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Merged
dweindl merged 1 commit into from
Dec 12, 2025
Merged

Require kwargs #3103

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77 changes: 15 additions & 62 deletions doc/examples/example_jax/ExampleJax.ipynb
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Expand Up @@ -304,11 +304,10 @@
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "beb890bd2f3d0880",
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"from amici.sim.sundials import SensitivityOrder\n",
"from amici.sim.sundials.petab.v1 import simulate_petab\n",
Expand All @@ -320,7 +319,7 @@
"def amici_callback_base(parameters: jnp.array):\n",
" ret = simulate_petab(\n",
" petab_problem,\n",
" amici_model,\n",
" amici_model=amici_model,\n",
" problem_parameters=dict(zip(petab_problem.x_free_ids, parameters)),\n",
" solver=amici_solver,\n",
" )\n",
Expand All @@ -329,7 +328,8 @@
" tuple(ret[\"sllh\"][par_id] for par_id in petab_problem.x_free_ids)\n",
" )\n",
" return llh, sllh"
]
],
"id": "3fa0df1128a9cb41"
},
{
"cell_type": "markdown",
Expand Down Expand Up @@ -477,75 +477,27 @@
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "48451b0e",
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"r = simulate_petab(\n",
" petab_problem,\n",
" amici_model,\n",
" amici_model=amici_model,\n",
" solver=amici_solver,\n",
" scaled_parameters=True,\n",
" scaled_gradients=True,\n",
" problem_parameters=scaled_parameters,\n",
")"
]
],
"id": "24a7792cc548dfe2"
},
{
"cell_type": "code",
"execution_count": 12,
"id": "2628db12",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>amici</th>\n",
" <th>jax</th>\n",
" <th>rel_diff</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>llh</th>\n",
" <td>-138.221997</td>\n",
" <td>-138.222</td>\n",
" <td>-2.135248e-08</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" amici jax rel_diff\n",
"llh -138.221997 -138.222 -2.135248e-08"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"import pandas as pd\n",
"\n",
Expand All @@ -557,7 +509,8 @@
" ),\n",
" index=(\"llh\",),\n",
")"
]
],
"id": "7f72eab3da313f24"
},
{
"cell_type": "code",
Expand Down
46 changes: 23 additions & 23 deletions doc/examples/example_jax_petab/ExampleJaxPEtab.ipynb
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Expand Up @@ -598,82 +598,82 @@
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "768fa60e439ca8b4",
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"%%timeit\n",
"simulate_petab(\n",
" petab_problem,\n",
" amici_model,\n",
" amici_model=amici_model,\n",
" solver=solver,\n",
" problem_parameters=problem_parameters,\n",
" scaled_parameters=True,\n",
" scaled_gradients=True,\n",
")"
]
],
"id": "42cbc67bc09b67dc"
},
{
"cell_type": "code",
"execution_count": null,
"id": "81fe95a6e7f613f1",
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"# Profile gradient computation using forward sensitivity analysis\n",
"solver.set_sensitivity_order(SensitivityOrder.first)\n",
"solver.set_sensitivity_method(SensitivityMethod.forward)"
]
],
"id": "4f1c06c5893a9c07"
},
{
"cell_type": "code",
"execution_count": null,
"id": "3bae1fab8c416122",
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"%%timeit\n",
"simulate_petab(\n",
" petab_problem,\n",
" amici_model,\n",
" amici_model=amici_model,\n",
" solver=solver,\n",
" problem_parameters=problem_parameters,\n",
" scaled_parameters=True,\n",
" scaled_gradients=True,\n",
")"
]
],
"id": "7367a19bcea98597"
},
{
"cell_type": "code",
"execution_count": null,
"id": "71e0358227e1dc74",
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"# Profile gradient computation using adjoint sensitivity analysis\n",
"solver.set_sensitivity_order(SensitivityOrder.first)\n",
"solver.set_sensitivity_method(SensitivityMethod.adjoint)"
]
],
"id": "a31e8eda806c2d7"
},
{
"cell_type": "code",
"execution_count": null,
"id": "e3cc7971002b6d06",
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"%%timeit\n",
"simulate_petab(\n",
" petab_problem,\n",
" amici_model,\n",
" amici_model=amici_model,\n",
" solver=solver,\n",
" problem_parameters=problem_parameters,\n",
" scaled_parameters=True,\n",
" scaled_gradients=True,\n",
")"
]
],
"id": "3f2ab1acb3ba818f"
}
],
"metadata": {
Expand Down
10 changes: 4 additions & 6 deletions doc/examples/example_petab/petab.ipynb
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Expand Up @@ -88,9 +88,7 @@
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"simulate_petab(petab_problem, amici_model)"
]
"source": "simulate_petab(petab_problem, amici_model=amici_model)"
},
{
"cell_type": "markdown",
Expand All @@ -100,10 +98,10 @@
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"cell_type": "code",
"outputs": [],
"execution_count": null,
"source": [
"parameters = {\n",
" x_id: x_val\n",
Expand All @@ -114,7 +112,7 @@
"}\n",
"simulate_petab(\n",
" petab_problem,\n",
" amici_model,\n",
" amici_model=amici_model,\n",
" problem_parameters=parameters,\n",
" scaled_parameters=True,\n",
")"
Expand Down
2 changes: 2 additions & 0 deletions python/sdist/amici/adapters/fiddy.py
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Expand Up @@ -240,6 +240,7 @@ def derivative(point: Type.POINT, return_dict: bool = False):

def simulate_petab_to_cached_functions(
petab_problem: petab.Problem,
*,
amici_model: Model,
free_parameter_ids: list[str] = None,
cache: bool = True,
Expand Down Expand Up @@ -363,6 +364,7 @@ def derivative(point: Type.POINT) -> Type.POINT:

def simulate_petab_v2_to_cached_functions(
petab_simulator: PetabSimulator,
*,
free_parameter_ids: list[str] = None,
cache: bool = True,
) -> tuple[Type.FUNCTION, Type.FUNCTION]:
Expand Down
4 changes: 2 additions & 2 deletions python/sdist/amici/importers/antimony/__init__.py
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Expand Up @@ -54,7 +54,7 @@ def antimony2sbml(ant_model: str | Path) -> str:
return sbml_str


def antimony2amici(ant_model: str | Path, *args, **kwargs):
def antimony2amici(ant_model: str | Path, **kwargs):
"""Convert Antimony model to AMICI model.

Converts the Antimony model provided as string or file to SBML and then
Expand All @@ -66,4 +66,4 @@ def antimony2amici(ant_model: str | Path, *args, **kwargs):

sbml_str = antimony2sbml(ant_model)
sbml_importer = SbmlImporter(sbml_str, from_file=False)
return sbml_importer.sbml2amici(*args, **kwargs)
return sbml_importer.sbml2amici(**kwargs)
7 changes: 2 additions & 5 deletions python/sdist/amici/importers/bngl/__init__.py
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Expand Up @@ -16,22 +16,19 @@
]


def bngl2amici(bngl_model: str, *args, **kwargs) -> None:
def bngl2amici(bngl_model: str, **kwargs) -> None:
r"""
Generate AMICI C++ files for the provided model.

:param bngl_model:
bngl model file, model name will determine the name of the generated
module

:param args:
see :func:`amici.importers.pysb.pysb2amici` for additional arguments

:param kwargs:
see :func:`amici.importers.pysb.pysb2amici` for additional arguments

"""
if "model" in kwargs:
raise ValueError("model argument not allowed")
pysb_model = model_from_bngl(bngl_model)
pysb2amici(pysb_model, *args, **kwargs)
pysb2amici(pysb_model, **kwargs)
1 change: 1 addition & 0 deletions python/sdist/amici/importers/petab/v1/petab_import.py
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Expand Up @@ -41,6 +41,7 @@
def import_petab_problem(
petab_problem: petab.Problem,
model_output_dir: str | Path | None = None,
*,
model_name: str = None,
compile_: bool = None,
non_estimated_parameters_as_constants=True,
Expand Down
2 changes: 2 additions & 0 deletions python/sdist/amici/importers/pysb/__init__.py
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Expand Up @@ -66,6 +66,7 @@
def pysb2jax(
model: pysb.Model,
output_dir: str | Path | None = None,
*,
observation_model: list[MeasurementChannel] = None,
verbose: int | bool = False,
compute_conservation_laws: bool = True,
Expand Down Expand Up @@ -163,6 +164,7 @@ def pysb2jax(
def pysb2amici(
model: pysb.Model,
output_dir: str | Path | None = None,
*,
observation_model: list[MeasurementChannel] = None,
fixed_parameters: list[str] = None,
verbose: int | bool = False,
Expand Down
2 changes: 2 additions & 0 deletions python/sdist/amici/importers/sbml/__init__.py
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Expand Up @@ -97,6 +97,7 @@ class SbmlImporter:
def __init__(
self,
sbml_source: str | Path | libsbml.Model,
*,
show_sbml_warnings: bool = False,
from_file: bool = True,
discard_annotations: bool = False,
Expand Down Expand Up @@ -261,6 +262,7 @@ def sbml2amici(
self,
model_name: str,
output_dir: str | Path = None,
*,
fixed_parameters: Iterable[str] = None,
observation_model: list[MeasurementChannel] = None,
verbose: int | bool = logging.ERROR,
Expand Down
1 change: 1 addition & 0 deletions python/sdist/amici/importers/utils.py
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Expand Up @@ -132,6 +132,7 @@ class MeasurementChannel:
def __init__(
self,
id_: str,
*,
name: str | None = None,
formula: str | sp.Expr | None = None,
noise_distribution: str | Callable[[str], str] | None = None,
Expand Down
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