[Doc] Eliminate some Doxygen and Sphinx warnings

doc/doxygen/Doxyfile

@@ -571,8 +571,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = src/apps \
-                         src/base \
+INPUT                  = src/base \
                          src/equil \
                          src/kinetics \
                          src/numerics \
@@ -1179,18 +1178,6 @@ GENERATE_XML           = NO
 
 XML_OUTPUT             = xml
 
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_SCHEMA             =
-
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
-XML_DTD                =
-
 # If the XML_PROGRAMLISTING tag is set to YES Doxygen will
 # dump the program listings (including syntax highlighting
 # and cross-referencing information) to the XML output. Note that
@@ -1397,17 +1384,6 @@ HIDE_UNDOC_RELATIONS   = YES
 
 HAVE_DOT               = YES
 
-# By default doxygen will write a font called FreeSans.ttf to the output
-# directory and reference it in all dot files that doxygen generates. This
-# font does not include all possible unicode characters however, so when you need
-# these (or just want a differently looking font) you can specify the font name
-# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
-# which can be done by putting it in a standard location or by setting the
-# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
-# containing the font.
-
-DOT_FONTNAME           = FreeSans
-
 # The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
 # The default size is 10pt.
 

doc/sphinx/cxx-guide/thermo.rst

@@ -27,8 +27,8 @@ prints its temperature is shown below:
 Class :ct:`ThermoPhase` is the base class for Cantera classes that represent
 phases of matter. It defines the public interface for all classes that represent
 phases. For example, it specifies that they all have a method :ct:`temperature
-<ThermoPhase::temperature>` that returns the current temperature, a method
-:ct:`setTemperature(double T) <ThermoPhase::setTemperature>` that sets the
+<Phase::temperature>` that returns the current temperature, a method
+:ct:`setTemperature(double T) <Phase::setTemperature>` that sets the
 temperature, a method :ct:`getChemPotentials(double* mu)
 <ThermoPhase::getChemPotentials>` that writes the species chemical potentials
 into array ``mu``, and so on.

doc/sphinx/install.rst

@@ -132,7 +132,7 @@ directions :ref:`above <sec-install-conda>`.
      version of Python 2.7, and will include Numpy as well as many other
      packages useful for scientific users.
 
-3. **Install the Visual C++ Redistributable for Visual Studio 2015
+3. **Install the Visual C++ Redistributable for Visual Studio 2015**
 
    - If you are using Python 3.5, you can skip this step as this will have
      already been installed when you installed Python.

include/cantera/base/global.h

@@ -193,7 +193,7 @@ void writelog(const std::string& fmt, const Args&... args) {
  * and then feed it into writelog().
  *
  * @param fmt  c format string for the following arguments
- * #param args arguments used to interpolate the format string
+ * @param args arguments used to interpolate the format string
  * @ingroup textlogs
  */
 template <typename... Args>

interfaces/cython/cantera/onedim.pyx

@@ -1081,8 +1081,10 @@ cdef class Sim1D:
             perturbs parameter ``i`` by a relative factor of ``dp``. To
             perturb a reaction rate constant, this function could be defined
             as::
+
                 def perturb(sim, i, dp):
                     sim.gas.set_multiplier(1+dp, i)
+
             Calling ``perturb(sim, i, 0)`` should restore that parameter to its
             default value.
         :param n_params: