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theislab / scgen

Single cell perturbation prediction

Home Page:https://scgen.readthedocs.io

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ImportError: cannot import name 'setup_anndata' from 'scvi.data'

GA-1101 opened this issue · comments

commented

Hi,
Thanks for your excellent contribution. I recently met an import issue: cannot import name 'setup_anndata' from 'scvi.data'

The initial script try to import 'setup_anndata' from the */scvi/data/__init__.py.
It seems that the latest version of scvi-tools have no more 'setup_anndata' in 'init.py'. It showed error:
ImportError: cannot import name 'setup_anndata' from 'scvi.data'

The latest version I installed of scvi-tools is '0.15.4', I downgrade the scvi-tools version to '0.9.0' so that the scgen can be import normally.

I think that may be an issue of the basic usage of scGen, could you please check the initial script and update related code to match the latest version of scvi-tools.

Lei