Move parameter mapping, private petab helpers (#3136)

* Move petab simulation code from `.importers` to `.sim`
* Separate sundials and non-sundials related code so the jax-related modules don't import the cpp extension
* Make helpers private

Closes #3041.

Author: dweindl

python/sdist/amici/adapters/fiddy.py

@@ -20,7 +20,6 @@
 from fiddy import CachedFunction, Type, fiddy_array
 from petab.v1.C import LIN, LOG, LOG10
 
-from amici.importers.petab.v1.parameter_mapping import create_parameter_mapping
 from amici.sim.sundials import (
     AmiciExpData,
     AmiciModel,
@@ -31,6 +30,9 @@
     run_simulation,
 )
 from amici.sim.sundials.petab.v1 import LLH, SLLH, create_edatas
+from amici.sim.sundials.petab.v1._parameter_mapping import (
+    create_parameter_mapping,
+)
 
 if TYPE_CHECKING:
     from amici.sim.sundials.petab import PetabSimulationResult, PetabSimulator

python/sdist/amici/importers/petab/_cli/import_petab.py

@@ -1,7 +1,7 @@
 import argparse
 
 import petab.v1 as petab
-from amici.importers.petab.v1.petab_import import import_model_sbml
+from amici.importers.petab.v1._petab_import import import_model_sbml
 
 
 def _parse_cli_args():

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

@@ -26,7 +26,7 @@
 from amici.logging import get_logger
 from amici.sim.jax.petab import JAXProblem
 
-from .v1.sbml_import import _add_global_parameter
+from .v1._sbml_import import _add_global_parameter
 
 if TYPE_CHECKING:
     import pysb
@@ -329,7 +329,7 @@ def _do_import_sbml(self):
             for change in self.petab_problem[condition_id].changes
         }
 
-        from .v1.sbml_import import show_model_info
+        from .v1._sbml_import import show_model_info
 
         show_model_info(self.petab_problem.model.sbml_model)
         sbml_importer = amici.SbmlImporter(

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

@@ -4,7 +4,7 @@
 #  preequilibration
 PREEQ_INDICATOR_ID = "preequilibration_indicator"
 
-from .petab_import import import_petab_problem
+from ._petab_import import import_petab_problem
 
 __all__ = [
     "import_petab_problem",

…ici/importers/petab/v1/import_helpers.py …ci/importers/petab/v1/_import_helpers.pypython/sdist/amici/importers/petab/v1/import_helpers.py renamed to python/sdist/amici/importers/petab/v1/_import_helpers.py python/sdist/amici/importers/petab/v1/import_helpers.py renamed to python/sdist/amici/importers/petab/v1/_import_helpers.py

@@ -18,16 +18,16 @@
 import amici
 from amici.logging import get_logger
 
-from .import_helpers import (
+from ._import_helpers import (
     _can_import_model,
     _create_model_name,
     _get_package_name_and_path,
     check_model,
 )
-from .sbml_import import import_model_sbml
+from ._sbml_import import import_model_sbml
 
 try:
-    from .pysb_import import import_model_pysb
+    from ._pysb_import import import_model_pysb
 except ModuleNotFoundError:
     # pysb not available
     import_model_pysb = None

…amici/importers/petab/v1/petab_import.py …mici/importers/petab/v1/_petab_import.pypython/sdist/amici/importers/petab/v1/petab_import.py renamed to python/sdist/amici/importers/petab/v1/_petab_import.py python/sdist/amici/importers/petab/v1/petab_import.py renamed to python/sdist/amici/importers/petab/v1/_petab_import.py

@@ -24,11 +24,11 @@
 from amici.logging import get_logger, log_execution_time, set_log_level
 
 from . import PREEQ_INDICATOR_ID
-from .import_helpers import (
+from ._import_helpers import (
     get_fixed_parameters,
     petab_noise_distribution_to_amici,
 )
-from .util import get_states_in_condition_table
+from ._util import get_states_in_condition_table
 
 logger = get_logger(__name__, logging.WARNING)
 

…/amici/importers/petab/v1/pysb_import.py …amici/importers/petab/v1/_pysb_import.pypython/sdist/amici/importers/petab/v1/pysb_import.py renamed to python/sdist/amici/importers/petab/v1/_pysb_import.py python/sdist/amici/importers/petab/v1/pysb_import.py renamed to python/sdist/amici/importers/petab/v1/_pysb_import.py

@@ -16,12 +16,12 @@
 from amici.logging import log_execution_time, set_log_level
 
 from . import PREEQ_INDICATOR_ID
-from .import_helpers import (
+from ._import_helpers import (
     check_model,
     get_fixed_parameters,
     get_observation_model,
 )
-from .util import get_states_in_condition_table
+from ._util import get_states_in_condition_table
 
 logger = logging.getLogger(__name__)
 

…/amici/importers/petab/v1/sbml_import.py …amici/importers/petab/v1/_sbml_import.pypython/sdist/amici/importers/petab/v1/sbml_import.py renamed to python/sdist/amici/importers/petab/v1/_sbml_import.py python/sdist/amici/importers/petab/v1/sbml_import.py renamed to python/sdist/amici/importers/petab/v1/_sbml_import.py

@@ -1 +1,3 @@
 """Functionality for simulating AMICI models."""
+
+from __future__ import annotations