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AttributeError: module 'scipy' has no attribute 'spatial' #20

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SachinLearns opened this issue Nov 28, 2023 · 1 comment
Open

AttributeError: module 'scipy' has no attribute 'spatial' #20

SachinLearns opened this issue Nov 28, 2023 · 1 comment
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@SachinLearns
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Describe the bug
I am using Python 3.8.13 and installed pyFlowSOM as explained here: https://pypi.org/project/pyFlowSOM/.
The module is giving me a basic error: AttributeError: module 'scipy' has no attribute 'spatial'
I anticipated a normal return of the output. Since it is written in C, I cannot locate/debug the code. Even if someone can guide me where to explore, it would be a help.

To Reproduce
I ran the following code:

node_output = som(data, seed = 30)

Note that the data was a 2D numpy array.

The following error was encountered:

Traceback (most recent call last):
File "main.py", line 27, in
node_output = som(data, seed = 30)
File "src/pyFlowSOM/cyFlowSOM.pyx", line 100, in pyFlowSOM.cyFlowSOM.som
File "src/pyFlowSOM/cyFlowSOM.pyx", line 46, in pyFlowSOM.cyFlowSOM.neighborhood_distance
AttributeError: module 'scipy' has no attribute 'spatial'

@SachinLearns SachinLearns added the bug Something isn't working label Nov 28, 2023
@cliu72
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cliu72 commented Dec 8, 2023

Please check the version of scipy you are using in your environment. As the error indicates, scipy.spatial (https://docs.scipy.org/doc/scipy/reference/spatial.html) does not seem to be available in your version of scipy. I just created a new conda environment in python 3.8.13 and was able to install and run pyFlowSOM without any error.

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