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Process returns tuple with array equal to duration (patch to PR 123) #143

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gvegayon
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@gvegayon gvegayon commented May 30, 2024

This addresses and should close #142. The PR does the following:

  • Corrects all classes in pyrenew.process to return tuples with arrays of shape (duration,).
  • Makes n_timepoints optional for models under pyrenew.model. Only required when observed data is not passed, the length of the time series is inferred from the observed data.
  • Consequently, updates tests and tutorials, only using the n_timepoints argument when simulating data.
  • It also adds additional assertions to the process testing to make sure the length of the output matches duration.

Notice this PR will be merged in to #123.

cc @damonbayer and @dylanhmorris

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codecov bot commented May 30, 2024

Codecov Report

Attention: Patch coverage is 52.94118% with 8 lines in your changes are missing coverage. Please review.

Project coverage is 93.04%. Comparing base (b603eb5) to head (8ead934).

Files Patch % Lines
...odel/src/pyrenew/model/rtinfectionsrenewalmodel.py 37.50% 5 Missing ⚠️
model/src/pyrenew/model/admissionsmodel.py 57.14% 3 Missing ⚠️
Additional details and impacted files
@@                      Coverage Diff                       @@
##           9-infection-feedback-in-rt     #143      +/-   ##
==============================================================
- Coverage                       93.86%   93.04%   -0.83%     
==============================================================
  Files                              35       35              
  Lines                             734      748      +14     
==============================================================
+ Hits                              689      696       +7     
- Misses                             45       52       +7     
Flag Coverage Δ
unittests 93.04% <52.94%> (-0.83%) ⬇️

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@gvegayon
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Hold my horses, I realized this should be merged into #131 instead! Thank goodness we have git cherry-pick. I'm closing this.

@gvegayon gvegayon closed this May 30, 2024
@dylanhmorris dylanhmorris deleted the 9-infection-feedback-array-length-patch branch July 30, 2024 01:07
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