.serialization_utils? Is that going to change the ability to use the top.save("top.json") method?

Otherwise, minus just some questions for my understanding this is good to go.

[daico007]

The reason JSONHandler got removed is because pydantic decided to deprecate the ability to have our own Json handler altogether (we used it before to handle non-serializable property, like unyt and sympy expression). The new way they try to make people do is having the custom json writer determined for each class (this is part of the work in this PR). The JSON reader and writer still works (the unit tests for those are kept mostly intact).

[CalCraven]

Excellent, good to know. I'm about to push fixes to these conflicts with the main branch, then we can get this merged.