Issues with scikit-bio on Mac M1

Question

I tried installing scikit-bio by running conda install -c https://conda.anaconda.org/biocore scikit-bio per the documentation, but verifying the installation via python -m skbio.test yielded the following error: Error while finding module specification for 'skbio.test' (ModuleNotFoundError: No module named 'skbio').

Next, I tried installing with pip install numpy and pip install scikit-bio, but that yielded a huge wall of errors. Tried the installation test anyway, got the same ModuleNotFoundError.

I'm on a MacBook Air 2020 with a M1 processor, so not sure if that's causing the issue.

Answer 1

I don't know if you still have problems with scikit-bio but the solution that worked for me was using sse2neon package: https://github.com/DLTcollab/sse2neon

Following instructions should work

git clone https://github.com/biocore/scikit-bio
cd scikit-bio
wget https://github.com/DLTcollab/sse2neon/blob/master/sse2neon.h

Open the simde-sse2.h file and replace each of the following two lines:

#include <xmmintrin.h>
#include <emmintrin.h>

with:

#include "sse2neon.h"

then run:

pip install .

!Note that this solution doesn't work for newer python releases. I used python 3.8 for this solution.