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Make which quantities are sampled more readily configurable #326

Merged
merged 37 commits into from
Feb 13, 2025
Merged

Make which quantities are sampled more readily configurable #326

merged 37 commits into from
Feb 13, 2025

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dylanhmorris
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@dylanhmorris dylanhmorris commented Feb 5, 2025 •
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This PR creates a clearer interface for configuring what quantities are sampled during fitting and posterior prediction. This will make it easier to use the same infrastructure for the various Pyrenew-{H,E,W} combinations.

To do:

  • Unit tests to confirm that configuration of what is sampled works as expected
  • Fix end to end test
  • Test fit/forecast flag combinations.

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codecov bot commented Feb 5, 2025 •
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Codecov Report

Attention: Patch coverage is 75.00000% with 16 lines in your changes missing coverage. Please review.

Project coverage is 26.86%. Comparing base (5bd8178) to head (58dfda3).
Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
pipelines/forecast_state.py 0.00% 14 Missing ⚠️
pipelines/fit_pyrenew_model.py 0.00% 1 Missing ⚠️
pipelines/generate_predictive.py 0.00% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #326      +/-   ##
==========================================
+ Coverage   23.15%   26.86%   +3.70%     
==========================================
  Files          22       24       +2     
  Lines        1710     1768      +58     
==========================================
+ Hits          396      475      +79     
+ Misses       1314     1293      -21
Flag Coverage Δ
hewr 35.35% <ø> (ø)
pipelines 14.83% <65.21%> (+9.83%) ⬆️
pyrenew_hew 30.37% <100.00%> (+2.40%) ⬆️

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@dylanhmorris dylanhmorris marked this pull request as ready for review February 6, 2025 00:47
damonbayer
damonbayer reviewed Feb 7, 2025
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What do you think about an approach that parsed the model name? We already use model_name as an argument to many functions in the pipeline.

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What do you think about an approach that parsed the model name? We already use model_name as an argument to many functions in the pipeline.

Per F2F discussion, the model name approach will not be taken in this PR. In the future, we could implement is and make use of the switches approach implemented in this PR.

@dylanhmorris dylanhmorris mentioned this pull request Feb 10, 2025
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Per F2F discussion, the model name approach will not be taken in this PR. In the future, we could implement is and make use of the switches approach implemented in this PR.

Update: I think it's fairly straightforward and arguably more robust to name the model based on the values of the switches, which I've done here:

pyrenew-hew/pipelines/forecast_state.py

Lines 216 to 220 in b8dc990

pyrenew_model_name = pyrenew_model_name_from_flags(
fit_ed_visits=fit_ed_visits,
fit_hospital_admissions=fit_hospital_admissions,
fit_wastewater=fit_wastewater,
)

damonbayer
damonbayer reviewed Feb 11, 2025
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@damonbayer damonbayer self-requested a review February 11, 2025 19:40
@dylanhmorris dylanhmorris mentioned this pull request Feb 11, 2025
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@dylanhmorris dylanhmorris requested review from damonbayer and removed request for damonbayer February 13, 2025 01:40
damonbayer
damonbayer approved these changes Feb 13, 2025
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Thanks @dylanhmorris!

@dylanhmorris dylanhmorris enabled auto-merge (squash) February 13, 2025 22:06
@dylanhmorris dylanhmorris merged commit 026f1eb into main Feb 13, 2025
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@dylanhmorris dylanhmorris deleted the dhm-configure-which-fit branch February 13, 2025 22:25
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@damonbayer damonbayer damonbayer approved these changes

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

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