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Add NHSN data pull to forecast_state #261

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@damonbayer damonbayer commented Dec 19, 2024

Adds NHSN data pull to process_and_save_state. This in turn modifies data_for_model_fit. The new data_for_model_fit is backwards compatible with existing pyrenew-e models and has the necessary data to fit a pyrenew-he model.

We also save combined_training_dat.tsv which is necessary for post-processing pyrenew-he models. We contintue to save data.tsv to maintain compatibility with current pyrenew-e models.

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codecov bot commented Dec 19, 2024

Codecov Report

Attention: Patch coverage is 0% with 32 lines in your changes missing coverage. Please review.

Project coverage is 16.75%. Comparing base (f9ac57d) to head (287e4b1).

Files with missing lines Patch % Lines
pipelines/prep_data.py 0.00% 32 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #261      +/-   ##
==========================================
- Coverage   17.08%   16.75%   -0.34%     
==========================================
  Files          21       21              
  Lines        1346     1373      +27     
==========================================
  Hits          230      230              
- Misses       1116     1143      +27     
Flag Coverage Δ
hewr 48.79% <ø> (ø)
pipelines 0.00% <0.00%> (ø)
pyrenew_hew 1.91% <ø> (ø)

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@damonbayer damonbayer marked this pull request as ready for review December 20, 2024 23:10
@damonbayer damonbayer changed the title (Draft) Add NHSN data pull to forecast_state Add NHSN data pull to forecast_state Dec 20, 2024
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