[Bug]: The jsanitize function does not behave as expected with recursive_msonable=True

[Andrew-S-Rosen]

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Version

2024.10.21

Which OS(es) are you using?

• MacOS
• Windows
• Linux

What happened?

Currently, jsanitize(recursive_msonable=True) does not (as the name might suggest) recursively crawl an MSONable object and make it fully sanitized. If an MSONable object is within an attribute of the parent MSONable object, the former will not be sanitized.

For instance, try the following:

from monty.json import jsanitize
from pymatgen.core import Structure
from copy import deepcopy
structure = Structure(
   lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
   species=["Mg", "O"],
   coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
   )
structure.properties = {"test": deepcopy(structure)}
sanitized = jsanitize(structure, recursive_msonable=True)

You will see the output is as follows:

{'@module': 'pymatgen.core.structure',
 '@class': 'Structure',
 'charge': 0,
 'lattice': {'matrix': [[0.0, 2.13, 2.13],
   [2.13, 0.0, 2.13],
   [2.13, 2.13, 0.0]],
  'pbc': (True, True, True),
  'a': 3.012274887854692,
  'b': 3.012274887854692,
  'c': 3.012274887854692,
  'alpha': 60.00000000000001,
  'beta': 60.00000000000001,
  'gamma': 60.00000000000001,
  'volume': 19.327193999999995},
 'properties': {'test': Structure Summary
  Lattice
      abc : 3.012274887854692 3.012274887854692 3.012274887854692
   angles : 60.00000000000001 60.00000000000001 60.00000000000001
   volume : 19.327193999999995
        A : 0.0 2.13 2.13
        B : 2.13 0.0 2.13
        C : 2.13 2.13 0.0
      pbc : True True True
  PeriodicSite: Mg (0.0, 0.0, 0.0) [0.0, 0.0, 0.0]
  PeriodicSite: O (2.13, 2.13, 2.13) [0.5, 0.5, 0.5]},
 'sites': [{'species': [{'element': 'Mg', 'occu': 1}],
   'abc': [0.0, 0.0, 0.0],
   'properties': {},
   'label': 'Mg',
   'xyz': [0.0, 0.0, 0.0]},
  {'species': [{'element': 'O', 'occu': 1}],
   'abc': [0.5, 0.5, 0.5],
   'properties': {},
   'label': 'O',
   'xyz': [2.13, 2.13, 2.13]}]}

Note how the properties key has an actual Structure object in it.

Code snippet

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Log output

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