[Python] Add ability to instantiate objects from YAML files

interfaces/cython/cantera/_cantera.pxd

@@ -5,6 +5,7 @@
 from libcpp.vector cimport vector
 from libcpp.string cimport string
 from libcpp.map cimport map as stdmap
+from libcpp.unordered_map cimport unordered_map
 from libcpp.pair cimport pair
 from libcpp cimport bool as cbool
 from cpython cimport bool as pybool
@@ -43,6 +44,21 @@ cdef extern from "cantera/base/xml.h" namespace "Cantera":
         XML_Node* findID(string)
         int nChildren()
 
+cdef extern from "cantera/base/AnyMap.h" namespace "Cantera":
+    cdef cppclass CxxAnyValue "Cantera::AnyValue"
+
+    cdef cppclass CxxAnyMap "Cantera::AnyMap":
+        CxxAnyMap()
+        CxxAnyValue& operator[](string) except +translate_exception
+        string keys_str()
+
+    cdef cppclass CxxAnyValue "Cantera::AnyValue":
+        CxxAnyValue()
+        unordered_map[string, CxxAnyMap*] asMap(string) except +translate_exception
+
+    CxxAnyMap AnyMapFromYamlFile "Cantera::AnyMap::fromYamlFile" (string) except +translate_exception
+    CxxAnyMap AnyMapFromYamlString "Cantera::AnyMap::fromYamlString" (string) except +translate_exception
+
 cdef extern from "cantera/base/stringUtils.h" namespace "Cantera":
     cdef Composition parseCompString(string) except +translate_exception
 
@@ -610,10 +626,12 @@ cdef extern from "cantera/zerodim.h" namespace "Cantera":
 cdef extern from "cantera/thermo/ThermoFactory.h" namespace "Cantera":
     cdef CxxThermoPhase* newPhase(string, string) except +translate_exception
     cdef CxxThermoPhase* newPhase(XML_Node&) except +translate_exception
+    cdef shared_ptr[CxxThermoPhase] newPhase(CxxAnyMap&, CxxAnyMap&) except +translate_exception
     cdef CxxThermoPhase* newThermoPhase(string) except +translate_exception
 
 cdef extern from "cantera/kinetics/KineticsFactory.h" namespace "Cantera":
     cdef CxxKinetics* newKineticsMgr(XML_Node&, vector[CxxThermoPhase*]) except +translate_exception
+    cdef shared_ptr[CxxKinetics] newKinetics(vector[CxxThermoPhase*], CxxAnyMap&, CxxAnyMap&) except +translate_exception
     cdef CxxKinetics* CxxNewKinetics "Cantera::newKineticsMgr" (string) except +translate_exception
 
 cdef extern from "cantera/transport/TransportFactory.h" namespace "Cantera":

interfaces/cython/cantera/base.pyx

@@ -3,8 +3,8 @@
 
 cdef class _SolutionBase:
     def __cinit__(self, infile='', phaseid='', phases=(), origin=None,
-                  source=None, thermo=None, species=(), kinetics=None,
-                  reactions=(), **kwargs):
+                  source=None, yaml=None, thermo=None, species=(),
+                  kinetics=None, reactions=(), **kwargs):
         # Shallow copy of an existing Solution (for slicing support)
         cdef _SolutionBase other
         if origin is not None:
@@ -21,7 +21,9 @@ cdef class _SolutionBase:
             self._selected_species = other._selected_species.copy()
             return
 
-        if infile or source:
+        if infile.endswith('.yml') or infile.endswith('.yaml') or yaml:
+            self._init_yaml(infile, phaseid, phases, yaml)
+        elif infile or source:
             self._init_cti_xml(infile, phaseid, phases, source)
         elif thermo and species:
             self._init_parts(thermo, species, kinetics, phases, reactions)
@@ -37,6 +39,55 @@ cdef class _SolutionBase:
         if isinstance(self, Transport):
             assert self.transport is not NULL
 
+    def _init_yaml(self, infile, phaseid, phases, source):
+        """
+        Instantiate a set of new Cantera C++ objects from a YAML
+        phase definition
+        """
+        cdef CxxAnyMap root
+        if infile:
+            root = AnyMapFromYamlFile(stringify(infile))
+        elif source:
+            root = AnyMapFromYamlString(stringify(source))
+
+        phaseNodes = root[stringify("phases")].asMap(stringify("name"))
+        phaseNames = []
+        for item in phaseNodes:
+            phaseNames.append(pystr(item.first))
+
+        if not phaseNames:
+            raise ValueError("YAML document doesn't contain any phase definitions")
+
+        if phaseid:
+            if phaseid in phaseNames:
+                phaseNode = phaseNodes[stringify(phaseid)]
+            else:
+                raise ValueError("YAML document doesn't contain"
+                    " a phase named '{}'".format(phaseid))
+        else:
+            phaseNode = phaseNodes[stringify(phaseNames[0])]
+
+        # Thermo
+        if isinstance(self, ThermoPhase):
+            self._thermo = newPhase(deref(phaseNode), root)
+            self.thermo = self._thermo.get()
+        else:
+            self.thermo = NULL
+
+        # Kinetics
+        cdef vector[CxxThermoPhase*] v
+        cdef _SolutionBase phase
+
+        if isinstance(self, Kinetics):
+            v.push_back(self.thermo)
+            for phase in phases:
+                # adjacent bulk phases for a surface phase
+                v.push_back(phase.thermo)
+            self._kinetics = newKinetics(v, deref(phaseNode), root)
+            self.kinetics = self._kinetics.get()
+        else:
+            self.kinetics = NULL
+
     def _init_cti_xml(self, infile, phaseid, phases, source):
         """
         Instantiate a set of new Cantera C++ objects from a CTI or XML

interfaces/cython/cantera/test/test_thermo.py

@@ -919,6 +919,18 @@ ideal_gas(name='spam', elements='O H',
         with self.assertRaisesRegex(ct.CanteraError, 'reaction is unbalanced'):
             ct.Solution('h2o2_unbalancedReaction.xml')
 
+    def test_yaml_ideal_gas_simple(self):
+        gas = ct.ThermoPhase('ideal-gas.yaml', 'simple')
+        self.check(gas, 'simple', 500, 10 * ct.one_atm, 3, 2)
+
+    def test_yaml_ideal_gas_remote_species(self):
+        gas = ct.ThermoPhase('ideal-gas.yaml', 'species-remote')
+        self.check(gas, 'species-remote', 300, ct.one_atm, 4, 2)
+
+    def test_yaml_duplicate(self):
+        with self.assertRaisesRegex(ct.CanteraError, 'duplicate'):
+            gas = ct.ThermoPhase('ideal-gas.yaml', 'duplicate-species')
+
 
 class TestSpecies(utilities.CanteraTest):
     def setUp(self):