..

python/sdist/amici/__main__.py

@@ -1,6 +1,5 @@
 """Package-level entrypoint"""
 
-import os
 import sys
 
 from . import __version__, compiledWithOpenMP, has_clibs, hdf5_enabled

python/sdist/amici/petab/cli/import_petab.py

@@ -1,7 +1,8 @@
 import argparse
 
 import petab
-from amici.petab_import import import_model
+
+from ..petab_import import import_model_sbml
 
 
 def _parse_cli_args():
@@ -142,7 +143,7 @@ def _main():
     if args.flatten:
         petab.flatten_timepoint_specific_output_overrides(pp)
 
-    import_model(
+    import_model_sbml(
         model_name=args.model_name,
         sbml_model=pp.sbml_model,
         condition_table=pp.condition_df,

python/sdist/amici/petab/simulator.py

@@ -0,0 +1,109 @@
+"""
+PEtab Simulator
+---------------
+Functionality related to the use of AMICI for simulation with :class:`petab.Simulator`.
+
+Use cases:
+
+- generate data for use with PEtab's plotting methods
+- generate synthetic data
+"""
+
+import inspect
+import sys
+from typing import Callable
+
+import pandas as pd
+import petab
+from amici import AmiciModel, SensitivityMethod_none
+
+from .petab_import import import_petab_problem
+from .simulations import RDATAS, rdatas_to_measurement_df, simulate_petab
+
+AMICI_MODEL = "amici_model"
+AMICI_SOLVER = "solver"
+MODEL_NAME = "model_name"
+MODEL_OUTPUT_DIR = "model_output_dir"
+
+PETAB_PROBLEM = "petab_problem"
+
+
+class PetabSimulator(petab.simulate.Simulator):
+    """Implementation of the PEtab `Simulator` class that uses AMICI."""
+
+    def __init__(self, *args, amici_model: AmiciModel = None, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.amici_model = amici_model
+
+    def simulate_without_noise(self, **kwargs) -> pd.DataFrame:
+        """
+        See :py:func:`petab.simulate.Simulator.simulate()` docstring.
+
+        Additional keyword arguments can be supplied to specify arguments for
+        the AMICI PEtab import, simulate, and export methods. See the
+        docstrings for the respective methods for argument options:
+        - :py:func:`amici.petab_import.import_petab_problem`, and
+        - :py:func:`amici.petab_objective.simulate_petab`.
+
+        Note that some arguments are expected to have already been specified
+        in the Simulator constructor (including the PEtab problem).
+        """
+        if AMICI_MODEL in {*kwargs, *dir(self)} and (
+            any(
+                k in kwargs
+                for k in inspect.signature(import_petab_problem).parameters
+            )
+        ):
+            print(
+                "Arguments related to the PEtab import are unused if "
+                f"`{AMICI_MODEL}` is specified, or the "
+                "`PetabSimulator.simulate()` method was previously called."
+            )
+
+        kwargs[PETAB_PROBLEM] = self.petab_problem
+
+        # The AMICI model instance for the PEtab problem is saved in the state,
+        # such that it need not be supplied with each request for simulated
+        # data. Any user-supplied AMICI model will overwrite the model saved
+        # in the state.
+        if AMICI_MODEL not in kwargs:
+            if self.amici_model is None:
+                if MODEL_NAME not in kwargs:
+                    kwargs[MODEL_NAME] = AMICI_MODEL
+                    # If the model name is the name of a module that is already
+                    # cached, it can cause issues during import.
+                    while kwargs[MODEL_NAME] in sys.modules:
+                        kwargs[MODEL_NAME] += str(self.rng.integers(10))
+                if MODEL_OUTPUT_DIR not in kwargs:
+                    kwargs[MODEL_OUTPUT_DIR] = self.working_dir
+                self.amici_model = _subset_call(import_petab_problem, kwargs)
+            kwargs[AMICI_MODEL] = self.amici_model
+        self.amici_model = kwargs[AMICI_MODEL]
+
+        if AMICI_SOLVER not in kwargs:
+            kwargs[AMICI_SOLVER] = self.amici_model.getSolver()
+            kwargs[AMICI_SOLVER].setSensitivityMethod(SensitivityMethod_none)
+
+        result = _subset_call(simulate_petab, kwargs)
+        return rdatas_to_measurement_df(
+            result[RDATAS], self.amici_model, self.petab_problem.measurement_df
+        )
+
+
+def _subset_call(method: Callable, kwargs: dict):
+    """
+    Helper function to call a method with the intersection of arguments in the
+    method signature and the supplied arguments.
+
+    :param method:
+        The method to be called.
+    :param kwargs:
+        The argument superset as a dictionary, similar to ``**kwargs`` in
+        method signatures.
+    :return:
+        The output of ``method``, called with the applicable arguments in
+        ``kwargs``.
+    """
+    method_args = inspect.signature(method).parameters
+    subset_kwargs = {k: v for k, v in kwargs.items() if k in method_args}
+    return method(**subset_kwargs)

python/sdist/amici/petab_import.py

@@ -11,15 +11,15 @@
     DeprecationWarning,
 )
 
-from .petab.import_helpers import (
+from .petab.import_helpers import (  # noqa # pylint: disable=unused-import
     get_fixed_parameters,
     get_observation_model,
     petab_noise_distributions_to_amici,
     petab_scale_to_amici_scale,
 )
 
 # DEPRECATED - DON'T ADD ANYTHING NEW HERE
-from .petab.petab_import import (
+from .petab.petab_import import (  # noqa # pylint: disable=unused-import
     check_model,
     import_model,
     import_model_sbml,

python/sdist/amici/petab_simulate.py

@@ -1,113 +1,10 @@
-"""
-PEtab Simulate
---------------
-Functionality related to the use of AMICI for simulation with PEtab's
-Simulator class.
+# THIS FILE IS TO BE REMOVED - DON'T ADD ANYTHING HERE!
 
-Use cases:
+import warnings
 
-- generate data for use with PEtab's plotting methods
-- generate synthetic data
-"""
-
-import inspect
-import sys
-from typing import Callable
-
-import pandas as pd
-import petab
-from amici import AmiciModel, SensitivityMethod_none
-from amici.petab_import import import_petab_problem
-from amici.petab_objective import (
-    RDATAS,
-    rdatas_to_measurement_df,
-    simulate_petab,
+warnings.warn(
+    f"Importing {__name__} is deprecated. Use `amici.petab.simulator` instead.",
+    DeprecationWarning,
 )
 
-AMICI_MODEL = "amici_model"
-AMICI_SOLVER = "solver"
-MODEL_NAME = "model_name"
-MODEL_OUTPUT_DIR = "model_output_dir"
-
-PETAB_PROBLEM = "petab_problem"
-
-
-class PetabSimulator(petab.simulate.Simulator):
-    """Implementation of the PEtab `Simulator` class that uses AMICI."""
-
-    def __init__(self, *args, amici_model: AmiciModel = None, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.amici_model = amici_model
-
-    def simulate_without_noise(self, **kwargs) -> pd.DataFrame:
-        """
-        See :py:func:`petab.simulate.Simulator.simulate()` docstring.
-
-        Additional keyword arguments can be supplied to specify arguments for
-        the AMICI PEtab import, simulate, and export methods. See the
-        docstrings for the respective methods for argument options:
-        - :py:func:`amici.petab_import.import_petab_problem`, and
-        - :py:func:`amici.petab_objective.simulate_petab`.
-
-        Note that some arguments are expected to have already been specified
-        in the Simulator constructor (including the PEtab problem).
-        """
-        if AMICI_MODEL in {*kwargs, *dir(self)} and (
-            any(
-                k in kwargs
-                for k in inspect.signature(import_petab_problem).parameters
-            )
-        ):
-            print(
-                "Arguments related to the PEtab import are unused if "
-                f"`{AMICI_MODEL}` is specified, or the "
-                "`PetabSimulator.simulate()` method was previously called."
-            )
-
-        kwargs[PETAB_PROBLEM] = self.petab_problem
-
-        # The AMICI model instance for the PEtab problem is saved in the state,
-        # such that it need not be supplied with each request for simulated
-        # data. Any user-supplied AMICI model will overwrite the model saved
-        # in the state.
-        if AMICI_MODEL not in kwargs:
-            if self.amici_model is None:
-                if MODEL_NAME not in kwargs:
-                    kwargs[MODEL_NAME] = AMICI_MODEL
-                    # If the model name is the name of a module that is already
-                    # cached, it can cause issues during import.
-                    while kwargs[MODEL_NAME] in sys.modules:
-                        kwargs[MODEL_NAME] += str(self.rng.integers(10))
-                if MODEL_OUTPUT_DIR not in kwargs:
-                    kwargs[MODEL_OUTPUT_DIR] = self.working_dir
-                self.amici_model = _subset_call(import_petab_problem, kwargs)
-            kwargs[AMICI_MODEL] = self.amici_model
-        self.amici_model = kwargs[AMICI_MODEL]
-
-        if AMICI_SOLVER not in kwargs:
-            kwargs[AMICI_SOLVER] = self.amici_model.getSolver()
-            kwargs[AMICI_SOLVER].setSensitivityMethod(SensitivityMethod_none)
-
-        result = _subset_call(simulate_petab, kwargs)
-        return rdatas_to_measurement_df(
-            result[RDATAS], self.amici_model, self.petab_problem.measurement_df
-        )
-
-
-def _subset_call(method: Callable, kwargs: dict):
-    """
-    Helper function to call a method with the intersection of arguments in the
-    method signature and the supplied arguments.
-
-    :param method:
-        The method to be called.
-    :param kwargs:
-        The argument superset as a dictionary, similar to ``**kwargs`` in
-        method signatures.
-    :return:
-        The output of ``method``, called with the applicable arguments in
-        ``kwargs``.
-    """
-    method_args = inspect.signature(method).parameters
-    subset_kwargs = {k: v for k, v in kwargs.items() if k in method_args}
-    return method(**subset_kwargs)
+from .petab.simulator import PetabSimulator  # noqa: F401

python/tests/splines_utils.py

@@ -17,7 +17,7 @@
 import sympy as sp
 from amici.gradient_check import _check_results
 from amici.petab.petab_import import import_petab_problem
-from amici.petab_objective import EDATAS, LLH, RDATAS, SLLH, simulate_petab
+from amici.petab.simulations import EDATAS, LLH, RDATAS, SLLH, simulate_petab
 from amici.sbml_utils import (
     add_compartment,
     add_inflow,

python/tests/test_conserved_quantities_rref.py

@@ -1,5 +1,3 @@
-import os
-
 import numpy as np
 import pytest
 import sympy as sp

python/tests/test_parameter_mapping.py

@@ -1,7 +1,5 @@
 """Test for ``amici.parameter_mapping``"""
-import os
 
-import pytest
 from amici.petab.parameter_mapping import (
     ParameterMapping,
     ParameterMappingForCondition,

python/tests/test_petab_objective.py

@@ -4,13 +4,12 @@
 from pathlib import Path
 
 import amici
-import amici.petab_objective
 import numpy as np
 import pandas as pd
 import petab
 import pytest
 from amici.petab.petab_import import import_petab_problem
-from amici.petab_objective import SLLH
+from amici.petab.simulations import SLLH, simulate_petab
 
 # Absolute and relative tolerances for finite difference gradient checks.
 ATOL: float = 1e-3
@@ -54,7 +53,7 @@ def test_simulate_petab_sensitivities(lotka_volterra):
                     problem_parameters
                 )
             results[(scaled_parameters, scaled_gradients)] = pd.Series(
-                amici.petab_objective.simulate_petab(
+                simulate_petab(
                     petab_problem=petab_problem,
                     amici_model=amici_model,
                     solver=amici_solver,

python/tests/test_petab_simulate.py

@@ -5,7 +5,7 @@
 import petab
 import petabtests
 import pytest
-from amici.petab_simulate import PetabSimulator
+from amici.petab.simulator import PetabSimulator
 from amici.testing import skip_on_valgrind
 
 

tests/benchmark-models/test_petab_benchmark.py

@@ -3,7 +3,6 @@
 from pathlib import Path
 
 import amici
-import amici.petab_objective
 import numpy as np
 import pandas as pd
 import petab

tests/benchmark-models/test_petab_model.py

@@ -16,7 +16,7 @@
 import petab
 import yaml
 from amici.logging import get_logger
-from amici.petab_objective import (
+from amici.petab.simulations import (
     LLH,
     RDATAS,
     rdatas_to_measurement_df,

tests/petab_test_suite/test_petab_suite.py

@@ -13,12 +13,9 @@
 from amici import SteadyStateSensitivityMode
 from amici.gradient_check import check_derivatives as amici_check_derivatives
 from amici.logging import get_logger, set_log_level
+from amici.petab.conditions import create_parameterized_edatas
 from amici.petab.petab_import import import_petab_problem
-from amici.petab_objective import (
-    create_parameterized_edatas,
-    rdatas_to_measurement_df,
-    simulate_petab,
-)
+from amici.petab.simulations import rdatas_to_measurement_df, simulate_petab
 
 logger = get_logger(__name__, logging.DEBUG)
 set_log_level(get_logger("amici.petab_import"), logging.DEBUG)