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Python 3.9.18 | packaged by conda-forge | (main, Dec 23 2023, 16:36:46)
[Clang 16.0.6 ] on darwin
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I installed muon and tried to run one of the tutorial and got the following error, please help
import numpy as np
import pandas as pd
import scanpy as sc
import anndata as adimport muon as mu
Traceback (most recent call last):
File "", line 1, in
File "/Users/naseersangwan/Desktop/Conda/envs/R_2024/lib/python3.9/site-packages/muon/init.py", line 6, in
from ._core import preproc as pp
File "/Users/naseersangwan/Desktop/Conda/envs/R_2024/lib/python3.9/site-packages/muon/_core/preproc.py", line 15, in
from scanpy.neighbors import _compute_connectivities_umap
ImportError: cannot import name '_compute_connectivities_umap' from 'scanpy.neighbors' (
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bio-la commentedon Mar 27, 2024
hi, got the same error since updating scanpy in the last 12 hours
scanpy 1.10.0, muon 0.1.5, anndata 0.8.0dorzhey commentedon Mar 29, 2024
hello, yes same dependencies, same problem
WLYYYYY commentedon Mar 29, 2024
Same here, it seems like the last version of Scanpy compatible with muon is v1.9.8.
seyoon-lee commentedon Apr 9, 2024
seems like I'm two weeks late, but still with the same issue.
zijunmeng commentedon Apr 30, 2024
same errors with scanpy 1.10.1, muon 0.1.5, anndata 0.10.6 ,
grst commentedon Apr 30, 2024
Oh, I think we still need a patch release @gtca?
gtca commentedon May 1, 2024
@grst, the
0.1.5is the version for which this issue has been open for, the0.1.6has already been released to fix that for the new version of scanpy.@zijunmeng, can you check that it fixed the issue for you?
grst commentedon May 1, 2024
Sorry, got confused by that release missing on github. But I've seen it's there now :)
zijunmeng commentedon May 2, 2024
yes, thank you, i have solved this problem. In my env, I have installed scvi, scglue, and muon. Two days ago, I encountered conflicts between muon's functions and scvi. I have now uninstalled the original 0.1.5 version and reinstalled the 0.1.6 version using pip. The conflicts have indeed disappeared. Thank you again for your help.