free/fixed

Author: dweindl

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": [],

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,
             )

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

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,
             )

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()

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