Updating pipeline

[SamuelBrand1]

This PR is aimed at addressing two issues, I found it tricky to sensibly separate them.

Pipeline update to work with latest version of EpiAware

• Fixes where prepended missing data were causing errors.
• Update of observation model so that the latest helper version of day of week effect on ascertainment was involved.

This closes #287 .

Modify setting observation model for pipeline

Given we are changing the observation model to reflect changes in EpiAware it was easier to refactor so the observation model wasn't hardcoded but rather a default constructor option (as per other aspects of pipeline).

This closes #288 .

Minor changes

• Fixing a fix in QUICK FIX: fix InferenceConfig constructor for latest version of EpiAware #283; this highlights need for resolution to Work out how to use @testitem in pipeline #206, Setup CI for analysis pipeline #209, Test environment for the pipeline #240
• Renaming functions e.g. when only latent models are used I've renamed to latentmodel in constructors.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.85%. Comparing base (e506f7d) to head (0ff4dc1).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #290   +/-   ##
=======================================
  Coverage   92.85%   92.85%           
=======================================
  Files          47       47           
  Lines         490      490           
=======================================
  Hits          455      455           
  Misses         35       35           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.