Some time ago I asked the question:

RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP'

It was solved by following the answer in it, however, it is still not working when I run a python script from terminal, giving the same error:

python python/umap.py -path 
"/Users/nikitavlasenko/python_scripts/output/" -data 

Traceback (most recent call last): File "python/umap.py", line 26, in result = umap.UMAP().fit_transform(data.T) AttributeError: module 'umap' has no attribute 'UMAP'

From inside spyder the same script runs perfectly, but somehow when running it from the terminal it is not successful. I am new to python, so maybe I am not pointing correctly to umap library? Maybe it should be imported in a different way? Here is the whole script:

import umap
import numpy as np

def getopts(argv):
opts = {}  # Empty dictionary to store key-value pairs.
while argv:  # While there are arguments left to parse...
    if argv[0][0] == '-':  # Found a "-name value" pair.
        opts[argv[0]] = argv[1]  # Add key and value to the dictionary.
    argv = argv[1:]  
return opts

if __name__ == '__main__':
  from sys import argv
  myargs = getopts(argv)
  path_to_save = myargs['-path']
  path_to_data = myargs['-data']
  data = np.loadtxt(open(path_to_data, "rb"), delimiter=",", skiprows=1)
  result = umap.UMAP().fit_transform(data.T)
  np.savetxt(path_to_save + "/umap.csv", result, delimiter=",")

Python version that is used by spyder and in the terminal seems to be the same: 3.6. I am using Mac OSX.

  • 1
    $\begingroup$ Add a print(umap.__file__) early on. It's likely that you're getting a different copy of umap. $\endgroup$
    – Devon Ryan
    Commented Jun 13, 2018 at 10:22

2 Answers 2


You answered your own question, yet it is not a coincidence that you have to change the name of your script.

When Python executes your custom script, it reads:

import umap

Python will first search the local sources (the directory of the script) , and afterwards the installed sources.

In this case Python identifies the local source to be umap.py, and imports the (currently executed) script, while foregoing the installed sources. Since you are calling functions, not defined in your current script, Python will not be able to fully execute your script.

For more information on importing see Module search path at docs.pyhton.org


It is pretty weird but the only thing that I needed to do is to rename my python script from umap.py to umap_gen.py and right away it started to work. So, I guess there can be such name collisions which we should avoid. Although I would prefer the file to be named as umap.py still...


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