Import error involving numpy and cobra

[CNelias]

When trying to import mass (or cobra), I get the following error:

ImportError: cannot import name 'object' from 'numpy' (C:\Users\Corentin offline\AppData\Roaming\Python\Python310\site-packages\numpy\__init__.py)

The full stack trace goes as follow:

C:\ProgramData\anaconda3\lib\site-packages\cobra\io\mat.py:13: FutureWarning: In the future `np.object` will be defined as the corresponding NumPy scalar.
  from numpy import object as np_object
Traceback (most recent call last):

  Cell In[2], line 1
    import mass

  File C:\ProgramData\anaconda3\lib\site-packages\mass\__init__.py:7
    from mass import enzyme_modules, io

  File C:\ProgramData\anaconda3\lib\site-packages\mass\enzyme_modules\__init__.py:2
    from mass.enzyme_modules.enzyme_module import EnzymeModule

  File C:\ProgramData\anaconda3\lib\site-packages\mass\enzyme_modules\enzyme_module.py:58
    from cobra.core.dictlist import DictList

  File C:\ProgramData\anaconda3\lib\site-packages\cobra\__init__.py:17
    from cobra import io

  File C:\ProgramData\anaconda3\lib\site-packages\cobra\io\__init__.py:6
    from cobra.io.mat import load_matlab_model, save_matlab_model

  File C:\ProgramData\anaconda3\lib\site-packages\cobra\io\mat.py:13
    from numpy import object as np_object

Any idea what's causing it and how I can fix this? I'm running Python 3.10 on windows 11. I have tried on another machine (also windows 11) and get the same error.

[AlbanMariette]

Hi @CNelias, did you find a fix for this issue? I some how have the same issue with MassPy, updating numpy and scipy does not fix the issue and updating Cobra to the last version does not work because of incompatibilities

[CNelias]

Unfortunately not, and I decided to switch to another framework at some point.

[AlbanMariette]

Hi @CNelias, thanks for your answer, may I ask to which framework you switched because I do not think COBRA would allow me to simulate enzyme inhibition or to integrate enzyme activities as MASSPY would have allowed me?

[luciansmith]

According to https://stackoverflow.com/questions/75069062/module-numpy-has-no-attribute-object, the 'object' child of numpy was removed in 1.24.0, so until masspy updates their code to match the new numpy, you'll need to install 1.23.5 or earlier (pip install numpy==1.23.5)