add epiweekly other forecast samples to standard pipeline

[dylanhmorris]

Key changes

• Pipeline now outputs two kinds of epiweekly proportion forecasts:

  • Ones in which both the target disease and other ed visits are forecast daily and then aggregated to epiweekly
  • One in which only the target disease is forecast daily and aggregated; the other ed visits are forecast epiweekly

• Pipeline automatically produces (and collates) plots of epiweekly aggregate predictions as well as daily-scale predictions, for better analysis of the actual forecast. For proportions, this includes both denominator options.

• End to end test runs, and all plots are successfully collated.

• to_epiweekly_quantile_table() in hewr now uses the pre-aggregated epiweekly trajectories rather than doing aggregation, and can be configured to use either of the two options (aggregated daily or directly forecast epiweekly) for the Other forecast.

Out of scope

Incorporation of epiweekly plots into diagnostic report (should be done, separate issue imo)

[codecov]

Codecov Report

Attention: Patch coverage is 23.65591% with 142 lines in your changes missing coverage. Please review.

Project coverage is 16.54%. Comparing base (591b416) to head (6998961).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
hewr/R/process_state_forecast.R	8.66%	137 Missing ⚠️
pipelines/postprocess_forecast_batches.py	0.00%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #270      +/-   ##
==========================================
- Coverage   18.46%   16.54%   -1.93%     
==========================================
  Files          21       21              
  Lines        1446     1481      +35     
==========================================
- Hits          267      245      -22     
- Misses       1179     1236      +57     

Flag	Coverage Δ
hewr	47.79% <24.30%> (-8.01%)	⬇️
pipelines	0.00% <0.00%> (ø)
pyrenew_hew	1.89% <ø> (ø)

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[damonbayer]

Could be merged if needed, but I think some of my comments are clear and easy improvements.