Incompatibility with pydantic version 2 about cobrapy HOT 6 CLOSED

Seems reasonable to me. Feel free to send a PR with a newer requirement. That way we will see if the CI passes.

from cobrapy.

Maybe just >=1.6 would allow both users of <2 and >2 to happily use cobrapy.

from cobrapy.

The PR above just changes the ~ here to a > as @Midnighter suggests.

I think the CI is just waiting for a maintainer to approve before it sets off.

from cobrapy.

Now fixed in 0.27.0.

from cobrapy.

Problem description

From a quick look I don't think cobrapy uses pydantic except for in this file, which I think is compatible with pydantic version 2 as is. It therefore doesn't seem like a very hard bug to fix: just remove the pin or change it to a version greater than 2.

@teddygroves or @cdiener, did you test whether the file referenced is compatible with pydantic v2? I ask because when setting up a new environment with conda, I get the following import error when importing cobra (cobra=0.29.0, pydantic=2.5.6):

Traceback (most recent call last):
File "", line 1, in
File "/home/a/.conda/envs/cobra/lib/python3.12/site-packages/cobra/init.py", line 17, in
from cobra import io
File "/home/a/.conda/envs/cobra/lib/python3.12/site-packages/cobra/io/init.py", line 9, in
from cobra.io.web import AbstractModelRepository, BiGGModels, BioModels, load_model
File "/home/a/.conda/envs/cobra/lib/python3.12/site-packages/cobra/io/web/init.py", line 6, in
from .biomodels_repository import BioModels
File "/home/a/.conda/envs/cobra/lib/python3.12/site-packages/cobra/io/web/biomodels_repository.py", line 14, in
class BioModelsFile(pydantic.BaseModel):
^^^^^^^^^^^^^^^^^^
File "/home/a/.conda/envs/cobra/lib/python3.12/site-packages/pydantic/init.py", line 372, in getattr
module = import_module(module_name, package=package)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/a/.conda/envs/cobra/lib/python3.12/importlib/init.py", line 90, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/a/.conda/envs/cobra/lib/python3.12/site-packages/pydantic/main.py", line 13, in
from pydantic_core import PydanticUndefined
ImportError: cannot import name 'PydanticUndefined' from 'pydantic_core' (unknown location)

I forced conda to install pydantic-1.10.0 and import cobra works fine. I do not have experience with pydantic, so I'm not clear if this is an issue with the requirements or not, but it appears that something does break when upgrading to pydantic v2.

from cobrapy.

Hi this error seems to be raised in pydantic itself and there seems to have been a bug in the conda package. Can you update your pedantic in the environment to a newer build and try again?

from cobrapy.