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Adjoint sensitivities for Python-imported models with events#1539

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dweindl merged 115 commits intomainfrom
adjoint_event
Jun 25, 2025
Merged

Adjoint sensitivities for Python-imported models with events#1539
dweindl merged 115 commits intomainfrom
adjoint_event

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@paulstapor paulstapor commented Aug 5, 2021

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@paulstapor paulstapor changed the base branch from master to develop August 5, 2021 11:31
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codecov bot commented Aug 5, 2021 •
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Codecov Report

❌ Patch coverage is 79.16667% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.71%. Comparing base (635a227) to head (83a665e).
⚠️ Report is 94 commits behind head on main.

Files with missing lines Patch % Lines
src/model.cpp 60.00% 6 Missing ⚠️
src/abstract_model.cpp 0.00% 4 Missing ⚠️
Additional details and impacted files

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@@            Coverage Diff             @@
##             main    #1539      +/-   ##
==========================================
+ Coverage   75.69%   79.71%   +4.01%     
==========================================
  Files         323      328       +5     
  Lines       22195    22403     +208     
  Branches     1513     1514       +1     
==========================================
+ Hits        16801    17859    +1058     
+ Misses       5019     4533     -486     
+ Partials      375       11     -364
Flag Coverage Δ
cpp 75.43% <79.16%> (?)
cpp_python 33.87% <39.58%> (+0.02%) ⬆️
petab 39.31% <25.00%> (?)
python 34.25% <52.08%> (-40.22%) ⬇️
sbmlsuite-jax ?

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
include/amici/abstract_model.h 100.00% <ø> (ø)
include/amici/forwardproblem.h 97.00% <ø> (+7.00%) ⬆️
include/amici/model.h 85.71% <ø> (+17.85%) ⬆️
python/sdist/amici/_codegen/cxx_functions.py 96.29% <ø> (ø)
python/sdist/amici/de_export.py 97.42% <100.00%> (+0.01%) ⬆️
python/sdist/amici/de_model.py 93.34% <100.00%> (-0.09%) ⬇️
src/backwardproblem.cpp 93.18% <100.00%> (+3.86%) ⬆️
src/forwardproblem.cpp 95.90% <100.00%> (+3.09%) ⬆️
src/abstract_model.cpp 8.69% <0.00%> (+1.23%) ⬆️
src/model.cpp 86.83% <60.00%> (+6.62%) ⬆️

... and 48 files with indirect coverage changes

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sonarqubecloud bot commented Oct 17, 2021

SonarCloud Quality Gate failed.    Quality Gate failed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 7 Code Smells

15.4% 15.4% Coverage
13.3% 13.3% Duplication

@dweindl dweindl linked an issue Nov 22, 2021 that may be closed by this pull request
adjoint sensitivies for models with events #18
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FFroehlich
FFroehlich reviewed Jun 24, 2025
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@dweindl dweindl changed the title Adjoint event Adjoint sensitivities for Python-import models with events Jun 25, 2025
@dweindl dweindl marked this pull request as ready for review June 25, 2025 12:04
@dweindl dweindl requested a review from a team as a code owner June 25, 2025 12:04
@dweindl dweindl requested a review from FFroehlich June 25, 2025 12:06
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dweindl commented Jun 25, 2025

This PR extends support for adjoint sensitivity analysis for models with events.
This does not yet cover all cases. Checking gradients for a given model is still highly recommended.

Changes:

  • Generate functions for computing the adjoint state and quadrature updates (fdeltaxB, fdeltaqB) during Python model import
  • Add Python-specific functions with updated signature for fdeltaxB, fdeltaqB
  • Store additional information at discontinuities
  • Test adjoint sensitivities in existing test cases. Some failure are currently ignored and require further investigation.

@dweindl dweindl self-assigned this Jun 25, 2025
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sonarqubecloud bot commented Jun 25, 2025

Quality Gate Passed Quality Gate passed

Issues
12 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@dweindl dweindl merged commit 68ed3b5 into main Jun 25, 2025
44 of 47 checks passed
@dweindl dweindl deleted the adjoint_event branch June 25, 2025 15:13
@dweindl dweindl changed the title Adjoint sensitivities for Python-import models with events Adjoint sensitivities for Python-imported models with events Jun 25, 2025
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adjoint sensitivies for models with events

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@paulstapor @dweindl @FFroehlich @stephanmg