Import cobra

[Alejandro Cano]

Hi everyone,

I'm a new user of CobraPy that used to work with Cobra toolbox in Matlab. I followed all the steps to install CobraPy in a Conda enviroment but when I run the "import cobra" line I get the following message.

Traceback (most recent call last):
  File "C:\Conda\lib\site-packages\IPython\core\interactiveshell.py", line 3437, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-2-e8543d93f282>", line 1, in <module>
    import cobra
  File "C:\Program Files\JetBrains\PyCharm Community Edition 2021.1.2\plugins\python-ce\helpers\pydev\_pydev_bundle\pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "C:\Conda\lib\site-packages\cobra\__init__.py", line 17, in <module>
    from cobra import io
  File "C:\Program Files\JetBrains\PyCharm Community Edition 2021.1.2\plugins\python-ce\helpers\pydev\_pydev_bundle\pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "C:\Conda\lib\site-packages\cobra\io\__init__.py", line 9, in <module>
    from cobra.io.web import AbstractModelRepository, BiGGModels, BioModels, load_model
  File "C:\Program Files\JetBrains\PyCharm Community Edition 2021.1.2\plugins\python-ce\helpers\pydev\_pydev_bundle\pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "C:\Conda\lib\site-packages\cobra\io\web\__init__.py", line 6, in <module>
    from .biomodels_repository import BioModels
  File "C:\Program Files\JetBrains\PyCharm Community Edition 2021.1.2\plugins\python-ce\helpers\pydev\_pydev_bundle\pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  File "C:\Conda\lib\site-packages\cobra\io\web\biomodels_repository.py", line 14, in <module>
    class BioModelsFile(pydantic.BaseModel):
  File "C:\Conda\lib\site-packages\cobra\io\web\biomodels_repository.py", line 18, in BioModelsFile
    size: int = pydantic.Field(alias="fileSize")

AttributeError: module 'pydantic' has no attribute 'Field'

Hope some of you can help me with this issue. Thank you.

[Dennis van den Berg]

Hi Alejandro,

Can you try to import cobrapy in a jupyter notebook instead of JetBrains? Just to see if it is not a problem with the IDE.

Kind regards,

Dennis

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[Alejandro Cano]

[Dennis van den Berg]

Hi Alejandro,

Do you happen to be running python 3.10?

And is your version of pydantic 1.9.0? Older versions are incompatible with python 3.10.

Regards,

Dennis

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[Alejandro Cano]

Currently I'm running python 3.8.8 and the version of pydantic that I have is 0.18.2.

Should I update both of them?

Regards,

Alejandro.

[Dennis van den Berg]

That version of pydantic is really low. My environment with python 3.8.12 is running pydantic 1.8.2 and cobra 0.22.1

That runs fine, so can you check in your ' conda list' command if pydantic is not from the pip channel. If so you can update it using ' conda install -c conda-forge pydantic'

Hope this helps,

Dennis

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[Dennis van den Berg]

My bad, I meant channel Pypi not pip.

[ch.d...@gmail.com]

Ye, as others said the pydantic version is too low. The smallest supported version is 1.6. There is a missing version requirement in the conda package. I'll add it there to avoid this in the furure.