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tyjo / luminate

Denoising longitudinal microbiome data.
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logsumexp has moved to scipy.special in newer versions of scipy #1

Closed fig-foodisgood closed 4 years ago

fig-foodisgood commented 4 years ago

http://pageperso.lif.univ-mrs.fr/~francois.denis/IAAM1/scipy-html-1.0.0/generated/scipy.special.logsumexp.html.

Get a few errors when running examples because import location has to be updated.

tyjo commented 4 years ago

This should be fixed now, thanks!

apascualgarcia commented 4 years ago

Dear Tyler,

The problem still persists, after installing requirements in a conda environment, running ./run-examples.sh leads to the error:

ImportError: cannot import name 'logsumexp' from 'scipy.misc'

The issue can be solved installing scipy==1.2.1 instead, for some reason in the version suggested in requirements.txt the function seems to be in another module. With the version 1.2.1 the code works.

tyjo commented 4 years ago

Thanks for bringing this to my attention.

The import statement in main.pydid not get updated with the rest of the code. I believe this should be resolved now, but let me know if you run into any trouble.

apascualgarcia commented 4 years ago

I confirm I can run it now with scipy-1.5.3, thanks for the quick response.