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AttributeError: module 'scipy.sparse' has no attribute 'csgraph'

See original GitHub issue

Hello,

Thank you for the great contribution.

I can’t seem to get it running. Any help is appreciated.

Here are my versions:

Requirement already satisfied: umap-learn in ./anaconda3/lib/python3.6/site-packages
Requirement already satisfied: numba>=0.34 in ./anaconda3/lib/python3.6/site-packages (from umap-learn)
Requirement already satisfied: scipy>=0.19 in ./anaconda3/lib/python3.6/site-packages (from umap-learn)
Requirement already satisfied: scikit-learn>=0.16 in ./anaconda3/lib/python3.6/site-packages (from umap-learn)
Requirement already satisfied: llvmlite in ./anaconda3/lib/python3.6/site-packages (from numba>=0.34->umap-learn)
Requirement already satisfied: numpy in ./anaconda3/lib/python3.6/site-packages (from numba>=0.34->umap-learn)

Running the example,

import umap
from sklearn.datasets import load_digits

digits = load_digits()

embedding = umap.UMAP().fit_transform(digits.data)

outputs:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-32-e5c7a5ee7150> in <module>()
      4 digits = load_digits()
      5 
----> 6 embedding = umap.UMAP().fit_transform(digits.data)

~/anaconda3/lib/python3.6/site-packages/umap/umap_.py in fit_transform(self, X, y)

~/anaconda3/lib/python3.6/site-packages/umap/umap_.py in fit(self, X, y)

~/anaconda3/lib/python3.6/site-packages/umap/umap_.py in simplicial_set_embedding(graph, n_components, initial_alpha, a, b, gamma, negative_sample_rate, n_epochs, init, random_state, verbose)

~/anaconda3/lib/python3.6/site-packages/umap/umap_.py in spectral_layout(graph, dim, random_state)

AttributeError: module 'scipy.sparse' has no attribute 'csgraph'

But I can import csgraph witout problems from scipy, from scipy.sparse import csgraph

Issue Analytics

State:
Created 6 years ago
Reactions:3
Comments:26 (8 by maintainers)

Top GitHub Comments

1reaction

wangchuan2008888commented, Jul 17, 2018

Scipy 1.1.0 has release, so in ubuntu python 3.6.4 just pip install -U scipy scipy 1.1.0 installed, problem sloved!

1reaction

gokceneraslancommented, Feb 21, 2018

You can maybe exclude scipy==1.0 in setup.py.

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