text: user2005: 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 
  "/Users/nikitavlasenko/python_scripts/data_files/WT_SCID_CCA.csv"
  
  
  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)
    print(myargs)
    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.
  
  user2153: 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
  
original_text: 2005: <p>Some time ago I asked the question: </p>
  
  <p><a href="https://bioinformatics.stackexchange.com/questions/4357/runumap-in-seurat-not-working-module-umap-has-no-attribute-umap">RunUMAP in Seurat not working: module &#39;umap&#39; has no attribute &#39;UMAP&#39;</a></p>
  
  <p>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:</p>
  
  <pre><code>python python/umap.py -path 
  "/Users/nikitavlasenko/python_scripts/output/" -data 
  "/Users/nikitavlasenko/python_scripts/data_files/WT_SCID_CCA.csv"
  </code></pre>
  
  <blockquote>
    <p>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'</p>
  </blockquote>
  
  <p>From inside <code>spyder</code> 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 <code>umap</code> library? Maybe it should be imported in a different way? Here is the whole script:</p>
  
  <pre><code>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)
    print(myargs)
    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=",")
  </code></pre>
  
  <p>Python version that is used by <code>spyder</code> and in the terminal seems to be the same: <code>3.6</code>. I am using <code>Mac OSX</code>.</p>
   2153: <p>You answered your own question, yet it is not a coincidence that you have to change the name of your script.</p>
  
  <p>When Python executes your custom script, it reads:</p>
  
  <blockquote>
    <p>import umap</p>
  </blockquote>
  
  <p>Python will first search the local sources (the directory of the script) , and afterwards the installed sources.</p>
  
  <p>In this case Python identifies the local source to be <code>umap.py</code>, 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.</p>
  
  <p>For more information on importing see <a href="https://docs.python.org/2/tutorial/modules.html#the-module-search-path" rel="nofollow noreferrer">Module search path</a> at docs.pyhton.org</p>
  