The initial version of pyCapsid associated with the publication in Bioinformatics (2024) didn't follow the standard lab project structure and included several bad coding practices. The code should be restructured, adapted to be object-oriented and give a more straightforward account of inputs used, data obtained, and outputs.

Ideally, this milestone should be developed parallel to the disassembly milestone. That milestone focuses more on the work needed for the follow-up publication as an application of pyCapsid. This milestone would focus more on the computer science part and programming crafting.