Petab Importer reforge

doc/example/petab_import.ipynb

@@ -105,7 +105,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The model must be imported to pyPESTO and AMICI. Therefore, we create a `pypesto.PetabImporter` from the problem. The importer itself creates a `pypesto.petab.Factory`, which is used to create the AMICI objective and model."
+    "In order to import the model into pyPESTO, we additionally need a simulator. We can clarify the simulator through the `, simulator_type` argument. Supported simulators are e.g.`amici` and `roadrunner`. We will use AMICI as our example simulator. Therefore, we create a `pypesto.PetabImporter` from the problem. The importer itself creates a `pypesto.petab.Factory`, which is used to create the AMICI objective and model."
    ]
   },
   {
@@ -116,7 +116,7 @@
    },
    "outputs": [],
    "source": [
-    "importer = pypesto.petab.PetabImporter(petab_problem)\n",
+    "importer = pypesto.petab.PetabImporter(petab_problem, simulator_type=\"amici\")\n",
     "factory = importer.create_objective_creator()\n",
     "\n",
     "model = factory.create_model(verbose=False)\n",
@@ -155,7 +155,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "importer = pypesto.petab.PetabImporter.from_yaml(yaml_config)\n",
+    "importer = pypesto.petab.PetabImporter.from_yaml(yaml_config, simulator_type=\"amici\")\n",
     "problem = importer.create_problem()  # creating the problem from the importer. The objective can be found at problem.objective"
    ]
   },

pypesto/C.py

@@ -84,6 +84,10 @@ class EnsembleType(Enum):
 X0 = "x0"
 ID = "id"
 
+AMICI = "amici"
+ROADRUNNER = "roadrunner"
+PETAB = "petab"
+
 
 ###############################################################################
 # HIERARCHICAL SCALING + OFFSET

pypesto/petab/factory.py

@@ -62,7 +62,7 @@
 
 
 class ObjectiveCreator(ABC):
-    """Abstract factory for creating an objective function."""
+    """Abstract Creator for creating an objective function."""
 
     @abstractmethod
     def create_objective(self, **kwargs) -> ObjectiveBase:
@@ -84,7 +84,7 @@ def __init__(
         validate_petab: bool = True,
     ):
         """
-        Initialize the factory.
+        Initialize the creator.
 
         Parameters
         ----------

pypesto/petab/importer.py

@@ -21,9 +21,12 @@
     roadrunner = None
 
 from ..C import (
+    AMICI,
     CENSORED,
     ORDINAL,
     ORDINAL_OPTIONS,
+    PETAB,
+    ROADRUNNER,
     SEMIQUANTITATIVE,
     SPLINE_APPROXIMATION_OPTIONS,
 )
@@ -74,7 +77,7 @@ def __init__(
         validate_petab_hierarchical: bool = True,
         hierarchical: bool = False,
         inner_options: dict | None = None,
-        simulator_type: str = "amici",
+        simulator_type: str = AMICI,
         simulator: petab.Simulator | None = None,
         rr: roadrunner.RoadRunner | None = None,
     ):
@@ -168,7 +171,7 @@ def __init__(
 
         self.simulator_type = simulator_type
         self.simulator = simulator
-        if simulator_type == "petab" and simulator is None:
+        if simulator_type == PETAB and simulator is None:
             raise ValueError(
                 "A petab simulator object must be provided if the simulator "
                 "type is 'petab'."
@@ -180,7 +183,7 @@ def from_yaml(
         yaml_config: dict | str,
         output_folder: str = None,
         model_name: str = None,
-        simulator_type: str = "amici",
+        simulator_type: str = AMICI,
     ) -> PetabImporter:
         """Simplified constructor using a petab yaml file."""
         petab_problem = petab.Problem.from_yaml(yaml_config)
@@ -288,7 +291,7 @@ def create_startpoint_method(self, **kwargs) -> StartpointMethod:
 
     def create_objective_creator(self) -> ObjectiveCreator:
         """Choose factory depending on the simulator type."""
-        if self.simulator_type == "amici":
+        if self.simulator_type == AMICI:
             return AmiciObjectiveCreator(
                 petab_problem=self.petab_problem,
                 output_folder=self.output_folder,
@@ -298,11 +301,11 @@ def create_objective_creator(self) -> ObjectiveCreator:
                 non_quantitative_data_types=self._non_quantitative_data_types,
                 validate_petab=self.validate_petab,
             )
-        elif self.simulator_type == "petab":
+        elif self.simulator_type == PETAB:
             return PetabSimulatorObjectiveCreator(
                 petab_problem=self.petab_problem, simulator=self.simulator
             )
-        elif self.simulator_type == "roadrunner":
+        elif self.simulator_type == ROADRUNNER:
             return RoadRunnerObjectiveCreator(
                 petab_problem=self.petab_problem, rr=self.roadrunner_instance
             )
@@ -447,7 +450,7 @@ def create_predictor(
         condition_ids: Sequence[str] = None,
     ) -> AmiciPredictor:
         """See :meth:`AmiciObjectiveCreator.create_predictor`."""
-        if self.simulator_type != "amici":
+        if self.simulator_type != AMICI:
             raise ValueError(
                 "Predictor can only be created for amici models and is "
                 "supposed to be created from the AmiciObjectiveCreator."