Fix: Figure 2 script

[SamuelBrand1]

This PR fixes the script for creating figure 2 so that it runs with the current inference data structure. Also, I've refactored plotting functions within EpiAwarePipeline where ever I've found myself reusing for figure 2 functions that seems specific to fig 1.

As per #555 I've swapped to using Makie directly.

[github-actions]

Try this Pull Request!

Open Julia and type:

import Pkg
Pkg.activate(temp=true)
Pkg.add(url="https://github.com/CDCgov/Rt-without-renewal", rev="refactor-fig2", subdir="EpiAware")
using EpiAware

[seabbs]

Nice looks good to me

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.96%. Comparing base (ccbbed3) to head (d601ab6).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #558   +/-   ##
=======================================
  Coverage   90.96%   90.96%           
=======================================
  Files          60       60           
  Lines         863      863           
=======================================
  Hits          785      785           
  Misses         78       78           

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