Questions about GimVI

Help scvi-tools
1

Hi, I find that I cannot run the tutorial of GimVI successfully:

ImportError Traceback (most recent call last)
Cell In[3], line 8
5 import matplotlib.pyplot as plt
7 from scipy.stats import spearmanr
----> 8 from scvi.data import (
9 smfish,
10 cortex,
11 setup_anndata
12 )
13 from scvi.model import GIMVI
15 train_size = 0.8

ImportError: cannot import name ‘setup_anndata’ from ‘scvi.data’ (/gpfs/gibbs/project/zhao/tl688/conda_envs/spaben/lib/python3.8/site-packages/scvi/data/init.py)

I also find that the colab link of GimVI failed. Could you please help me? Thanks a lot.

(Introduction to gimVI — scvi 0.8.0 documentation)

2

Hi, this is an outdated version of our gimVI tutorial (0.8.0). Please refer to the most recent version (1.0.2).

I also see that you might have the old scvi package installed instead of the newer scvi-tools. You can install this with pip install -U scvi-tools or conda install scvi-tools -c conda-forge.

3

Hello, I have updated scvi, but I still cannot use setup_anndata:

AttributeError Traceback (most recent call last)
Cell In[11], line 1
----> 1 scvi.data.setup_anndata

AttributeError: module ‘scvi.data’ has no attribute ‘setup_anndata’

4

Hi, please refer to the tutorial I linked above. You can call the setup method as follows:

scvi.external.GIMVI.setup_anndata(...
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