Implement event assignments in JAX #3080

BSnelling · 2025-12-01T11:42:29Z

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codecov · 2025-12-01T12:03:14Z

Codecov Report

❌ Patch coverage is 95.52239% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.27%. Comparing base (2b036e9) to head (c4a4166).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
python/sdist/amici/jax/model.py	89.65%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3080      +/-   ##
==========================================
+ Coverage   78.23%   78.27%   +0.03%     
==========================================
  Files         315      315              
  Lines       20478    20524      +46     
  Branches     1500     1500              
==========================================
+ Hits        16021    16065      +44     
- Misses       4448     4450       +2     
  Partials        9        9

Flag	Coverage Δ
cpp	`71.75% <86.56%> (+0.02%)`	⬆️
cpp_python	`37.71% <17.91%> (-0.05%)`	⬇️
petab	`46.54% <67.16%> (+0.05%)`	⬆️
petab_sciml	`13.95% <64.17%> (+0.16%)`	⬆️
python	`70.41% <91.04%> (+0.04%)`	⬆️
sbmlsuite-jax	`33.38% <88.05%> (+0.53%)`	⬆️

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

Files with missing lines	Coverage Δ
python/sdist/amici/_symbolic/de_model.py	`91.92% <100.00%> (+0.06%)`	⬆️
...hon/sdist/amici/importers/petab/_petab_importer.py	`86.78% <ø> (ø)`
...thon/sdist/amici/importers/petab/v1/sbml_import.py	`97.75% <ø> (ø)`
python/sdist/amici/importers/sbml/__init__.py	`94.35% <100.00%> (+0.02%)`	⬆️
python/sdist/amici/jax/_simulation.py	`97.05% <100.00%> (+0.33%)`	⬆️
python/sdist/amici/jax/ode_export.py	`89.23% <100.00%> (+0.89%)`	⬆️
python/sdist/amici/jax/model.py	`87.50% <89.65%> (+0.49%)`	⬆️

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python/sdist/amici/importers/sbml/__init__.py

python/sdist/amici/jax/_simulation.py

…heaviside init

support explicit initial value event assignments fix deltax tcl

Co-authored-by: Fabian Fröhlich <fabian.frohlich@crick.ac.uk>

This reverts commit 82caa94.

python/sdist/amici/_symbolic/de_model.py

FFroehlich · 2025-12-12T08:33:08Z

Let‘s temporarily disable SalazarCavazos_MBoC2020

FFroehlich

@dweindl only minor changes to non-jax bits but feel free to weigh in as well

dweindl

Cool, thanks. Can't say much on the JAX part. The rest looks good to me, except for the x_old thing.

python/sdist/amici/_symbolic/de_model.py

python/sdist/amici/importers/sbml/__init__.py

dweindl · 2025-12-13T08:30:27Z

python/sdist/amici/jax/model.py

        ...

+    @abstractmethod
+    def _delta_x(


Fine as is, but it's a bit funny that $\Delta x$ updates $y$. This might be something to harmonize at some point. Using state $y$ would also be more in line with SUNDIALS.

IIUC this is a matter of different naming conventions in different parts of the code base so shouldn't be too hard to harmonise, but I'd want to check with @FFroehlich to be sure of that.

open to changing that, but if we do so, let's do it in a separate PR.

python/sdist/amici/jax/ode_export.py

sonarqubecloud · 2025-12-15T14:48:24Z

Quality Gate passed

Issues
0 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

FFroehlich reviewed Dec 5, 2025

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python/sdist/amici/importers/sbml/__init__.py Outdated Show resolved Hide resolved

python/sdist/amici/importers/sbml/__init__.py Outdated Show resolved Hide resolved

python/sdist/amici/jax/_simulation.py Outdated Show resolved Hide resolved

BSnelling force-pushed the bes/jax_event_assignments branch 2 times, most recently from cab120b to 7698822 Compare December 9, 2025 10:57

BSnelling marked this pull request as ready for review December 9, 2025 11:45

BSnelling requested a review from a team as a code owner December 9, 2025 11:45

FFroehlich reviewed Dec 10, 2025

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python/sdist/amici/jax/_simulation.py Show resolved Hide resolved

BSnelling and others added 22 commits December 11, 2025 09:14

event assignments jax - sbml cases 348 - 404

6cea00b

fix up sbml test cases - not implemented priority, update t_eps, fix …

46ff884

…heaviside init

initialValue False not implemented

728e828

try fix other test cases

20495d2

Matrix only for JAX event assignments

1533f8f

params only in explicit triggers - and matrix only in JAX again

67c2eb0

oops committed breakpoint

533b97e

fix delta variables in deltax

6b53bb4

new param _delta_x missing in solve calls

af08ed3

try simpler roots direction logic in handle event

b4b3219

try not logic in handle event

0545a07

looking for initialValue test cases

06a208b

support explicit initial value event assignments fix deltax tcl

add h = 0 check to handle event

8398a38

do not update h pre-solve

9aa9866

handle_t0_event

523cf20

reinstate time skip (hack diffrax bug?)

7f5fdab

Update python/sdist/amici/jax/_simulation.py

3b9471e

Co-authored-by: Fabian Fröhlich <fabian.frohlich@crick.ac.uk>

Revert "Update python/sdist/amici/jax/_simulation.py"

b93d884

This reverts commit 82caa94.

rm clip controller

a4be718

handle t0 event near zero

0ab7c68

skip non-time dependent event assignment cases

4a47d3b

fix sbml _symbols

bc51bb4

BSnelling force-pushed the bes/jax_event_assignments branch from c1b8809 to bc51bb4 Compare December 11, 2025 09:17

skip some more tests - NotImplemented discs

449ed78

FFroehlich reviewed Dec 12, 2025

View reviewed changes

python/sdist/amici/_symbolic/de_model.py Outdated Show resolved Hide resolved

FFroehlich reviewed Dec 12, 2025

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python/sdist/amici/_symbolic/de_model.py Outdated Show resolved Hide resolved

BSnelling added 4 commits December 12, 2025 09:19

update implicit check and skip SalazarCavazos_MBoC2020 benchmark

e9f47e3

empty set is not None

3618db8

update solver settings for jax benchmarks

900eaef

keep Weber settings specific

51a7e9c

FFroehlich approved these changes Dec 12, 2025

View reviewed changes

dweindl reviewed Dec 13, 2025

View reviewed changes

review comments - remove x_old usage and add TODO/FIXMEs

d49572e

dweindl approved these changes Dec 15, 2025

View reviewed changes

BSnelling added this pull request to the merge queue Dec 15, 2025

github-merge-queue bot removed this pull request from the merge queue due to failed status checks Dec 15, 2025

Merge branch 'main' into bes/jax_event_assignments

c4a4166

BSnelling added this pull request to the merge queue Dec 15, 2025

Merged via the queue into main with commit aa85fb9 Dec 15, 2025
40 of 41 checks passed

Implement event assignments in JAX #3080

Implement event assignments in JAX #3080

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BSnelling commented Dec 1, 2025

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sonarqubecloud bot commented Dec 15, 2025

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codecov bot commented Dec 1, 2025 •

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