Include day of week effect in pipeline analysis

[SamuelBrand1]

Small PR which implements the day of week observation effect introduced by #253 and #258 to the pipeline generative model. Also removes older "truth data" sims.

Closes #257 .

[seabbs]

Suggest using a .gitignore in truth data and adding these file types + getting rid of the placeholder file. Or do we want to commit this data as fixes the sims for onwards analysis?

I've added ignore *.jld2 files to gitignore and if we commit this as a fix I think this works.

[SamuelBrand1]

This looks good but has there been a git history issue here? Looks like a bunch of changes I thought we had merged already.

I started this branch before these changes were merged to main and squashed them into this branch.

[seabbs]

That doesn't sound like the right git flow to me? I've rebase so maybe will fix

[seabbs]

Rebased fixed the issue with old stuff here but commited files are still here. Are they meant to be?

[SamuelBrand1]

Rebased fixed the issue with old stuff here but commited files are still here. Are they meant to be?

I don't see any committed files except some placeholder.md files?

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.34%. Comparing base (4688d20) to head (aab078b).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #264   +/-   ##
=======================================
  Coverage   93.34%   93.34%           
=======================================
  Files          45       45           
  Lines         451      451           
=======================================
  Hits          421      421           
  Misses         30       30           

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