Merge branch 'develop' into release_0_11_7

python/amici/__init__.py

@@ -136,6 +136,22 @@ def _imported_from_setup() -> bool:
 hdf5_enabled = 'readSolverSettingsFromHDF5' in dir()
 
 
+def _get_ptr(obj: Union[AmiciModel, AmiciExpData, AmiciSolver]
+             ) -> Union['amici.Model', 'amici.ExpData', 'amici.Solver']:
+    """
+    Convenience wrapper that returns the smart pointer pointee, if applicable
+
+    :param obj:
+        Potential smart pointer
+
+    :returns:
+        Non-smart pointer
+    """
+    if isinstance(obj, (amici.ModelPtr, amici.ExpDataPtr, amici.SolverPtr)):
+        return obj.get()
+    return obj
+
+
 def runAmiciSimulation(
         model: AmiciModel,
         solver: AmiciSolver,
@@ -159,11 +175,9 @@ def runAmiciSimulation(
         ReturnData object with simulation results
     """
 
-    if edata and isinstance(edata, amici.ExpDataPtr):
-        edata = edata.get()
-
     with capture_cstdout():
-        rdata = amici.runAmiciSimulation(solver.get(), edata, model.get())
+        rdata = amici.runAmiciSimulation(_get_ptr(solver), _get_ptr(edata),
+                                         _get_ptr(model))
     return numpy.ReturnDataView(rdata)
 
 
@@ -177,13 +191,13 @@ def ExpData(*args) -> 'amici.ExpData':
     """
     if isinstance(args[0], ReturnDataView):
         return amici.ExpData(args[0]['ptr'].get(), *args[1:])
-    elif isinstance(args[0], amici.ExpDataPtr):
+    elif isinstance(args[0], (amici.ExpData, amici.ExpDataPtr)):
         # the *args[:1] should be empty, but by the time you read this,
         # the constructor signature may have changed and you are glad this
         # wrapper did not break.
-        return amici.ExpData(args[0].get(), *args[1:])
-    elif isinstance(args[0], amici.ModelPtr):
-        return amici.ExpData(args[0].get())
+        return amici.ExpData(_get_ptr(args[0]), *args[1:])
+    elif isinstance(args[0], (amici.Model, amici.ModelPtr)):
+        return amici.ExpData(_get_ptr(args[0]))
     else:
         return amici.ExpData(*args)
 
@@ -209,9 +223,9 @@ def runAmiciSimulations(
     """
     with capture_cstdout():
         edata_ptr_vector = amici.ExpDataPtrVector(edata_list)
-        rdata_ptr_list = amici.runAmiciSimulations(solver.get(),
+        rdata_ptr_list = amici.runAmiciSimulations(_get_ptr(solver),
                                                    edata_ptr_vector,
-                                                   model.get(),
+                                                   _get_ptr(model),
                                                    failfast,
                                                    num_threads)
     return [numpy.ReturnDataView(r) for r in rdata_ptr_list]
@@ -229,10 +243,7 @@ def readSolverSettingsFromHDF5(
     :param solver: Solver instance to which settings will be transferred
     :param location: location of solver settings in hdf5 file
     """
-    if isinstance(solver, amici.SolverPtr):
-        amici.readSolverSettingsFromHDF5(file, solver.get(), location)
-    else:
-        amici.readSolverSettingsFromHDF5(file, solver, location)
+    amici.readSolverSettingsFromHDF5(file, _get_ptr(solver), location)
 
 
 def writeSolverSettingsToHDF5(
@@ -248,10 +259,7 @@ def writeSolverSettingsToHDF5(
     :param solver: Solver instance from which settings will stored
     :param location: location of solver settings in hdf5 file
     """
-    if isinstance(solver, amici.SolverPtr):
-        amici.writeSolverSettingsToHDF5(solver.get(), file, location)
-    else:
-        amici.writeSolverSettingsToHDF5(solver, file, location)
+    amici.writeSolverSettingsToHDF5(_get_ptr(solver), file, location)
 
 
 class add_path: