SCVI problem

Question

[Andy]

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

[Andy]

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.

[LChart]

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.

[Andy]

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

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

[LChart]

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

[Andy]

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

Answer 1

[Andy]

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