Merge from Doxygen_for_GUDHI_1.3.0.

Doxygen fixes for Gudhi version 1.3.0


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1111 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3f5c37263f802621ba818fdb4ab73eba1fec29c8

37 files changed, 2627 insertions, 161 deletions

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 19d10535..20767813 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,5 +1,5 @@
 set (GUDHI_MAJOR_VERSION 1)
-set (GUDHI_MINOR_VERSION 2)
+set (GUDHI_MINOR_VERSION 3)
 set (GUDHI_PATCH_VERSION 0)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ecd1f7fd..6ad3a58f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -34,6 +34,11 @@ else()
   # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
   # but it implies to use cmake version 3.1 at least.
   find_package(CGAL)
+  # Only CGAL versions > 4.4 supports what Gudhi uses from CGAL
+  if (CGAL_VERSION VERSION_LESS 4.4.0)
+    message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
+    unset(CGAL_FOUND)
+  endif()
   if(CGAL_FOUND)
     include( ${CGAL_USE_FILE} )
   endif()
@@ -58,6 +63,10 @@ else()
   # Find TBB package for parallel sort - not mandatory, just optional.
   set(TBB_FIND_QUIETLY ON)
   find_package(TBB)
+  if (TBB_FOUND)
+    message("TBB found in ${TBB_LIBRARY_DIRS}")
+    add_definitions(-DGUDHI_USE_TBB)
+  endif()
 
   # Required programs for unitary tests purpose
   FIND_PROGRAM( GCOVR_PATH gcovr )
diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index 9d0dcefa..226bb257 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -65,7 +65,7 @@ namespace alphacomplex {
  * 
  * Then, it is asked to display information about the alpha complex.
  * 
- * \include Alpha_complex_from_points.cpp
+ * \include Alpha_complex/Alpha_complex_from_points.cpp
  * 
  * When launching:
  * 
@@ -74,7 +74,7 @@ namespace alphacomplex {
  *
  * the program output is:
  * 
- * \include alphaoffreader_for_doc_60.txt
+ * \include Alpha_complex/alphaoffreader_for_doc_60.txt
  * 
  * \section algorithm Algorithm
  * 
@@ -145,7 +145,7 @@ namespace alphacomplex {
  * 
  * Then, it is asked to display information about the alpha complex.
  * 
- * \include Alpha_complex_from_off.cpp
+ * \include Alpha_complex/Alpha_complex_from_off.cpp
  * 
  * When launching:
  * 
@@ -154,7 +154,7 @@ namespace alphacomplex {
  *
  * the program output is:
  * 
- * \include alphaoffreader_for_doc_32.txt
+ * \include Alpha_complex/alphaoffreader_for_doc_32.txt
  * 
  * \copyright GNU General Public License v3.                         
  * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index debb440d..f1346867 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -14,12 +14,16 @@ if(CGAL_FOUND)
 
       add_executable ( alphapoints Alpha_complex_from_points.cpp )
       target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
+      add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
+      target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      if (TBB_FOUND)
+        target_link_libraries(alphapoints ${TBB_RELEASE_LIBRARY})
+        target_link_libraries(alphaoffreader ${TBB_RELEASE_LIBRARY})
+      endif()
 
+      add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
       # Do not forget to copy test files in current binary dir
       file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-      add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
-      target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
       add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt)
       add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt)
       if (DIFF_PATH)
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index 2e5d6c3d..e24588d7 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -24,6 +24,9 @@ if(CGAL_FOUND)
 
       add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
       target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+      if (TBB_FOUND)
+        target_link_libraries(AlphaComplexUT ${TBB_RELEASE_LIBRARY})
+      endif()
 
       # Do not forget to copy test files in current binary dir
       file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
diff --git a/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.ipe b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.ipe
new file mode 100644
index 00000000..bec245e7
--- /dev/null
+++ b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.ipe
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diff --git a/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.png b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.png
new file mode 100644
index 00000000..afb2a75e
--- /dev/null
+++ b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.png
diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
index cde0b2fc..83921427 100644
--- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
+++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
@@ -76,7 +76,7 @@ namespace Cubical_complex {
  * directions, allows to determine, dimension, neighborhood, boundary and coboundary of every cube \f$C \in

  * \mathcal{K}\f$.

  *

- * \image html "bitmapAllCubes.png" "Cubical complex.

+ * \image html "Cubical_complex_representation.png" Cubical complex.

  *

  * Note that the cubical complex in the figure above is, in a natural way, a product of one dimensional cubical

  * complexes in \f$\mathbb{R}\f$. The number of all cubes in each direction is equal \f$2n+1\f$, where \f$n\f$ is the

@@ -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/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt
index 8f9cfa80..ad86b763 100644
--- a/src/Bitmap_cubical_complex/example/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt
@@ -2,16 +2,25 @@ cmake_minimum_required(VERSION 2.6)
 project(GUDHIBitmap)
 
 add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp )
-target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})	
+target_link_libraries(Bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Bitmap_cubical_complex ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(Bitmap_cubical_complex_one_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt)
 add_test(Bitmap_cubical_complex_two_sphere ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
 
 add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp )
-target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})	
+target_link_libraries(Random_bitmap_cubical_complex ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Random_bitmap_cubical_complex ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(Random_bitmap_cubical_complex ${CMAKE_CURRENT_BINARY_DIR}/Random_bitmap_cubical_complex 2 100 100)
 
 add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp )
-target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})	
+target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${Boost_SYSTEM_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(Bitmap_cubical_complex_periodic_2d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt)
 add_test(Bitmap_cubical_complex_periodic_3d_torus ${CMAKE_CURRENT_BINARY_DIR}/Bitmap_cubical_complex_periodic_boundary_conditions ${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt)
 
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..56fa297c 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 +46,14 @@ 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
+ * @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:
@@ -321,7 +317,7 @@ class Bitmap_cubical_complex : public T {
   };
 
   /**
-   * Filtration_simplex_range provides the ranges for Filtration_simplex_iterator.
+   * @brief Filtration_simplex_range provides the ranges for Filtration_simplex_iterator.
    **/
   class Filtration_simplex_range {
     // Range over the simplices of the complex in the order of the filtration.
@@ -492,7 +488,7 @@ class Bitmap_cubical_complex : public T {
   };
 
   /**
-   * Class needed for compatibility with Gudhi. Not useful for other purposes.
+   * @brief Class needed for compatibility with Gudhi. Not useful for other purposes.
    **/
   class Skeleton_simplex_range {
     // Range over the simplices of the complex in the order of the filtration.
@@ -549,7 +545,8 @@ void Bitmap_cubical_complex<T>::initialize_simplex_associated_to_key() {
   this->simplex_associated_to_key = std::vector<size_t>(this->data.size());
   std::iota(std::begin(simplex_associated_to_key), std::end(simplex_associated_to_key), 0);
 #ifdef GUDHI_USE_TBB
-  tbb::parallel_sort(simplex_associated_to_key, is_before_in_filtration<T>(this));
+  tbb::parallel_sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(),
+                     is_before_in_filtration<T>(this));
 #else
   std::sort(simplex_associated_to_key.begin(), simplex_associated_to_key.end(), is_before_in_filtration<T>(this));
 #endif
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..3a8c3988 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
@@ -31,8 +31,8 @@ namespace Gudhi {
 namespace Cubical_complex {
 
 /**
- * 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. 
+ * @brief This is an implementation of a counter being a vector of integers. 
+ * @details The constructor of the class takes as an input two vectors W and V. 
  * It assumes that W < V coordinatewise.
  * If the initial counter W is not specified, it is assumed to be vector of zeros. 
  * The class allows to iterate between W and V by using increment() function.
@@ -40,7 +40,6 @@ 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..2f74ba9e 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 +39,9 @@ namespace Gudhi {
 namespace Cubical_complex {
 
 /**
- * @class Bitmap_cubical_complex_base
  * @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
@@ -193,7 +189,7 @@ class Bitmap_cubical_complex_base {
   // ITERATORS
 
   /**
-   * Iterator through all cells in the complex (in order they appear in the structure -- i.e.
+   * @brief Iterator through all cells in the complex (in order they appear in the structure -- i.e.
    * in lexicographical order).
    **/
   class All_cells_iterator : std::iterator< std::input_iterator_tag, T > {
@@ -261,7 +257,7 @@ class Bitmap_cubical_complex_base {
   }
 
   /**
-   * All_cells_range class provides ranges for All_cells_iterator
+   * @brief All_cells_range class provides ranges for All_cells_iterator
    **/
   class All_cells_range {
    public:
@@ -312,7 +308,7 @@ class Bitmap_cubical_complex_base {
   }
 
   /**
-   * Iterator through top dimensional cells of the complex. The cells appear in order they are stored
+   * @brief Iterator through top dimensional cells of the complex. The cells appear in order they are stored
    * in the structure (i.e. in lexicographical order)
    **/
   class Top_dimensional_cells_iterator : std::iterator< std::input_iterator_tag, T > {
@@ -414,7 +410,7 @@ class Bitmap_cubical_complex_base {
   }
 
   /**
-   * Top_dimensional_cells_iterator_range class provides ranges for Top_dimensional_cells_iterator_range
+   * @brief Top_dimensional_cells_iterator_range class provides ranges for Top_dimensional_cells_iterator_range
    **/
   class Top_dimensional_cells_range {
    public:
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..0d0f2f84 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 +39,9 @@ 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
  * @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/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
index b6fc8a3b..0e5340c7 100644
--- a/src/Bitmap_cubical_complex/test/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -12,6 +12,9 @@ endif()
 
 add_executable ( BitmapCCUT Bitmap_test.cpp )
 target_link_libraries(BitmapCCUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(BitmapCCUT ${TBB_RELEASE_LIBRARY})
+endif()
 
 # Unitary tests
 add_test(NAME BitmapCCUT
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index f5dccbc1..1700ddaa 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -31,6 +31,11 @@ else()
   # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
   # but it implies to use cmake version 3.1 at least.
   find_package(CGAL)
+  # Only CGAL versions > 4.4 supports what Gudhi uses from CGAL
+  if (CGAL_VERSION VERSION_LESS 4.4.0)
+    message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
+    unset(CGAL_FOUND)
+  endif()
   if(CGAL_FOUND)
     include( ${CGAL_USE_FILE} )
   endif()
@@ -55,6 +60,10 @@ else()
   # Find TBB package for parallel sort - not mandatory, just optional.
   set(TBB_FIND_QUIETLY ON)
   find_package(TBB)
+  if (TBB_FOUND)
+    message("TBB found in ${TBB_LIBRARY_DIRS}")
+    add_definitions(-DGUDHI_USE_TBB)
+  endif()
 
   # BOOST ISSUE result_of vs C++11
   add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
diff --git a/src/Contraction/doc/sphere_contraction_representation.png b/src/Contraction/doc/sphere_contraction_representation.png
new file mode 100644
index 00000000..edf37bf3
--- /dev/null
+++ b/src/Contraction/doc/sphere_contraction_representation.png
diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index a4c786be..1b2cdee9 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -46,7 +46,7 @@ namespace contraction {
 The purpose of this package is to offer a user-friendly interface for edge contraction simplification of huge simplicial complexes.
 It uses the \ref skbl data-structure whose size remains small  during simplification  
 of  most used geometrical complexes of topological data analysis such as the Rips or the Delaunay complexes. In practice, the 
-size of this data-structure is even uch lower than the total number of simplices.
+size of this data-structure is even much lower than the total number of simplices.
 
 The edge contraction operation consists in identifying two vertices of a simplicial complex. 
 A lot of algorithms have been developed in computer graphics that allows to reduce efficiently the size of 2-dimensional simplicial complexes
@@ -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 b0afb876..6ddfb55d 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -32,19 +32,19 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "Gudhi"
+PROJECT_NAME           = "GUDHI"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "1.2.0"
+PROJECT_NUMBER         = "1.3.0"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          =
+PROJECT_BRIEF          = "C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding."
 
 # With the PROJECT_LOGO tag one can specify an logo or icon that is included in
 # the documentation. The maximum height of the logo should not exceed 55 pixels
@@ -153,7 +153,7 @@ STRIP_FROM_PATH        =
 # specify the list of include paths that are normally passed to the compiler
 # using the -I flag.
 
-STRIP_FROM_INC_PATH    =
+STRIP_FROM_INC_PATH    = include concept
 
 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
 # less readable) file names. This can be useful is your file systems doesn't
@@ -580,27 +580,27 @@ STRICT_PROTO_MATCHING  = NO
 # documentation.
 # The default value is: YES.
 
-GENERATE_TODOLIST      = YES
+GENERATE_TODOLIST      = NO
 
 # The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the
 # test list. This list is created by putting \test commands in the
 # documentation.
 # The default value is: YES.
 
-GENERATE_TESTLIST      = YES
+GENERATE_TESTLIST      = NO
 
 # The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug
 # list. This list is created by putting \bug commands in the documentation.
 # The default value is: YES.
 
-GENERATE_BUGLIST       = YES
+GENERATE_BUGLIST       = NO
 
 # The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO)
 # the deprecated list. This list is created by putting \deprecated commands in
 # the documentation.
 # The default value is: YES.
 
-GENERATE_DEPRECATEDLIST= YES
+GENERATE_DEPRECATEDLIST= NO
 
 # The ENABLED_SECTIONS tag can be used to enable conditional documentation
 # sections, marked by \if <section_label> ... \endif and \cond <section_label>
@@ -780,7 +780,9 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = 
+EXCLUDE                = data/ \
+	                     example/ \
+	                     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
@@ -814,15 +816,14 @@ EXCLUDE_SYMBOLS        =
 # command).
 
 EXAMPLE_PATH           = biblio/ \
-    example/common/ \
-    example/Alpha_complex/
+	example/
 
 # 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 and
 # *.h) to filter out the source-files in the directories. If left blank all
 # files are included.
 
-EXAMPLE_PATTERNS       =
+EXAMPLE_PATTERNS       = 
 
 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
 # searched for input files to be used with the \include or \dontinclude commands
@@ -839,6 +840,8 @@ IMAGE_PATH             = doc/Skeleton_blocker/ \
 	doc/Alpha_complex/ \
 	doc/common/ \
 	doc/Contraction/ \
+	doc/Simplex_tree/ \
+	doc/Persistent_cohomology/ \
 	doc/Witness_complex/ \
 	doc/Bitmap_cubical_complex/
 
@@ -1044,7 +1047,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            =
+HTML_HEADER            = doc/common/header.html
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1054,7 +1057,7 @@ HTML_HEADER            =
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            =
+HTML_FOOTER            = doc/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 fine-tune the look of
@@ -1066,7 +1069,7 @@ HTML_FOOTER            =
 # obsolete.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_STYLESHEET        =
+HTML_STYLESHEET        = doc/common/stylesheet.css
 
 # The HTML_EXTRA_STYLESHEET tag can be used to specify an additional user-
 # defined cascading style sheet that is included after the standard style sheets
@@ -1549,7 +1552,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index d58d0bd4..a7e64319 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -57,6 +57,9 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
 	
   target_link_libraries( GudhUI ${QT_LIBRARIES} ${QGLVIEWER_LIBRARIES} )
   target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
+if (TBB_FOUND)
+  target_link_libraries( GudhUI ${TBB_RELEASE_LIBRARY})
+endif()
 
 ###############################################################################
 
diff --git a/src/Persistent_cohomology/doc/3DTorus_poch.png b/src/Persistent_cohomology/doc/3DTorus_poch.png
new file mode 100644
index 00000000..1c9d8328
--- /dev/null
+++ b/src/Persistent_cohomology/doc/3DTorus_poch.png
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 779a9e89..2f94ed15 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -7,57 +7,55 @@ add_definitions( -DBOOST_ALL_DYN_LINK )
 
 add_executable(plain_homology plain_homology.cpp)
 target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
-add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
 
 add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
 target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
-add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
 
 add_executable(rips_persistence rips_persistence.cpp)
 target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-   
-add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100)
-   
+
 add_executable(parallel_rips_persistence parallel_rips_persistence.cpp)
 target_link_libraries(parallel_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-   
-add_test(parallel_rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/parallel_rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100)
-   
+
 add_executable(persistence_from_file persistence_from_file.cpp)
 target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+if (TBB_FOUND)
+  target_link_libraries(plain_homology ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(persistence_from_simple_simplex_tree ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(rips_persistence ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(parallel_rips_persistence ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(persistence_from_file ${TBB_RELEASE_LIBRARY})
+endif()
+
+add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
+add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
+add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
+add_test(parallel_rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/parallel_rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100)
 add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0)
 add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
-
+   
 if(GMPXX_FOUND AND GMP_FOUND)
-  message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
-  message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
+   message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
+   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
 
-  add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
-  target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
-  add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100)
+   add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
+   target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+   add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
+   target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+   if (TBB_FOUND)
+     target_link_libraries(rips_multifield_persistence ${TBB_RELEASE_LIBRARY})
+     target_link_libraries(performance_rips_persistence ${TBB_RELEASE_LIBRARY})
+   endif()
 
-  add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
-  target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100)
 
   if(CGAL_FOUND)
-    include( ${CGAL_USE_FILE} )
-    # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-    # A workaround is to add "-std=c++11" again.
-    # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-    # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-    # but it implies to use cmake version 3.1 at least.
-    if(NOT MSVC)
-      include(CheckCXXCompilerFlag)
-      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-      if(COMPILER_SUPPORTS_CXX11)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-      endif()
-    endif()
-    # - End of workaround
-
     add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
     target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
+    if (TBB_FOUND)
+      target_link_libraries(alpha_complex_3d_persistence ${TBB_RELEASE_LIBRARY})
+    endif()
     add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
 
     if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
@@ -70,6 +68,9 @@ if(GMPXX_FOUND AND GMP_FOUND)
       
         add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
         target_link_libraries(alpha_complex_persistence  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+        if (TBB_FOUND)
+          target_link_libraries(alpha_complex_persistence ${TBB_RELEASE_LIBRARY})
+        endif()
 
       else()
         message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 643b810c..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 
@@ -63,15 +64,6 @@ namespace persistent_cohomology {
   composed of three elements: 
   topological spaces, their homology groups and an evolution scheme.
 
- The theory of homology consists in attaching to a topological space a sequence of
- (homology) groups,
- capturing global topological features
- like connected components, holes, cavities, etc. Persistent homology studies the evolution
- -- birth, life and death -- of
- these features when the topological space is changing. Consequently, the theory is essentially
- composed of three elements:
- topological spaces, their homology groups and an evolution scheme.
-
  <DT>Topological Spaces:</DT>
  Topological spaces are represented by simplicial complexes.
  Let \f$V = \{1, \cdots ,|V|\}\f$ be a set of <EM>vertices</EM>.
@@ -178,11 +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/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index d16be5be..459cc000 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -12,6 +12,9 @@ endif()
 
 add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp )
 target_link_libraries(PersistentCohomologyUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(PersistentCohomologyUT ${TBB_RELEASE_LIBRARY})
+endif()
 
 # Unitary tests
 add_test(NAME PersistentCohomologyUT 
@@ -22,7 +25,10 @@ add_test(NAME PersistentCohomologyUT
 
 if(GMPXX_FOUND AND GMP_FOUND)
   add_executable ( PersistentCohomologyMultiFieldUT persistent_cohomology_unit_test_multi_field.cpp )
-  target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+target_link_libraries(PersistentCohomologyMultiFieldUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+if (TBB_FOUND)
+  target_link_libraries(PersistentCohomologyMultiFieldUT ${TBB_RELEASE_LIBRARY})
+endif()
 
   # Unitary tests
   add_test(NAME PersistentCohomologyMultiFieldUT
diff --git a/src/Simplex_tree/doc/Simplex_tree_representation.png b/src/Simplex_tree/doc/Simplex_tree_representation.png
new file mode 100644
index 00000000..9d401520
--- /dev/null
+++ b/src/Simplex_tree/doc/Simplex_tree_representation.png
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index 200161a6..89a4e053 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -2,10 +2,16 @@ cmake_minimum_required(VERSION 2.6)
 project(GUDHISimplexTreeFromFile)
 
 add_executable ( simplex_tree_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp )
+if (TBB_FOUND)
+  target_link_libraries(simplex_tree_from_cliques_of_graph ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(simplex_tree_from_cliques_of_graph_2 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 2)
 add_test(simplex_tree_from_cliques_of_graph_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_cliques_of_graph ${CMAKE_SOURCE_DIR}/data/points/Klein_bottle_complex.txt 3)
 
 add_executable ( simple_simplex_tree simple_simplex_tree.cpp )
+if (TBB_FOUND)
+  target_link_libraries(simple_simplex_tree ${TBB_RELEASE_LIBRARY})
+endif()
 add_test(simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/simple_simplex_tree)
 
 add_executable ( mini_simplex_tree mini_simplex_tree.cpp )
@@ -16,5 +22,8 @@ add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree)
 if(GMP_FOUND AND CGAL_FOUND)
   add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp )
   target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(simplex_tree_from_alpha_shapes_3 ${TBB_RELEASE_LIBRARY})
+  endif()
   add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000)
 endif()
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 9388fedb..b6dc8e13 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -51,6 +51,7 @@
 
 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
@@ -71,16 +72,13 @@ namespace Gudhi {
  The simplex tree is an efficient and flexible
  data structure for representing general (filtered) simplicial complexes. The data structure
  is described in \cite boissonnatmariasimplextreealgorithmica
+ \image html "Simplex_tree_representation.png" "Simplex tree representation"
 
  The second one is the Hasse_complex. The Hasse complex is a data structure representing
  explicitly all co-dimension 1 incidence relations in a complex. It is consequently faster
  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.
  * @{
  */
@@ -88,6 +86,7 @@ namespace Gudhi {
 struct Simplex_tree_options_full_featured;
 
 /**
+ * \class Simplex_tree Simplex_tree.h gudhi/Simplex_tree.h
  * \brief Simplex Tree data structure for representing simplicial complexes.
  *
  * \details Every simplex \f$[v_0, \cdots ,v_d]\f$ admits a canonical orientation
@@ -825,10 +824,11 @@ class Simplex_tree {
      * possible.
      */
 #ifdef GUDHI_USE_TBB
-    tbb::parallel_sort(filtration_vect_, is_before_in_filtration(this));
+    std::cout << "TBB is ON !!!" << std::endl;
+    tbb::parallel_sort(filtration_vect_.begin(), filtration_vect_.end(), is_before_in_filtration(this));
 #else
-    std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(),
-                     is_before_in_filtration(this));
+    std::cout << "TBB is OFF..." << std::endl;
+    std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(), is_before_in_filtration(this));
 #endif
   }
 
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index 1f2f7d33..609d8669 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -12,6 +12,9 @@ endif()
 
 add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp )
 target_link_libraries(SimplexTreeUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(SimplexTreeUT ${TBB_RELEASE_LIBRARY})
+endif()
 
 # Do not forget to copy test files in current binary dir
 file(COPY "simplex_tree_for_unit_test.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index 1f495a7a..8584cd16 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/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h
index e9f78170..60dfd27b 100644
--- a/src/Witness_complex/doc/Witness_complex_doc.h
+++ b/src/Witness_complex/doc/Witness_complex_doc.h
@@ -6,6 +6,8 @@
 
    \author Siargey Kachanovich
 
+   \image html "Witness_complex_representation.png" "Witness complex representation"
+
    \section Definitions
 
    Witness complex \f$ Wit(W,L) \f$  is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$:
@@ -18,7 +20,9 @@
 
    \f$ \sigma \subset L \f$ is witnessed if there exists a point \f$w \in W\f$ such that 
    w is closer to the vertices of \f$ \sigma \f$ than other points in \f$ L \f$ and all of its faces are witnessed as well. 
-      
+ 
+   The data structure is described in \cite boissonnatmariasimplextreealgorithmica .
+
    \section Implementation
 
    The principal class of this module is Gudhi::Witness_complex.
diff --git a/src/Witness_complex/doc/Witness_complex_representation.png b/src/Witness_complex/doc/Witness_complex_representation.png
new file mode 100644
index 00000000..1d31a490
--- /dev/null
+++ b/src/Witness_complex/doc/Witness_complex_representation.png
diff --git a/src/common/doc/Gudhi_banner.jpg b/src/common/doc/Gudhi_banner.jpg
deleted file mode 100644
index ebd3d8af..00000000
--- a/src/common/doc/Gudhi_banner.jpg
+++ /dev/null
diff --git a/src/common/doc/Gudhi_banner.png b/src/common/doc/Gudhi_banner.png
new file mode 100644
index 00000000..18e8a672
--- /dev/null
+++ b/src/common/doc/Gudhi_banner.png
diff --git a/src/common/doc/footer.html b/src/common/doc/footer.html
new file mode 100644
index 00000000..7b4cdc5c
--- /dev/null
+++ b/src/common/doc/footer.html
@@ -0,0 +1,29 @@
+<!-- HTML footer for doxygen 1.8.6-->
+<!-- start footer part -->
+<table style="width:100%">
+  <tr class="no-bullet shadow-black">
+      <td class="network-entypo">
+<!--BEGIN PROJECT_NAME--> $projectname
+<!--BEGIN PROJECT_NUMBER-->&#160;Version $projectnumber<!--END PROJECT_NUMBER-->
+<!--BEGIN PROJECT_BRIEF-->&#160;-&#160;$projectbrief<!--END PROJECT_BRIEF-->
+<!--END PROJECT_NAME-->
+      </td>
+      <td class="network-entypo">
+<!--BEGIN GENERATE_TREEVIEW-->
+        $generatedby
+        <a href="http://www.doxygen.org/index.html">
+        <img class="footer" src="$relpath^doxygen.png" alt="doxygen"/></a> $doxygenversion
+<!--END GENERATE_TREEVIEW-->
+      </td>
+  </tr>
+</table>
+
+<!--BEGIN !GENERATE_TREEVIEW-->
+<hr class="footer"/><address class="footer"><small> tralala
+$generatedby &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="$relpath^doxygen.png" alt="doxygen"/>
+</a> $doxygenversion
+</small></address>
+<!--END !GENERATE_TREEVIEW-->
+</body>
+</html>
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
new file mode 100644
index 00000000..c958390c
--- /dev/null
+++ b/src/common/doc/header.html
@@ -0,0 +1,82 @@
+<!-- HTML header for doxygen 1.8.6-->
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!-- GUDHI website : class="no-js" lang="en" is necessary -->
+<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen $doxygenversion"/>
+<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
+<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
+<!-- GUDHI website css for header BEGIN -->
+<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" />
+<!-- GUDHI website css for header END -->
+<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="$relpath^jquery.js"></script>
+<script type="text/javascript" src="$relpath^dynsections.js"></script>
+$treeview
+$search
+$mathjax
+<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
+$extrastylesheet
+</head>
+<body>
+
+<!-- GUDHI website header BEGIN -->
+<div id="navigation" class="sticky">
+  <nav class="top-bar" role="navigation" data-topbar>
+    <section class="top-bar-section">
+      <ul class="right">
+              <li class="divider"></li>
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+      </ul>
+      <ul class="left">
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+                      <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li>
+                  </ul>
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+                <a href="#">Download</a>
+                  <ul class="dropdown">
+                      <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li>
+                      <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li>
+                      <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">Installation manual</a></li>
+                  </ul>
+              </li>
+              <li class="divider"></li>
+              <li><a href="http://gudhi.gforge.inria.fr/doc/latest/modules.html">Documentation</a></li>
+              <li class="divider"></li>
+              <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li>
+              <li class="divider"></li>
+      </ul>
+    </section>
+  </nav>
+</div><!-- /#navigation -->
+<!-- GUDHI website header BEGIN -->
+    
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+
+<!--BEGIN TITLEAREA-->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 30px;">
+  <!--BEGIN DISABLE_INDEX-->
+   <!--BEGIN SEARCHENGINE-->
+   <td>$searchbox</td>
+   <!--END SEARCHENGINE-->
+  <!--END DISABLE_INDEX-->
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+</div>
+<!--END TITLEAREA-->
+<!-- end header part -->
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 3c42f72d..063e0a11 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -1,15 +1,14 @@
 /*! \mainpage
- * \image html "Gudhi_banner.jpg" "" width=20cm
+ *  \tableofcontents
+ * \image html "Gudhi_banner.png" "" width=20cm
  * 
  * \section Introduction Introduction
- * The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic open source C++ library for
+ * The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic open source C++ library for
  * Computational Topology and Topological Data Analysis
  * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>).
- * The GUDHI library is developed as part of the
- * <a class="el" target="_blank" href="https://project.inria.fr/gudhi/">GUDHI project</a> supported by the European
- * Research Council. The GUDHI library intends  to help the development of new algorithmic solutions in TDA and their
- * transfer to applications. It provides robust, efficient, flexible and easy to use implementations of
- * state-of-the-art algorithms and data structures.
+ * The GUDHI library intends  to help the development of new algorithmic solutions in TDA and their transfer to
+ * applications. It provides robust, efficient, flexible and easy to use implementations of state-of-the-art
+ * algorithms and data structures.
  * 
  * The current release of the GUDHI library includes:
  * 
@@ -20,24 +19,138 @@
  * All data-structures are generic and several of their aspects can be parameterized via template classes.
  * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library.
  *
- * The library is available <a class="el" target="_blank" href="https://gforge.inria.fr/frs/?group_id=3865">here</a>
- * and the documentation is available at this <a class="el" href="http://gudhi.gforge.inria.fr/doc/latest/">
- * webpage</a>.
- * 
- * The library comes with data sets, \ref demos and \ref testsuites.
- * 
- * Gudhi is also accessible though the
- * <a class="el" target="_blank" href="https://cran.r-project.org/web/packages/TDA/index.html">R package TDA</a>
- * (Statistical Tools for Topological Data Analysis).
- * 
- * The development of the GUDHI library is steered by an Editorial Board composed of:
- * 
- * \li <a class="el" target="_blank" href="http://www-sop.inria.fr/members/Jean-Daniel.Boissonnat/">
- * Jean-Daniel Boissonnat</a> | INRIA Sophia Antipolis - Méditerranée
- * \li <a class="el" target="_blank" href="http://geometrica.saclay.inria.fr/team/Marc.Glisse/">Marc Glisse</a> | INRIA Saclay - Ile de France
- * \li Clément Jamin | INRIA Sophia Antipolis - Méditerranée
- * \li Vincent Rouvreau | INRIA Saclay - Ile de France
- * 
+ \section DataStructures Data structures
+ \subsection AlphaComplexDataStructure Alpha complex
+ \image html "alpha_complex_representation.png" "Alpha complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Vincent Rouvreau<br>
+      <b>Introduced in:</b> GUDHI 1.3.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.<br>
+    The filtration value of each simplex is computed as the square of the circumradius of the simplex if the
+    circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration
+    values of the codimension 1 cofaces that make it not Gabriel otherwise.
+    All simplices that have a filtration value strictly greater than a given alpha squared value are not inserted into
+    the complex.<br>
+    <b>User manual:</b> \ref alpha_complex - <b>Reference manual:</b> Gudhi::alphacomplex::Alpha_complex
+    </td>
+ </tr>
+</table>
+ \subsection CubicalComplexDataStructure Cubical complex
+ \image html "Cubical_complex_representation.png" "Cubical complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Pawel Dlotko<br>
+      <b>Introduced in:</b> GUDHI 1.3.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The cubical complex is an example of a structured complex useful in computational mathematics (specially
+    rigorous numerics) and image analysis.<br>
+    <b>User manual:</b> \ref cubical_complex - <b>Reference manual:</b> Gudhi::Cubical_complex::Bitmap_cubical_complex
+    </td>
+ </tr>
+</table>
+ \subsection SimplexTreeDataStructure Simplex tree
+ \image html "Simplex_tree_representation.png" "Simplex tree representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Cl&eacute;ment Maria<br>
+      <b>Introduced in:</b> GUDHI 1.0.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The simplex tree is an efficient and flexible
+ data structure for representing general (filtered) simplicial complexes. The data structure
+ is described in \cite boissonnatmariasimplextreealgorithmica .<br>
+    <b>User manual:</b> \ref simplex_tree - <b>Reference manual:</b> Gudhi::Simplex_tree
+    </td>
+ </tr>
+</table>
+ \subsection SkeletonBlockerDataStructure Skeleton blocker
+ \image html "ds_representation.png" "Skeleton blocker representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> David Salinas<br>
+      <b>Introduced in:</b> GUDHI 1.1.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit*
+    representation of its simplices \cite socg_blockers_2011,\cite blockers2012. Intuitively, it just stores the
+    1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that is very small in practice.
+    This data-structure handles all simplicial complexes operations such as simplex enumeration or simplex removal but
+    operations that are particularly efficient are operations that do not require simplex enumeration such as edge
+    iteration, link computation or simplex contraction.<br>
+    <b>User manual:</b> \ref skbl - <b>Reference manual:</b> Gudhi::skbl::Skeleton_blocker_complex
+    </td>
+ </tr>
+</table>
+ \subsection WitnessComplexDataStructure Witness complex
+ \image html "Witness_complex_representation.png" "Witness complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Siargey Kachanovich<br>
+      <b>Introduced in:</b> GUDHI 1.3.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    Witness complex \f$ Wit(W,L) \f$  is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$.
+    The data structure is described in \cite boissonnatmariasimplextreealgorithmica .<br>
+    <b>User manual:</b> \ref witness_complex - <b>Reference manual:</b> Gudhi::witness_complex::SimplicialComplexForWitness
+    </td>
+ </tr>
+</table>
+ 
+ \section Toolbox Toolbox
+ \subsection ContractionToolbox Contraction
+ \image html "sphere_contraction_representation.png" "Sphere contraction example"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> David Salinas<br>
+      <b>Introduced in:</b> GUDHI 1.1.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The purpose of this package is to offer a user-friendly interface for edge contraction simplification of huge
+    simplicial complexes. It uses the \ref skbl data-structure whose size remains small  during simplification of most
+    used geometrical complexes of topological data analysis such as the Rips or the Delaunay complexes. In practice,
+    the size of this data-structure is even much lower than the total number of simplices.<br>
+    <b>User manual:</b> \ref contr
+    </td>
+ </tr>
+</table>
+ \subsection PersistentCohomologyToolbox Persistent Cohomology
+ \image html "3DTorus_poch.png" "Rips Persistent Cohomology on a 3D Torus"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Cl&eacute;ment Maria<br>
+      <b>Introduced in:</b> GUDHI 1.0.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The theory of homology consists in attaching to a topological space a sequence of (homology) groups, capturing
+    global topological features like connected components, holes, cavities, etc. Persistent homology studies the
+    evolution -- birth, life and death -- of these features when the topological space is changing. Consequently, the
+    theory is essentially composed of three elements: topological spaces, their homology groups and an evolution
+    scheme.
+    Computation of persistent cohomology using the algorithm of \cite DBLP:journals/dcg/SilvaMV11 and
+    \cite DBLP:journals/corr/abs-1208-5018 and the Compressed Annotation Matrix implementation of
+    \cite DBLP:conf/esa/BoissonnatDM13 .<br>
+    <b>User manual:</b> \ref persistent_cohomology - <b>Reference manual:</b> Gudhi::persistent_cohomology::Persistent_cohomology
+    </td>
+ </tr>
+</table>
 */
 
 /*! \page installation Gudhi installation
@@ -47,7 +160,7 @@
  * 
  * \section compiling Compiling
  * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or
- * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013.
+ * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
  * 
  * \subsection gmp GMP:
  * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
@@ -55,31 +168,114 @@
  * 
  * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic
  * Library</a> (GMP) and will not be built if GMP is not installed:
- * \li Persistent_cohomology/rips_multifield_persistence
+ * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/performance_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_multifield_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
  *
  * Having GMP version 4.2 or higher installed is recommended.
  * 
  * \subsection cgal CGAL:
  * CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms.
  * 
+ * Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to
+ * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
+ * 
  * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
  * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed:
- * \li GudhUI
- * \li Persistent_cohomology/alpha_shapes_persistence
- * \li Simplex_tree/simplex_tree_from_alpha_shapes_3
- * \li Alpha_complex/Alpha_complex_from_off
- * \li Alpha_complex/Alpha_complex_from_points
+ * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ *  Alpha_complex/Alpha_complex_from_off.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ *  Alpha_complex/Alpha_complex_from_points.cpp</a>
  * 
- * Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to
- * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
+ * The following example requires CGAL version &ge; 4.6:
+ * \li <a href="_witness_complex_2witness_complex_sphere_8cpp-example.html">
+ * Witness_complex/witness_complex_sphere.cpp</a>
+ * 
+ * The following example requires CGAL version &ge; 4.7:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_off.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="common_2_c_g_a_l_points_off_reader_8cpp-example.html">
+ * common/CGAL_points_off_reader.cpp</a>
+ * 
+ * \subsection eigen3 Eigen3:
+ * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra:
+ * matrices, vectors, numerical solvers, and related algorithms.
+ * 
+ * The following example requires the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be
+ * built if Eigen3 is not installed:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_off.cpp</a> (requires also Eigen3)
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a> (requires also Eigen3)
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
+ * 
+ * \subsection tbb Threading Building Blocks:
+ * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel&reg; TBB</a> lets you easily write parallel
+ * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have
+ * future-proof scalability.
+ * 
+ * Having Intel&reg; TBB installed is recommended to parallelize and accelerate some GUDHI computations.
+ * 
+ * The following examples are using Intel&reg; TBB if installed:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_off.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
+ * Bitmap_cubical_complex/Bitmap_cubical_complex.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
+ * Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp</a>
+ * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html">
+ * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
+ * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
+ * Simplex_tree/simple_simplex_tree.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
+ * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html">
+ * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2parallel_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/parallel_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2performance_rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/performance_rips_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html">
+ * Persistent_cohomology/persistence_from_file.cpp</a>
+ * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html">
+ * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a>
+ * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html">
+ * Persistent_cohomology/plain_homology.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_multifield_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html">
+ * Persistent_cohomology/rips_persistence.cpp</a>
  * 
  * \subsection demos Demos and examples
- * To build the demos and libraries, run the following commands in a terminal:
+ * To build the demos and examples, run the following commands in a terminal:
 \verbatim  cd /path-to-gudhi/
 mkdir build
 cd build/
 cmake ..
 make \endverbatim
+ * A list of examples is available <a href="examples.html">here</a>.
  * 
  * \subsection testsuites Test suites
  * To test your build, run the following command in a terminal:
@@ -93,17 +289,6 @@ make \endverbatim
  * 
 */
 
-/*! \page Upcoming Upcoming
- *
- * The library is under active development. New packages to be released next include:
- * \li Alpha complex.
- * \li Bottleneck distance.
- * \li Zig zag persistence.
- * \li Witness complex.
- * \li Tangential complex.
- * \li Clustering.
-*/
-
 /*! \page Citation Acknowledging the GUDHI library
  * We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use
  * of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages.
@@ -115,3 +300,33 @@ make \endverbatim
  * \verbinclude  biblio/how_to_cite_gudhi.bib
 */
 
+// List of Gudhi examples - Doxygen needs at least a file tag to analyse comments
+/*! @file Examples
+ * @example Alpha_complex/Alpha_complex_from_off.cpp
+ * @example Alpha_complex/Alpha_complex_from_points.cpp
+ * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp
+ * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
+ * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
+ * @example common/CGAL_points_off_reader.cpp
+ * @example Contraction/Garland_heckbert.cpp
+ * @example Contraction/Rips_contraction.cpp
+ * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp
+ * @example Persistent_cohomology/alpha_complex_persistence.cpp
+ * @example Persistent_cohomology/parallel_rips_persistence.cpp
+ * @example Persistent_cohomology/performance_rips_persistence.cpp
+ * @example Persistent_cohomology/persistence_from_file.cpp
+ * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
+ * @example Persistent_cohomology/plain_homology.cpp
+ * @example Persistent_cohomology/rips_multifield_persistence.cpp
+ * @example Persistent_cohomology/rips_persistence.cpp
+ * @example Simplex_tree/mini_simplex_tree.cpp
+ * @example Simplex_tree/simple_simplex_tree.cpp
+ * @example Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp
+ * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp
+ * @example Skeleton_blocker/Skeleton_blocker_link.cpp
+ * @example Witness_complex/witness_complex_from_file.cpp
+ * @example Witness_complex/witness_complex_sphere.cpp
+ */
+
diff --git a/src/common/doc/stylesheet.css b/src/common/doc/stylesheet.css
new file mode 100644
index 00000000..1df177a4
--- /dev/null
+++ b/src/common/doc/stylesheet.css
@@ -0,0 +1,1367 @@
+/* The standard CSS for doxygen 1.8.6 */
+
+body, table, div, p, dl {
+	font: 400 14px/22px Roboto,sans-serif;
+}
+
+/* @group Heading Levels */
+
+h1.groupheader {
+	font-size: 150%;
+}
+
+.title {
+	font: 400 14px/28px Roboto,sans-serif;
+	font-size: 150%;
+	font-weight: bold;
+	margin: 10px 2px;
+}
+
+h2.groupheader {
+	border-bottom: 1px solid #879ECB;
+	color: #354C7B;
+	font-size: 150%;
+	font-weight: normal;
+	margin-top: 1.75em;
+	padding-top: 8px;
+	padding-bottom: 4px;
+	width: 100%;
+}
+
+h3.groupheader {
+	font-size: 100%;
+}
+
+h1, h2, h3, h4, h5, h6 {
+	-webkit-transition: text-shadow 0.5s linear;
+	-moz-transition: text-shadow 0.5s linear;
+	-ms-transition: text-shadow 0.5s linear;
+	-o-transition: text-shadow 0.5s linear;
+	transition: text-shadow 0.5s linear;
+	margin-right: 15px;
+}
+
+h1.glow, h2.glow, h3.glow, h4.glow, h5.glow, h6.glow {
+	text-shadow: 0 0 15px cyan;
+}
+
+dt {
+	font-weight: bold;
+}
+
+div.multicol {
+	-moz-column-gap: 1em;
+	-webkit-column-gap: 1em;
+	-moz-column-count: 3;
+	-webkit-column-count: 3;
+}
+
+p.startli, p.startdd {
+	margin-top: 2px;
+}
+
+p.starttd {
+	margin-top: 0px;
+}
+
+p.endli {
+	margin-bottom: 0px;
+}
+
+p.enddd {
+	margin-bottom: 4px;
+}
+
+p.endtd {
+	margin-bottom: 2px;
+}
+
+/* @end */
+
+caption {
+	font-weight: bold;
+}
+
+span.legend {
+        font-size: 70%;
+        text-align: center;
+}
+
+h3.version {
+        font-size: 90%;
+        text-align: center;
+}
+
+div.qindex, div.navtab{
+	background-color: #EBEFF6;
+	border: 1px solid #A3B4D7;
+	text-align: center;
+}
+
+div.qindex, div.navpath {
+	width: 100%;
+	line-height: 140%;
+}
+
+div.navtab {
+	margin-right: 15px;
+}
+
+/* @group Link Styling */
+
+a {
+	color: #3D578C;
+	font-weight: normal;
+	text-decoration: none;
+}
+
+.contents a:visited {
+	color: #4665A2;
+}
+
+a:hover {
+	text-decoration: underline;
+}
+
+a.qindex {
+	font-weight: bold;
+}
+
+a.qindexHL {
+	font-weight: bold;
+	background-color: #9CAFD4;
+	color: #ffffff;
+	border: 1px double #869DCA;
+}
+
+.contents a.qindexHL:visited {
+        color: #ffffff;
+}
+
+a.el {
+	font-weight: bold;
+}
+
+a.elRef {
+}
+
+a.code, a.code:visited, a.line, a.line:visited {
+	color: #4665A2; 
+}
+
+a.codeRef, a.codeRef:visited, a.lineRef, a.lineRef:visited {
+	color: #4665A2; 
+}
+
+/* @end */
+
+dl.el {
+	margin-left: -1cm;
+}
+
+pre.fragment {
+        border: 1px solid #C4CFE5;
+        background-color: #FBFCFD;
+        padding: 4px 6px;
+        margin: 4px 8px 4px 2px;
+        overflow: auto;
+        word-wrap: break-word;
+        font-size:  9pt;
+        line-height: 125%;
+        font-family: monospace, fixed;
+        font-size: 105%;
+}
+
+div.fragment {
+        padding: 4px 6px;
+        margin: 4px 8px 4px 2px;
+	background-color: #FBFCFD;
+	border: 1px solid #C4CFE5;
+}
+
+div.line {
+	font-family: monospace, fixed;
+        font-size: 13px;
+	min-height: 13px;
+	line-height: 1.0;
+	text-wrap: unrestricted;
+	white-space: -moz-pre-wrap; /* Moz */
+	white-space: -pre-wrap;     /* Opera 4-6 */
+	white-space: -o-pre-wrap;   /* Opera 7 */
+	white-space: pre-wrap;      /* CSS3  */
+	word-wrap: break-word;      /* IE 5.5+ */
+	text-indent: -53px;
+	padding-left: 53px;
+	padding-bottom: 0px;
+	margin: 0px;
+	-webkit-transition-property: background-color, box-shadow;
+	-webkit-transition-duration: 0.5s;
+	-moz-transition-property: background-color, box-shadow;
+	-moz-transition-duration: 0.5s;
+	-ms-transition-property: background-color, box-shadow;
+	-ms-transition-duration: 0.5s;
+	-o-transition-property: background-color, box-shadow;
+	-o-transition-duration: 0.5s;
+	transition-property: background-color, box-shadow;
+	transition-duration: 0.5s;
+}
+
+div.line.glow {
+	background-color: cyan;
+	box-shadow: 0 0 10px cyan;
+}
+
+
+span.lineno {
+	padding-right: 4px;
+	text-align: right;
+	border-right: 2px solid #0F0;
+	background-color: #E8E8E8;
+        white-space: pre;
+}
+span.lineno a {
+	background-color: #D8D8D8;
+}
+
+span.lineno a:hover {
+	background-color: #C8C8C8;
+}
+
+div.ah {
+	background-color: black;
+	font-weight: bold;
+	color: #ffffff;
+	margin-bottom: 3px;
+	margin-top: 3px;
+	padding: 0.2em;
+	border: solid thin #333;
+	border-radius: 0.5em;
+	-webkit-border-radius: .5em;
+	-moz-border-radius: .5em;
+	box-shadow: 2px 2px 3px #999;
+	-webkit-box-shadow: 2px 2px 3px #999;
+	-moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+	background-image: -webkit-gradient(linear, left top, left bottom, from(#eee), to(#000),color-stop(0.3, #444));
+	background-image: -moz-linear-gradient(center top, #eee 0%, #444 40%, #000);
+}
+
+div.groupHeader {
+	margin-left: 16px;
+	margin-top: 12px;
+	font-weight: bold;
+}
+
+div.groupText {
+	margin-left: 16px;
+	font-style: italic;
+}
+
+body {
+	background-color: white;
+	color: black;
+        margin: 0;
+}
+
+div.contents {
+	margin-top: 10px;
+	margin-left: 12px;
+	margin-right: 8px;
+}
+
+td.indexkey {
+	background-color: #EBEFF6;
+	font-weight: bold;
+	border: 1px solid #C4CFE5;
+	margin: 2px 0px 2px 0;
+	padding: 2px 10px;
+        white-space: nowrap;
+        vertical-align: top;
+}
+
+td.indexvalue {
+	background-color: #EBEFF6;
+	border: 1px solid #C4CFE5;
+	padding: 2px 10px;
+	margin: 2px 0px;
+}
+
+tr.memlist {
+	background-color: #EEF1F7;
+}
+
+p.formulaDsp {
+	text-align: center;
+}
+
+img.formulaDsp {
+	
+}
+
+img.formulaInl {
+	vertical-align: middle;
+}
+
+div.center {
+	text-align: center;
+        margin-top: 0px;
+        margin-bottom: 0px;
+        padding: 0px;
+}
+
+div.center img {
+	border: 0px;
+}
+
+address.footer {
+	text-align: right;
+	padding-right: 12px;
+}
+
+img.footer {
+	border: 0px;
+	vertical-align: middle;
+}
+
+/* @group Code Colorization */
+
+span.keyword {
+	color: #008000
+}
+
+span.keywordtype {
+	color: #604020
+}
+
+span.keywordflow {
+	color: #e08000
+}
+
+span.comment {
+	color: #800000
+}
+
+span.preprocessor {
+	color: #806020
+}
+
+span.stringliteral {
+	color: #002080
+}
+
+span.charliteral {
+	color: #008080
+}
+
+span.vhdldigit { 
+	color: #ff00ff 
+}
+
+span.vhdlchar { 
+	color: #000000 
+}
+
+span.vhdlkeyword { 
+	color: #700070 
+}
+
+span.vhdllogic { 
+	color: #ff0000 
+}
+
+blockquote {
+        background-color: #F7F8FB;
+        border-left: 2px solid #9CAFD4;
+        margin: 0 24px 0 4px;
+        padding: 0 12px 0 16px;
+}
+
+/* @end */
+
+/*
+.search {
+	color: #003399;
+	font-weight: bold;
+}
+
+form.search {
+	margin-bottom: 0px;
+	margin-top: 0px;
+}
+
+input.search {
+	font-size: 75%;
+	color: #000080;
+	font-weight: normal;
+	background-color: #e8eef2;
+}
+*/
+
+td.tiny {
+	font-size: 75%;
+}
+
+.dirtab {
+	padding: 4px;
+	border-collapse: collapse;
+	border: 1px solid #A3B4D7;
+}
+
+th.dirtab {
+	background: #EBEFF6;
+	font-weight: bold;
+}
+
+hr {
+	height: 0px;
+	border: none;
+	border-top: 1px solid #4A6AAA;
+}
+
+hr.footer {
+	height: 1px;
+}
+
+/* @group Member Descriptions */
+
+table.memberdecls {
+	border-spacing: 0px;
+	padding: 0px;
+}
+
+.memberdecls td, .fieldtable tr {
+	-webkit-transition-property: background-color, box-shadow;
+	-webkit-transition-duration: 0.5s;
+	-moz-transition-property: background-color, box-shadow;
+	-moz-transition-duration: 0.5s;
+	-ms-transition-property: background-color, box-shadow;
+	-ms-transition-duration: 0.5s;
+	-o-transition-property: background-color, box-shadow;
+	-o-transition-duration: 0.5s;
+	transition-property: background-color, box-shadow;
+	transition-duration: 0.5s;
+}
+
+.memberdecls td.glow, .fieldtable tr.glow {
+	background-color: cyan;
+	box-shadow: 0 0 15px cyan;
+}
+
+.mdescLeft, .mdescRight,
+.memItemLeft, .memItemRight,
+.memTemplItemLeft, .memTemplItemRight, .memTemplParams {
+	background-color: #F9FAFC;
+	border: none;
+	margin: 4px;
+	padding: 1px 0 0 8px;
+}
+
+.mdescLeft, .mdescRight {
+	padding: 0px 8px 4px 8px;
+	color: #555;
+}
+
+.memSeparator {
+        border-bottom: 1px solid #DEE4F0;
+        line-height: 1px;
+        margin: 0px;
+        padding: 0px;
+}
+
+.memItemLeft, .memTemplItemLeft {
+        white-space: nowrap;
+}
+
+.memItemRight {
+	width: 100%;
+}
+
+.memTemplParams {
+	color: #4665A2;
+        white-space: nowrap;
+	font-size: 80%;
+}
+
+/* @end */
+
+/* @group Member Details */
+
+/* Styles for detailed member documentation */
+
+.memtemplate {
+	font-size: 80%;
+	color: #4665A2;
+	font-weight: normal;
+	margin-left: 9px;
+}
+
+.memnav {
+	background-color: #EBEFF6;
+	border: 1px solid #A3B4D7;
+	text-align: center;
+	margin: 2px;
+	margin-right: 15px;
+	padding: 2px;
+}
+
+.mempage {
+	width: 100%;
+}
+
+.memitem {
+	padding: 0;
+	margin-bottom: 10px;
+	margin-right: 5px;
+        -webkit-transition: box-shadow 0.5s linear;
+        -moz-transition: box-shadow 0.5s linear;
+        -ms-transition: box-shadow 0.5s linear;
+        -o-transition: box-shadow 0.5s linear;
+        transition: box-shadow 0.5s linear;
+        display: table !important;
+        width: 100%;
+}
+
+.memitem.glow {
+         box-shadow: 0 0 15px cyan;
+}
+
+.memname {
+        font-weight: bold;
+        margin-left: 6px;
+}
+
+.memname td {
+	vertical-align: bottom;
+}
+
+.memproto, dl.reflist dt {
+        border-top: 1px solid #A8B8D9;
+        border-left: 1px solid #A8B8D9;
+        border-right: 1px solid #A8B8D9;
+        padding: 6px 0px 6px 0px;
+        color: #253555;
+        font-weight: bold;
+        text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+        background-image:url('nav_f.png');
+        background-repeat:repeat-x;
+        background-color: #E2E8F2;
+        /* opera specific markup */
+        box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+        border-top-right-radius: 4px;
+        border-top-left-radius: 4px;
+        /* firefox specific markup */
+        -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+        -moz-border-radius-topright: 4px;
+        -moz-border-radius-topleft: 4px;
+        /* webkit specific markup */
+        -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+        -webkit-border-top-right-radius: 4px;
+        -webkit-border-top-left-radius: 4px;
+
+}
+
+.memdoc, dl.reflist dd {
+        border-bottom: 1px solid #A8B8D9;      
+        border-left: 1px solid #A8B8D9;      
+        border-right: 1px solid #A8B8D9; 
+        padding: 6px 10px 2px 10px;
+        background-color: #FBFCFD;
+        border-top-width: 0;
+        background-image:url('nav_g.png');
+        background-repeat:repeat-x;
+        background-color: #FFFFFF;
+        /* opera specific markup */
+        border-bottom-left-radius: 4px;
+        border-bottom-right-radius: 4px;
+        box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+        /* firefox specific markup */
+        -moz-border-radius-bottomleft: 4px;
+        -moz-border-radius-bottomright: 4px;
+        -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+        /* webkit specific markup */
+        -webkit-border-bottom-left-radius: 4px;
+        -webkit-border-bottom-right-radius: 4px;
+        -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
+}
+
+dl.reflist dt {
+        padding: 5px;
+}
+
+dl.reflist dd {
+        margin: 0px 0px 10px 0px;
+        padding: 5px;
+}
+
+.paramkey {
+	text-align: right;
+}
+
+.paramtype {
+	white-space: nowrap;
+}
+
+.paramname {
+	color: #602020;
+	white-space: nowrap;
+}
+.paramname em {
+	font-style: normal;
+}
+.paramname code {
+        line-height: 14px;
+}
+
+.params, .retval, .exception, .tparams {
+        margin-left: 0px;
+        padding-left: 0px;
+}       
+
+.params .paramname, .retval .paramname {
+        font-weight: bold;
+        vertical-align: top;
+}
+        
+.params .paramtype {
+        font-style: italic;
+        vertical-align: top;
+}       
+        
+.params .paramdir {
+        font-family: "courier new",courier,monospace;
+        vertical-align: top;
+}
+
+table.mlabels {
+	border-spacing: 0px;
+}
+
+td.mlabels-left {
+	width: 100%;
+	padding: 0px;
+}
+
+td.mlabels-right {
+	vertical-align: bottom;
+	padding: 0px;
+	white-space: nowrap;
+}
+
+span.mlabels {
+        margin-left: 8px;
+}
+
+span.mlabel {
+        background-color: #728DC1;
+        border-top:1px solid #5373B4;
+        border-left:1px solid #5373B4;
+        border-right:1px solid #C4CFE5;
+        border-bottom:1px solid #C4CFE5;
+	text-shadow: none;
+	color: white;
+	margin-right: 4px;
+	padding: 2px 3px;
+	border-radius: 3px;
+	font-size: 7pt;
+	white-space: nowrap;
+	vertical-align: middle;
+}
+
+
+
+/* @end */
+
+/* these are for tree view when not used as main index */
+
+div.directory {
+        margin: 10px 0px;
+        border-top: 1px solid #A8B8D9;
+        border-bottom: 1px solid #A8B8D9;
+        width: 100%;
+}
+
+.directory table {
+        border-collapse:collapse;
+}
+
+.directory td {
+        margin: 0px;
+        padding: 0px;
+	vertical-align: top;
+}
+
+.directory td.entry {
+        white-space: nowrap;
+        padding-right: 6px;
+	padding-top: 3px;
+}
+
+.directory td.entry a {
+        outline:none;
+}
+
+.directory td.entry a img {
+        border: none;
+}
+
+.directory td.desc {
+        width: 100%;
+        padding-left: 6px;
+	padding-right: 6px;
+	padding-top: 3px;
+	border-left: 1px solid rgba(0,0,0,0.05);
+}
+
+.directory tr.even {
+	padding-left: 6px;
+	background-color: #F7F8FB;
+}
+
+.directory img {
+	vertical-align: -30%;
+}
+
+.directory .levels {
+        white-space: nowrap;
+        width: 100%;
+        text-align: right;
+        font-size: 9pt;
+}
+
+.directory .levels span {
+        cursor: pointer;
+        padding-left: 2px;
+        padding-right: 2px;
+	color: #3D578C;
+}
+
+div.dynheader {
+        margin-top: 8px;
+	-webkit-touch-callout: none;
+	-webkit-user-select: none;
+	-khtml-user-select: none;
+	-moz-user-select: none;
+	-ms-user-select: none;
+	user-select: none;
+}
+
+address {
+	font-style: normal;
+	color: #2A3D61;
+}
+
+table.doxtable {
+	border-collapse:collapse;
+        margin-top: 4px;
+        margin-bottom: 4px;
+}
+
+table.doxtable td, table.doxtable th {
+	border: 1px solid #2D4068;
+	padding: 3px 7px 2px;
+}
+
+table.doxtable th {
+	background-color: #374F7F;
+	color: #FFFFFF;
+	font-size: 110%;
+	padding-bottom: 4px;
+	padding-top: 5px;
+}
+
+table.fieldtable {
+        /*width: 100%;*/
+        margin-bottom: 10px;
+        border: 1px solid #A8B8D9;
+        border-spacing: 0px;
+        -moz-border-radius: 4px;
+        -webkit-border-radius: 4px;
+        border-radius: 4px;
+        -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+        -webkit-box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+        box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+}
+
+.fieldtable td, .fieldtable th {
+        padding: 3px 7px 2px;
+}
+
+.fieldtable td.fieldtype, .fieldtable td.fieldname {
+        white-space: nowrap;
+        border-right: 1px solid #A8B8D9;
+        border-bottom: 1px solid #A8B8D9;
+        vertical-align: top;
+}
+
+.fieldtable td.fieldname {
+        padding-top: 3px;
+}
+
+.fieldtable td.fielddoc {
+        border-bottom: 1px solid #A8B8D9;
+        /*width: 100%;*/
+}
+
+.fieldtable td.fielddoc p:first-child {
+        margin-top: 0px;
+}       
+        
+.fieldtable td.fielddoc p:last-child {
+        margin-bottom: 2px;
+}
+
+.fieldtable tr:last-child td {
+        border-bottom: none;
+}
+
+.fieldtable th {
+        background-image:url('nav_f.png');
+        background-repeat:repeat-x;
+        background-color: #E2E8F2;
+        font-size: 90%;
+        color: #253555;
+        padding-bottom: 4px;
+        padding-top: 5px;
+        text-align:left;
+        -moz-border-radius-topleft: 4px;
+        -moz-border-radius-topright: 4px;
+        -webkit-border-top-left-radius: 4px;
+        -webkit-border-top-right-radius: 4px;
+        border-top-left-radius: 4px;
+        border-top-right-radius: 4px;
+        border-bottom: 1px solid #A8B8D9;
+}
+
+
+.tabsearch {
+	top: 0px;
+	left: 10px;
+	height: 36px;
+	background-image: url('tab_b.png');
+	z-index: 101;
+	overflow: hidden;
+	font-size: 13px;
+}
+
+.navpath ul
+{
+	font-size: 11px;
+	background-image:url('tab_b.png');
+	background-repeat:repeat-x;
+	background-position: 0 -5px;
+	height:30px;
+	line-height:30px;
+	color:#8AA0CC;
+	border:solid 1px #C2CDE4;
+	overflow:hidden;
+	margin:0px;
+	padding:0px;
+}
+
+.navpath li
+{
+	list-style-type:none;
+	float:left;
+	padding-left:10px;
+	padding-right:15px;
+	background-image:url('bc_s.png');
+	background-repeat:no-repeat;
+	background-position:right;
+	color:#364D7C;
+}
+
+.navpath li.navelem a
+{
+	height:32px;
+	display:block;
+	text-decoration: none;
+	outline: none;
+	color: #283A5D;
+	font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
+	text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+	text-decoration: none;        
+}
+
+.navpath li.navelem a:hover
+{
+	color:#6884BD;
+}
+
+.navpath li.footer
+{
+        list-style-type:none;
+        float:right;
+        padding-left:10px;
+        padding-right:15px;
+        background-image:none;
+        background-repeat:no-repeat;
+        background-position:right;
+        color:#364D7C;
+        font-size: 8pt;
+}
+
+
+div.summary
+{
+	float: right;
+	font-size: 8pt;
+	padding-right: 5px;
+	width: 50%;
+	text-align: right;
+}       
+
+div.summary a
+{
+	white-space: nowrap;
+}
+
+div.ingroups
+{
+	font-size: 8pt;
+	width: 50%;
+	text-align: left;
+}
+
+div.ingroups a
+{
+	white-space: nowrap;
+}
+
+div.header
+{
+        background-image:url('nav_h.png');
+        background-repeat:repeat-x;
+	background-color: #F9FAFC;
+	margin:  0px;
+	border-bottom: 1px solid #C4CFE5;
+}
+
+div.headertitle
+{
+	padding: 5px 5px 5px 10px;
+}
+
+dl
+{
+        padding: 0 0 0 10px;
+}
+
+/* dl.note, dl.warning, dl.attention, dl.pre, dl.post, dl.invariant, dl.deprecated, dl.todo, dl.test, dl.bug */
+dl.section
+{
+	margin-left: 0px;
+	padding-left: 0px;
+}
+
+dl.note
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #D0C000;
+}
+
+dl.warning, dl.attention
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #FF0000;
+}
+
+dl.pre, dl.post, dl.invariant
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #00D000;
+}
+
+dl.deprecated
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #505050;
+}
+
+dl.todo
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #00C0E0;
+}
+
+dl.test
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #3030E0;
+}
+
+dl.bug
+{
+        margin-left:-7px;
+        padding-left: 3px;
+        border-left:4px solid;
+        border-color: #C08050;
+}
+
+dl.section dd {
+	margin-bottom: 6px;
+}
+
+
+#projectlogo
+{
+	text-align: center;
+	vertical-align: bottom;
+	border-collapse: separate;
+}
+ 
+#projectlogo img
+{ 
+	border: 0px none;
+}
+ 
+#projectname
+{
+	border: 0px none;
+	font: 300% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 2px 0px;
+}
+    
+#projectbrief
+{
+	font: 60% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 0px;
+}
+
+#projectnumber
+{
+	font: 80% Tahoma, Arial,sans-serif;
+	margin: 0px;
+	padding: 0px;
+}
+
+#titlearea
+{
+	padding: 0px;
+	margin: 0px;
+	width: 100%;
+	border-bottom: 1px solid #5373B4;
+}
+
+.image
+{
+        text-align: center;
+}
+
+.dotgraph
+{
+        text-align: center;
+}
+
+.mscgraph
+{
+        text-align: center;
+}
+
+.diagraph
+{
+        text-align: center;
+}
+
+.caption
+{
+	font-weight: bold;
+}
+
+div.zoom
+{
+	border: 1px solid #90A5CE;
+}
+
+dl.citelist {
+        margin-bottom:50px;
+}
+
+dl.citelist dt {
+        color:#334975;
+        float:left;
+        font-weight:bold;
+        margin-right:10px;
+        padding:5px;
+}
+
+dl.citelist dd {
+        margin:2px 0;
+        padding:5px 0;
+}
+
+div.toc {
+        padding: 14px 25px;
+        background-color: #F4F6FA;
+        border: 1px solid #D8DFEE;
+        border-radius: 7px 7px 7px 7px;
+        float: right;
+        height: auto;
+        margin: 0 20px 10px 10px;
+        width: 200px;
+}
+
+div.toc li {
+        background: url("bdwn.png") no-repeat scroll 0 5px transparent;
+        font: 10px/1.2 Verdana,DejaVu Sans,Geneva,sans-serif;
+        margin-top: 5px;
+        padding-left: 10px;
+        padding-top: 2px;
+}
+
+div.toc h3 {
+        font: bold 12px/1.2 Arial,FreeSans,sans-serif;
+	color: #4665A2;
+        border-bottom: 0 none;
+        margin: 0;
+}
+
+div.toc ul {
+        list-style: none outside none;
+        border: medium none;
+        padding: 0px;
+}       
+
+div.toc li.level1 {
+        margin-left: 0px;
+}
+
+div.toc li.level2 {
+        margin-left: 15px;
+}
+
+div.toc li.level3 {
+        margin-left: 30px;
+}
+
+div.toc li.level4 {
+        margin-left: 45px;
+}
+
+.inherit_header {
+        font-weight: bold;
+        color: gray;
+        cursor: pointer;
+	-webkit-touch-callout: none;
+	-webkit-user-select: none;
+	-khtml-user-select: none;
+	-moz-user-select: none;
+	-ms-user-select: none;
+	user-select: none;
+}
+
+.inherit_header td {
+        padding: 6px 0px 2px 5px;
+}
+
+.inherit {
+        display: none;
+}
+
+tr.heading h2 {
+        margin-top: 12px;
+        margin-bottom: 4px;
+}
+
+/* tooltip related style info */
+
+.ttc {
+        position: absolute;
+        display: none;
+}
+
+#powerTip {
+	cursor: default;
+	white-space: nowrap;
+	background-color: white;
+	border: 1px solid gray;
+	border-radius: 4px 4px 4px 4px;
+	box-shadow: 1px 1px 7px gray;
+	display: none;
+	font-size: smaller;
+	max-width: 80%;
+	opacity: 0.9;
+	padding: 1ex 1em 1em;
+	position: absolute;
+	z-index: 2147483647;
+}
+
+#powerTip div.ttdoc {
+        color: grey;
+	font-style: italic;
+}
+
+#powerTip div.ttname a {
+        font-weight: bold;
+}
+
+#powerTip div.ttname {
+        font-weight: bold;
+}
+
+#powerTip div.ttdeci {
+        color: #006318;
+}
+
+#powerTip div {
+        margin: 0px;
+        padding: 0px;
+        font: 12px/16px Roboto,sans-serif;
+}
+
+#powerTip:before, #powerTip:after {
+	content: "";
+	position: absolute;
+	margin: 0px;
+}
+
+#powerTip.n:after,  #powerTip.n:before,
+#powerTip.s:after,  #powerTip.s:before,
+#powerTip.w:after,  #powerTip.w:before,
+#powerTip.e:after,  #powerTip.e:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.nw:after, #powerTip.nw:before,
+#powerTip.sw:after, #powerTip.sw:before {
+	border: solid transparent;
+	content: " ";
+	height: 0;
+	width: 0;
+	position: absolute;
+}
+
+#powerTip.n:after,  #powerTip.s:after,
+#powerTip.w:after,  #powerTip.e:after,
+#powerTip.nw:after, #powerTip.ne:after,
+#powerTip.sw:after, #powerTip.se:after {
+	border-color: rgba(255, 255, 255, 0);
+}
+
+#powerTip.n:before,  #powerTip.s:before,
+#powerTip.w:before,  #powerTip.e:before,
+#powerTip.nw:before, #powerTip.ne:before,
+#powerTip.sw:before, #powerTip.se:before {
+	border-color: rgba(128, 128, 128, 0);
+}
+
+#powerTip.n:after,  #powerTip.n:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.nw:after, #powerTip.nw:before {
+	top: 100%;
+}
+
+#powerTip.n:after, #powerTip.ne:after, #powerTip.nw:after {
+	border-top-color: #ffffff;
+	border-width: 10px;
+	margin: 0px -10px;
+}
+#powerTip.n:before {
+	border-top-color: #808080;
+	border-width: 11px;
+	margin: 0px -11px;
+}
+#powerTip.n:after, #powerTip.n:before {
+	left: 50%;
+}
+
+#powerTip.nw:after, #powerTip.nw:before {
+	right: 14px;
+}
+
+#powerTip.ne:after, #powerTip.ne:before {
+	left: 14px;
+}
+
+#powerTip.s:after,  #powerTip.s:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.sw:after, #powerTip.sw:before {
+	bottom: 100%;
+}
+
+#powerTip.s:after, #powerTip.se:after, #powerTip.sw:after {
+	border-bottom-color: #ffffff;
+	border-width: 10px;
+	margin: 0px -10px;
+}
+
+#powerTip.s:before, #powerTip.se:before, #powerTip.sw:before {
+	border-bottom-color: #808080;
+	border-width: 11px;
+	margin: 0px -11px;
+}
+
+#powerTip.s:after, #powerTip.s:before {
+	left: 50%;
+}
+
+#powerTip.sw:after, #powerTip.sw:before {
+	right: 14px;
+}
+
+#powerTip.se:after, #powerTip.se:before {
+	left: 14px;
+}
+
+#powerTip.e:after, #powerTip.e:before {
+	left: 100%;
+}
+#powerTip.e:after {
+	border-left-color: #ffffff;
+	border-width: 10px;
+	top: 50%;
+	margin-top: -10px;
+}
+#powerTip.e:before {
+	border-left-color: #808080;
+	border-width: 11px;
+	top: 50%;
+	margin-top: -11px;
+}
+
+#powerTip.w:after, #powerTip.w:before {
+	right: 100%;
+}
+#powerTip.w:after {
+	border-right-color: #ffffff;
+	border-width: 10px;
+	top: 50%;
+	margin-top: -10px;
+}
+#powerTip.w:before {
+	border-right-color: #808080;
+	border-width: 11px;
+	top: 50%;
+	margin-top: -11px;
+}
+
+@media print
+{
+  #top { display: none; }
+  #side-nav { display: none; }
+  #nav-path { display: none; }
+  body { overflow:visible; }
+  h1, h2, h3, h4, h5, h6 { page-break-after: avoid; }
+  .summary { display: none; }
+  .memitem { page-break-inside: avoid; }
+  #doc-content
+  {
+    margin-left:0 !important;
+    height:auto !important;
+    width:auto !important;
+    overflow:inherit;
+    display:inline;
+  }
+}
+
diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h
index 1bd5c1e6..77f36be2 100644
--- a/src/common/include/gudhi/Points_off_io.h
+++ b/src/common/include/gudhi/Points_off_io.h
@@ -113,7 +113,7 @@ class Points_off_visitor_reader {
  * This example loads points from an OFF file and builds a vector of CGAL points in dimension d.
  * Then, it is asked to display the points.
  * 
- * \include CGAL_points_off_reader.cpp
+ * \include common/CGAL_points_off_reader.cpp
  * 
  * When launching:
  * 
@@ -122,7 +122,7 @@ class Points_off_visitor_reader {
  *
  * the program output is:
  * 
- * \include cgaloffreader_result.txt
+ * \include common/cgaloffreader_result.txt
  */
 template<typename Point_d>
 class Points_off_reader {