Epic: Upgrade I/O

[jrihon]

💡 Summary

The current approach in reading in commandline argument is extremely manual and error-prone.

This should be changed by using validation using pydantic or something similar

🔎 Scope & Requirements

This epic would touch the following parts of the code :

• the preprocessing script

• getting rid of the binp, tinp files etc.

• Adding secure cli parsing

• The output functionality should receive a better layer as well, so this requires refactoring as well

This needs to be finished in order for this epic to be considered done :

• Tests tests tests
  • tests for the new pydantic models
  • tests for the new functions written
  • tests for matching input and output
• A friendlier CLI experience

Not in scope

What we are not including is the following :

1. xyz-to-pdb . This we will just deprecate. Perhaps we can host a simple script online in the documentation so people can do it themselves.
2. nucleobase. This will be reworked in a different feature
3. The GUI. This is a pandora's box I am not opening yet.

Linked Tasks / Features

• Feature: Rework I/O Build module #24
• Feature: Reworked I/O Transmute model #25
• Feature: Reworked I/O randomiser module #26