Biopython, pip and Python-2 deprecation

Microbial community profiling ShortBRED
1

Initially I opened this issue on github, before I realized that this forum existed.

Pip no longer supports Python-2 because Python-2 was deprecated 01/01/2020. Biopython is only available for Python-3 (at least via pip ). It appears that your code does not support Python-3 (e.g. shortbred_quantify.py : 320).

Questions :

  1. Are there any plans on updating your code to make it Python-3 compatible?
  2. Is there a Python-3 compatible version of this project? Maybe a successor project?
  3. Do you have specific installation instructions to work around these incompatibilities?

Thanks!

2

A work around solution is that I managed to get this to work using the Docker image : Docker Hub

This should be suggested on the github page.

Thanks!