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SCVI problem

Good morning,

I am trying to use SCVI-tool to integrate my data, however, I meet a problem. I hope you guys could help me out.

I meet the error message- "module 'scvi' has no attribute 'data' when I run scvi.model.SCVI.setup_anndata(adata) command.

My SCVI - tool version is "scvi-tools 0.20.3".

Thanks for your support.

Andy

scvi
• 3,975 views • link
written by Andy • Andy

enter image description here

Really weird, I import scvi without any error message, and when I check the package version inside the python, and python replies "scvi package not found". I use pip install dcvi-tools, and I indeed have scvi tools in my condo environment.

• 0 views • link
written by Andy • Andy

I have noticed on occasion that conda does not properly set its environment variables; so even though I have the "(packagename)" in the prompt, which python gives me a binary in a different location than $CONDA_LIB/envs/packagename. Try deactivating all the way back to base, and then reactivating to the library of interest, and see if that sets your environment variables correctly.

• 0 views • link
written by LChart LChart

Could you please elaborate? I think I did not really follow you.

I did check echo $CONDA_PREFIX and the path are same.

• 0 views • link
written by Andy • Andy

I just mean conda deactivate until it says (base), and then conda activate yourenv

• 0 views • link
written by LChart LChart

Thanks for the clarification! I think I solved the problem.

• 0 views • link
written by Andy • Andy

1 answer

UPDATE: problem solved by remove SCVI package, remove old environment, recreate a new condo environment and pip install SCVI-tools.

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written by Andy • Andy

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