[Cython] Improve support for building derived Cython modules

The .pxd file now contains declarations for all of the cdef classes,
and is installed with the module.

interfaces/cython/cantera/_cantera.pxd

@@ -564,6 +564,8 @@ cdef extern from "wrappers.h":
 
 cdef string stringify(x)
 
+ctypedef void (*thermoMethod1d)(CxxThermoPhase*, double*) except +
+
 cdef class _SolutionBase:
     cdef CxxThermoPhase* thermo
     cdef CxxKinetics* kinetics
@@ -572,9 +574,28 @@ cdef class _SolutionBase:
     cdef np.ndarray _selected_species
     cdef object parent
 
+cdef class ThermoPhase(_SolutionBase):
+    cdef double _mass_factor(self)
+    cdef double _mole_factor(self)
+    cpdef int element_index(self, element) except *
+    cpdef int species_index(self, species) except *
+    cdef np.ndarray _getArray1(self, thermoMethod1d method)
+    cdef void _setArray1(self, thermoMethod1d method, values) except *
+
+cdef class InterfacePhase(ThermoPhase):
+    cdef CxxSurfPhase* surf
+
 cdef class Kinetics(_SolutionBase):
     pass
 
+cdef class InterfaceKinetics(Kinetics):
+    pass
+
+cdef class Mixture:
+    cdef CxxMultiPhase* mix
+    cdef list _phases
+    cpdef int element_index(self, element) except *
+
 cdef class Func1:
     cdef CxxFunc1* func
     cdef object callable
@@ -591,6 +612,21 @@ cdef class Reactor(ReactorBase):
     cdef CxxReactor* reactor
     cdef object _kinetics
 
+cdef class Reservoir(ReactorBase):
+    pass
+
+cdef class ConstPressureReactor(Reactor):
+    pass
+
+cdef class IdealGasReactor(Reactor):
+    pass
+
+cdef class IdealGasConstPressureReactor(Reactor):
+    pass
+
+cdef class FlowReactor(Reactor):
+    pass
+
 cdef class WallSurface:
     cdef CxxWall* cxxwall
     cdef object wall
@@ -613,3 +649,65 @@ cdef class FlowDevice:
     cdef str name
     cdef ReactorBase _upstream
     cdef ReactorBase _downstream
+
+cdef class MassFlowController(FlowDevice):
+    pass
+
+cdef class Valve(FlowDevice):
+    pass
+
+cdef class PressureController(FlowDevice):
+    pass
+
+cdef class ReactorNet:
+    cdef CxxReactorNet net
+    cdef list _reactors
+
+cdef class Domain1D:
+    cdef CxxDomain1D* domain
+
+cdef class Boundary1D(Domain1D):
+    cdef CxxBdry1D* boundary
+    cdef _SolutionBase phase
+
+cdef class Inlet1D(Boundary1D):
+    cdef CxxInlet1D* inlet
+
+cdef class Outlet1D(Boundary1D):
+    cdef CxxOutlet1D* outlet
+
+cdef class OutletReservoir1D(Boundary1D):
+    cdef CxxOutletRes1D* outlet
+
+cdef class SymmetryPlane1D(Boundary1D):
+    cdef CxxSymm1D* symm
+
+cdef class Surface1D(Boundary1D):
+    cdef CxxSurf1D* surf
+
+cdef class ReactingSurface1D(Boundary1D):
+    cdef CxxReactingSurf1D* surf
+
+cdef class _FlowBase(Domain1D):
+    cdef CxxStFlow* flow
+    cdef _SolutionBase gas
+
+cdef class FreeFlow(_FlowBase):
+    pass
+
+cdef class AxisymmetricStagnationFlow(_FlowBase):
+    pass
+
+cdef class Sim1D:
+    cdef CxxSim1D* sim
+    cdef readonly object domains
+    cdef object _initialized
+    cdef Func1 interrupt
+
+cdef class ReactionPathDiagram:
+    cdef CxxReactionPathDiagram diagram
+    cdef CxxReactionPathBuilder builder
+    cdef Kinetics kinetics
+    cdef str element
+    cdef pybool built
+    cdef CxxStringStream _log

interfaces/cython/cantera/mixture.pyx

@@ -27,10 +27,6 @@ cdef class Mixture:
     Each one stores its own state information locally, and synchronizes the
     phases objects whenever it requires phase properties.
     """
-
-    cdef CxxMultiPhase* mix
-    cdef list _phases
-
     def __cinit__(self, phases):
         self.mix = new CxxMultiPhase()
         self._phases = []

interfaces/cython/cantera/onedim.pyx

@@ -8,7 +8,6 @@ except ImportError:
     from scipy.special import erf
 
 cdef class Domain1D:
-    cdef CxxDomain1D* domain
     def __cinit__(self, *args, **kwargs):
         self.domain = NULL
 
@@ -169,9 +168,6 @@ cdef class Boundary1D(Domain1D):
     :param phase:
         The (gas) phase corresponding to the adjacent flow domain
     """
-    cdef CxxBdry1D* boundary
-    cdef _SolutionBase phase
-
     def __cinit__(self, *args, **kwargs):
         self.boundary = NULL
 
@@ -238,7 +234,6 @@ cdef class Inlet1D(Boundary1D):
     domain - it must be either the leftmost or rightmost domain in a
     stack.
     """
-    cdef CxxInlet1D* inlet
     def __cinit__(self, *args, **kwargs):
         self.inlet = new CxxInlet1D()
         self.boundary = <CxxBdry1D*>(self.inlet)
@@ -258,7 +253,6 @@ cdef class Outlet1D(Boundary1D):
     A one-dimensional outlet. An outlet imposes a zero-gradient boundary
     condition on the flow.
     """
-    cdef CxxOutlet1D* outlet
     def __cinit__(self, *args, **kwargs):
         self.outlet = new CxxOutlet1D()
         self.boundary = <CxxBdry1D*>(self.outlet)
@@ -271,7 +265,6 @@ cdef class OutletReservoir1D(Boundary1D):
     """
     A one-dimensional outlet into a reservoir.
     """
-    cdef CxxOutletRes1D* outlet
     def __cinit__(self, *args, **kwargs):
         self.outlet = new CxxOutletRes1D()
         self.boundary = <CxxBdry1D*>(self.outlet)
@@ -282,7 +275,6 @@ cdef class OutletReservoir1D(Boundary1D):
 
 cdef class SymmetryPlane1D(Boundary1D):
     """A symmetry plane."""
-    cdef CxxSymm1D* symm
     def __cinit__(self, *args, **kwargs):
         self.symm = new CxxSymm1D()
         self.boundary = <CxxBdry1D*>(self.symm)
@@ -293,7 +285,6 @@ cdef class SymmetryPlane1D(Boundary1D):
 
 cdef class Surface1D(Boundary1D):
     """A solid surface."""
-    cdef CxxSurf1D* surf
     def __cinit__(self, *args, **kwargs):
         self.surf = new CxxSurf1D()
         self.boundary = <CxxBdry1D*>(self.surf)
@@ -304,7 +295,6 @@ cdef class Surface1D(Boundary1D):
 
 cdef class ReactingSurface1D(Boundary1D):
     """A reacting solid surface."""
-    cdef CxxReactingSurf1D* surf
     def __cinit__(self, *args, **kwargs):
         self.surf = new CxxReactingSurf1D()
         self.boundary = <CxxBdry1D*>(self.surf)
@@ -328,8 +318,6 @@ cdef class ReactingSurface1D(Boundary1D):
 
 cdef class _FlowBase(Domain1D):
     """ Base class for 1D flow domains """
-    cdef CxxStFlow* flow
-    cdef _SolutionBase gas
     def __cinit__(self, *args, **kwargs):
         self.flow = NULL
 
@@ -451,11 +439,6 @@ cdef class Sim1D:
 
     Domains are ordered left-to-right, with domain number 0 at the left.
     """
-    cdef CxxSim1D* sim
-    cdef readonly object domains
-    cdef object _initialized
-    cdef Func1 interrupt
-
     def __cinit__(self, *args, **kwargs):
         self.sim = NULL
 

interfaces/cython/cantera/reactionpath.pyx

@@ -1,11 +1,4 @@
 cdef class ReactionPathDiagram:
-    cdef CxxReactionPathDiagram diagram
-    cdef CxxReactionPathBuilder builder
-    cdef Kinetics kinetics
-    cdef str element
-    cdef pybool built
-    cdef CxxStringStream _log
-
     def __init__(self, Kinetics kin, str element):
         """
         Create a reaction path diagram for the fluxes of the element *element*

interfaces/cython/cantera/reactor.pyx

@@ -712,9 +712,6 @@ cdef class ReactorNet:
     >>> reactor_network = ReactorNet([r1, r2])
     >>> reactor_network.advance(time)
     """
-    cdef CxxReactorNet net
-    cdef list _reactors
-
     def __init__(self, reactors=()):
         self._reactors = []  # prevents premature garbage collection
         for R in reactors:

interfaces/cython/cantera/thermo.pyx

@@ -2,8 +2,6 @@ cdef enum Thermasis:
     mass_basis = 0
     molar_basis = 1
 
-ctypedef void (*thermoMethod1d)(CxxThermoPhase*, double*) except +
-
 cdef class ThermoPhase(_SolutionBase):
     """
     A phase with an equation of state.
@@ -814,7 +812,6 @@ cdef class ThermoPhase(_SolutionBase):
 
 cdef class InterfacePhase(ThermoPhase):
     """ A class representing a surface or edge phase"""
-    cdef CxxSurfPhase* surf
     def __cinit__(self, *args, **kwargs):
         if self.thermo.eosType() not in (thermo_type_surf, thermo_type_edge):
             raise TypeError('Underlying ThermoPhase object is of the wrong type.')

interfaces/cython/setup.py.in

@@ -61,4 +61,5 @@ setup(name="Cantera",
       ext_modules = exts,
       package_data = {'cantera.data': ['*.*'],
                       'cantera.test.data': ['*.*'],
-                      'cantera.examples': ['*/*.*']})
+                      'cantera.examples': ['*/*.*'],
+                      'cantera': ['*.pxd']})