[Doc] Include all Python classes/functions in Sphinx

doc/sphinx/cython/importing.rst

@@ -44,9 +44,3 @@ Representing Multiple States
 ----------------------------
 
 .. autoclass:: SolutionArray
-
-Utility Functions
------------------
-
-.. autofunction:: add_directory
-.. autofunction:: get_data_directories

doc/sphinx/cython/index.rst

@@ -15,3 +15,4 @@ Contents:
    zerodim
    onedim
    constants
+   utilities

doc/sphinx/cython/kinetics.rst

@@ -38,6 +38,17 @@ FalloffReaction
 .. autoclass:: FalloffReaction
    :no-undoc-members:
 
+ChemicallyActivatedReaction
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. autoclass:: ChemicallyActivatedReaction
+   :no-undoc-members:
+
+CustomReaction
+^^^^^^^^^^^^^^
+.. autoclass:: CustomReaction
+   :no-undoc-members:
+
+
 Reaction Rates
 --------------
 

doc/sphinx/cython/onedim.rst

@@ -27,6 +27,10 @@ CounterflowPremixedFlame
 ^^^^^^^^^^^^^^^^^^^^^^^^
 .. autoclass:: CounterflowPremixedFlame
 
+CounterflowTwinPremixedFlame
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. autoclass:: CounterflowTwinPremixedFlame
+
 ImpingingJet
 ^^^^^^^^^^^^
 .. autoclass:: ImpingingJet

doc/sphinx/cython/utilities.rst

@@ -0,0 +1,58 @@
+.. py:currentmodule:: cantera
+
+Utilities
+=========
+
+.. contents::
+   :local:
+
+YAML Output
+-----------
+
+YamlWriter
+^^^^^^^^^^
+.. autoclass:: YamlWriter
+
+Unit Conversions
+----------------
+
+UnitSystem
+^^^^^^^^^^
+.. autoclass:: UnitSystem
+   :no-undoc-members:
+
+Units
+^^^^^
+.. autoclass:: Units
+   :no-undoc-members:
+
+
+Global Functions
+----------------
+
+.. autofunction:: add_directory
+.. autofunction:: get_data_directories
+.. autofunction:: import_phases
+.. autofunction:: appdelete
+.. autofunction:: use_sparse
+
+.. autofunction:: make_deprecation_warnings_fatal
+.. autofunction:: suppress_deprecation_warnings
+.. autofunction:: suppress_thermo_warnings
+.. autofunction:: use_legacy_rate_constants
+.. autofunction:: debug_mode_enabled
+.. autofunction:: add_module_directory
+
+Exceptions
+----------
+
+CanteraError
+^^^^^^^^^^^^
+.. autoclass:: CanteraError
+   :no-undoc-members:
+
+
+ThermoModelMethodError
+^^^^^^^^^^^^^^^^^^^^^^
+.. autoclass:: ThermoModelMethodError
+   :no-undoc-members:

doc/sphinx/cython/zerodim.rst

@@ -13,6 +13,8 @@ Defining Functions
 
 .. autoclass:: Func1
 
+.. autoclass:: TabulatedFunction
+
 Base Classes
 ------------
 

interfaces/cython/cantera/base.pyx

@@ -337,7 +337,8 @@ cdef class _SolutionBase:
             output file
         :param units:
             A `UnitSystem` object or dictionary of the units to be used for
-            each dimension. See `YamlWriter.output_units`.
+            each dimension.
+            See `YamlWriter.output_units <cantera.YamlWriter.output_units>`.
         :param precision:
             For output floating point values, the maximum number of digits to
             the right of the decimal point. The default is 15 digits.

interfaces/cython/cantera/kinetics.pyx

@@ -370,7 +370,7 @@ cdef class Kinetics(_SolutionBase):
         The computed values include all temperature-dependent and pressure-dependent
         contributions. By default, third-body concentrations are only considered if
         they are part of the reaction rate definition; for a legacy implementation that
-        includes third-body concentrations @see Cantera::use_legacy_rate_constants().
+        includes third-body concentrations, see `use_legacy_rate_constants`.
         """
         def __get__(self):
             return get_reaction_array(self, kin_getFwdRateConstants)
@@ -382,7 +382,7 @@ cdef class Kinetics(_SolutionBase):
         The computed values include all temperature-dependent and pressure-dependent
         contributions. By default, third-body concentrations are only considered if
         they are part of the reaction rate definition; for a legacy implementation that
-        includes third-body concentrations @see Cantera::use_legacy_rate_constants().
+        includes third-body concentrations, see `use_legacy_rate_constants`.
         """
         def __get__(self):
             return get_reaction_array(self, kin_getRevRateConstants)