Respect ExpData settings in gradient checks

python/sdist/amici/gradient_check.py

@@ -66,20 +66,29 @@ def check_finite_difference(
         finite difference step-size
 
     """
+    p = copy.deepcopy(x0)
+    plist = [ip]
+
+    # store original settings and apply new ones
     og_sensitivity_order = solver.get_sensitivity_order()
     og_parameters = model.get_parameters()
     og_plist = model.get_parameter_list()
     if edata:
         og_eplist = edata.plist
+        og_eparameters = edata.parameters
 
-    # sensitivity
-    p = copy.deepcopy(x0)
-    plist = [ip]
+        edata.plist = plist
+        # we always set parameters via the model below
+        edata.parameters = []
+        pscale = (
+            edata.pscale if len(edata.pscale) else model.get_parameter_scale()
+        )
+    else:
+        pscale = model.get_parameter_scale()
+        model.set_parameter_list(plist)
 
+    model.set_parameter_scale(pscale)
     model.set_parameters(p)
-    model.set_parameter_list(plist)
-    if edata:
-        edata.plist = plist
 
     # simulation with gradient
     if int(og_sensitivity_order) < int(SensitivityOrder.first):
@@ -93,8 +102,7 @@ def check_finite_difference(
 
     pf = copy.deepcopy(x0)
     pb = copy.deepcopy(x0)
-    pscale = model.get_parameter_scale()[ip]
-    if x0[ip] == 0 or pscale != int(ParameterScaling.none):
+    if x0[ip] == 0 or pscale[ip] != int(ParameterScaling.none):
         pf[ip] += epsilon / 2
         pb[ip] -= epsilon / 2
     else:
@@ -142,6 +150,7 @@ def check_finite_difference(
     model.set_parameter_list(og_plist)
     if edata:
         edata.plist = og_eplist
+        edata.parameters = og_eparameters
 
 
 def check_derivatives(
@@ -160,7 +169,8 @@ def check_derivatives(
 
     :param model: amici model
     :param solver: amici solver
-    :param edata: exp data
+    :param edata: ExpData instance. If provided, ExpData settings will
+        override model settings where applicable (`plist`, `parmeters`, ...).
     :param atol: absolute tolerance for comparison
     :param rtol: relative tolerance for comparison
     :param epsilon: finite difference step-size
@@ -169,7 +179,10 @@ def check_derivatives(
         are zero
     :param skip_fields: list of fields to skip
     """
-    p = np.array(model.get_parameters())
+    if edata and edata.parameters:
+        p = np.array(edata.parameters)
+    else:
+        p = np.array(model.get_parameters())
 
     og_sens_order = solver.get_sensitivity_order()
 

tests/petab_test_suite/test_petab_suite.py

@@ -203,12 +203,6 @@ def check_derivatives(
         petab_problem=problem,
         problem_parameters=problem_parameters,
     ):
-        # check_derivatives does currently not support parameters in ExpData
-        # set parameter scales before setting parameter values!
-        model.set_parameter_scale(edata.pscale)
-        model.set_parameters(edata.parameters)
-        edata.parameters = []
-        edata.pscale = amici.parameter_scaling_from_int_vector([])
         amici_check_derivatives(model, solver, edata)