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Merged
damonbayer merged 19 commits into from
Jan 14, 2026
Merged

Data Cleanup #822

damonbayer merged 19 commits into from
Jan 14, 2026

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@damonbayer damonbayer commented Jan 6, 2026 •
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  • Training and eval data are combined in a single file, rather than separate files.
  • Removes ability to pull non-latest NSSP data (mirroring NHSN capabilities) (closes Remove functionality for pulling non-latest data. #591)
  • Allows plotting for eval wastewater data
  • Fixes an issue where computing epiweekly data on datasets where the transition from training to eval data occurs in the middle of an epiweek resulted in an epiweek being dropped (e8e9e31)
  • Cleans up some type hints

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codecov bot commented Jan 6, 2026 •
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Codecov Report

❌ Patch coverage is 16.66667% with 40 lines in your changes missing coverage. Please review.
✅ Project coverage is 41.97%. Comparing base (cfa1864) to head (569ebff).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
pipelines/prep_data.py 19.04% 17 Missing ⚠️
hewr/R/process_loc_forecast.R 0.00% 11 Missing ⚠️
pipelines/forecast_timeseries.py 0.00% 4 Missing ⚠️
pipelines/common_utils.py 25.00% 3 Missing ⚠️
pipelines/forecast_pyrenew.py 0.00% 3 Missing ⚠️
hewr/R/timeseries_utils.R 0.00% 1 Missing ⚠️
pipelines/generate_test_data_lib.py 0.00% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #822      +/-   ##
==========================================
- Coverage   42.78%   41.97%   -0.82%     
==========================================
  Files          30       29       -1     
  Lines        2896     2809      -87     
==========================================
- Hits         1239     1179      -60     
+ Misses       1657     1630      -27
Flag Coverage Δ
hewr 37.87% <0.00%> (-0.17%) ⬇️
pipelines 36.45% <22.22%> (-1.89%) ⬇️
pyrenew_hew 62.29% <ø> (ø)

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damonbayer and others added 15 commits January 6, 2026 16:48
@damonbayer
everything running with some known bugs
ec31885
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
6210446 
for more information, see https://pre-commit.ci
@damonbayer
fix python tests
e564a26
@damonbayer
Merge branch 'dmb_non_latest' of https://github.com/CDCgov/pyrenew-hew …
775d130 
…into dmb_non_latest
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
37b8d81 
for more information, see https://pre-commit.ci
@damonbayer
tests passing
d0c06f5
@damonbayer
Merge branch 'dmb_non_latest' of https://github.com/CDCgov/pyrenew-hew …
52fd46d 
…into dmb_non_latest
@damonbayer
missed a test
a9a18c8
@damonbayer
update hewr docs
330dbcf
@damonbayer
correct treatment of nwss train/eval data
23a14fc
@damonbayer
Discard changes to pipelines/tests/test_end_to_end.sh
26e5b60
@damonbayer
fix issue where training data spans partial epiweeks
e8e9e31
@damonbayer
Merge branch 'main' into dmb_non_latest
96c5f07 
# Conflicts:
#	pipelines/common_utils.py
#	pipelines/tests/test_common_utils.py
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
7670878 
for more information, see https://pre-commit.ci
@damonbayer
small simplification
f343848
@damonbayer damonbayer marked this pull request as ready for review January 9, 2026 17:12
dylanhmorris
dylanhmorris reviewed Jan 14, 2026
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dylanhmorris
dylanhmorris reviewed Jan 14, 2026
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@damonbayer damonbayer merged commit b14ddd4 into main Jan 14, 2026
69 of 71 checks passed
@damonbayer damonbayer deleted the dmb_non_latest branch January 14, 2026 22:03
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@dylanhmorris dylanhmorris dylanhmorris approved these changes

@sbidari sbidari Awaiting requested review from sbidari sbidari is a code owner

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@damonbayer @dylanhmorris