module 'umap' has no attribute '__version__'

Hey!

I hope you are doing well.

I run into the error AttributeError: module ‘umap’ has no attribute ‘version’ when running this code:

import pandas as pd
#pd.set_option("display.max_columns", None)
import numpy as np
import anndata
import scanpy as sc

%store -r df

adata = anndata.AnnData(df)
sc.pp.neighbors(adata, n_neighbors=10, n_pcs=40)
sc.tl.paga(adata)
sc.pl.paga(adata, plot=False)
sc.tl.umap(adata, init_pos='paga')

I am using Python 3.8 on Jupyter Notebooks on Mac M1.

Please find below the error in a more detailed fashion:

AttributeError                            Traceback (most recent call last)
<ipython-input-7-7cfb2fb3103e> in <module>
----> 1 sc.tl.umap(adata, init_pos='paga')
      2 sc.pl.umap(adata)

~/opt/anaconda3/lib/python3.8/site-packages/scanpy/tools/_umap.py in umap(adata, min_dist, spread, n_components, maxiter, alpha, gamma, negative_sample_rate, init_pos, random_state, a, b, copy, method, neighbors_key)
    141         import umap
    142 
--> 143     if version.parse(umap.__version__) >= version.parse("0.5.0"):
    144 
    145         def simplicial_set_embedding(*args, **kwargs):

AttributeError: module 'umap' has no attribute '__version__'

Would you have any idea on how to solve this? I think it is a package dependency problem.

Thank you in advance for your help!

[hurleyLi]

@hurleyLi, would you mind opening an issue over on umap that you’re unable to get a __version__ from it? It would be nice to have that fixed/ at least tracked down upstream.

Figure it out. In my case it’s because I have both umap and umap-learn installed, see here: https://github.com/theislab/scanpy/issues/2045#issuecomment-963533994

[flying-sheep]

Why are we using umap.__version__ instead of importlib.metadata.version('umap-learn')?