Reapply "amici.importers.petab" until AMICI-dev/AMICI#3039

dweindl · dweindl · commit f6a593ee133f · 2025-11-15T22:12:18.000+01:00
This reverts commit 70e3af0.
diff --git a/doc/example/synthetic_data.ipynb b/doc/example/synthetic_data.ipynb
@@ -38,7 +38,7 @@
    "outputs": [],
    "source": [
     "import petab\n",
-    "from amici.petab.simulator import PetabSimulator\n",
+    "from amici.importers.petab.v1.simulator import PetabSimulator\n",
     "\n",
     "import pypesto.optimize\n",
     "import pypesto.petab\n",
diff --git a/pypesto/hierarchical/inner_calculator_collector.py b/pypesto/hierarchical/inner_calculator_collector.py
@@ -48,7 +48,7 @@
 try:
     import amici
     import petab.v1 as petab
-    from amici.petab.parameter_mapping import ParameterMapping
+    from amici.importers.petab.v1.parameter_mapping import ParameterMapping
 except ImportError:
     petab = None
     ParameterMapping = None
@@ -336,7 +336,7 @@ def __call__(
             Whether to use the FIM (if available) instead of the Hessian (if
             requested).
         """
-        from amici.petab.conditions import fill_in_parameters
+        from amici.importers.petab.v1.conditions import fill_in_parameters
 
         if mode == MODE_RES and any(
             data_type in self.data_types
diff --git a/pypesto/hierarchical/ordinal/calculator.py b/pypesto/hierarchical/ordinal/calculator.py
@@ -34,8 +34,8 @@
 
 try:
     import amici
-    from amici.petab.conditions import fill_in_parameters
-    from amici.petab.parameter_mapping import ParameterMapping
+    from amici.importers.petab.v1.conditions import fill_in_parameters
+    from amici.importers.petab.v1.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 
diff --git a/pypesto/hierarchical/ordinal/solver.py b/pypesto/hierarchical/ordinal/solver.py
@@ -37,7 +37,7 @@
 from .problem import OrdinalProblem
 
 try:
-    from amici.petab.parameter_mapping import ParameterMapping
+    from amici.importers.petab.v1.parameter_mapping import ParameterMapping
 except ImportError:
     ParameterMapping = None
 
diff --git a/pypesto/hierarchical/relative/calculator.py b/pypesto/hierarchical/relative/calculator.py
@@ -7,8 +7,8 @@
 
 try:
     import amici
-    from amici.petab.conditions import fill_in_parameters
-    from amici.petab.parameter_mapping import ParameterMapping
+    from amici.importers.petab.v1.conditions import fill_in_parameters
+    from amici.importers.petab.v1.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 
diff --git a/pypesto/hierarchical/relative/solver.py b/pypesto/hierarchical/relative/solver.py
@@ -33,7 +33,7 @@
 
 try:
     import amici
-    from amici.petab.parameter_mapping import ParameterMapping
+    from amici.importers.petab.v1.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 
diff --git a/pypesto/hierarchical/semiquantitative/calculator.py b/pypesto/hierarchical/semiquantitative/calculator.py
@@ -34,8 +34,8 @@
 
 try:
     import amici
-    from amici.petab.conditions import fill_in_parameters
-    from amici.petab.parameter_mapping import ParameterMapping
+    from amici.importers.petab.v1.conditions import fill_in_parameters
+    from amici.importers.petab.v1.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 
diff --git a/pypesto/hierarchical/semiquantitative/solver.py b/pypesto/hierarchical/semiquantitative/solver.py
@@ -29,7 +29,7 @@
 from .problem import SemiquantProblem
 
 try:
-    from amici.petab.parameter_mapping import ParameterMapping
+    from amici.importers.petab.v1.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 
diff --git a/pypesto/objective/amici/amici.py b/pypesto/objective/amici/amici.py
@@ -40,7 +40,7 @@
 
     try:
         import amici
-        from amici.petab.parameter_mapping import ParameterMapping
+        from amici.importers.petab.v1.parameter_mapping import ParameterMapping
     except ImportError:
         pass
 
@@ -113,7 +113,7 @@ def __init__(
         parameter_mapping:
             Mapping of optimization parameters to model parameters. Format
             as created by
-            `amici.petab.parameter_mapping.create_parameter_mapping`.
+            `amici.importers.petab.v1.parameter_mapping.create_parameter_mapping`.
             The default is just to assume that optimization and simulation
             parameters coincide.
         guess_steadystate:
diff --git a/pypesto/objective/amici/amici_calculator.py b/pypesto/objective/amici/amici_calculator.py
@@ -26,10 +26,14 @@
     sim_sres_to_opt_sres,
 )
 
+try:
+    import amici
+except ImportError:
+    amici = None
+
 if TYPE_CHECKING:
     try:
-        import amici
-        from amici.petab.parameter_mapping import ParameterMapping
+        from amici.importers.petab.v1.parameter_mapping import ParameterMapping
     except ImportError:
         ParameterMapping = None
 
@@ -87,7 +91,7 @@ def __call__(
             Whether to use the FIM (if available) instead of the Hessian (if
             requested).
         """
-        import amici.petab.conditions
+        from amici.importers.petab.v1.conditions import fill_in_parameters
 
         # set order in solver
         sensi_order = 0
@@ -101,7 +105,7 @@ def __call__(
             amici_solver.set_sensitivity_order(sensi_order)
 
         # fill in parameters
-        amici.petab.conditions.fill_in_parameters(
+        fill_in_parameters(
             edatas=edatas,
             problem_parameters=x_dct,
             scaled_parameters=True,
diff --git a/pypesto/objective/amici/amici_util.py b/pypesto/objective/amici/amici_util.py
@@ -24,7 +24,7 @@
 if TYPE_CHECKING:
     try:
         import amici
-        from amici.petab.parameter_mapping import (
+        from amici.importers.petab.v1.parameter_mapping import (
             ParameterMapping,
             ParameterMappingForCondition,
         )
@@ -124,7 +124,7 @@ def create_identity_parameter_mapping(
     both in preequilibration and simulation, are assumed to be provided
     correctly in model or edatas already.
     """
-    from amici.petab.parameter_mapping import (
+    from amici.importers.petab.v1.parameter_mapping import (
         ParameterMapping,
         ParameterMappingForCondition,
         amici_to_petab_scale,
diff --git a/pypesto/petab/importer.py b/pypesto/petab/importer.py
@@ -47,7 +47,6 @@
 
 try:
     import amici
-    import amici.petab.simulations
 except ImportError:
     amici = None
 
diff --git a/pypesto/petab/objective_creator.py b/pypesto/petab/objective_creator.py
@@ -43,11 +43,6 @@
 
 try:
     import amici
-    import amici.petab
-    import amici.petab.conditions
-    import amici.petab.parameter_mapping
-    import amici.petab.simulations
-    from amici.petab.import_helpers import check_model
 except ImportError:
     amici = None
 try:
@@ -166,6 +161,8 @@ def create_model(
 
     def _create_model(self) -> amici.Model:
         """Load model module and return the model, no checks/compilation."""
+        from amici.importers.petab.v1.import_helpers import check_model
+
         # load moduĺe
         module = amici.import_model_module(
             module_name=self.model_name, module_path=self.output_folder
@@ -217,11 +214,13 @@ def compile_model(self, **kwargs):
             Extra arguments passed to :meth:`amici.sbml_import.SbmlImporter.sbml2amici`
             or :func:`amici.pysb_import.pysb2amici`.
         """
+        from amici.importers.petab.v1 import import_petab_problem
+
         # delete output directory
         if os.path.exists(self.output_folder):
             shutil.rmtree(self.output_folder)
 
-        amici.petab.import_petab_problem(
+        import_petab_problem(
             petab_problem=self.petab_problem,
             model_name=self.model_name,
             model_output_dir=self.output_folder,
@@ -248,11 +247,13 @@ def create_edatas(
         verbose: bool = True,
     ) -> list[amici.ExpData]:
         """Create list of :class:`amici.amici.ExpData` objects."""
+        from amici.importers.petab.v1.conditions import create_edatas
+
         # create model
         if model is None:
             model = self.create_model(verbose=verbose)
 
-        return amici.petab.conditions.create_edatas(
+        return create_edatas(
             amici_model=model,
             petab_problem=self.petab_problem,
             simulation_conditions=simulation_conditions,
@@ -292,6 +293,11 @@ def create_objective(
         -------
         A :class:`pypesto.objective.AmiciObjective` for the model and the data.
         """
+        from amici.importers.petab.v1.conditions import fill_in_parameters
+        from amici.importers.petab.v1.parameter_mapping import (
+            create_parameter_mapping,
+        )
+
         simulation_conditions = petab.get_simulation_conditions(
             self.petab_problem.measurement_df
         )
@@ -306,14 +312,12 @@ def create_objective(
             edatas = self.create_edatas(
                 model=model, simulation_conditions=simulation_conditions
             )
-        parameter_mapping = (
-            amici.petab.parameter_mapping.create_parameter_mapping(
-                petab_problem=self.petab_problem,
-                simulation_conditions=simulation_conditions,
-                scaled_parameters=True,
-                amici_model=model,
-                fill_fixed_parameters=False,
-            )
+        parameter_mapping = create_parameter_mapping(
+            petab_problem=self.petab_problem,
+            simulation_conditions=simulation_conditions,
+            scaled_parameters=True,
+            amici_model=model,
+            fill_fixed_parameters=False,
         )
         par_ids = self.petab_problem.x_ids
 
@@ -322,7 +326,7 @@ def create_objective(
         problem_parameters = dict(
             zip(self.petab_problem.x_ids, self.petab_problem.x_nominal_scaled)
         )
-        amici.petab.conditions.fill_in_parameters(
+        fill_in_parameters(
             edatas=edatas,
             problem_parameters=problem_parameters,
             scaled_parameters=True,
@@ -512,14 +516,16 @@ def rdatas_to_measurement_df(
         A dataframe built from the rdatas in the format as in
         ``self.petab_problem.measurement_df``.
         """
+        from amici.importers.petab.v1.simulations import (
+            rdatas_to_measurement_df,
+        )
+
         # create model
         if model is None:
             model = self.create_model(verbose=verbose)
 
-        measurement_df = self.petab_problem.measurement_df
-
-        return amici.petab.simulations.rdatas_to_measurement_df(
-            rdatas, model, measurement_df
+        return rdatas_to_measurement_df(
+            rdatas, model, self.petab_problem.measurement_df
         )
 
     def rdatas_to_simulation_df(
diff --git a/pypesto/visualize/model_fit.py b/pypesto/visualize/model_fit.py
@@ -15,8 +15,8 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import petab.v1 as petab
-from amici.petab.conditions import fill_in_parameters
-from amici.petab.simulations import rdatas_to_simulation_df
+from amici.importers.petab.v1.conditions import fill_in_parameters
+from amici.importers.petab.v1.simulations import rdatas_to_simulation_df
 from petab.v1.visualize import plot_problem
 
 from ..C import CENSORED, ORDINAL, RDATAS, SEMIQUANTITATIVE
diff --git a/pypesto/visualize/observable_mapping.py b/pypesto/visualize/observable_mapping.py
@@ -25,7 +25,7 @@
 
 try:
     import amici
-    from amici.petab.conditions import fill_in_parameters
+    from amici.importers.petab.v1.conditions import fill_in_parameters
 
     from ..hierarchical import InnerCalculatorCollector
     from ..hierarchical.base_problem import scale_back_value_dict
diff --git a/pypesto/visualize/ordinal_categories.py b/pypesto/visualize/ordinal_categories.py
@@ -9,7 +9,7 @@
 
 try:
     import amici
-    from amici.petab.conditions import fill_in_parameters
+    from amici.importers.petab.v1.conditions import fill_in_parameters
     from petab.v1.C import OBSERVABLE_ID
 
     from ..hierarchical.ordinal.calculator import OrdinalCalculator
diff --git a/test/petab/test_petab_suite.py b/test/petab/test_petab_suite.py
@@ -2,10 +2,10 @@
 
 import logging
 
-import amici.petab.simulations
 import petab.v1 as petab
 import petabtests
 import pytest
+from amici.importers.petab.v1.simulations import rdatas_to_measurement_df
 
 import pypesto
 import pypesto.petab
@@ -96,7 +96,7 @@ def _execute_case(case, model_type, version):
     rdatas = ret["rdatas"]
     chi2 = sum(rdata["chi2"] for rdata in rdatas)
     llh = -ret["fval"]
-    simulation_df = amici.petab.simulations.rdatas_to_measurement_df(
+    simulation_df = rdatas_to_measurement_df(
         rdatas, model, importer.petab_problem.measurement_df
     )
 
