free_par

dweindl · dweindl · commit dcc0257a32cd · 2025-11-17T14:46:04.000+01:00
diff --git a/doc/example/amici.ipynb b/doc/example/amici.ipynb
@@ -152,9 +152,9 @@
     }
    },
    "source": [
-    "#### Constant parameters\n",
+    "#### Fixed parameters\n",
     "\n",
-    "Constant parameters, i.e., parameters with respect to which no sensitivities are to be computed (these are often parameters specifying a certain experimental condition) are provided as a list of parameter names."
+    "Fixed parameters, i.e., parameters with respect to which no sensitivities are to be computed (these are often parameters specifying a certain experimental condition) are provided as a list of parameter IDs."
    ]
   },
   {
@@ -168,9 +168,7 @@
      "name": "#%%\n"
     }
    },
-   "source": [
-    "constant_parameters = [\"ratio\", \"specC17\"]"
-   ],
+   "source": "fixed_parameters = [\"ratio\", \"specC17\"]",
    "outputs": [],
    "execution_count": null
   },
@@ -255,7 +253,7 @@
     "    model_output_dir,\n",
     "    verbose=False,\n",
     "    observation_model=observables,\n",
-    "    constant_parameters=constant_parameters,\n",
+    "    fixed_parameters=fixed_parameters,\n",
     ")"
    ],
    "outputs": [],
@@ -324,7 +322,7 @@
    "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 +480,7 @@
     "\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",
diff --git a/doc/example/conversion_reaction.ipynb b/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",
diff --git a/doc/example/petab_import.ipynb b/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\")"
diff --git a/pypesto/hierarchical/inner_calculator_collector.py b/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:
diff --git a/pypesto/hierarchical/ordinal/calculator.py b/pypesto/hierarchical/ordinal/calculator.py
@@ -216,7 +216,7 @@ def __call__(
                 ssigma=ssigma,
                 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(),
                 par_edatas_indices=[edata.plist for edata in edatas],
                 snllh=snllh,
             )
diff --git a/pypesto/hierarchical/relative/calculator.py b/pypesto/hierarchical/relative/calculator.py
@@ -355,7 +355,7 @@ def calculate_directly(
                 inner_parameters=inner_parameters,
                 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(),
                 snllh=snllh,
             )
         # apply the computed inner parameters to the ReturnData
diff --git a/pypesto/hierarchical/semiquantitative/calculator.py b/pypesto/hierarchical/semiquantitative/calculator.py
@@ -220,7 +220,7 @@ def __call__(
                 amici_ssigma=ssigma,
                 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(),
                 par_edatas_indices=[edata.plist for edata in edatas],
                 snllh=snllh,
             )
diff --git a/pypesto/objective/amici/amici.py b/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
diff --git a/pypesto/objective/amici/amici_util.py b/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):
diff --git a/test/base/test_engine.py b/test/base/test_engine.py
@@ -103,8 +103,8 @@ def test_deepcopy_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()
@@ -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()
diff --git a/test/petab/test_amici_objective.py b/test/petab/test_amici_objective.py
@@ -122,7 +122,7 @@ def test_preeq_guesses():
     assert obj.steadystate_guesses["fval"] < np.inf
     assert len(obj.steadystate_guesses["data"]) == len(obj.edatas)
     # check that we have test a problem where plist is nontrivial
-    assert any(len(e.plist) != len(e.parameters) for e in obj.edatas)
+    assert any(len(e.plist) != len(e.free_parameters) for e in obj.edatas)
 
     df = obj.check_grad(
         problem.get_reduced_vector(
diff --git a/test/petab/test_amici_predictor.py b/test/petab/test_amici_predictor.py
@@ -73,8 +73,8 @@ def create_intial_assignment(sbml_model, spec_id):
             create_observable(sbml_importer.sbml, spec)
             create_intial_assignment(sbml_importer.sbml, spec)
 
-        # add constant parameters and observables to AMICI model
-        constant_parameters = ["A0", "B0"]
+        # add fixed parameters and observables to AMICI model
+        fixed_parameters = ["A0", "B0"]
         observables = amici.assignment_rules_to_observables(
             sbml_importer.sbml,  # the libsbml model object
             filter_function=lambda variable: variable.getId().startswith(
@@ -87,7 +87,7 @@ def create_intial_assignment(sbml_model, spec_id):
             model_output_dir,
             verbose=False,
             observation_model=observables,
-            constant_parameters=constant_parameters,
+            fixed_parameters=fixed_parameters,
         )
 
         # Importing the module and loading the model
@@ -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()
 
diff --git a/test/petab/test_petab_import.py b/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]
diff --git a/test/petab/test_sbml_conversion.py b/test/petab/test_sbml_conversion.py
@@ -39,7 +39,7 @@ class AmiciObjectiveTest(unittest.TestCase):
     def runTest(self):
         for example in ["conversion_reaction"]:
             objective, model = load_amici_objective(example)
-            x0 = np.array(list(model.get_parameters()))
+            x0 = np.array(list(model.get_free_parameters()))
 
             df = objective.check_grad(
                 x0,
@@ -98,7 +98,7 @@ def parameter_estimation(objective, library, solver, fixed_pars, n_starts):
     dim = len(objective.x_ids)
     lb = -2 * np.ones((1, dim))
     ub = 2 * np.ones((1, dim))
-    pars = objective.amici_model.get_parameters()
+    pars = objective.amici_model.get_free_parameters()
     problem = pypesto.Problem(
         objective,
         lb,
diff --git a/test/util.py b/test/util.py
@@ -321,7 +321,7 @@ def load_amici_objective(example_name):
     model.require_sensitivities_for_all_parameters()
     model.set_timepoints(np.linspace(0, 10, 11))
     model.set_parameter_scale(amici.ParameterScaling.log10)
-    model.set_parameters([-0.3, -0.7])
+    model.set_free_parameters([-0.3, -0.7])
     solver = model.create_solver()
     solver.set_sensitivity_method(amici.SensitivityMethod.forward)
     solver.set_sensitivity_order(amici.SensitivityOrder.first)

Original file line number	Diff line number	Diff line change
`@@ -515,7 +515,7 @@ def __call__(`
`515`	`515`	`dim=dim,`
`516`	`516`	`parameter_mapping=parameter_mapping,`
`517`	`517`	`par_opt_ids=x_ids,`
`518`		`- par_sim_ids=amici_model.get_parameter_ids(),`
	`518`	`+ par_sim_ids=amici_model.get_free_parameter_ids(),`
`519`	`519`	`)`
`520`	`520`	`nllh += quantitative_result[FVAL]`
`521`	`521`	`if 1 in sensi_orders:`
Original file line number	Diff line number	Diff line change
`@@ -216,7 +216,7 @@ def __call__(`
`216`	`216`	`ssigma=ssigma,`
`217`	`217`	`parameter_mapping=parameter_mapping,`
`218`	`218`	`par_opt_ids=x_ids,`
`219`		`- par_sim_ids=amici_model.get_parameter_ids(),`
	`219`	`+ par_sim_ids=amici_model.get_free_parameter_ids(),`
`220`	`220`	`par_edatas_indices=[edata.plist for edata in edatas],`
`221`	`221`	`snllh=snllh,`
`222`	`222`	`)`
Original file line number	Diff line number	Diff line change
`@@ -355,7 +355,7 @@ def calculate_directly(`
`355`	`355`	`inner_parameters=inner_parameters,`
`356`	`356`	`parameter_mapping=parameter_mapping,`
`357`	`357`	`par_opt_ids=x_ids,`
`358`		`- par_sim_ids=amici_model.get_parameter_ids(),`
	`358`	`+ par_sim_ids=amici_model.get_free_parameter_ids(),`
`359`	`359`	`snllh=snllh,`
`360`	`360`	`)`
`361`	`361`	`# apply the computed inner parameters to the ReturnData`
Original file line number	Diff line number	Diff line change
`@@ -220,7 +220,7 @@ def __call__(`
`220`	`220`	`amici_ssigma=ssigma,`
`221`	`221`	`parameter_mapping=parameter_mapping,`
`222`	`222`	`par_opt_ids=x_ids,`
`223`		`- par_sim_ids=amici_model.get_parameter_ids(),`
	`223`	`+ par_sim_ids=amici_model.get_free_parameter_ids(),`
`224`	`224`	`par_edatas_indices=[edata.plist for edata in edatas],`
`225`	`225`	`snllh=snllh,`
`226`	`226`	`)`