[Python] Fix derived pointer initialization for Jacobians

Author: speth

interfaces/cython/cantera/jacobians.pxd

@@ -46,20 +46,16 @@ cdef extern from "cantera/numerics/SystemJacobianFactory.h" namespace "Cantera":
 cdef class SystemJacobian:
     @staticmethod
     cdef wrap(shared_ptr[CxxSystemJacobian])
-    cdef set_cxx_object(self)
     cdef shared_ptr[CxxSystemJacobian] _base
 
 cdef class EigenSparseJacobian(SystemJacobian):
-    cdef set_cxx_object(self)
     cdef CxxEigenSparseJacobian* sparse_jac
 
 cdef class EigenSparseDirectJacobian(EigenSparseJacobian):
     pass
 
 cdef class AdaptivePreconditioner(EigenSparseJacobian):
-    cdef set_cxx_object(self)
     cdef CxxAdaptivePreconditioner* adaptive
 
 cdef class BandedJacobian(SystemJacobian):
-    cdef set_cxx_object(self)
     cdef CxxMultiJac* band_jac

interfaces/cython/cantera/jacobians.pyx

@@ -48,7 +48,7 @@ cdef class SystemJacobian:
         jac.set_cxx_object()
         return jac
 
-    cdef set_cxx_object(self):
+    def set_cxx_object(self):
         pass
 
     property side:
@@ -67,10 +67,10 @@ cdef class SystemJacobian:
         """ Get/Set the value of gamma used in the expression P = (I - gamma * J).
         """
         def __get__(self):
-            return self.pbase.get().gamma()
+            return self._base.get().gamma()
 
         def __set__(self, value):
-            self.pbase.get().setGamma(value)
+            self._base.get().setGamma(value)
 
 
 cdef class EigenSparseJacobian(SystemJacobian):
@@ -81,7 +81,8 @@ cdef class EigenSparseJacobian(SystemJacobian):
 
     _type = "eigen-sparse"
 
-    cdef set_cxx_object(self):
+    def set_cxx_object(self):
+        super().set_cxx_object()
         self.sparse_jac = <CxxEigenSparseJacobian*>self._base.get()
 
     def print_contents(self):
@@ -117,7 +118,8 @@ cdef class AdaptivePreconditioner(EigenSparseJacobian):
     _type = "Adaptive"
     linear_solver_type = "GMRES"
 
-    cdef set_cxx_object(self):
+    def set_cxx_object(self):
+        super().set_cxx_object()
         self.adaptive = <CxxAdaptivePreconditioner*>self._base.get()
 
     property threshold:
@@ -188,5 +190,6 @@ cdef class BandedJacobian(SystemJacobian):
     _type = "banded-direct"
     linear_solver_type = "direct"
 
-    cdef set_cxx_object(self):
+    def set_cxx_object(self):
+        super().set_cxx_object()
         self.band_jac = <CxxMultiJac*>self._base.get()