Refactor code

[tare]

What

Refactor the whole code base.

Why

The code base is old and it was put together without a good structure. Additionally, the use of CmdStan introduced some complicated steps when it comes to input data generation and downstream analysis. Finally, the code was not going to work on Visium data.

How

Here is a list of the main changes:

• replace CmdStan with NumPyro
• replace CAR prior using HSGP
• use Poetry
• implement unit tests
• implement graph-based tissue section detection and separation
• simplify the code base
• add type hinting
• add GitHub actions
• add some pre-commit hooks
• use ruff

Testing

Experimented with the package and implemented tests to ensure that the package works as expected.

Anything else

There are many breaking changes.