Improve code

[llrs]

This program is getting some users, so it might be worth to improve it a bit more:

• Make it easy to install with pip
• Add tests (To avoid issues like Hello, I tried your code but despite the different real .pdbs I used as input, I got the following error:  #3 )
• Add to PyPi?

Relevant sources:

• Packaging (Official)
• Python Packaging
• The hitchhikers guide to packaging

[durvasa]

I agree it might be worth putting some extra time to improve this.
@llrs I like the points you raise.
It might also be convenient to:

• add jupyter notebooks to portray functionality
• refurbish the README

[llrs]

Created a new branch packaging to test this (I'm not that familiar with distributing python packages).

Not sure how does the version dependencies work on python work (I think they are usually set up as exactly as possible and then dealt with environments), but there is a problem with the biopython 1.78 and the Bio.Alphabet we import:

sudo -H python3 -m pip install -e . # On the packaging branch
python3
>>> import cozmic
...

ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.