Refactor Naghavi case study

[radka-j]

Closes #532
Closes #553
Closes #637
Closes #648
Closes #716
Closes #796

Contributes to #748

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Codecov Report

❌ Patch coverage is 93.21888% with 79 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.90%. Comparing base (cecf95d) to head (04db678).
⚠️ Report is 158 commits behind head on main.

Files with missing lines	Patch %	Lines
autoemulate/core/sensitivity_analysis.py	17.94%	32 Missing ⚠️
autoemulate/calibration/history_matching.py	58.82%	14 Missing ⚠️
autoemulate/simulations/base.py	95.06%	4 Missing ⚠️
autoemulate/simulations/flow_problem.py	33.33%	4 Missing ⚠️
autoemulate/emulators/base.py	89.28%	3 Missing ⚠️
autoemulate/core/compare.py	92.00%	2 Missing ⚠️
autoemulate/datasets/__init__.py	0.00%	2 Missing ⚠️
autoemulate/datasets/datasets.py	0.00%	2 Missing ⚠️
autoemulate/emulators/gaussian_process/__init__.py	80.00%	2 Missing ⚠️
autoemulate/simulations/reaction_diffusion.py	0.00%	2 Missing ⚠️
... and 11 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #632      +/-   ##
==========================================
+ Coverage   80.20%   81.90%   +1.70%     
==========================================
  Files         155       81      -74     
  Lines       11132     5559    -5573     
==========================================
- Hits         8928     4553    -4375     
+ Misses       2204     1006    -1198     

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Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
autoemulate/calibration
history_matching.py					319, 325-326, 384-388, 392, 579-608
autoemulate/core
sensitivity_analysis.py					235-240, 374-379, 791-793, 820-872
Project Total

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