[Python] Added "slicing" support to Solution

Slicing a Solution object (with the [] operator) creates a view where all
species-specific properties are returned for the specified subset of the
species.

interfaces/cython/cantera/_cantera.pxd

@@ -1,6 +1,10 @@
 from libcpp.vector cimport vector
 from libcpp.string cimport string
 from libcpp cimport bool as cbool
+from cpython cimport bool as pybool
+
+import numpy as np
+cimport numpy as np
 
 cdef extern from "cantera/base/xml.h" namespace "Cantera":
     cdef cppclass XML_Node:
@@ -271,6 +275,8 @@ cdef class _SolutionBase:
     cdef CxxKinetics* kinetics
     cdef CxxTransport* transport
     cdef int thermoBasis
+    cdef np.ndarray _selectedSpecies
+    cdef object parent
 
 cdef class Mixture:
     cdef CxxMultiPhase* mix

interfaces/cython/cantera/base.pyx

@@ -1,5 +1,23 @@
 cdef class _SolutionBase:
-    def __cinit__(self, infile, phaseid='', phases=()):
+    def __cinit__(self, infile='', phaseid='', phases=(), source=None):
+        # Shallow copy of an existing Solution (for slicing support)
+        cdef _SolutionBase other
+        if source is not None:
+            other = <_SolutionBase?>source
+
+            # keep a reference to the parent to prevent the underlying
+            # C++ objects from being deleted
+            self.parent = other
+
+            self.thermo = other.thermo
+            self.kinetics = other.kinetics
+            self.transport = other.transport
+
+            self.thermoBasis = other.thermoBasis
+            self._selectedSpecies = other._selectedSpecies.copy()
+            return
+
+        # Instantiate a set of new Cantera C++ objects
         rootNode = getCtmlTree(stringify(infile))
 
         # Get XML data
@@ -33,11 +51,34 @@ cdef class _SolutionBase:
         # Initialization of transport is deferred to Transport.__init__
         self.transport = NULL
 
+        self._selectedSpecies = np.ndarray(0, dtype=np.integer)
+
     def __init__(self, *args, **kwargs):
         if isinstance(self, Transport):
             assert self.transport is not NULL
 
+    def __getitem__(self, selection):
+        copy = self.__class__(source=self)
+        if isinstance(selection, slice):
+            selection = range(selection.start or 0,
+                              selection.stop or self.nSpecies,
+                              selection.step or 1)
+        copy.selectedSpecies = selection
+        return copy
+
+    property selectedSpecies:
+        def __get__(self):
+            return list(self._selectedSpecies)
+        def __set__(self, species):
+            if isinstance(species, (str, int)):
+                species = (species,)
+            self._selectedSpecies.resize(len(species))
+            for i,spec in enumerate(species):
+                self._selectedSpecies[i] = self.speciesIndex(spec)
+
     def __dealloc__(self):
-        del self.thermo
-        del self.kinetics
-        del self.transport
+        # only delete the C++ objects if this is the parent object
+        if self.parent is None:
+            del self.thermo
+            del self.kinetics
+            del self.transport

interfaces/cython/cantera/thermo.pyx

@@ -7,7 +7,8 @@ ctypedef void (*thermoMethod1d)(CxxThermoPhase*, double*) except +
 cdef class ThermoPhase(_SolutionBase):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.thermoBasis = massBasis
+        if 'source' not in kwargs:
+            self.thermoBasis = massBasis
 
     def report(self, show_thermo=True):
         return pystr(self.thermo.report(bool(show_thermo)))
@@ -85,7 +86,11 @@ cdef class ThermoPhase(_SolutionBase):
 
     property speciesNames:
         def __get__(self):
-            return [self.speciesName(k) for k in range(self.nSpecies)]
+            if self._selectedSpecies.size:
+                indices = self._selectedSpecies
+            else:
+                indices = range(self.nSpecies)
+            return [self.speciesName(k) for k in indices]
 
     cpdef int speciesIndex(self, species) except *:
         if isinstance(species, str):
@@ -107,7 +112,10 @@ cdef class ThermoPhase(_SolutionBase):
     cdef np.ndarray _getArray1(self, thermoMethod1d method):
         cdef np.ndarray[np.double_t, ndim=1] data = np.empty(self.nSpecies)
         method(self.thermo, &data[0])
-        return data
+        if self._selectedSpecies.size:
+            return data[self._selectedSpecies]
+        else:
+            return data
 
     cdef void _setArray1(self, thermoMethod1d method, values) except *:
         if len(values) != self.nSpecies:
@@ -121,9 +129,6 @@ cdef class ThermoPhase(_SolutionBase):
         def __get__(self):
             return self._getArray1(thermo_getMolecularWeights)
 
-    def molecularWeight(self, species):
-        return self.thermo.molecularWeight(self.speciesIndex(species))
-
     property meanMolecularWeight:
         def __get__(self):
             return self.thermo.meanMolecularWeight()
@@ -137,9 +142,6 @@ cdef class ThermoPhase(_SolutionBase):
             else:
                 self._setArray1(thermo_setMassFractions, Y)
 
-    def massFraction(self, species):
-        return self.thermo.massFraction(self.speciesIndex(species))
-
     property X:
         def __get__(self):
             return self._getArray1(thermo_getMoleFractions)
@@ -149,18 +151,12 @@ cdef class ThermoPhase(_SolutionBase):
             else:
                 self._setArray1(thermo_setMoleFractions, X)
 
-    def moleFraction(self, species):
-        return self.thermo.moleFraction(self.speciesIndex(species))
-
     property concentrations:
         def __get__(self):
             return self._getArray1(thermo_getConcentrations)
         def __set__(self, C):
             self._setArray1(thermo_setConcentrations, C)
 
-    def concentration(self, species):
-        return self.thermo.concentration(self.speciesIndex(species))
-
     ######## Read-only thermodynamic properties ########
 
     property P: