[Python] Implement Species constructors from YAML files/strings

include/cantera/thermo/Species.h

@@ -79,6 +79,9 @@ unique_ptr<Species> newSpecies(const AnyMap& node);
 //! respectively, where the string or file is formatted as either CTI or XML.
 std::vector<shared_ptr<Species> > getSpecies(const XML_Node& node);
 
+//! Generate Species objects for each item (an AnyMap) in `items`.
+std::vector<shared_ptr<Species>> getSpecies(const AnyValue& items);
+
 }
 
 #endif

interfaces/cython/cantera/_cantera.pxd

@@ -116,6 +116,8 @@ cdef extern from "cantera/thermo/Species.h" namespace "Cantera":
 
     cdef shared_ptr[CxxSpecies] CxxNewSpecies "newSpecies" (XML_Node&)
     cdef vector[shared_ptr[CxxSpecies]] CxxGetSpecies "getSpecies" (XML_Node&)
+    cdef shared_ptr[CxxSpecies] CxxNewSpecies "newSpecies" (CxxAnyMap&) except +translate_exception
+    cdef vector[shared_ptr[CxxSpecies]] CxxGetSpecies "getSpecies" (CxxAnyValue&) except +translate_exception
 
 cdef extern from "cantera/thermo/ThermoPhase.h" namespace "Cantera":
     cdef cppclass CxxThermoPhase "Cantera::ThermoPhase":

interfaces/cython/cantera/test/test_thermo.py

@@ -1022,6 +1022,10 @@ class TestSpecies(utilities.CanteraTest):
         self.assertEqual({sp.name for sp in S},
                          set(self.gas.species_names))
 
+    def test_listfromFile_yaml(self):
+        S = ct.Species.listFromFile('ideal-gas.yaml')
+        self.assertEqual(S[0].name, 'O2')
+
     def test_listFromCti(self):
         p = os.path.dirname(__file__)
         with open(pjoin(p, '..', 'data', 'h2o2.cti')) as f:
@@ -1030,6 +1034,20 @@ class TestSpecies(utilities.CanteraTest):
         self.assertEqual({sp.name for sp in S},
                          set(self.gas.species_names))
 
+    def test_listFomYaml(self):
+        yaml = '''
+        - name: H2O
+          composition: {H: 2, O: 1}
+          thermo: {model: constant-cp, h0: 100}
+        - name: HO2
+          composition: {H: 1, O: 2}
+          thermo: {model: constant-cp, h0: 200}
+        '''
+        species = ct.Species.listFromYaml(yaml)
+        self.assertEqual(species[0].name, 'H2O')
+        self.assertEqual(species[1].composition, {'H': 1, 'O': 2})
+        self.assertNear(species[0].thermo.h(300), 100)
+
     def test_listFromXml(self):
         p = os.path.dirname(__file__)
         with open(pjoin(p, '..', 'data', 'h2o2.xml')) as f:

interfaces/cython/cantera/thermo.pyx

@@ -37,15 +37,14 @@ cdef class Species:
         ch4.transport = tran
         gas = ct.Solution(thermo='IdealGas', species=[ch4])
 
-    The static methods `fromCti`, `fromXml`, `listFromFile`, `listFromCti`, and
-    `listFromXml` can be used to create `Species` objects from existing
-    definitions in the CTI or XML formats. All of the following will produce a
-    list of 53 `Species` objects containing the species defined in the GRI 3.0
-    mechanism::
+    The static methods `fromYaml`, `fromCti`, `fromXml`, `listFromFile`,
+    `listFromYaml`, `listFromCti`, and `listFromXml` can be used to create
+    `Species` objects from existing definitions in the CTI or XML formats.
+    Either of the following will produce a list of 53 `Species` objects
+    containing the species defined in the GRI 3.0 mechanism::
 
-        S = ct.Species.listFromFile('gri30.cti')
-        S = ct.Species.listFromCti(open('path/to/gri30.cti').read())
-        S = ct.Species.listFromXml(open('path/to/gri30.xml').read())
+        S = ct.Species.listFromFile('gri30.yaml')
+        S = ct.Species.listFromYaml(open('path/to/gri30.yaml').read())
 
     """
     def __cinit__(self, *args, init=True, **kwargs):
@@ -96,10 +95,21 @@ cdef class Species:
         return species
 
     @staticmethod
-    def listFromFile(filename):
+    def fromYaml(text):
+        """
+        Create a Species object from its YAML string representation.
+        """
+        cxx_species = CxxNewSpecies(AnyMapFromYamlString(stringify(text)))
+        species = Species(init=False)
+        species._assign(cxx_species)
+        return species
+
+    @staticmethod
+    def listFromFile(filename, section='species'):
         """
         Create a list of Species objects from all of the species defined in a
-        CTI or XML file.
+        YAML, CTI or XML file. For YAML files, return species from the section
+        *section*.
 
         Directories on Cantera's input file path will be searched for the
         specified file.
@@ -108,7 +118,12 @@ cdef class Species:
         children of the ``<speciesData>`` node in a document with a ``<ctml>``
         root node, as in the XML files produced by conversion from CTI files.
         """
-        cxx_species = CxxGetSpecies(deref(CxxGetXmlFile(stringify(filename))))
+        if filename.lower().split('.')[-1] in ('yml', 'yaml'):
+            root = AnyMapFromYamlFile(stringify(filename))
+            cxx_species = CxxGetSpecies(root[stringify(section)])
+        else:
+            cxx_species = CxxGetSpecies(deref(CxxGetXmlFile(stringify(filename))))
+
         species = []
         for a in cxx_species:
             b = Species(init=False)
@@ -148,6 +163,21 @@ cdef class Species:
             species.append(b)
         return species
 
+    @staticmethod
+    def listFromYaml(text):
+        """
+        Create a list of Species objects from all the species defined in a YAML
+        string.
+        """
+        root = AnyMapFromYamlString(stringify(text))
+        cxx_species = CxxGetSpecies(root[stringify("items")])
+        species = []
+        for a in cxx_species:
+            b = Species(init=False)
+            b._assign(a)
+            species.append(b)
+        return species
+
     property name:
         """ The name of the species. """
         def __get__(self):

src/base/AnyMap.cpp

@@ -149,7 +149,11 @@ struct convert<Cantera::AnyMap> {
     }
     static bool decode(const Node& node, Cantera::AnyMap& target) {
         target.setLoc(node.Mark().line, node.Mark().column);
-        if (!node.IsMap()) {
+        if (node.IsSequence()) {
+            // Convert a top-level list to a map with the key "items"
+            target["items"] = node.as<AnyValue>();
+            return true;
+        } else if (!node.IsMap()) {
             std::string text = YAML::Dump(node);
             if (text.size() > 300) {
                 text.resize(300);

src/thermo/Species.cpp

@@ -127,4 +127,13 @@ std::vector<shared_ptr<Species> > getSpecies(const XML_Node& node)
     return all_species;
 }
 
+std::vector<shared_ptr<Species>> getSpecies(const AnyValue& items)
+{
+    std::vector<shared_ptr<Species> > all_species;
+    for (const auto& node : items.asVector<AnyMap>()) {
+        all_species.emplace_back(newSpecies(node));
+    }
+    return all_species;
+}
+
 }