Scanpy: ImportError: cannot import name 'IndexMixin'

[genecell]

Hi,

When I ran

import scanpy.api as sc

I met this error:

     19 from scipy import sparse
     20 from scipy.sparse import issparse
---> 21 from scipy.sparse.sputils import IndexMixin
     22 from natsort import natsorted
     23 

ImportError: cannot import name 'IndexMixin'

Is there any requirements for the version of scipy?

Thanks in advance,
BP

[genecell]

Hi, I just tried install a higher version of scipy, and it works now.

pip install scipy==1.2.1

Refer to: https://www.scipy.org

[wir963]

I also ran into this issue when using scanpy==1.4.2 and scipy==1.3.0 (which are the versions installed when I install using conda). Enforcing scipy==1.2.1 in my conda environment file fixed it.

[bgruening]

This problem also exists in 1.4.3.

[flying-sheep]

duplicate of theislab/anndata#146

[levinhein]

Hi. I'm struggling with the same issue that is not resolved with the suggestions above (using other scipy version==1.2.1). I have scanpy==1.6.0 and scipy==1.5.2 in my environment. I am using Ubuntu in Windows.

And when I import scanpy in jupyter notebook, I get the error:

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

Please advise!

[wfma]

I have the same issue as @levinhein!

[YubinXie]

Same issue here. Downgrading scipy from 1.5.4 to 1.2.1 helps.