pytorch_geometric: AttributeError: module 'scipy.sparse' has no attribute 'coo_array'

🐛 Describe the bug

code: from torch_geometric.datasets import KarateClub dataset = KarateClub()

bug: Traceback (most recent call last): File “F:\study\python\test\test4pyg.py”, line 2, in <module> dataset = KarateClub() File “F:\anaconda\envs\ai\lib\site-packages\torch_geometric\datasets\karate.py”, line 50, in init adj = nx.to_scipy_sparse_array(G).tocoo() File “F:\anaconda\envs\ai\lib\site-packages\networkx\convert_matrix.py”, line 921, in to_scipy_sparse_array A = sp.sparse.coo_array((d, (r, c)), shape=(nlen, nlen), dtype=dtype) AttributeError: module ‘scipy.sparse’ has no attribute ‘coo_array’

Environment

PyG version:2.0.4
PyTorch versn:1.10.1
OS:windows10
Python version:3.9.7
CUDA/cuDNN version:CU113
How you installed PyTorch and PyG (conda, pip, source):conda
Any other relevant information (e.g., version of torch-scatter):
pytorch-scatter:2.0.9
pytorch-sparse:0.6.13
pytorch-spline-conv:1.2.1
pytorch-cluster:1.6.0

About this issue

Original URL
State: closed
Created 2 years ago
Reactions: 5
Comments: 22 (3 by maintainers)

Commits related to this issue

SciPy 1.8.0 required — committed to QSMxT/QSMxT by astewartau 2 years ago

Most upvoted comments

coo_array appears only in scipy version 1.8.0

+27

Godofnothing on Mar 31, 2022

Looks like this is a version conflict between networkx and scipy. Can you upgrade both to see if this resolves your issues?

+17

rusty1s on Mar 30, 2022

Same error using pyg-nightly and networkx 2.7.1. Downgrading to networkx==2.6.3 ‘solves’ the error for me.

+14

david-AH on May 9, 2022

Upgrading the networkx caused the same problem. These ones solved the problem for me scipy==1.8.0 networkx==2.6

decanbay on Aug 17, 2022

I upgraded networkx and scipy, restarted vscode (powershell) and now it works.

lfcc1 on May 10, 2022

I was calculating the network.pagerank of a graph on Google Colab when I encountered this problem. After going through all the suggestions, I executed the following to resolve the issue:
!pip install --upgrade scipy networkx

I tried this but still shows the same error. Can anyone suggest something that works? (My networkX version = 3.0 , scipy = 1.10)

dharrypotter on Feb 14, 2023

I’m having the same problem, already upgraded both modules (networkx and scipy) but still getting the same error… AttributeError: module ‘scipy.sparse’ has no attribute ‘coo_array’

lfcc1 on Apr 23, 2022

For me conda couldnt update to correct version but this works:

pip install --upgrade scipy networkx

kakkapriyesh on Sep 8, 2022