update end to end test

[sbidari]

Key changes:

Adds generate_fake_nwss_data function in generate_test_data.R
Modifies end_to_end_test.sh to fit Pyrenew-HEW model for COVID-19

Adds PyrenewWastewaterData class to handle wastewater data.
Modifies build_model_from_dir and related functions to incorporate wastewater data.
Adds priors for wastewater-related parameters in prod_priors.py and build_pyrenew_model.py
Modifies forecast_state.py to handle wastewater data:
-scan for NWSS data conditional on fit_wastewater flag
-raise errors if wastewater data is not available for the requested report date.
Moved calculation of pop_fraction from PyrenewHEWData to prep_data.py (required arg for LatentInfectionProcess)

[codecov]

Codecov Report

Attention: Patch coverage is 82.05128% with 21 lines in your changes missing coverage. Please review.

Project coverage is 30.47%. Comparing base (128ae86) to head (5d52a5e).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
pipelines/forecast_state.py	0.00%	12 Missing ⚠️
pipelines/prep_data.py	0.00%	6 Missing ⚠️
pyrenew_hew/pyrenew_wastewater_data.py	97.36%	2 Missing ⚠️
pyrenew_hew/pyrenew_hew_data.py	94.11%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #353      +/-   ##
==========================================
+ Coverage   29.26%   30.47%   +1.21%     
==========================================
  Files          25       26       +1     
  Lines        1910     1939      +29     
==========================================
+ Hits          559      591      +32     
+ Misses       1351     1348       -3     

Flag	Coverage Δ
hewr	35.35% <ø> (ø)
pipelines	14.41% <25.00%> (+0.24%)	⬆️
pyrenew_hew	42.02% <96.77%> (+3.31%)	⬆️

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[dylanhmorris]

This is looking very good. Thanks, @sbidari! Just a few questions before I review further.

[sbidari]

@dylanhmorris I have made the changes we discussed yesterday.

This passes the pipeline run check but fails on a test for PyrenewWastewaterData. The issue is that site_pop (within site_subpop_spine) is interpreted as Object when accessed from build_model_from_dir but is interpreted as Float when called from test_pyrenew_wastewater_data leading to this error. I don't really understand what's causing this difference

[dylanhmorris]

One question and one suggestion. Thanks, @sbidari!

[dylanhmorris]

LGTM provided tests pass, thanks @sbidari!. In the future we should more fully separate the subpopulation specification from the wastewater data specification (so you can do multi-subpop models without observed wastewater). This should also help with the pop-fraction stuff. But it's out of scope for now.