Move petab v1 simulation code to amici.sim...

doc/examples/example_errors.ipynb

@@ -29,10 +29,7 @@
     "    import_model_module,\n",
     ")\n",
     "from amici.importers.petab.v1 import (\n",
-    "    EDATAS,\n",
-    "    RDATAS,\n",
     "    import_petab_problem,\n",
-    "    simulate_petab,\n",
     ")\n",
     "from amici.sim.sundials import (\n",
     "    AMICI_SUCCESS,\n",
@@ -44,6 +41,11 @@
     "    simulation_status_to_str,\n",
     "    unscale_parameter,\n",
     ")\n",
+    "from amici.sim.sundials.petab.v1 import (\n",
+    "    EDATAS,\n",
+    "    RDATAS,\n",
+    "    simulate_petab,\n",
+    ")\n",
     "from amici.sim.sundials.plotting import plot_jacobian, plot_state_trajectories\n",
     "from petab.v1.sbml import get_sbml_model\n",
     "\n",

doc/examples/example_jax/ExampleJax.ipynb

@@ -310,8 +310,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from amici.importers.petab.v1 import simulate_petab\n",
     "from amici.sim.sundials import SensitivityOrder\n",
+    "from amici.sim.sundials.petab.v1 import simulate_petab\n",
     "\n",
     "amici_solver = amici_model.create_solver()\n",
     "amici_solver.set_sensitivity_order(SensitivityOrder.first)\n",

doc/examples/example_jax_petab/ExampleJaxPEtab.ipynb

@@ -565,8 +565,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from amici.importers.petab.v1 import simulate_petab\n",
     "from amici.sim.sundials import SensitivityMethod, SensitivityOrder\n",
+    "from amici.sim.sundials.petab.v1 import simulate_petab\n",
     "\n",
     "# Import the PEtab problem as a standard AMICI model\n",
     "amici_model = import_petab_problem(\n",

doc/examples/example_petab/petab.ipynb

@@ -18,12 +18,9 @@
    "outputs": [],
    "source": [
     "import petab\n",
-    "from amici.importers.petab.v1 import (\n",
-    "    import_petab_problem,\n",
-    "    simulate_petab,\n",
-    ")\n",
-    "from amici.importers.petab.v1.petab_problem import PetabProblem\n",
+    "from amici.importers.petab.v1 import import_petab_problem\n",
     "from amici.sim.sundials import run_simulation\n",
+    "from amici.sim.sundials.petab.v1 import PetabProblem, simulate_petab\n",
     "from amici.sim.sundials.plotting import plot_state_trajectories"
    ]
   },

doc/python_modules.rst

@@ -18,18 +18,16 @@ AMICI Python API
    amici.importers.antimony
    amici.importers.petab
    amici.importers.petab.v1
-   amici.importers.petab.v1.conditions
    amici.importers.petab.v1.import_helpers
    amici.importers.petab.v1.parameter_mapping
    amici.importers.petab.v1.petab_import
    amici.importers.petab.v1.pysb_import
    amici.importers.petab.v1.sbml_import
-   amici.importers.petab.v1.simulations
-   amici.importers.petab.v1.simulator
    amici.jax
    amici.exporters.sundials.de_export
    amici.sim.sundials
    amici.sim.sundials.plotting
    amici.sim.sundials.gradient_check
+   amici.sim.sundials.petab.v1
    amici.logging
    amici.adapters.fiddy

python/sdist/amici/adapters/fiddy.py

@@ -17,10 +17,7 @@
 from fiddy import CachedFunction, Type, fiddy_array
 from petab.v1.C import LIN, LOG, LOG10
 
-import amici
-import amici.importers.petab.v1.simulations
 from amici.importers.petab import LLH, SLLH
-from amici.importers.petab.v1.conditions import create_edatas
 from amici.importers.petab.v1.parameter_mapping import create_parameter_mapping
 from amici.sim.sundials import (
     AmiciExpData,
@@ -31,6 +28,7 @@
     SensitivityOrder,
     run_simulation,
 )
+from amici.sim.sundials.petab.v1._conditions import create_edatas
 
 if TYPE_CHECKING:
     from amici.importers.petab import PetabSimulator
@@ -297,7 +295,7 @@ def simulate_petab_to_cached_functions(
     **kwargs,
 ) -> tuple[Type.FUNCTION, Type.FUNCTION]:
     """
-    Convert :func:`amici.petab.simulations.simulate_petab`
+    Convert :func:`amici.sim.sundials.petab.v1.simulate_petab`
     (PEtab v1 simulations) to fiddy functions.
 
     Note that all gradients are provided on linear scale. The correction from
@@ -333,7 +331,7 @@ def simulate_petab_to_cached_functions(
         free_parameter_ids = list(petab_problem.parameter_df.index)
 
     if simulate_petab is None:
-        simulate_petab = amici.importers.petab.v1.simulations.simulate_petab
+        from amici.sim.sundials.petab.v1._simulations import simulate_petab
 
     edatas = None
     if precreate_edatas:

python/sdist/amici/importers/petab/_petab_importer.py

@@ -26,9 +26,17 @@
 from amici.importers.utils import MeasurementChannel, amici_time_symbol
 from amici.logging import get_logger
 from amici.sim.sundials import SensitivityOrder
+from amici.sim.sundials.petab.v1._simulations import (
+    EDATAS,
+    LLH,
+    RDATAS,
+    RES,
+    S2LLH,
+    SLLH,
+    SRES,
+)
 
 from .v1.sbml_import import _add_global_parameter
-from .v1.simulations import EDATAS, LLH, RDATAS, RES, S2LLH, SLLH, SRES
 
 if TYPE_CHECKING:
     import pysb

python/sdist/amici/importers/petab/v1/__init__.py

@@ -5,31 +5,7 @@
 PREEQ_INDICATOR_ID = "preequilibration_indicator"
 
 from .petab_import import import_petab_problem
-from .simulations import (
-    EDATAS,
-    FIM,
-    LLH,
-    RDATAS,
-    RES,
-    S2LLH,
-    SLLH,
-    SRES,
-    rdatas_to_measurement_df,
-    rdatas_to_simulation_df,
-    simulate_petab,
-)
 
 __all__ = [
     "import_petab_problem",
-    "simulate_petab",
-    "rdatas_to_simulation_df",
-    "rdatas_to_measurement_df",
-    "LLH",
-    "SLLH",
-    "FIM",
-    "S2LLH",
-    "RES",
-    "SRES",
-    "RDATAS",
-    "EDATAS",
 ]

python/sdist/amici/sim/sundials/petab/v1/__init__.py

@@ -0,0 +1,34 @@
+from ._conditions import create_edatas, create_parameterized_edatas
+from ._petab_problem import PetabProblem
+from ._simulations import (
+    EDATAS,
+    FIM,
+    LLH,
+    RDATAS,
+    RES,
+    S2LLH,
+    SLLH,
+    SRES,
+    rdatas_to_measurement_df,
+    rdatas_to_simulation_df,
+    simulate_petab,
+)
+from ._simulator import PetabSimulator
+
+__all__ = [
+    "simulate_petab",
+    "rdatas_to_simulation_df",
+    "rdatas_to_measurement_df",
+    "LLH",
+    "SLLH",
+    "FIM",
+    "S2LLH",
+    "RES",
+    "SRES",
+    "RDATAS",
+    "EDATAS",
+    "PetabProblem",
+    "PetabSimulator",
+    "create_edatas",
+    "create_parameterized_edatas",
+]

python/sdist/amici/importers/petab/v1/conditions.py → python/sdist/amici/sim/sundials/petab/v1/_conditions.py

@@ -19,20 +19,19 @@
     TIME,
 )
 
-from amici.sim.sundials import (
-    AmiciModel,
-    ExpData,
-    parameter_scaling_from_int_vector,
-)
-
-from .parameter_mapping import (
+from amici.importers.petab.v1.parameter_mapping import (
     ParameterMapping,
     ParameterMappingForCondition,
     petab_to_amici_scale,
     scale_parameters_dict,
     unscale_parameters_dict,
 )
-from .util import get_states_in_condition_table
+from amici.importers.petab.v1.util import get_states_in_condition_table
+from amici.sim.sundials import (
+    AmiciModel,
+    ExpData,
+    parameter_scaling_from_int_vector,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -283,7 +282,9 @@ def create_parameterized_edatas(
 
     # Get parameter mapping
     if parameter_mapping is None:
-        from .parameter_mapping import create_parameter_mapping
+        from amici.importers.petab.v1.parameter_mapping import (
+            create_parameter_mapping,
+        )
 
         parameter_mapping = create_parameter_mapping(
             petab_problem=petab_problem,

python/sdist/amici/importers/petab/v1/petab_problem.py → python/sdist/amici/sim/sundials/petab/v1/_petab_problem.py

@@ -9,9 +9,11 @@
 from petab.v1.C import PREEQUILIBRATION_CONDITION_ID, SIMULATION_CONDITION_ID
 
 import amici
-
-from .conditions import create_edatas, fill_in_parameters
-from .parameter_mapping import create_parameter_mapping
+from amici.importers.petab.v1.parameter_mapping import create_parameter_mapping
+from amici.sim.sundials.petab.v1._conditions import (
+    create_edatas,
+    fill_in_parameters,
+)
 
 
 class PetabProblem:
@@ -50,7 +52,7 @@ def __init__(
         if amici_model is not None:
             self._amici_model = amici_model
         else:
-            from .petab_import import import_petab_problem
+            from amici.importers.petab.v1 import import_petab_problem
 
             self._amici_model = import_petab_problem(petab_problem)
 

python/sdist/amici/importers/petab/v1/simulations.py → python/sdist/amici/sim/sundials/petab/v1/_simulations.py

@@ -17,6 +17,10 @@
 from petab.v1.C import *  # noqa: F403
 
 import amici
+from amici.importers.petab.v1.parameter_mapping import (
+    ParameterMapping,
+    create_parameter_mapping,
+)
 from amici.logging import get_logger, log_execution_time
 from amici.sim.sundials import (
     AMICI_SUCCESS,
@@ -27,15 +31,10 @@
     SensitivityOrder,
     run_simulations,
 )
-
-from .conditions import (
+from amici.sim.sundials.petab.v1._conditions import (
     create_edatas,
     fill_in_parameters,
 )
-from .parameter_mapping import (
-    ParameterMapping,
-    create_parameter_mapping,
-)
 
 logger = get_logger(__name__)
 

python/sdist/amici/importers/petab/v1/simulator.py → python/sdist/amici/sim/sundials/petab/v1/_simulator.py

@@ -18,10 +18,10 @@
 import pandas as pd
 import petab.v1 as petab
 
+from amici.importers.petab.v1.petab_import import import_petab_problem
 from amici.sim.sundials import AmiciModel, SensitivityMethod
 
-from .petab_import import import_petab_problem
-from .simulations import RDATAS, rdatas_to_measurement_df, simulate_petab
+from ._simulations import RDATAS, rdatas_to_measurement_df, simulate_petab
 
 AMICI_MODEL = "amici_model"
 AMICI_SOLVER = "solver"

python/tests/adapters/test_fiddy.py

@@ -4,7 +4,7 @@
 
 import amici
 import amici.importers.petab.v1.petab_import
-import amici.importers.petab.v1.simulations
+import amici.sim.sundials.petab.v1._simulations
 import numpy as np
 import pytest
 from amici.adapters.fiddy import (

python/tests/petab_/test_petab_problem.py

@@ -1,5 +1,5 @@
 from amici.importers.petab.v1 import import_petab_problem
-from amici.importers.petab.v1.petab_problem import PetabProblem
+from amici.sim.sundials.petab.v1._petab_problem import PetabProblem
 from amici.testing import skip_on_valgrind
 from benchmark_models_petab import get_problem
 

python/tests/splines_utils.py

@@ -18,12 +18,7 @@
 import petab.v1 as petab
 import sympy as sp
 from amici.importers.petab.v1 import (
-    EDATAS,
-    LLH,
-    RDATAS,
-    SLLH,
     import_petab_problem,
-    simulate_petab,
 )
 from amici.importers.sbml.splines import (
     AbstractSpline,
@@ -41,6 +36,13 @@
 )
 from amici.sim.sundials import run_simulation
 from amici.sim.sundials.gradient_check import _check_results
+from amici.sim.sundials.petab.v1 import (
+    EDATAS,
+    LLH,
+    RDATAS,
+    SLLH,
+    simulate_petab,
+)
 from amici.testing import TemporaryDirectoryWinSafe as TemporaryDirectory
 from petab.v1.models.sbml_model import SbmlModel
 

python/tests/test_petab_objective.py

@@ -7,8 +7,9 @@
 import pandas as pd
 import petab.v1 as petab
 import pytest
-from amici.importers.petab.v1 import SLLH, import_petab_problem, simulate_petab
+from amici.importers.petab.v1 import import_petab_problem
 from amici.sim.sundials import SensitivityOrder
+from amici.sim.sundials.petab.v1 import SLLH, simulate_petab
 from amici.testing import skip_on_valgrind
 
 # Absolute and relative tolerances for finite difference gradient checks.

python/tests/test_petab_simulate.py

@@ -6,7 +6,7 @@
 import petab.v1 as petab
 import petabtests
 import pytest
-from amici.importers.petab.v1.simulator import PetabSimulator
+from amici.sim.sundials.petab.v1 import PetabSimulator
 from amici.testing import skip_on_valgrind
 
 

tests/benchmark_models/test_petab_benchmark.py

@@ -25,12 +25,7 @@
     simulate_petab_v2_to_cached_functions,
 )
 from amici.importers.petab.v1 import (
-    LLH,
-    RDATAS,
-    SLLH,
     import_petab_problem,
-    rdatas_to_measurement_df,
-    simulate_petab,
 )
 from amici.logging import get_logger
 from amici.sim.sundials import (
@@ -40,6 +35,13 @@
     SteadyStateComputationMode,
     SteadyStateSensitivityMode,
 )
+from amici.sim.sundials.petab.v1 import (
+    LLH,
+    RDATAS,
+    SLLH,
+    rdatas_to_measurement_df,
+    simulate_petab,
+)
 from fiddy import MethodId, get_derivative
 from fiddy.derivative_check import NumpyIsCloseDerivativeCheck
 from fiddy.success import Consistency