Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ImportError: cannot import name '_compute_connectivities_umap' from 'scanpy.neighbors' #135

Closed
nbutyrate opened this issue Mar 27, 2024 · 9 comments · Fixed by #136
Closed
Labels
bug Something isn't working

Comments

@nbutyrate
Copy link

Python 3.9.18 | packaged by conda-forge | (main, Dec 23 2023, 16:36:46)
[Clang 16.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.

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 ad

import 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' (

@nbutyrate nbutyrate added the bug Something isn't working label Mar 27, 2024
@bio-la
Copy link

bio-la commented 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 0.8.0

@dorzhey
Copy link

dorzhey commented Mar 29, 2024

hello, yes same dependencies, same problem

@WLYYYYY
Copy link

WLYYYYY commented Mar 29, 2024

Same here, it seems like the last version of Scanpy compatible with muon is v1.9.8.

@seyoon-lee
Copy link

seems like I'm two weeks late, but still with the same issue.

@zijunmeng
Copy link

same errors with scanpy 1.10.1, muon 0.1.5, anndata 0.10.6 ,

@grst
Copy link
Contributor

grst commented Apr 30, 2024

Oh, I think we still need a patch release @gtca?

@gtca
Copy link
Collaborator

gtca commented May 1, 2024

@grst, the 0.1.5 is the version for which this issue has been open for, the 0.1.6 has already been released to fix that for the new version of scanpy.

@zijunmeng, can you check that it fixed the issue for you?

@grst
Copy link
Contributor

grst commented May 1, 2024

Sorry, got confused by that release missing on github. But I've seen it's there now :)

@zijunmeng
Copy link

@grst, the 0.1.5 is the version for which this issue has been open for, the 0.1.6 has already been released to fix that for the new version of scanpy.

@zijunmeng, can you check that it fixed the issue for you?

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

Successfully merging a pull request may close this issue.

8 participants