Issue 532: Change deps and remove Dagger for pipeline

[SamuelBrand1]

This PR closes #532 .

The way in which I've addressed problems described in #532 around using RCall and Dagger in the pipeline execution is to:

1. Move the usage of RCall into an extension of EpiAwarePipeline. This means we can still call to scoringutils in post-processing but it doesn't need to installed for a pipeline main inference compute.
2. Removed Dagger and replace with pmap. This is a bit disappointing but it works fine for this problem.

[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="532-reduce-pipeline-deps-and-simplify-pipeline-compute", subdir="EpiAware")
using EpiAware

[seabbs]

Nice good solution. A shame about Dagger

[SamuelBrand1]

Nice good solution. A shame about Dagger

Agreed.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.54%. Comparing base (ae73647) to head (a308479).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #534   +/-   ##
=======================================
  Coverage   90.54%   90.54%           
=======================================
  Files          57       57           
  Lines         825      825           
=======================================
  Hits          747      747           
  Misses         78       78           

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