Rearranging Cython module into a single shared object

This is necessary to deal with DLL linking limitations on Windows

interfaces/cython/cantera/__init__.py

@@ -1,3 +1 @@
-from .solution import *
-from .constants import *
-from .mixture import *
+from ._cantera import *

interfaces/cython/cantera/_cantera.pxd

@@ -1,5 +1,14 @@
 from libcpp.vector cimport vector
-from utils cimport *
+from libcpp.string cimport string
+
+cdef extern from "cantera/base/xml.h" namespace "Cantera":
+    cdef cppclass XML_Node:
+        XML_Node* findByName(string)
+        XML_Node* findID(string)
+        int nChildren()
+
+cdef extern from "cantera/base/ctml.h" namespace "ctml":
+    XML_Node getCtmlTree(string) except +
 
 cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
     cdef cppclass CxxThermoPhase "Cantera::ThermoPhase":
@@ -11,34 +20,50 @@ cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
         int nSpecies()
         XML_Node& xml()
 
-
 cdef extern from "cantera/kinetics/Kinetics.h" namespace "Cantera":
     cdef cppclass CxxKinetics "Cantera::Kinetics":
         CxxKinetics()
         int nReactions()
 
-
 cdef extern from "cantera/transport/TransportBase.h" namespace "Cantera":
     cdef cppclass CxxTransport "Cantera::Transport":
         CxxTransport(CxxThermoPhase*)
         double viscosity() except +
 
+cdef extern from "cantera/transport/DustyGasTransport.h" namespace "Cantera":
+    cdef cppclass CxxDustyGasTransport "Cantera::DustyGasTransport":
+        void setPorosity(double) except +
+
+
+cdef extern from "cantera/equil/MultiPhase.h" namespace "Cantera":
+    cdef cppclass CxxMultiPhase "Cantera::MultiPhase":
+        CxxMultiPhase()
+        void addPhase(CxxThermoPhase*, double) except +
+        void init() except +
+        double nSpecies()
+        void setTemperature(double)
+        double temperature()
+        void setPressure(double)
+        double pressure()
 
 cdef extern from "cantera/thermo/ThermoFactory.h" namespace "Cantera":
     cdef CxxThermoPhase* newPhase(string, string) except +
     cdef CxxThermoPhase* newPhase(XML_Node&) except +
 
-
 cdef extern from "cantera/kinetics/KineticsFactory.h" namespace "Cantera":
     cdef CxxKinetics* newKineticsMgr(XML_Node&, vector[CxxThermoPhase*]) except +
 
-
 cdef extern from "cantera/transport/TransportFactory.h" namespace "Cantera":
     cdef CxxTransport* newDefaultTransportMgr(CxxThermoPhase*) except +
     cdef CxxTransport* newTransportMgr(string, CxxThermoPhase*) except +
 
+cdef string stringify(x)
 
 cdef class _SolutionBase:
     cdef CxxThermoPhase* thermo
     cdef CxxKinetics* kinetics
     cdef CxxTransport* transport
+
+cdef class Mixture:
+    cdef CxxMultiPhase* mix
+    cdef list _phases

interfaces/cython/cantera/_cantera.pyx

@@ -0,0 +1,17 @@
+import numpy as np
+cimport numpy as np
+
+from cython.operator cimport dereference as deref
+
+from _cantera cimport *
+
+include "utils.pyx"
+include "constants.pyx"
+
+include "base.pyx"
+include "thermo.pyx"
+include "kinetics.pyx"
+include "transport.pyx"
+include "composite.pyx"
+
+include "mixture.pyx"

interfaces/cython/cantera/base.pyx

@@ -0,0 +1,38 @@
+cdef class _SolutionBase:
+    def __cinit__(self, infile, phaseid=''):
+        rootNode = getCtmlTree(stringify(infile))
+
+        # Get XML data
+        cdef XML_Node* phaseNode
+        if phaseid:
+            phaseNode = rootNode.findID(stringify(phaseid))
+        else:
+            phaseNode = rootNode.findByName(stringify('phase'))
+        if phaseNode is NULL:
+            raise ValueError("Couldn't read phase node from XML file")
+
+        # Thermo
+        if isinstance(self, ThermoPhase):
+            self.thermo = newPhase(deref(phaseNode))
+        else:
+            self.thermo = NULL
+
+        # Kinetics
+        cdef vector[CxxThermoPhase*] v
+
+        if isinstance(self, Kinetics):
+            v.push_back(self.thermo)
+            self.kinetics = newKineticsMgr(deref(phaseNode), v)
+        else:
+            self.kinetics = NULL
+
+        # Transport
+        if isinstance(self, Transport):
+            self.transport = newDefaultTransportMgr(self.thermo)
+        else:
+            self.transport = NULL
+
+    def __dealloc__(self):
+        del self.thermo
+        del self.kinetics
+        del self.transport

interfaces/cython/cantera/composite.pyx

@@ -0,0 +1,4 @@
+class Solution(ThermoPhase, Kinetics, Transport):
+    def __init__(self, *args, **kwars):
+        pass
+

interfaces/cython/cantera/kinetics.pyx

@@ -0,0 +1,4 @@
+cdef class Kinetics(_SolutionBase):
+    property nReactions:
+        def __get__(self):
+            return self.kinetics.nReactions()

interfaces/cython/cantera/mixture.pxd

@@ -1,16 +0,0 @@
-from solution cimport *
-
-cdef extern from "cantera/equil/MultiPhase.h" namespace "Cantera":
-    cdef cppclass CxxMultiPhase "Cantera::MultiPhase":
-        CxxMultiPhase()
-        void addPhase(CxxThermoPhase*, double) except +
-        void init() except +
-        double nSpecies()
-        void setTemperature(double)
-        double temperature()
-        void setPressure(double)
-        double pressure()
-
-cdef class Mixture:
-    cdef CxxMultiPhase* mix
-    cdef list _phases

interfaces/cython/cantera/mixture.pyx

@@ -1,5 +1,3 @@
-from mixture cimport *
-
 cdef class Mixture:
     def __cinit__(self, phases):
         self.mix = new CxxMultiPhase()

interfaces/cython/cantera/substance.pyx

@@ -1,88 +0,0 @@
-import numpy as np
-cimport numpy as np
-
-from cython.operator cimport dereference as deref
-
-from utils cimport *
-
-cdef class _SolutionBase:
-    def __cinit__(self, infile, phaseid=''):
-        rootNode = getCtmlTree(stringify(infile))
-
-        # Get XML data
-        cdef XML_Node* phaseNode
-        if phaseid:
-            phaseNode = rootNode.findID(stringify(phaseid))
-        else:
-            phaseNode = rootNode.findByName(stringify('phase'))
-        if phaseNode is NULL:
-            raise ValueError("Couldn't read phase node from XML file")
-
-        # Thermo
-        if isinstance(self, ThermoPhase):
-            self.thermo = newPhase(deref(phaseNode))
-        else:
-            self.thermo = NULL
-
-        # Kinetics
-        cdef vector[CxxThermoPhase*] v
-
-        if isinstance(self, Kinetics):
-            v.push_back(self.thermo)
-            self.kinetics = newKineticsMgr(deref(phaseNode), v)
-        else:
-            self.kinetics = NULL
-
-        # Transport
-        if isinstance(self, Transport):
-            self.transport = newDefaultTransportMgr(self.thermo)
-        else:
-            self.transport = NULL
-
-    def __dealloc__(self):
-        del self.thermo
-        del self.kinetics
-        del self.transport
-
-
-cdef class ThermoPhase(_SolutionBase):
-    property nSpecies:
-        def __get__(self):
-            return self.thermo.nSpecies()
-
-    property pressure:
-        def __get__(self):
-            return self.thermo.pressure()
-
-    property temperature:
-        def __get__(self):
-            return self.thermo.temperature()
-
-    def setMoleFractions(self, X):
-        if len(X) != self.nSpecies:
-            raise ValueError("Mole fraction array has incorrect length")
-        cdef np.ndarray[np.double_t, ndim=1] X_c = np.ascontiguousarray(X, dtype=np.double)
-        self.thermo.setMoleFractions(&X_c[0])
-
-    property massFractions:
-        def __get__(self):
-            cdef np.ndarray[np.double_t, ndim=1] X_c = np.empty(self.nSpecies)
-            self.thermo.getMassFractions(&X_c[0])
-            return X_c
-
-
-cdef class Kinetics(_SolutionBase):
-    property nReactions:
-        def __get__(self):
-            return self.kinetics.nReactions()
-
-
-cdef class Transport(_SolutionBase):
-    property viscosity:
-        def __get__(self):
-            return self.transport.viscosity()
-
-
-class Solution(ThermoPhase, Kinetics, Transport):
-    def __init__(self, *args, **kwars):
-        pass

interfaces/cython/cantera/thermo.pyx

@@ -0,0 +1,24 @@
+cdef class ThermoPhase(_SolutionBase):
+    property nSpecies:
+        def __get__(self):
+            return self.thermo.nSpecies()
+
+    property pressure:
+        def __get__(self):
+            return self.thermo.pressure()
+
+    property temperature:
+        def __get__(self):
+            return self.thermo.temperature()
+
+    def setMoleFractions(self, X):
+        if len(X) != self.nSpecies:
+            raise ValueError("Mole fraction array has incorrect length")
+        cdef np.ndarray[np.double_t, ndim=1] X_c = np.ascontiguousarray(X, dtype=np.double)
+        self.thermo.setMoleFractions(&X_c[0])
+
+    property massFractions:
+        def __get__(self):
+            cdef np.ndarray[np.double_t, ndim=1] X_c = np.empty(self.nSpecies)
+            self.thermo.getMassFractions(&X_c[0])
+            return X_c

interfaces/cython/cantera/transport.pyx

@@ -0,0 +1,4 @@
+cdef class Transport(_SolutionBase):
+    property viscosity:
+        def __get__(self):
+            return self.transport.viscosity()

interfaces/cython/cantera/utils.pxd

@@ -1,14 +0,0 @@
-from libcpp.string cimport string
-
-cdef extern from "cantera/base/xml.h" namespace "Cantera":
-    cdef cppclass XML_Node:
-        XML_Node* findByName(string)
-        XML_Node* findID(string)
-        int nChildren()
-
-
-cdef extern from "cantera/base/ctml.h" namespace "ctml":
-    XML_Node getCtmlTree(string) except +
-
-
-cdef string stringify(x)

interfaces/cython/cantera/utils.pyx

@@ -1,5 +1,3 @@
-from utils cimport *
-
 cdef string stringify(x):
     """ Converts Python strings to std::string. """
     # This method works with both Python 2.x and 3.x.

interfaces/cython/setup.py.in

@@ -9,21 +9,14 @@ if os.name == 'nt':
 else:
     dataFiles.append('libcantera_shared.so')
 
-exts = []
-
-def addExtension(name):
-    exts.append(Extension("cantera.%s" % name,
-                          ["cantera/%s.pyx" % name],
-                          include_dirs=@py_include_dirs@,
-                          language="c++",
-                          libraries=@py_cantera_libs@,
-                          library_dirs=@py_libdirs@,
-                          extra_link_args=@py_extra_link_args@))
-
-addExtension('solution')
-addExtension('mixture')
-addExtension('utils')
-addExtension('constants')
+exts = [Extension("cantera._cantera",
+                  ["cantera/_cantera.pyx"],
+                  include_dirs=@py_include_dirs@,
+                  language="c++",
+                  libraries=@py_cantera_libs@,
+                  library_dirs=@py_libdirs@,
+                  extra_compile_args=@py_extra_compiler_args@,
+                  extra_link_args=@py_extra_link_args@)]
 
 setup(name="Cantera",
       version="@cantera_version@",

src/python/SConscript

@@ -117,13 +117,15 @@ libDirs = ('../../build/lib', localenv['sundials_libdir'],
            localenv['boost_lib_dir'])
 
 localenv['py_include_dirs'] = repr([x for x in incDirs if x])
-localenv['py_cantera_libs'] = repr(localenv['cantera_shared_libs'])
+localenv['py_cantera_libs'] = repr(localenv['cantera_libs'])
 localenv['py_libdirs'] = repr([x for x in libDirs if x])
 
 if localenv['CC'] == 'cl':
     localenv['py_extra_link_args'] = repr([])
+    localenv['py_extra_compiler_args'] = repr(['/EHsc'])
 else:
     localenv['py_extra_link_args'] = repr(['-Wl,-rpath=$$ORIGIN'])
+    localenv['py_extra_compiler_args'] = repr([])
 
 make_setup = localenv.SubstFile('#interfaces/cython/setup.py',
                                 '#interfaces/cython/setup.py.in')