Forecasting code cleanup

[JeffreyCovington]

Miscellaneous cleanup which includes:

• Renaming likelihoods to be more explicit.
• Adding more validation checks.
• Adding better type annotations.
• Adding and updating documentation.
• Fixing typos.

[JavadocMD]

Looking much better, thanks! Just a few minor things, see inline.

[Averydx]

Is it possible to split up some of the code in pipeline.py? I'm having difficulties with the dreaded circular imports. For example some of the dataclasses I'm using for type hinting like UnknownParam and PipelineOutput.

[JavadocMD]

Is it possible to split up some of the code in pipeline.py?

There are a number of tricks to accomplish this. For instance, notice the epymorph.tools.data module defines its own Output as a Protocol rather than importing the real Output from epymorph.simulator.basic.output. Breaking out of circular imports was the main reason for doing that.

You can also move certain foundational entities to a third module, if they don't require many imports themselves.

There are certain guidelines that can help organize imports; I thought about enforcing them with tools at one point. Anyway, I'm happy to chat about specifics if it's helpful.

[Averydx]

Thank you! That’s very helpful.