modernatx / seqlike

Unified biological sequence manipulation in Python
https://modernatx.github.io/seqlike
Apache License 2.0
207 stars 21 forks source link

Add missing setup.py deps, add notebook extras, and move test deps to extras #64

Closed JacobHayes closed 2 years ago

JacobHayes commented 2 years ago

I had a couple import errors (see below) when testing this package out that are related to undeclared dependencies in setup.py. Some were in requirements.txt, but not declared in setup.py's install_requires, so I moved them all to setup.py and removed requirements.txt (so this doesn't happen again :crossed_fingers:).

I also added 2 extras:


Here are the errors I saw:

.../lib/python3.7/site-packages/seqlike/SeqLike.py in <module>
      9 from typing import Callable, Optional, Union
     10
---> 11 import lazy_loader as lazy
     12
     13 from Bio.Seq import Seq

ModuleNotFoundError: No module named 'lazy_loader'
.../lib/python3.7/site-packages/seqlike/draw_utils.py in <module>
     19 try:
     20     get_ipython
---> 21     from bokeh.io import output_notebook
     22
     23     output_notebook()

ModuleNotFoundError: No module named 'bokeh'
ericmjl commented 2 years ago

Hi @JacobHayes, my many apologies for responding late here! I've just seen the code changes and everything looks good from my view. I think we can merge and cut a new release as soon as all tests pass. Thank you for taking the time to help us make SeqLike better! :smile:

ericmjl commented 2 years ago

Things are only failing at building notebooks as docs, but everything else should be fine here. I'm going to merge.