Add cubical complex to main page

Homogeneize the author/copyright sections of modules
Exclude data and GudhUI from doxygen



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Doxygen_for_GUDHI_1.3.0@1085 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1b89161f3253553a02935885334b2fc6cf58055e

11 files changed, 17 insertions, 32 deletions

diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
index be4caaad..83921427 100644
--- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
+++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
@@ -145,7 +145,8 @@ namespace Cubical_complex {
 

  * \section BitmapExamples Examples

  * End user programs are available in example/Bitmap_cubical_complex folder.

-

+ * 

+ * \copyright GNU General Public License v3.

  */

 /** @} */  // end defgroup cubical_complex

 

diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
index 67e1fed3..54ae47d0 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
@@ -46,18 +46,15 @@ const bool globalDbg = false;
 template <typename T> class is_before_in_filtration;
 
 /**
- * This is a Bitmap_cubical_complex class. It joints a functionalities of Bitmap_cubical_complex_base and
+ * @class Bitmap_cubical_complex Bitmap_cubical_complex.h gudhi/Bitmap_cubical_complex.h
+ * @brief Cubical complex represented as a bitmap.
+ * @ingroup cubical_complex
+ * @details This is a Bitmap_cubical_complex class. It joints a functionalities of Bitmap_cubical_complex_base and
  * Bitmap_cubical_complex_periodic_boundary_conditions_base classes into
  * Gudhi persistent homology engine. It is a template class that inherit from its template parameter. The template
  * parameter is supposed to be either Bitmap_cubical_complex_base or
  * Bitmap_cubical_complex_periodic_boundary_conditions_base class.
  **/
-
-/**
- *@class Bitmap_cubical_complex
- *@brief Cubical complex represented as a bitmap.
- *@ingroup cubical_complex
- */
 template <typename T>
 class Bitmap_cubical_complex : public T {
  public:
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
index 266ce051..bee19344 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
@@ -31,6 +31,7 @@ namespace Gudhi {
 namespace Cubical_complex {
 
 /**
+ * @class counter counter.h gudhi/Bitmap_cubical_complex/counter.h
  * This is an implementation of a counter being a vector of integers. 
  * The constructor of the class takes as an input two vectors W and V. 
  * It assumes that W < V coordinatewise.
@@ -40,7 +41,6 @@ namespace Cubical_complex {
  * The current counter reach the end counter V if the value returned by the increment function is FALSE.
  * This class is needed for the implementation of a bitmapCubicalComplex.
  **/
-
 class counter {
  public:
   /**
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
index 7294da98..4bdc94ef 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
@@ -39,13 +39,10 @@ namespace Gudhi {
 namespace Cubical_complex {
 
 /**
- * @class Bitmap_cubical_complex_base
+ * @class Bitmap_cubical_complex_base Bitmap_cubical_complex_base.h gudhi/Bitmap_cubical_complex_base.h
  * @brief Cubical complex represented as a bitmap, class with basic implementation.
  * @ingroup cubical_complex
- */
-
-/**
- * This is a class implementing a basic bitmap data structure to store cubical complexes.
+ * @details This is a class implementing a basic bitmap data structure to store cubical complexes.
  * It implements only the most basic subroutines.
  * The idea of the bitmap is the following. Our aim is to have a memory efficient
  * data structure to store d-dimensional cubical complex
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
index a446c0e8..5b7e4115 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
@@ -39,12 +39,10 @@ namespace Cubical_complex {
 // the cells on the right / top are not in the Bitmap_cubical_complex_periodic_boundary_conditions_base
 
 /**
- * @class Bitmap_cubical_complex_periodic_boundary_conditions_base
+ * @class Bitmap_cubical_complex_periodic_boundary_conditions_base Bitmap_cubical_complex_periodic_boundary_conditions_base.h gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
  * @brief Cubical complex with periodic boundary conditions represented as a bitmap.
  * @ingroup cubical_complex
- */
-/**
- * This is a class implementing a bitmap data structure with periodic boundary conditions. Most of the functions are
+ * @details This is a class implementing a bitmap data structure with periodic boundary conditions. Most of the functions are
  * identical to the functions from Bitmap_cubical_complex_base.
  * The ones that needed to be updated are the constructors and get_boundary_of_a_cell and get_coboundary_of_a_cell.
  */
diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index 73236db9..1fe563d6 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -226,7 +226,6 @@ Time to simplify and enumerate simplices:
 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
 */
 /** @} */  // end defgroup
 }  // namespace contraction
diff --git a/src/Doxyfile b/src/Doxyfile
index 8fe41755..f7fba3e6 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -779,7 +779,8 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = 
+EXCLUDE                = data/ \
+	GudhUI/
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 3c331f0f..1b86f1f9 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -48,6 +48,7 @@ namespace persistent_cohomology {
 
 /** \defgroup persistent_cohomology Persistent Cohomology
   *
+ \author    Clément Maria
 
   Computation of persistent cohomology using the algorithm of 
    \cite DBLP:journals/dcg/SilvaMV11 and \cite DBLP:journals/corr/abs-1208-5018 
@@ -169,11 +170,6 @@ points sampling a Klein bottle in \f$\mathbb{R}^5\f$ with a simplex tree, its co
 Hasse diagram and the computation of persistent homology and multi-field persistent homology for the 
 different representations.
 
-
-
- \author    Clément Maria
- \version   1.0
- \date      2014
  \copyright GNU General Public License v3.
  @{  
  */
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 46670b85..ba09db63 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -48,6 +48,7 @@
 namespace Gudhi {
 
 /** \defgroup simplex_tree Filtered Complexes
+ * \author    Cl&eacute;ment Maria
  *
  * A simplicial complex \f$\mathbf{K}\f$
  * on a set of vertices \f$V = \{1, \cdots ,|V|\}\f$ is a collection of simplices
@@ -75,10 +76,6 @@ namespace Gudhi {
  when accessing the boundary of a simplex, but is less compact and harder to construct from
  scratch.
 
-
- * \author    Clément Maria
- * \version   1.0
- * \date      2014
  * \copyright GNU General Public License v3.
  * @{
  */
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index 615b3a81..74c6a71d 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
@@ -240,7 +240,6 @@ their collaboration to write the two initial papers
 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
 */
 /** @} */  // end defgroup
 
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 56cb82bb..6f3d8603 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -41,7 +41,7 @@
 <table border="0">
   <tr>
     <td width="25%">
-      <b>Author:</b> Clément Maria<br>
+      <b>Author:</b> Cl&eacute;ment Maria<br>
       <b>Introduced in:</b> GUDHI 1.0.0<br>
       <b>Copyright:</b> GPL v3<br>
     </td>
@@ -114,7 +114,7 @@
 <table border="0">
   <tr>
     <td width="25%">
-      <b>Author:</b> Clément Maria<br>
+      <b>Author:</b> Cl&eacute;ment Maria<br>
       <b>Introduced in:</b> GUDHI 1.0.0<br>
       <b>Copyright:</b> GPL v3<br>
     </td>