Add calculate processes function to pipeline

[SamuelBrand1]

This PR adds a function that calculates the three process targets for inference:

• log incidence
• exponential growth rate
• (Instantaneous) reproduction number.

Adds a simple rt calculation, and wraps EpiAware.expected_Rt, but with left truncation effect dealt with backwards exponential growth according to first value of rt.

Closes #116

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.18%. Comparing base (788ddce) to head (33f60a5).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #314   +/-   ##
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  Coverage   93.18%   93.18%           
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  Files          50       50           
  Lines         528      528           
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  Hits          492      492           
  Misses         36       36           

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[SamuelBrand1]

I've kept the functionality the same here, but added an internal method for seeding the infections. The backwards exponential is now a default dispatching on the pipeline type. This should make it easier to address new functionality later as flagged by @seabbs .

[seabbs]

Good idea