Added deepcpy functionality and small test for roadrunner.

pypesto/objective/base.py

@@ -56,13 +56,6 @@ def __init__(
         self.pre_post_processor = PrePostProcessor()
         self.history = NoHistory()
 
-    def __deepcopy__(self, memodict=None) -> "ObjectiveBase":
-        """Create deepcopy of objective object."""
-        other = type(self)()  # maintain type for derived classes
-        for attr, val in self.__dict__.items():
-            other.__dict__[attr] = copy.deepcopy(val)
-        return other
-
     # The following has_ properties can be used to find out what values
     # the objective supports.
     @property

pypesto/objective/roadrunner/road_runner.py

@@ -2,6 +2,7 @@
 
 Currently does not support sensitivities.
 """
+import copy
 from collections import OrderedDict
 from collections.abc import Sequence
 from typing import Optional, Union
@@ -70,6 +71,23 @@ def __init__(
         self.solver_options = solver_options
         super().__init__(x_names=x_names)
 
+    def __deepcopy__(
+        self, memodict: Optional[dict] = None
+    ) -> "RoadRunnerObjective":
+        """Deepcopy function for RoadRunner objective."""
+        import roadrunner
+
+        other = self.__class__.__new__(self.__class__)
+
+        for key in set(self.__dict__.keys()) - {"roadrunner_instance"}:
+            other.__dict__[key] = copy.deepcopy(self.__dict__[key])
+        other_rr = roadrunner.RoadRunner()
+        state = self.roadrunner_instance.saveStateS()
+        other_rr.loadStateS(state=state)
+        other.roadrunner_instance = other_rr
+
+        return other
+
     def get_config(self) -> dict:
         """Return basic information of the objective configuration."""
         info = super().get_config()

test/base/test_roadrunner.py

@@ -1,7 +1,9 @@
 """Test the roadrunner interface."""
-
+import copy
 import logging
+import os
 
+import benchmark_models_petab as models
 import petab
 import petabtests
 import pytest
@@ -104,3 +106,33 @@ def _execute_case_rr(case, model_type, version):
         )
 
     logger.info(f"Case {version}/{model_type}/{case} passed.")
+
+
+def test_deepcopy():
+    "Test that deepcopy works as intended"
+    model_name = "Boehm_JProteomeRes2014"
+    petab_problem = petab.Problem.from_yaml(
+        os.path.join(models.MODELS_DIR, model_name, model_name + ".yaml")
+    )
+    petab_problem.model_name = model_name
+    importer = objective_rr.PetabImporterRR(petab_problem)
+    problem_parameters = petab_problem.x_nominal_free_scaled
+
+    problem = importer.create_problem()
+    obj = problem.objective
+
+    problem_copied = copy.deepcopy(problem)
+    copied_objective = problem_copied.objective
+
+    assert obj(problem_parameters) == copied_objective(problem_parameters)
+
+    # !!not adviced, only done here for testing purposes!!
+    obj.roadrunner_instance.removeParameter(
+        "pSTAT5A_rel", forceRegenerate=False
+    )
+    obj.roadrunner_instance.addParameter("pSTAT5A_rel", 0.0, False)
+    obj.roadrunner_instance.addAssignmentRule(
+        "pSTAT5A_rel", "(100 * pApB + 200 * pApA * specC17)"
+    )
+
+    assert obj(problem_parameters) != copied_objective(problem_parameters)