Hi, I find that I cannot run the tutorial of GimVI successfully:
ImportError Traceback (most recent call last)
Cell In, line 8
5 import matplotlib.pyplot as plt
7 from scipy.stats import spearmanr
----> 8 from scvi.data import (
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)
Hi, this is an outdated version of our gimVI tutorial (0.8.0).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.
Hello, I have updated scvi, but I still cannot use setup_anndata:
AttributeError Traceback (most recent call last)
Cell In, line 1
----> 1 scvi.data.setup_anndata
AttributeError: module ‘scvi.data’ has no attribute ‘setup_anndata’
Hi, please refer to the tutorial I linked above. You can call the setup method as follows: