Closed as not planned
Description
Code snippet
# pip install maggma ase==3.23.0 pymatgen==2024.10.25 numpy==1.26.4
from ase.build import bulk
from pymatgen.io.ase import AseAtomsAdaptor
from maggma.stores import MemoryStore
atoms = bulk("Cu")
structure = AseAtomsAdaptor.get_structure(atoms)
print(type(structure[0].lattice.pbc[0])) # np.bool_
store = MemoryStore()
with store as s:
s.update(structure, key="charge")What happened?
When trying to store a document with a numpy 1.x np.bool_ entry, the underlying bson dependency raises an InvalidDocument error and maggma can't store the document in the connected store. Some sanitization should likely be done to address this.
Hmm, but the following works okay, so there is something in-between here:
with store as s:
s.update({"test": 1, "val": (np.bool_)}, key="test")Version
0.70.0
Which OS?
- MacOS
- Windows
- Linux
Log output
Cell In[1], line 11
9 store = MemoryStore()
10 with store as s:
---> 11 s.update(structure, key="charge")
File ~\miniconda\envs\test\Lib\site-packages\maggma\stores\mongolike.py:395, in MongoStore.update(self, docs, key)
393 if len(requests) > 0:
394 try:
--> 395 self._collection.bulk_write(requests, ordered=False)
396 except (OperationFailure, DocumentTooLarge) as e:
397 if self.safe_update:
File ~\miniconda\envs\test\Lib\site-packages\mongomock\collection.py:1852, in Collection.bulk_write(self, requests, ordered, bypass_document_validation, session)
1850 for operation in requests:
1851 operation._add_to_bulk(bulk)
-> 1852 return BulkWriteResult(bulk.execute(), True)
File ~\miniconda\envs\test\Lib\site-packages\mongomock\collection.py:331, in BulkOperationBuilder.execute(self, write_concern)
329 exec_name = execute_func.__name__
330 try:
--> 331 op_result = execute_func()
332 except WriteError as error:
333 result['writeErrors'].append({
334 'index': index,
335 'code': error.code,
336 'errmsg': str(error),
337 })
File ~\miniconda\envs\test\Lib\site-packages\mongomock\collection.py:157, in BulkWriteOperation.register_update_op.<locals>.exec_update()
156 def exec_update():
--> 157 result = collection._update(spec=selector, document=document,
158 multi=multi, upsert=self.is_upsert,
159 **extra_args)
160 ret_val = {}
161 if result.get('upserted'):
File ~\miniconda\envs\test\Lib\site-packages\mongomock\collection.py:896, in Collection._update(self, spec, document, upsert, manipulate, multi, check_keys, hint, session, collation, let, array_filters, **kwargs)
894 if not check_keys:
895 _validate_data_fields(document)
--> 896 BSON.encode(document, check_keys=check_keys)
897 existing_document.update(self._internalize_dict(document))
898 if existing_document['_id'] != _id:
File ~\miniconda\envs\test\Lib\site-packages\bson\__init__.py:1429, in BSON.encode(cls, document, check_keys, codec_options)
1403 @classmethod
1404 def encode(
1405 cls: Type[BSON],
(...)
1408 codec_options: CodecOptions[Any] = DEFAULT_CODEC_OPTIONS,
1409 ) -> BSON:
1410 """Encode a document to a new :class:`BSON` instance.
1411
1412 A document can be any mapping type (like :class:`dict`).
(...)
1427 Replaced `uuid_subtype` option with `codec_options`.
1428 """
-> 1429 return cls(encode(document, check_keys, codec_options))
File ~\miniconda\envs\test\Lib\site-packages\bson\__init__.py:1050, in encode(document, check_keys, codec_options)
1047 if not isinstance(codec_options, CodecOptions):
1048 raise _CODEC_OPTIONS_TYPE_ERROR
-> 1050 return _dict_to_bson(document, check_keys, codec_options)
InvalidDocument: cannot encode object: True, of type: <class 'numpy.bool_'>