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Fix JAX test failures related to diffrax/optimistix release #3129

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Merged
BSnelling merged 7 commits into from
Feb 23, 2026
Merged

Fix JAX test failures related to diffrax/optimistix release #3129

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53cead4
adjust test_jax tols
BSnelling Feb 23, 2026
0221c46
increase max steps for jax benchmarks
BSnelling Feb 23, 2026
5790bbe
pin optax for notebook test
BSnelling Feb 23, 2026
26ccdf6
increase max steps for petab tests
BSnelling Feb 23, 2026
61aa312
increase petab max steps again
BSnelling Feb 23, 2026
6a433e9
even higher max steps for Weber benchmark
BSnelling Feb 23, 2026
11b9c90
pin optax in docs build
BSnelling Feb 23, 2026
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2 changes: 1 addition & 1 deletion doc/rtd_requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ setuptools>=67.7.2
git+https://github.com/jmuhlich/pysb@22d69a350b472f33d85ba64ffb10b190483c1c98
# For forward type definition in generate_equinox
matplotlib>=3.7.1
optax
optax==0.2.6
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@BSnelling BSnelling Feb 23, 2026 •
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Opened #3130 to keep track of this.

nbsphinx
nbformat
myst-parser
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4 changes: 2 additions & 2 deletions python/sdist/amici/jax/petab.py
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Expand Up @@ -1550,7 +1550,7 @@ def run_simulations(
steady_state_event: Callable[
..., diffrax._custom_types.BoolScalarLike
] = diffrax.steady_state_event(),
max_steps: int = 2**10,
max_steps: int = 2**13,
ret: ReturnValue | str = ReturnValue.llh,
):
"""
Expand Down Expand Up @@ -1653,7 +1653,7 @@ def petab_simulate(
steady_state_event: Callable[
..., diffrax._custom_types.BoolScalarLike
] = diffrax.steady_state_event(),
max_steps: int = 2**10,
max_steps: int = 2**13,
):
"""
Run simulations for a problem and return the results as a petab simulation dataframe.
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2 changes: 1 addition & 1 deletion python/tests/test_jax.py
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Original file line number Diff line number Diff line change
Expand Up @@ -204,7 +204,7 @@ def check_fields_jax(
"iy_trafos": jnp.array(iy_trafos),
"x_preeq": jnp.array([]),
"solver": diffrax.Kvaerno5(),
"controller": diffrax.PIDController(atol=ATOL_SIM, rtol=RTOL_SIM),
"controller": diffrax.PIDController(atol=1e-8, rtol=1e-8),
"root_finder": optimistix.Newton(atol=ATOL_SIM, rtol=RTOL_SIM),
"adjoint": diffrax.RecursiveCheckpointAdjoint(),
"steady_state_event": diffrax.steady_state_event(),
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2 changes: 1 addition & 1 deletion scripts/installAmiciSource.sh
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Expand Up @@ -39,7 +39,7 @@ python -m pip install --upgrade pip wheel
python -m pip install --upgrade pip setuptools cmake_build_extension==0.6.0 numpy petab swig
python -m pip install git+https://github.com/pysb/pysb@master # for SPM with compartments
python -m pip install git+https://github.com/patrick-kidger/diffrax@main # for events with direction
python -m pip install optax # for jax petab notebook
python -m pip install 'optax<0.2.7' # for jax petab notebook
AMICI_BUILD_TEMP="${AMICI_PATH}/python/sdist/build/temp" \
python -m pip install --verbose -e "${AMICI_PATH}/python/sdist[petab,test,vis,jax]" --no-build-isolation
deactivate
11 changes: 7 additions & 4 deletions tests/benchmark_models/test_petab_benchmark_jax.py
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Expand Up @@ -10,7 +10,7 @@
from amici.importers.petab.v1 import (
import_petab_problem,
)
from amici.jax.petab import run_simulations
from amici.jax.petab import run_simulations, DEFAULT_CONTROLLER_SETTINGS
from amici.sim.sundials import SensitivityMethod, SensitivityOrder
from amici.sim.sundials.petab.v1 import (
LLH,
Expand Down Expand Up @@ -113,11 +113,11 @@ def test_jax_llh(benchmark_problem):
if problem_id == "Weber_BMC2015":
atol = cur_settings.atol_sim
rtol = cur_settings.rtol_sim
max_steps = 2 * 10**5
max_steps = 4 * 10**7
else:
atol = 1e-8
rtol = 1e-8
max_steps = 1024
max_steps = 2 * 10**5
beartype(run_simulations)(jax_problem)
(llh_jax, _), sllh_jax = eqx.filter_value_and_grad(
run_simulations, has_aux=True
Expand All @@ -130,7 +130,10 @@ def test_jax_llh(benchmark_problem):
),
)
else:
llh_jax, _ = beartype(run_simulations)(jax_problem)
llh_jax, _ = beartype(run_simulations)(
jax_problem,
max_steps=2 * 10**5,
)

np.testing.assert_allclose(
llh_jax,
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