From 8d802d1616b4c7219f06e391248686a91dd0089c Mon Sep 17 00:00:00 2001
From: Nicholas Malaya <nicholas.malaya@gmail.com>
Date: Thu, 19 Jul 2012 15:32:34 +0000
Subject: [PATCH] [cantera]: fixing doxygen documentation test generation.

---
 doc/doxygen/cantera.dox | 30 +++++++++++++++---------------
 doc/doxygen/cantera.sty | 20 ++++++++++++++++++++
 2 files changed, 35 insertions(+), 15 deletions(-)
 create mode 100644 doc/doxygen/cantera.sty

diff --git a/doc/doxygen/cantera.dox b/doc/doxygen/cantera.dox
index c414c2cde..4d1d14084 100644
--- a/doc/doxygen/cantera.dox
+++ b/doc/doxygen/cantera.dox
@@ -570,18 +570,18 @@ WARN_LOGFILE           =
 
 INPUT                  = src/cantera.h src/cantera.f90 examples/pecos-input.txt \
 		         tutorial/laplacian.c tutorial/laplacian_utils.c tutorial/laplacian.h \
-		         $(SRCDIR)/doxygen/cantera.page \
-			 $(SRCDIR)/doxygen/fortran_interface.page \
-			 $(SRCDIR)/doxygen/txt_common/acknowledgment.page  \
-			 $(SRCDIR)/doxygen/txt_common/gpl.page  \
-                         $(SRCDIR)/doxygen/txt_common/lgpl.page \
-                         $(SRCDIR)/doxygen/txt_common/noop.page \
+		         $(SRCDIR)/doc/doxygen/cantera.page \
+			 $(SRCDIR)/doc/doxygen/fortran_interface.page \
+			 $(SRCDIR)/doc/doxygen/txt_common/acknowledgment.page  \
+			 $(SRCDIR)/doc/doxygen/txt_common/gpl.page  \
+                         $(SRCDIR)/doc/doxygen/txt_common/lgpl.page \
+                         $(SRCDIR)/doc/doxygen/txt_common/noop.page \
 			 ./doxygen/txt_common/about_vpath.page \
-		         $(SRCDIR)/doxygen/tutorial.page \
-		         $(SRCDIR)/doxygen/install.page \			 
-		         $(SRCDIR)/doxygen/add_sol.page \			 
-		         $(SRCDIR)/doxygen/auto_diff.page \			 
-			 $(SRCDIR)/doxygen/solutions    \
+		         $(SRCDIR)/doc/doxygen/tutorial.page \
+		         $(SRCDIR)/doc/doxygen/install.page \			 
+		         $(SRCDIR)/doc/doxygen/add_sol.page \			 
+		         $(SRCDIR)/doc/doxygen/auto_diff.page \			 
+			 $(SRCDIR)/doc/doxygen/solutions    \
 
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
@@ -638,7 +638,7 @@ EXCLUDE_SYMBOLS        =
 # directories that contain example code fragments that are included (see 
 # the \include command).
 
-EXAMPLE_PATH           = $(SRCDIR)/examples $(SRCDIR)/doxygen/fig_common
+EXAMPLE_PATH           = $(SRCDIR)/examples $(SRCDIR)/doc/doxygen/fig_common
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the 
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
@@ -658,7 +658,7 @@ EXAMPLE_RECURSIVE      = NO
 # directories that contain image that are included in the documentation (see 
 # the \image command).
 
-IMAGE_PATH             = $(SRCDIR)/doxygen/images/ $(SRCDIR)/doxygen/fig_common
+IMAGE_PATH             = $(SRCDIR)/doc/doxygen/images/ $(SRCDIR)/doc/doxygen/fig_common
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should 
 # invoke to filter for each input file. Doxygen will invoke the filter program 
@@ -799,7 +799,7 @@ HTML_HEADER            =
 # each generated HTML page. If it is left blank doxygen will generate a 
 # standard footer.
 
-HTML_FOOTER            = $(SRCDIR)/doxygen/txt_common/footer.html
+HTML_FOOTER            = $(SRCDIR)/doc/doxygen/txt_common/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
 # style sheet that is used by each HTML page. It can be used to 
@@ -1031,7 +1031,7 @@ PAPER_TYPE             = $(PAPER_SIZE)
 # The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
 # packages that should be included in the LaTeX output. 
 
-EXTRA_PACKAGES = $(SRCDIR)/../../doxygen/cantera
+EXTRA_PACKAGES = $(SRCDIR)/../../doc/doxygen/cantera
 
 # The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
 # the generated latex document. The header should contain everything until 
diff --git a/doc/doxygen/cantera.sty b/doc/doxygen/cantera.sty
new file mode 100644
index 000000000..fca692fa3
--- /dev/null
+++ b/doc/doxygen/cantera.sty
@@ -0,0 +1,20 @@
+\typeout{Document Style `masa'. Released  04 March 2011}
+\usepackage{pdflscape}
+\usepackage[authoryear]{natbib}
+%\usepackage[utf8x]{inputenc}
+\usepackage{amsmath}
+\usepackage{amsfonts}
+\usepackage{geometry}
+
+\newcommand{\D}{\partial}
+\newcommand{\Diff}[2] {\dfrac{\partial( #1)}{\partial #2}}
+\newcommand{\diff}[2] {\dfrac{\partial #1}{\partial #2}}
+\newcommand{\bv}[1]{\ensuremath{\mbox{\boldmath$ #1 $}}}
+\newcommand{\gv}[1]{\ensuremath{\mbox{\boldmath$ #1 $}}}
+\newcommand{\grad}[1]{\gv{\nabla} #1}
+\newcommand{\Rho}{\,\mathtt{Rho}}
+\newcommand{\PP}{\,\mathtt{P}}
+%\newcommand{\U}{\,\mathtt{U}}
+\newcommand{\V}{\,\mathtt{V}}
+\newcommand{\W}{\,\mathtt{W}}
+\newcommand{\Lo}{\,\mathcal{L}}