[Feature] Clean MoSDeN for Initial Release

[LukeSeifert]

Is your feature request related to a problem? Please describe.

MoSDeN has several issues that should be cleaned up before the initial release.

Describe the feature you'd like.

• JSON sensitivity reading is excessively slow; replace with HDF5 or some other data format (Update 01/12/26: The slowdown was actually caused by re-writing the file every sampled iteration. This has been fixed and the runtime is now greatly improved and does not decrease over time dramatically)
• Add tests for chemical removal expected behavior
• Remove various hard-coded values
• Give each unique DNP its own color
• Use the scientific Python dev guide
• Store literature data externally in CSVs
• Reduce code repetition (base.py can do more heavy lifting)

Optional features

• Add automated documentation
• Add more unit tests for better coverage
• Reduce function sizes and make stateless
• Clean up static typing and use mypy

How can this issue be closed?

All non-optional features are added