Cannot import modules from IAB even though scikit bio installed

Question

I am trying to use the Jupyter notebooks from "An Introduction to Applied Bioinformatics". My computer is a Mac M1 with the Ventura OS and I'm using Python 3.9.2. When I get to the cells using packages from iab I get error messages. For example

from iab.algorithms import show_F

error no module named iab.

I cannot find an iab package to load it, even though I installed scikit bio.

All code cells using the iab module failed.

Answer 1

If you are going to continue to work with the content from edition 1, see here.

I'd suggest try running in a new cell in your notebook the following:

%pip install https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics/archive/master.zip

Then restart the kernel and now from iab.algorithms import show_F should work. See my comment for further explanation.