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

[amirsani]

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

[lmcinnes]

I am a little puzzled by this -- scipy >= 0.19 does have that module according to the docs:

• https://docs.scipy.org/doc/scipy-1.0.0/reference/sparse.csgraph.html
• https://docs.scipy.org/doc/scipy-0.19.0/reference/sparse.csgraph.html
  I'm not sure why it wouldn't be found.

[amirsani]

I agree, the following works fine:
from scipy.sparse.csgraph import connected_components

If I add the following,
from scipy.sparse.csgraph import connected_components
before,
def spectral_layout(graph, dim, random_state):
It works fine.

Probably my install is messed up.

[lmcinnes]

It could be an issue in how some commits got merged in. I'll take a look soon just in case.

[amirsani]

Thanks Leland

[arnaudmiribel]

I have the same issue. Sorry, could you elaborate a little more on the solution that worked for you guys ?

[lmcinnes]

My understanding is that you should edit the file umap_.py to have

from scipy.sparse.csgraph import connected_components

Along with the other imports. In practice it may be worth grabbing the latest version on master here and installing from that (after uninstalling the pip version). That should fix this issue, but as I can't actually reproduce it myself I can't know for sure.

[arnaudmiribel]

Thanks @lmcinnes, that trick indeed worked for me :)

[sauln]

can't actually reproduce it myself

@arnaudmiribel and @amirsani, What system are you are using? Operating system w/ version and Python version.

We might be able add to add them to the Travis CI test runs. Currently, it's a little sparse running only on conda with 3.6 and 2.7.

Is this specific to Jupyter notebooks? I am on Ubuntu 16.04, python 3.5.2.

import umap
from sklearn.datasets import load_digits
#from scipy.sparse.csgraph import connected_components

digits = load_digits()

embedding = umap.UMAP(n_neighbors=5,
                      min_dist=0.3,
                      metric='correlation').fit_transform(digits.data)

The code above works if I start python from the command line, but doesn't work in a Jupyter notebook. If i uncomment the import it works in the notebook.

[amirsani]

Hello,

Yes. I was running on a Jupyter Notebook with Python 3.6.4 and Ubuntu 17.10.

from scipy.sparse.csgraph import connected_components
is all I had to add to umap_.py to get it working.

I installed umap-learn on my other system without any problems. I accidentally installed umap, as I did the first time, and wondered if this was causing any problems? I removed it and reinstalled umap-learn to get everything working on the other system.

[sauln]

Thanks for the info. Sounds like it could be Jupyter or Ubuntu related.

One more question for both of you, are you using conda or pip to install everything?

[amirsani]

pip install umap-learn

[wflynny]

This looks like it's related to SciPy version 1.0.0. I assume it's working for SciPy version =< 0.19.

I currently have SciPy version 1.0.0 (released October 25, 2017) installed via conda/pip and I also have this problem. This commit to SciPy a month ago adds back the import of csgraph to scipy.sparse but there hasn't been a new release of SciPy since.

It might be best to directly import from scipy.sparse.csgraph import connected_components as suggested.