Newest Version of Anndata incompatible with scvi-tools

[bykovam]

Please make sure these conditions are met

• [X] I have checked that this issue has not already been reported.
• [X] I have confirmed this bug exists on the latest version of anndata.
• [X] (optional) I have confirmed this bug exists on the master branch of anndata.

Report

import os
import anndata as ann
import numpy as np
import pandas as pd
import scanpy as sc
import scvi

Traceback:

File ~/beegfs/bykovam/anaconda3/envs/scvi-env/lib/python3.9/site-packages/scvi/data/_utils.py:13
     11 import scipy.sparse as sp_sparse
     12 from anndata import AnnData
---> 13 from anndata._core.sparse_dataset import SparseDataset
     15 # TODO use the experimental api once we lower bound to anndata 0.8
     16 try:

ImportError: cannot import name 'SparseDataset' from 'anndata._core.sparse_dataset' (/home/bykovam/beegfs/bykovam/anaconda3/envs/scvi-env/lib/python3.9/site-packages/anndata/_core/sparse_dataset.py)

Versions

Version of anndata is 0.10.1
Version of scvi-tools is 0.20.3

[ivirshup]

Thanks for the report.

This was fixed in the already released 0.10.2.

See also: https://github.com/scverse/scvi-tools/issues/2268