Merge branch 'develop' into update_refs

ICB-DCM · Nov 26, 2024 · f9ed4aa · f9ed4aa
2 parents d80148c + 6c049f5
commit f9ed4aa
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Showing 5 changed files with 34 additions and 10 deletions.
diff --git a/pypesto/objective/amici/amici.py b/pypesto/objective/amici/amici.py
@@ -713,3 +713,9 @@ def update_from_problem(
             ) in condition_mapping.map_sim_fix.items():
                 if (val := id_to_val.get(mapped_to_par)) is not None:
                     condition_mapping.map_sim_fix[model_par] = val
+            for (
+                model_par,
+                mapped_to_par,
+            ) in condition_mapping.map_preeq_fix.items():
+                if (val := id_to_val.get(mapped_to_par)) is not None:
+                    condition_mapping.map_preeq_fix[model_par] = val
diff --git a/setup.cfg b/setup.cfg
@@ -105,7 +105,8 @@ ipopt =
 dlib =
     dlib >= 19.19.0
 nlopt =
-    nlopt >= 2.6.2
+    # != 2.9.0: https://github.com/stevengj/nlopt/issues/575
+    nlopt >= 2.6.2, != 2.9.0
 pyswarm =
     pyswarm >= 0.6
 cma =

diff --git a/test/base/test_engine.py b/test/base/test_engine.py
@@ -86,7 +86,14 @@ def test_deepcopy_objective():
         )
     )
     factory = petab_importer.create_objective_creator()
-    objective = factory.create_objective()
+    amici_model = factory.create_model()
+    amici_model.setSteadyStateSensitivityMode(
+        amici.SteadyStateSensitivityMode.integrateIfNewtonFails
+    )
+    amici_model.setSteadyStateComputationMode(
+        amici.SteadyStateComputationMode.integrateIfNewtonFails
+    )
+    objective = factory.create_objective(model=amici_model)
 
     objective.amici_solver.setSensitivityMethod(
         amici.SensitivityMethod_adjoint

diff --git a/test/petab/test_amici_objective.py b/test/petab/test_amici_objective.py
@@ -86,12 +86,21 @@ def test_preeq_guesses():
     importer = pypesto.petab.PetabImporter.from_yaml(
         os.path.join(models.MODELS_DIR, model_name, model_name + ".yaml")
     )
-    problem = importer.create_problem()
-    obj = problem.objective
-    obj.amici_solver.setNewtonMaxSteps(0)
+    obj_creator = importer.create_objective_creator()
+    amici_model = obj_creator.create_model()
+    amici_model.setSteadyStateComputationMode(
+        amici.SteadyStateComputationMode.integrateIfNewtonFails
+    )
+    amici_model.setSteadyStateSensitivityMode(
+        amici.SteadyStateSensitivityMode.integrateIfNewtonFails
+    )
+    obj = obj_creator.create_objective(model=amici_model)
+    problem = importer.create_problem(objective=obj)
     obj.amici_model.setSteadyStateSensitivityMode(
         amici.SteadyStateSensitivityMode.integrationOnly
     )
+    obj = problem.objective
+    obj.amici_solver.setNewtonMaxSteps(0)
     obj.amici_solver.setAbsoluteTolerance(1e-12)
     obj.amici_solver.setRelativeTolerance(1e-12)
 

diff --git a/test/petab/test_petab_import.py b/test/petab/test_petab_import.py
@@ -36,12 +36,13 @@ def setUpClass(cls):
         cls.obj_edatas = []
 
     def test_0_import(self):
-        for model_name in ["Zheng_PNAS2012", "Boehm_JProteomeRes2014"]:
+        for model_name in [
+            "Zheng_PNAS2012",
+            "Boehm_JProteomeRes2014",
+            "Weber_BMC2015",
+        ]:
             # test yaml import for one model:
-            yaml_config = os.path.join(
-                models.MODELS_DIR, model_name, model_name + ".yaml"
-            )
-            petab_problem = petab.Problem.from_yaml(yaml_config)
+            petab_problem = models.get_problem(model_name)
             self.petab_problems.append(petab_problem)
 
     def test_1_compile(self):