free_par

Author: dweindl

doc/example/amici.ipynb

@@ -324,7 +324,7 @@
    "source": [
     "model = model_module.get_model()\n",
     "\n",
-    "print(\"Model parameters:\", list(model.get_parameter_ids()))\n",
+    "print(\"Model parameters:\", list(model.get_free_parameter_ids()))\n",
     "print(\"Model outputs:   \", list(model.get_observable_ids()))\n",
     "print(\"Model states:    \", list(model.get_state_ids()))"
    ],
@@ -482,7 +482,7 @@
     "\n",
     "# set parameters to optimal values found in the benchmark collection\n",
     "model.set_parameter_scale(amici.ParameterScaling.log10)\n",
-    "model.set_parameters(benchmark_parameters)\n",
+    "model.set_free_parameters(benchmark_parameters)\n",
     "\n",
     "# Create solver instance\n",
     "solver = model.create_solver()\n",

doc/example/conversion_reaction.ipynb

@@ -112,7 +112,7 @@
     "model.require_sensitivities_for_all_parameters()\n",
     "model.set_timepoints(np.linspace(0, 10, 11))\n",
     "model.set_parameter_scale(amici.ParameterScaling.log10)\n",
-    "model.set_parameters([-0.3, -0.7])\n",
+    "model.set_free_parameters([-0.3, -0.7])\n",
     "solver = model.create_solver()\n",
     "solver.set_sensitivity_method(amici.SensitivityMethod.forward)\n",
     "solver.set_sensitivity_order(amici.SensitivityOrder.first)\n",

doc/example/petab_import.ipynb

@@ -120,7 +120,7 @@
     "model = factory.create_model(verbose=False)\n",
     "\n",
     "# some model properties\n",
-    "print(\"Model parameters:\", list(model.get_parameter_ids()), \"\\n\")\n",
+    "print(\"Model parameters:\", list(model.get_free_parameter_ids()), \"\\n\")\n",
     "print(\"Model const parameters:\", list(model.get_fixed_parameter_ids()), \"\\n\")\n",
     "print(\"Model outputs:   \", list(model.get_observable_ids()), \"\\n\")\n",
     "print(\"Model states:    \", list(model.get_state_ids()), \"\\n\")"

pypesto/hierarchical/inner_calculator_collector.py

@@ -515,7 +515,7 @@ def __call__(
                 dim=dim,
                 parameter_mapping=parameter_mapping,
                 par_opt_ids=x_ids,
-                par_sim_ids=amici_model.get_parameter_ids(),
+                par_sim_ids=amici_model.get_free_parameter_ids(),
             )
             nllh += quantitative_result[FVAL]
             if 1 in sensi_orders:

pypesto/objective/amici/amici.py

@@ -169,7 +169,7 @@ def __init__(
         # optimization parameter ids
         if x_ids is None:
             # use model parameter ids as ids
-            x_ids = list(self.amici_model.get_parameter_ids())
+            x_ids = list(self.amici_model.get_free_parameter_ids())
         self.x_ids = x_ids
 
         # mapping of parameters

pypesto/objective/amici/amici_util.py

@@ -62,7 +62,7 @@ def map_par_opt_to_par_sim(
     """
     par_sim_vals = [
         condition_map_sim_var[par_id]
-        for par_id in amici_model.get_parameter_ids()
+        for par_id in amici_model.get_free_parameter_ids()
     ]
 
     # iterate over simulation parameter indices
@@ -130,7 +130,7 @@ def create_identity_parameter_mapping(
         amici_to_petab_scale,
     )
 
-    x_ids = list(amici_model.get_parameter_ids())
+    x_ids = list(amici_model.get_free_parameter_ids())
     x_scales = list(amici_model.get_parameter_scale())
     parameter_mapping = ParameterMapping()
     for _ in range(n_conditions):

pypesto/objective/petab.py

@@ -57,7 +57,7 @@ def replace_parameters(self, x: np.ndarray):
         x_unscaled = self.petab_problem.unscale_parameters(x_dict)
         par_df = self.petab_problem.parameter_df
         par_df["nominalValue"] = par_df.index.map(x_unscaled)
-        self.simulator.set_parameters(x_unscaled)
+        self.simulator.set_free_parameters(x_unscaled)
 
     def call_unprocessed(
         self,

test/base/test_engine.py

@@ -141,8 +141,8 @@ def test_pickle_objective():
 
     # test some properties
     assert (
-        objective.amici_model.get_parameter_ids()
-        == objective2.amici_model.get_parameter_ids()
+        objective.amici_model.get_free_parameter_ids()
+        == objective2.amici_model.get_free_parameter_ids()
     )
     assert (
         objective.amici_solver.get_sensitivity_order()

test/petab/test_amici_predictor.py

@@ -114,7 +114,7 @@ def edata_objects(conversion_reaction_model):
 
     # set timepoints for which we want to simulate the model
     testmodel.set_timepoints(np.linspace(0, 4, 10))
-    testmodel.set_parameters(np.array([4.0, 0.4]))
+    testmodel.set_free_parameters(np.array([4.0, 0.4]))
     # Create solver instance
     solver = testmodel.create_solver()
 

test/petab/test_petab_import.py

@@ -187,7 +187,7 @@ def test_plist_mapping():
     #  `plist` later on)
     fixed_model_par_ids = ["init_b10", "init_bcry"]
     fixed_model_par_idxs = [
-        objective.amici_model.get_parameter_ids().index(id)
+        objective.amici_model.get_free_parameter_ids().index(id)
         for id in fixed_model_par_ids
     ]
     fixed_idxs = [problem.x_names.index(id) for id in fixed_ids]