Merge of the branch for Doxygen to use MathJax.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2429 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7606538aabea730e4cef25c451a9db2041b84c61

3 files changed, 63 insertions, 28 deletions

diff --git a/data/points/SO3.COPYRIGHT b/data/points/SO3.COPYRIGHT
index 26bbb0ad..a9383f8f 100644
--- a/data/points/SO3.COPYRIGHT
+++ b/data/points/SO3.COPYRIGHT
@@ -7,3 +7,5 @@ This software is an implementation of the two following papers:
 J. C. Mitchell. Discrete Uniform Sampling of Rotation Groups Using Orthogonal Images. SIAM Journal of Scientific Computing, 30(1):525-547, 2007. 
 
 A. Yershova, S. Jain, S. M. LaValle, and J. C. Mitchell. Generating Uniform Incremental Grids on SO(3) Using the Hopf Fibration International Journal of Robotics Research, November 2009. 
+
+This software copyright is GNU General Public License as published by the Free Software Foundation version 2.
diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index 69959fc5..cf1a946a 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -89,31 +89,64 @@ namespace alpha_complex {
  * \image html "alpha_complex_doc.png" "Simplicial complex structure construction example"
  *
  * \subsection filtrationcomputation Filtration value computation algorithm
- * 
- * \f{algorithm}{ 
- * \caption{Filtration value computation algorithm}\label{alpha}
- * \begin{algorithmic}
- * \For{i : dimension $\rightarrow$ 0}
- *   \ForAll{$\sigma$ of dimension i}
- *     \If {filtration($\sigma$) is NaN}
- *       \State filtration($\sigma$) = $\alpha^2(\sigma)$
- *     \EndIf
- *     \ForAll{$\tau$ face of $\sigma$} \Comment{propagate alpha filtration value}
- *       \If {filtration($\tau$) is not NaN} 
- *         \State filtration($\tau$) = min (filtration($\tau$), filtration($\sigma$))
- *       \Else
- *         \If {$\tau$ is not Gabriel for $\sigma$} 
- *           \State filtration($\tau$) = filtration($\sigma$)
- *         \EndIf
- *       \EndIf
- *     \EndFor
- *   \EndFor
- * \EndFor
- * \State make\_filtration\_non\_decreasing()
- * \State prune\_above\_filtration()
- * \end{algorithmic}
- * \f}
- * 
+ *
+ *
+ *
+ * <ul>
+ *   <li style="list-style-type: none;">\f$ \textbf{for } i : dimension \rightarrow 0 \textbf{ do} \f$
+ *     <ul>
+ *       <li style="list-style-type: none;">\f$\textbf{for all } \sigma of dimension i \f$
+ *         <ul>
+ *           <li style="list-style-type: none;">\f$\textbf{if } filtration( \sigma ) is NaN \textbf{ then} \f$
+ *             <ul>
+ *               <li style="list-style-type: none;">\f$ filtration( \sigma ) = \alpha^2( \sigma ) \f$
+ *               </li>
+ *             </ul>
+ *           </li>
+ *           <li style="list-style-type: none;">\f$\textbf{end if}\f$
+ *           </li>
+ *           <li style="list-style-type: none;">\f$\textbf{for all } \tau face of \sigma \textbf{ do} \f$
+ *             &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;// propagate alpha filtration value
+ *             <ul>
+ *               <li style="list-style-type: none;">\f$\textbf{if } filtration( \tau ) is not NaN \textbf{ then} \f$
+ *                 <ul>
+ *                   <li style="list-style-type: none;">\f$ filtration( \tau ) = min ( filtration( \tau ), filtration( \sigma ) ) \f$
+ *                   </li>
+ *                 </ul>
+ *               </li>
+ *               <li style="list-style-type: none;">\f$\textbf{else}\f$
+ *                 <ul>
+ *                   <li style="list-style-type: none;">\f$\textbf{if } \tau is not Gabriel for \sigma \textbf{ then} \f$
+ *                     <ul>
+ *                       <li style="list-style-type: none;">\f$ filtration( \tau ) = filtration( \sigma ) \f$
+ *                       </li>
+ *                     </ul>
+ *                   </li>
+ *                   <li style="list-style-type: none;">\f$\textbf{end if}\f$
+ *                   </li>
+ *                 </ul>
+ *               </li>
+ *               <li style="list-style-type: none;">\f$\textbf{end if}\f$
+ *               </li>
+ *             </ul>
+ *           </li>
+ *           <li style="list-style-type: none;">\f$\textbf{end for}\f$
+ *           </li>
+ *         </ul>
+ *       </li>
+ *       <li style="list-style-type: none;">\f$\textbf{end for}\f$
+ *       </li>
+ *     </ul>
+ *   </li>
+ *   <li style="list-style-type: none;">\f$\textbf{end for}\f$
+ *   </li>
+ *   <li style="list-style-type: none;">\f$make\_filtration\_non\_decreasing()\f$
+ *   </li>
+ *   <li style="list-style-type: none;">\f$prune\_above\_filtration()\f$
+ *   </li>
+ * </ul>
+ *
+ *
  * \subsubsection dimension2 Dimension 2
  * 
  * From the example above, it means the algorithm looks into each triangle ([0,1,2], [0,2,4], [1,2,3], ...),
diff --git a/src/Doxyfile b/src/Doxyfile
index d2d0a447..9cd3894c 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -1427,7 +1427,7 @@ FORMULA_TRANSPARENT    = YES
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:
@@ -1450,14 +1450,14 @@ MATHJAX_FORMAT         = HTML-CSS
 # The default value is: http://cdn.mathjax.org/mathjax/latest.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+MATHJAX_RELPATH        = http://gudhi.gforge.inria.fr/doc
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example
 # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_EXTENSIONS     =
+MATHJAX_EXTENSIONS     = TeX/AMSmath TeX/AMSsymbols TeX/algorithm TeX/algpseudocode
 
 # The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
 # of code that will be used on startup of the MathJax code. See the MathJax site