fix: `JsonableData` strips `@module` and `@class` before passing dict to `from_dict()`, breaking MSONable round-trips

[rautaditya2606]

Describe the bug

JsonableData._get_object() calls .pop('@class') and .pop('@module') on the attributes dictionary before passing it to cls.from_dict(). This mutates the dict and strips both keys before deserialization. MSONable's contract (used by pymatgen and other materials science libraries) requires @module and @class to be present in the dict passed to from_dict() — the same dict that as_dict() produced. Stripping them silently breaks round-trip deserialization.

Steps to reproduce

from aiida.orm import JsonableData, load_node

class MyMSONable:
    def __init__(self, value):
        self.value = value

    def as_dict(self):
        return {
            '@module': self.__class__.__module__,
            '@class': self.__class__.__name__,
            'value': self.value,
        }

    @classmethod
    def from_dict(cls, d):
        # MSONable contract: @module and @class must be present
        if '@module' not in d or '@class' not in d:
            raise KeyError('`@module` and `@class` must be present')
        return cls(d['value'])

obj = MyMSONable(42)
node = JsonableData(obj)
node.store()

loaded = load_node(node.pk)
print(loaded.obj.value)  # Raises KeyError: @module and @class stripped

Expected behavior

loaded.obj.value should return 42. @module and @class should be preserved in the dict passed to cls.from_dict().

Your environment

• Operating system: Linux
• Python version: 3.11
• aiida-core version: 2.8.0 (main branch)

Additional context

File: src/aiida/orm/nodes/data/jsonable.py

The fix is to use non-destructive key access (attributes['@class']) instead of .pop(), so the full dict including @module and @class reaches from_dict(). A PR with the fix and a regression test is ready.

[agoscinski]

Yes because these are internal fields. The only issue might be that we don't document good enough in the docs (grep for JsonableData there its in source/topics/data_types.rst)