some more

Author: dweindl

doc/examples/example_splines/ExampleSplines.ipynb

@@ -90,7 +90,7 @@
     "    # Setup simulation timepoints and parameters\n",
     "    model = model_module.get_model()\n",
     "    for name, value in parameters.items():\n",
-    "        model.set_parameter_by_name(name, value)\n",
+    "        model.set_free_parameter_by_name(name, value)\n",
     "    if isinstance(T, int | float):\n",
     "        T = np.linspace(0, T, 100)\n",
     "    model.set_timepoints([float(t) for t in T])\n",

doc/examples/getting_started/GettingStarted.ipynb

@@ -73,12 +73,12 @@
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": "The model allows the user to manipulate model related properties of simulations. This includes the values of model parameters that can be set by using [amici.Model.set_parameter_by_name](https://amici.readthedocs.io/en/latest/generated/amici.amici.Model.html#amici.amici.Model.set_parameter_by_name). Here, we set the model parameter `p1` to a value of `1e-3`."
+   "source": "The model allows the user to manipulate model related properties of simulations. This includes the values of model parameters that can be set by using [amici.Model.set_free_parameter_by_name](https://amici.readthedocs.io/en/latest/generated/amici.amici.Model.html#amici.amici.Model.set_free_parameter_by_name). Here, we set the model parameter `p1` to a value of `1e-3`."
   },
   {
    "cell_type": "code",
    "metadata": {},
-   "source": "model.set_parameter_by_name(\"p1\", 1e-3)",
+   "source": "model.set_free_parameter_by_name(\"p1\", 1e-3)",
    "outputs": [],
    "execution_count": null
   },

python/sdist/amici/adapters/fiddy.py

@@ -153,7 +153,7 @@ def run_amici_simulation(
         point: Type.POINT, order: SensitivityOrder
     ) -> ReturnData:
         problem_parameters = dict(zip(free_parameter_ids, point, strict=True))
-        amici_model.set_parameter_by_id(problem_parameters)
+        amici_model.set_free_parameter_by_id(problem_parameters)
         amici_solver.set_sensitivity_order(order)
         rdata = amici.run_simulation(
             model=amici_model, solver=amici_solver, edata=amici_edata
@@ -198,7 +198,7 @@ def derivative(point: Type.POINT, return_dict: bool = False):
     # Get structure
     dummy_point = fiddy_array(
         [
-            amici_model.get_parameter_by_id(par_id)
+            amici_model.get_free_parameter_by_id(par_id)
             for par_id in free_parameter_ids
         ]
     )

python/sdist/amici/swig_wrappers.py

@@ -181,7 +181,7 @@ def write_solver_settings_to_hdf5(
     ),
     "minimum_sigma_residuals",
     ("n_max_event", "set_n_max_event"),
-    "parameters",
+    "free_parameters",
     "reinitialization_state_idxs",
     "reinitialize_fixed_parameter_initial_states",
     "state_is_non_negative",

python/tests/test_pysb.py

@@ -59,7 +59,7 @@ def test_compare_to_sbml_import(
         # check equilibrium initial parameters
         assert np.isclose(
             sum(rdata["x_ss"][[0, 3, 4, 5]]),
-            model.get_parameter_by_name("PROT_0"),
+            model.get_free_parameter_by_name("PROT_0"),
             atol=1e-6,
             rtol=1e-6,
         ), f"{importer} preequilibration"

tests/sbml/utils.py

@@ -36,7 +36,9 @@ def verify_results(
 
     # collect parameters
     for par in model.get_free_parameter_ids():
-        parameter_data[par] = rdata["ts"] * 0 + model.get_parameter_by_id(par)
+        parameter_data[par] = rdata["ts"] * 0 + model.get_free_parameter_by_id(
+            par
+        )
 
     expression_data = {}