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Move petab v2 simulation code to amici.sim #3093

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Merged
dweindl merged 1 commit into from
Dec 10, 2025
Merged

Move petab v2 simulation code to amici.sim #3093

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1 change: 1 addition & 0 deletions doc/examples/example_petab/petab_v2.ipynb
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Expand Up @@ -23,6 +23,7 @@
"\n",
"from amici.importers.petab import *\n",
"from amici.sim.sundials import AMICI_SUCCESS\n",
"from amici.sim.sundials.petab import *\n",
"from amici.sim.sundials.plotting import *\n",
"from petab.v2 import Problem"
]
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5 changes: 2 additions & 3 deletions python/sdist/amici/adapters/fiddy.py
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Expand Up @@ -17,7 +17,6 @@
from fiddy import CachedFunction, Type, fiddy_array
from petab.v1.C import LIN, LOG, LOG10

from amici.importers.petab import LLH, SLLH
from amici.importers.petab.v1.parameter_mapping import create_parameter_mapping
from amici.sim.sundials import (
AmiciExpData,
Expand All @@ -28,10 +27,10 @@
SensitivityOrder,
run_simulation,
)
from amici.sim.sundials.petab.v1._conditions import create_edatas
from amici.sim.sundials.petab.v1 import LLH, SLLH, create_edatas

if TYPE_CHECKING:
from amici.importers.petab import PetabSimulator
from amici.sim.sundials.petab import PetabSimulator

__all__ = [
"run_simulation_to_cached_functions",
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3 changes: 0 additions & 3 deletions python/sdist/amici/importers/petab/__init__.py
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Expand Up @@ -8,9 +8,6 @@
problems, the relevant classes are:

* :class:`PetabImporter`: Import a PEtab problem as an AMICI model.
* :class:`PetabSimulator`: Simulate PEtab problems with AMICI.
* :class:`ExperimentManager`: Create :class:`amici.ExpData` objects for PEtab
experiments.

See :doc:`/examples/example_petab/petab_v2` for example usage.
Note that the PEtab v2 API is still under development and may change in future
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