refactor pipeline smaller scripts and functions

[SamuelBrand1]

This PR aims to refactor, but not extend the functionality, of the analysis pipeline in such a way that:

1. It is more readable.
2. Its closer to DRY principles.
3. Its written in such a way that a next step for job scheduling is as easy as possible.

Concretely,

• Default variables are generated by calling a default function from the AnalysisPipeline module.
• Vectors of scenarios combinations are generated by calling make_... functions from the AnalysisPipeline module.
• Plotting functions are declared separately; I don't feel they belong inside the analysis module but open to changing this.
• The pipeline is now one script, which essentially follows an analogous sequence of steps to the opening example of targets.R.
• Inference scenarios are an inner loop of the the "truth data" generation process.
• Each function has a unit test, as does the whole pipeline for a randomly selected inference scenario on a short flat time series of fake data.

Closes #215 .

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.73%. Comparing base (4262a9b) to head (9180cd0).

Additional details and impacted files

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##             main     #217   +/-   ##
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  Coverage   92.73%   92.73%           
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  Files          42       42           
  Lines         399      399           
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  Hits          370      370           
  Misses         29       29           

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[seabbs]

I really like this. I had a few suggestions to make it more complicated/have more infra but not essential. We can discuss and port what we want to do into new issues and merge this I think

[SamuelBrand1]

I've made a few minor changes:

• More small(ish) functions with tests
• plotting functions to inside AnalysisPipeline
• moved some struct construction to inside a generate function to make the pipeline script a bit cleaner.

#218 Should cover some of the more exciting ideas we could do with pipeline analysis going forwards! But I think this pipeline (which runs) is currently a good template to layer on the rest the tasks in #195