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theislab / scgen

Single cell perturbation prediction
https://scgen.readthedocs.io
GNU General Public License v3.0
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ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' #28

Closed levinhein closed 3 years ago

levinhein commented 3 years ago

Hi. I'm having an import error. When I try to import scgen, I encounter the error below and attached as image. ALSO, whether I import scgen or scanpy alone, same "IndexMixin" error occurs. My scipy version is 1.5.2. I tried using version 1.4 and 1.2.1 (because I saw from other online issues that this should resolve it), but it didn't work for my case, the error is still the same. Help, please!

ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' (/home/levinbioinformatics/anaconda3/envs/scgen-env/lib/python3.7/site-packages/scipy/sparse/sputils.py)

image

M0hammadL commented 3 years ago

@levinhein hi, I think it is not scgen problem, it is just an inconsistency in your env, I saw you posted an issue in scanpy too, try to change the version of scipy then it will be fixed.

M0hammadL commented 3 years ago

Hi

We have released a new PyTorch version of the code. Please use this version.

Best Mo