update infectionswithfeedback process #440

sbidari · 2024-09-10T18:20:43Z

This PR modifies the following functions/files such that these now work when I0 and Rt are 2D arrays as is the case for site-level hierarchical model.

convolve.py : new_convolve_scanner and new_double_convolve_scanner
arrayutils.py : added a function pad_edges_to_match that pads multidimensional arrays using speficied edge values
Infections and InfectionWithFeedback classes in latent module
add tests of these functions using 2D arrays where appropriate
add more tests for convolve scanner functions (Additional tests for convolve scanner factory functions #189)
add additional tests for Infection and InfectionWithFeedback classes

Out of scope

multidimensional generational intervals

…-handle-batch-input-within-numpyro-plate-context

codecov · 2024-09-10T18:29:29Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.26%. Comparing base (ade84ce) to head (bafe3b0).
Report is 1 commits behind head on main.

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@@            Coverage Diff             @@
##             main     #440      +/-   ##
==========================================
+ Coverage   94.03%   94.26%   +0.23%     
==========================================
  Files          42       42              
  Lines         989      994       +5     
==========================================
+ Hits          930      937       +7     
+ Misses         59       57       -2

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…ate-infectionswithfeedback-process-to-handle-batch-input-within-numpyro-plate-context

pyrenew/arrayutils.py

test/test_infectionsrtfeedback.py

damonbayer

Looks nice @sbidari, but I think there are some opportunities to improve performance and clarity.

damonbayer · 2024-09-11T21:45:28Z

@sbidari Can you also look into addressing #394 and #189 in this PR?

…-handle-batch-input-within-numpyro-plate-context

…ch-input-within-numpyro-plate-context' of https://github.com/CDCgov/PyRenew into 435-update-infectionswithfeedback-process-to-handle-batch-input-within-numpyro-plate-context

sbidari · 2024-09-12T21:35:22Z

@sbidari Can you also look into addressing #394 and #189 in this PR?

Added more tests for the convolve factory functions in d933df4

damonbayer · 2024-09-12T22:35:37Z

@sbidari Can we also have tests that try to use numpyro.plate and make sure things work as expected?

pyrenew/latent/infectionswithfeedback.py

…-handle-batch-input-within-numpyro-plate-context

test/test_convolve_scanners.py

damonbayer

A few open questions. I would also like @dylanhmorris to take a look, if he can, since he just did similar work on the AR class.

…ch-input-within-numpyro-plate-context' of https://github.com/CDCgov/PyRenew into 435-update-infectionswithfeedback-process-to-handle-batch-input-within-numpyro-plate-context

dylanhmorris

This looks generally very good, thanks @sbidari. A few questions about scope on which I will defer to you and @damonbayer, and a suggestion about dot products that will be useful for future-proofing.

docs/source/tutorials/extending_pyrenew.qmd

pyrenew/convolve.py

pyrenew/latent/infectionswithfeedback.py

test/test_arrayutils.py

test/test_convolve_scanners.py

sbidari · 2024-09-13T21:19:28Z

Thanks @dylanhmorris
I think multidimensional gen_int is out of scope for this PR (I will make a note in the PR description) and this is ready for final review.

dylanhmorris

A key remaining question about the dimensionality check

pyrenew/convolve.py

pyrenew/latent/infections.py

pyrenew/latent/infectionswithfeedback.py

pyrenew/latent/infections.py

dylanhmorris

One final thing @sbidari, otherwise looks ready!

test/test_infectionwithfeedback_plate_compatibility.py

dylanhmorris

LGTM

dylanhmorris · 2024-09-16T21:44:51Z

@damonbayer can you confirm your concerns were resolved?

pyrenew/latent/infectionswithfeedback.py

test/test_infection_and_infectionwithfeedback.py

damonbayer

Thanks @sbidari!

sbidari added 2 commits September 10, 2024 14:08

add function to pad using edge values and tests

a10b95c

modify convolve and infectionwithfeedback to work with 2d array

f89aa9d

sbidari linked an issue Sep 10, 2024 that may be closed by this pull request

Update InfectionsWithFeedback process to handle batch input within numpyro plate context #435

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Merge branch 'main' into 435-update-infectionswithfeedback-process-to…

b7fb437

…-handle-batch-input-within-numpyro-plate-context

sbidari added 4 commits September 11, 2024 11:23

test convolve scanner for 2d arrays

b0e8a3d

Merge branch 'main' of https://github.com/CDCgov/PyRenew into 435-upd…

1862aee

…ate-infectionswithfeedback-process-to-handle-batch-input-within-numpyro-plate-context

add tests for 2d array, infectionsrtfeedback

114af6a

more tests

a625fde

sbidari marked this pull request as ready for review September 11, 2024 20:49

sbidari requested review from dylanhmorris, damonbayer and gvegayon as code owners September 11, 2024 20:49

damonbayer reviewed Sep 11, 2024

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sbidari and others added 8 commits September 12, 2024 11:52

remove pad to match functions

91be92f

remove tests

396c2d7

use list comprehension in test_infectionsrtfeedback

8197059

revert to using for loop

97d19d0

add more test for convolve scanner functions

d933df4

Merge branch 'main' into 435-update-infectionswithfeedback-process-to…

39667c1

…-handle-batch-input-within-numpyro-plate-context

add check for initial infections and Rt ndims

c210606

Merge branch '435-update-infectionswithfeedback-process-to-handle-bat…

5e91418

…ch-input-within-numpyro-plate-context' of https://github.com/CDCgov/PyRenew into 435-update-infectionswithfeedback-process-to-handle-batch-input-within-numpyro-plate-context

sbidari added 2 commits September 12, 2024 18:03

remove typos and superfluous print statements

f5557a3

add more tests

46e32e8

sbidari added 2 commits September 12, 2024 18:29

change value of inf_feedback in tests to cover diff scenarios

728aad3

add input array tests for infections.py

54c0527

add test with plate

a6ce6c6

sbidari requested a review from damonbayer September 13, 2024 13:27

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sbidari requested a review from damonbayer September 13, 2024 17:03

Merge branch 'main' into 435-update-infectionswithfeedback-process-to…

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…-handle-batch-input-within-numpyro-plate-context

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sbidari added 2 commits September 13, 2024 15:57

code review changes

cc61d0b

Merge branch '435-update-infectionswithfeedback-process-to-handle-bat…

a4a74f0

…ch-input-within-numpyro-plate-context' of https://github.com/CDCgov/PyRenew into 435-update-infectionswithfeedback-process-to-handle-batch-input-within-numpyro-plate-context

dylanhmorris reviewed Sep 13, 2024

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sbidari added 2 commits September 13, 2024 16:45

code review suggestion

0cd56ad

replace jnp.dot with einsum

0f3e2fd

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sbidari requested a review from dylanhmorris September 16, 2024 15:16

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sbidari requested a review from damonbayer September 17, 2024 20:03

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damonbayer merged commit ab8238a into main Sep 17, 2024
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damonbayer deleted the 435-update-infectionswithfeedback-process-to-handle-batch-input-within-numpyro-plate-context branch September 17, 2024 20:41

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update infectionswithfeedback process #440

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