pydantic error

[shoepfl]

Hi Matthias,

currently I get a pydantic error, when using sbmlutils 0.8.4:

UserWarning: Field "model_units" has conflict with protected namespace "model_".

You may be able to resolve this warning by setting model_config['protected_namespaces'] = ().
warnings.warn(
/home/basti/miniconda3/envs/sbmlutils/lib/python3.11/site-packages/pydantic/_internal/fields.py:127: UserWarning: Field "model_definitions" has conflict with protected namespace "model".

You may be able to resolve this warning by setting model_config['protected_namespaces'] = ().
warnings.warn(
───────────────────────────────────────────────────────────────────────────────────── Create SBML ──────────────────────────────────────────────────────────────────────────────────────
Traceback (most recent call last):
File "/mnt/c/Users/basti/Documents/Uni/11_Doktorarbeit/Python/BayModTS/test.py", line 74, in
results = create_model(
^^^^^^^^^^^^^
File "/home/basti/miniconda3/envs/sbmlutils/lib/python3.11/site-packages/sbmlutils/factory.py", line 3619, in create_model
m = Model.merge_models(model)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/basti/miniconda3/envs/sbmlutils/lib/python3.11/site-packages/sbmlutils/factory.py", line 3445, in merge_models
kind = m2._keys.get(key, None)
^^^^^^^^
File "/home/basti/miniconda3/envs/sbmlutils/lib/python3.11/site-packages/pydantic/main.py", line 711, in getattr
return self.pydantic_private[item] # type: ignore
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/basti/miniconda3/envs/sbmlutils/lib/python3.11/site-packages/pydantic/main.py", line 715, in getattr
pydantic_extra = object.getattribute(self, 'pydantic_extra')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'Model' object has no attribute 'pydantic_extra'. Did you mean: 'pydantic_complete'?

The error occours now in the file I already sent you for the RTD function:
test.py.txt

for me this seems to be a problem with my dependencies - can you help me here?

Thanks, Sebastian

[matthiaskoenig]

Hi @shoepfl,
this is most likely due to the latest pydantic release. Downgrading pydantic to <2.0 should fix this.
I will provide a bugfix asap.
Best Matthias

[shoepfl]

Thanks @matthiaskoenig,

i succeeded with pydantic 1.10.2

Best,
Sebastian

[harveymannering]

We also had this issue, which was causing tests to fail. We fixed this by downgrading pydantic to <2.0.

[matthiaskoenig]

This is fixed in the latest version 0.8.5