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MilsteinLab / FOCAL3D

Clustering Algorithm for single-molecular localization microscopy data
GNU General Public License v3.0
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requirement.txt for environment #1

Open SarahAufmkolk opened 3 years ago

SarahAufmkolk commented 3 years ago

Hello MilsteinLab, congratulation on an exciting paper/algorithm! It would be very helpful if you could provide a requirement file for the python environment. Best regards, Sarah

PS. I want to add to this request that the error of "No module named 'scipy._lib.six" occurs, since the newer scipy doesn't have the module. (See link below.) They suggest calling the module 'six' independently. But frankly said I'm too much of a beginner with python to see where to change the modules in your code. I hope you can help me or suggest a scipy version for your environment.

https://github.com/wrwrwr/scikit-gof/pull/5

MilsteinLab commented 3 years ago

Hi Sarah, apologies for the delay in response. We became aware of the issue with scipy._lib.six as well. We came up with a rough patch: There is a change in lines 4 and 5 for the file titled “binned_statistic_64bit.py” since “scipy._lib.six” is apparently no longer being supported by python. The required changes are:

4> from six import callable

5> from six.moves import xrange

We'll work on adding a more detailed requirement.txt. The python version that comes when you install Spyder with Anaconda seems to suffice. Thank you for the feedback.