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update end to end test#353

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dylanhmorris merged 35 commits intomainCDCgov/pyrenew-hew:mainfrom sb-update-end-to-end-testCDCgov/pyrenew-hew:sb-update-end-to-end-testCopy head branch name to clipboardMar 3, 2025

+605-296

Commits

Commits on Feb 19, 2025

• add wastewater data prep code

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  240cde2

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• update prep_data.py

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• pre-commit

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• add wastewater data in json file

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• move processing of wastewater data to pyrenew-hew-data

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• syn to use datetime.date for dates throughout, rename ww_sampled to ww_observed

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• add a test

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  1d8e2f0

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• fix test

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• n_datapoints -> n_data_days, move get_spines function to pyrenewHEWData

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• drop wastewater data with no LOD reported

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• create fake nwss data

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• add ww_data_dir to forecast_state.py, test_end_to_end.sh

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• add schema for ww dataframe, add placeholder path

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• pre-commit

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• code review suggestions

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• add schema override

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  f7dea09

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• fix test

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Commits on Feb 20, 2025

• add wastewater related priors

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• Merge branch 'main' of https://github.com/CDCgov/pyrenew-hew into sb-update-end-to-end-test

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Commits on Feb 24, 2025

• add PyrenewWastewaterData

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Commits on Feb 25, 2025

• code clean up

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• only render diagnostic report for pyrenew_e

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• update test ww data generation

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• nwss data handling, split end-to-end test by disease

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• remove unused imports

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Commits on Feb 26, 2025

• end-to-end run test for covid-19 in US

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• update create_more_model_test_data to exclude model_run_dir for covid

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• Update pipelines/generate_test_data.R

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Commits on Feb 27, 2025

• add PyRenewWasteWater args as a dict to PyrenewHewData

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• Apply suggestions from code review

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• coerce population_size to be an integer

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• Suggestion for how to handle the population calculation (#365)

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Commits on Feb 28, 2025

• add missing args to to_forecast_data, code review suggestions

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Commits on Mar 3, 2025

• Update pyrenew_hew/pyrenew_hew_model.py

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• Update pyrenew_hew/pyrenew_hew_model.py

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