[Python] Deprecate Kinetics.*_stoich_coeffs() method in favor of prop…

…erty

Methods are replaced by property Kinetics.*_stoich_coefficients

interfaces/cython/cantera/kinetics.pyx

@@ -235,8 +235,8 @@ cdef class Kinetics(_SolutionBase):
 
     def reactant_stoich_coeff(self, k_spec, int i_reaction):
         """
-        The stoichiometric coefficient of species *k_spec* as a reactant in
-        reaction *i_reaction*.
+        The stoichiometric coefficient of species ``k_spec`` as a reactant in
+        reaction ``i_reaction``.
         """
         cdef int k
         if isinstance(k_spec, (str, bytes)):
@@ -250,8 +250,8 @@ cdef class Kinetics(_SolutionBase):
 
     def product_stoich_coeff(self, k_spec, int i_reaction):
         """
-        The stoichiometric coefficient of species *k_spec* as a product in
-        reaction *i_reaction*.
+        The stoichiometric coefficient of species ``k_spec`` as a product in
+        reaction ``i_reaction``.
         """
         cdef int k
         if isinstance(k_spec, (str, bytes)):
@@ -268,28 +268,65 @@ cdef class Kinetics(_SolutionBase):
         The array of reactant stoichiometric coefficients. Element *[k,i]* of
         this array is the reactant stoichiometric coefficient of species *k* in
         reaction *i*.
+
+        .. deprecated:: 2.6
+
+            To be removed after Cantera 2.6; replaceable by property
+            `Kinetics.reactant_stoich_coefficients`.
+
         """
-        cdef np.ndarray[np.double_t, ndim=2] data = np.empty((self.n_total_species,
-                                                              self.n_reactions))
-        cdef int i,k
-        for i in range(self.n_reactions):
-            for k in range(self.n_total_species):
-                data[k,i] = self.kinetics.reactantStoichCoeff(k,i)
-        return data
+        warnings.warn("To be removed after Cantera 2.6; replaceable by "
+                      "property 'reactant_stoich_coefficients'.", DeprecationWarning)
+        return self.reactant_stoich_coefficients
+
+    property reactant_stoich_coefficients:
+        """
+        The array of reactant stoichiometric coefficients. Element ``[k,i]`` of
+        this array is the reactant stoichiometric coefficient of species ``k`` in
+        reaction ``i``.
+
+        For sparse output, set ``ct.use_sparse(True)``.
+        """
+        def __get__(self):
+            # ensure that output vectors have sufficient size
+            shape = self.n_total_species, self.n_reactions
+            max_size = shape[0] * shape[1]
+            if __use_sparse__:
+                data, ix_ij = get_sparse(self, kin_reactantStoichCoeffs, max_size)
+                return _scipy_sparse.coo_matrix((data, ix_ij), shape=shape)
+            return get_dense(self, kin_reactantStoichCoeffs, max_size, shape)
 
     def product_stoich_coeffs(self):
         """
         The array of product stoichiometric coefficients. Element *[k,i]* of
         this array is the product stoichiometric coefficient of species *k* in
         reaction *i*.
+
+        .. deprecated:: 2.6
+
+            To be removed after Cantera 2.6; replaceable by property
+            `Kinetics.product_stoich_coefficients`.
         """
-        cdef np.ndarray[np.double_t, ndim=2] data = np.empty((self.n_total_species,
-                                                              self.n_reactions))
-        cdef int i,k
-        for i in range(self.n_reactions):
-            for k in range(self.n_total_species):
-                data[k,i] = self.kinetics.productStoichCoeff(k,i)
-        return data
+        warnings.warn("To be removed after Cantera 2.6; replaceable by "
+                      "property 'product_stoich_coefficients'.", DeprecationWarning)
+        return self.product_stoich_coefficients
+
+    property product_stoich_coefficients:
+        """
+        The array of product stoichiometric coefficients. Element ``[k,i]`` of
+        this array is the product stoichiometric coefficient of species ``k`` in
+        reaction ``i``.
+
+        For sparse output, set ``ct.use_sparse(True)``.
+        """
+        def __get__(self):
+            # ensure that output vectors have sufficient size
+            shape = self.n_total_species, self.n_reactions
+            max_size = shape[0] * shape[1]
+            if __use_sparse__:
+                data, ix_ij = get_sparse(self, kin_productStoichCoeffs, max_size)
+                return _scipy_sparse.coo_matrix((data, ix_ij), shape=shape)
+            return get_dense(self, kin_productStoichCoeffs, max_size, shape)
 
     property forward_rates_of_progress:
         """

interfaces/cython/cantera/test/test_convert.py

@@ -39,8 +39,8 @@ def checkConversion(self, refFile, testFile):
 
         self.assertEqual(ref.element_names, gas.element_names)
         self.assertEqual(ref.species_names, gas.species_names)
-        coeffs_ref = ref.reactant_stoich_coeffs()
-        coeffs_gas = gas.reactant_stoich_coeffs()
+        coeffs_ref = ref.reactant_stoich_coefficients
+        coeffs_gas = gas.reactant_stoich_coefficients
         self.assertEqual(coeffs_gas.shape, coeffs_ref.shape)
         self.assertTrue((coeffs_gas == coeffs_ref).all())
 
@@ -154,7 +154,7 @@ def test_pathologicalSpeciesNames(self):
         self.assertEqual(gas.species_name(8), 'co')
 
         self.assertEqual(gas.n_reactions, 12)
-        nu = gas.product_stoich_coeffs() - gas.reactant_stoich_coeffs()
+        nu = gas.product_stoich_coefficients - gas.reactant_stoich_coefficients
         self.assertEqual(list(nu[:,0]), [-1, -1, 0, 2, 0, 0, 0, 0, 0])
         self.assertEqual(list(nu[:,1]), [-2, 3, 0, -1, 0, 0, 0, 0, 0])
         self.assertEqual(list(nu[:,2]), [-1, 0, 0, 0, 1, 0, 0, 0, 0])
@@ -233,8 +233,8 @@ def test_explicit_reverse_rate(self):
         self.assertEqual(Rr[2], 0.0)
         self.assertEqual(Rr[3], 0.0)
         self.assertEqual(Rr[4], 0.0)
-        Rstoich = gas.reactant_stoich_coeffs()
-        Pstoich = gas.product_stoich_coeffs()
+        Rstoich = gas.reactant_stoich_coefficients
+        Pstoich = gas.product_stoich_coefficients
         self.assertEqual(list(Rstoich[:, 0]), list(Pstoich[:, 1]))
         self.assertEqual(list(Rstoich[:, 1]), list(Pstoich[:, 0]))
         self.assertEqual(list(Rstoich[:, 2]), list(Pstoich[:, 3]))
@@ -289,8 +289,8 @@ def test_float_stoich_coeffs(self):
         output = self.convert('float-stoich.inp', thermo='dummy-thermo.dat')
         gas = ct.Solution(output)
 
-        R = gas.reactant_stoich_coeffs()
-        P = gas.product_stoich_coeffs()
+        R = gas.reactant_stoich_coefficients
+        P = gas.product_stoich_coefficients
         self.assertArrayNear(R[:,0], [0, 1.5, 0.5, 0])
         self.assertArrayNear(P[:,0], [1, 0, 0, 1])
         self.assertArrayNear(R[:,1], [1, 0, 0, 1])

interfaces/cython/cantera/test/test_kinetics.py

@@ -98,8 +98,8 @@ def test_reactants_products(self):
                     self.assertIn(self.phase.species_name(k), P)
 
     def test_stoich_coeffs(self):
-        nu_r = self.phase.reactant_stoich_coeffs()
-        nu_p = self.phase.product_stoich_coeffs()
+        nu_r = self.phase.reactant_stoich_coefficients
+        nu_p = self.phase.product_stoich_coefficients
 
         def check_reactant(s, i, value):
             k = self.phase.kinetics_species_index(s)
@@ -149,8 +149,8 @@ def test_rate_constants(self):
             self.phase.equilibrium_constants[ix])
 
     def test_species_rates(self):
-        nu_p = self.phase.product_stoich_coeffs()
-        nu_r = self.phase.reactant_stoich_coeffs()
+        nu_p = self.phase.product_stoich_coefficients
+        nu_r = self.phase.reactant_stoich_coefficients
         creation = (np.dot(nu_p, self.phase.forward_rates_of_progress) +
                     np.dot(nu_r, self.phase.reverse_rates_of_progress))
         destruction = (np.dot(nu_r, self.phase.forward_rates_of_progress) +
@@ -187,10 +187,10 @@ def test_idealgas(self):
         gas1.TPY = 800, 2*ct.one_atm, 'H2:0.3, O2:0.7, OH:2e-4, O:1e-3, H:5e-5'
         gas2.TPY = gas1.TPY
 
-        self.assertTrue((gas1.reactant_stoich_coeffs() ==
-                         gas2.reactant_stoich_coeffs()).all())
-        self.assertTrue((gas1.product_stoich_coeffs() ==
-                         gas2.product_stoich_coeffs()).all())
+        self.assertTrue((gas1.reactant_stoich_coefficients ==
+                         gas2.reactant_stoich_coefficients).all())
+        self.assertTrue((gas1.product_stoich_coefficients ==
+                         gas2.product_stoich_coefficients).all())
 
         self.assertArrayNear(gas1.delta_gibbs,
                              gas2.delta_gibbs)
@@ -265,10 +265,10 @@ def test_add_reaction(self):
 
         self.assertEqual(gas1.n_reactions, gas2.n_reactions)
 
-        self.assertTrue((gas1.reactant_stoich_coeffs() ==
-                         gas2.reactant_stoich_coeffs()).all())
-        self.assertTrue((gas1.product_stoich_coeffs() ==
-                         gas2.product_stoich_coeffs()).all())
+        self.assertTrue((gas1.reactant_stoich_coefficients ==
+                         gas2.reactant_stoich_coefficients).all())
+        self.assertTrue((gas1.product_stoich_coefficients ==
+                         gas2.product_stoich_coefficients).all())
 
         self.assertArrayNear(gas1.delta_gibbs,
                              gas2.delta_gibbs)