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AMICI-dev / AMICI Public

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Add support in JAX backend for PEtab v2#3115

Merged

BSnelling merged 43 commits intomainAMICI-dev/AMICI:mainfrom

bes/petabv2_jaxAMICI-dev/AMICI:bes/petabv2_jaxCopy head branch name to clipboard

Feb 24, 2026

Conversation Commits43 (43)Checks Files changed

Merged

Add support in JAX backend for PEtab v2#3115
BSnelling merged 43 commits intomainfrom
bes/petabv2_jax

Commits

Commits on Feb 24, 2026

event assignments jax - sbml cases 348 - 404
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fix up sbml test cases - not implemented priority, update t_eps, fix heaviside init
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initialValue False not implemented
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try fix other test cases
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params only in explicit triggers - and matrix only in JAX again
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oops committed breakpoint
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committed
looking for initialValue test cases
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committed
do not update h pre-solve
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committed
handle_t0_event
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committed
reinstate time skip (hack diffrax bug?)
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Update python/sdist/amici/jax/_simulation.py

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and
FFroehlich
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Revert "Update python/sdist/amici/jax/_simulation.py"
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rm clip controller
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handle t0 event near zero
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skip non-time dependent event assignment cases
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first pass petabv2 - updating JAXProblem init
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petabv2 test cases up to 15-ish
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petab v2 test cases up to 27-ish
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rework petabv2 jax test cases with ExperimentsToSbmlEvents and no v1 parameter_mapping
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committed
fix some rebase issues
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add test skip for petab v1
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remaining petab v2 test cases
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update workflows - deactivate petab_sciml wf for now
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update tests to skip on petab v2 type error
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skip some more tests and reinstate more specific implicit triggers check
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fixup benchmark skipping check
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tidying - add docstrings - rm outputs in notebook
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skip implicit benchmark case - and prior distribution cases
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review feedback - rm simultaneous event check - implement sequential event assignments with assumed priority
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fix test_jax tests and sbml cases with no y0
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fix pysb test case for jax
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use h symbol and update example notebook
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rm v1 instance checks and improve preeq conditionals
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implement implicit triggers using fixed parameters check
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temp workaround for pysb build issue
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pysb workaround in petab workflow too
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fix indentation errors in gen JAX code - restore petabv1 conditional
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skip JAXProblems with v1 problems
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skip JAXProblems with v1 problems - again
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check implicit triggers in sep function
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use petabv2 constants - avoid df usage in loops
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committed
restore pysb install to master
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tody petab file
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committed

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