16 files changed, 138 insertions, 210 deletions
diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index 5ab23720..41e5e16d 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -107,6 +107,7 @@ Table of Contents
  * \subsection filtrationcomputation Filtration value computation algorithm
  * <br>
  * \f$
+ * \begin{array}{l}
  * \textbf{for } \text{i : dimension } \rightarrow 0 \textbf{ do}\\
  * \quad \textbf{for all } \sigma \text{ of dimension i}\\
  * \quad\quad \textbf{if } \text{filtration(} \sigma ) \text{ is NaN} \textbf{ then}\\
@@ -127,6 +128,7 @@ Table of Contents
  * \textbf{end for}\\
  * \text{make_filtration_non_decreasing()}\\
  * \text{prune_above_filtration()}\\
+ * \end{array}
  * \f$
  *
  * \subsubsection dimension2 Dimension 2
@@ -164,11 +166,11 @@ Table of Contents
  * <b>Requires:</b> \ref eigen &ge; 3.1.0 and \ref cgal &ge; 5.1.0.
  * 
  * A weighted version for Alpha complex is available (cf. Alpha_complex). It is like a usual Alpha complex, but based
- * on a <a href="https://doc.cgal.org/latest/Triangulation/index.html#title20">CGAL regular triangulation</a> instead
+ * on a <a href="https://doc.cgal.org/latest/Triangulation/index.html#TriangulationSecRT">CGAL regular triangulation</a> instead
  * of Delaunay.
  *
  * This example builds the CGAL weighted alpha shapes from a small molecule, and initializes the alpha complex with
- * it. This example is taken from <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title13">CGAL 3d
+ * it. This example is taken from <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#AlphaShape_3DExampleforWeightedAlphaShapes">CGAL 3d
  * weighted alpha shapes</a>.
  *
  * Then, it is asked to display information about the alpha complex.
@@ -212,7 +214,7 @@ Table of Contents
  * Gudhi::alpha_complex::complexity::EXACT.
  *
  * This example builds the CGAL 3d weighted alpha shapes from a small molecule, and initializes the alpha complex with
- * it. This example is taken from <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title13">CGAL 3d
+ * it. This example is taken from <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#AlphaShape_3DExampleforWeightedAlphaShapes">CGAL 3d
  * weighted alpha shapes</a>.
  *
  * Then, it is asked to display information about the alpha complex.
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
index b3dbc9bb..562ef139 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
@@ -98,7 +98,7 @@ struct Value_from_iterator<complexity::EXACT> {
  * \tparam Periodic Boolean used to set/unset the periodic version of Alpha_complex_3d. Default value is false.
  *
  * For the weighted version, weights values are explained on CGAL
- * <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0">Alpha shapes 3d</a> and
+ * <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#Alpha_shapes_3Definitions">Alpha shapes 3d</a> and
  * <a href="https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation">Regular
  * triangulation</a> documentation.
  *
diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md
index 0d3c6027..1e3b8fab 100644
--- a/src/Alpha_complex/utilities/alphacomplex.md
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -64,7 +64,7 @@ N.B.:
 * Weights values are explained on CGAL
 [dD Triangulations](https://doc.cgal.org/latest/Triangulation/index.html)
 and
-[Regular triangulation](https://doc.cgal.org/latest/Triangulation/index.html#title20) documentation.
+[Regular triangulation](https://doc.cgal.org/latest/Triangulation/index.html#TriangulationSecRT) documentation.
 
 
 ## alpha_complex_3d_persistence ##
@@ -131,6 +131,6 @@ N.B.:
 * `alpha_complex_3d_persistence` only accepts OFF files in dimension 3.
 * Filtration values are alpha square values.
 * Weights values are explained on CGAL
-[Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0)
+[Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#Alpha_shapes_3Definitions)
 and
 [Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation.
diff --git a/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h
index 698f9749..095fd320 100644
--- a/src/Cech_complex/doc/Intro_cech_complex.h
+++ b/src/Cech_complex/doc/Intro_cech_complex.h
@@ -70,9 +70,8 @@ namespace cech_complex {
  * This radius computation is the reason why the Cech_complex is taking much more time to be computed than the
  * \ref rips_complex but it offers more topological guarantees.
  *
- * If the Cech_complex interfaces are not detailed enough for your need, please refer to
- * <a href="cech_complex_step_by_step_8cpp-example.html">
- * cech_complex_step_by_step.cpp</a> example, where the graph construction over the Simplex_tree is more detailed.
+ * If the Cech_complex interfaces are not detailed enough for your need, please refer to the example
+ * \gudhi_example_link{Cech_complex,cech_complex_step_by_step.cpp}, where the graph construction over the Simplex_tree is more detailed.
  *
  * \subsection cechpointscloudexample Example from a point cloud
  * 
diff --git a/src/Doxyfile.in b/src/Doxyfile.in
index f76ba2bd..54ec9078 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -229,7 +229,7 @@ TAB_SIZE               = 2
 # "Side Effects:". You can put \n's in the value part of an alias to insert
 # newlines.
 
-ALIASES                =
+ALIASES                = gudhi_example_link{2}="@ref \2 \"\1/\2\""
 
 # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
 # only. Doxygen will then generate output that is more tailored for C. For
@@ -1473,6 +1473,17 @@ FORMULA_TRANSPARENT    = YES
 
 USE_MATHJAX            = YES
 
+# With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
+# Note that the different versions of MathJax have different requirements with
+# regards to the different settings, so it is possible that also other MathJax
+# settings have to be changed when switching between the different MathJax
+# versions.
+# Possible values are: MathJax_2 and MathJax_3.
+# The default value is: MathJax_2.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+@GUDHI_DOXYGEN_MATHJAX_VERSION@
+
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:
 # http://docs.mathjax.org/en/latest/output.html) for more details.
@@ -1494,15 +1505,14 @@ MATHJAX_FORMAT         = HTML-CSS
 # The default value is: http://cdn.mathjax.org/mathjax/latest.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2
+MATHJAX_RELPATH        = 
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example
 # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_EXTENSIONS     = TeX/AMSmath \
-                         TeX/AMSsymbols
+MATHJAX_EXTENSIONS  = @GUDHI_DOXYGEN_MATHJAX_EXTENSIONS@
 
 # The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
 # of code that will be used on startup of the MathJax code. See the MathJax site
diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
index a6098860..e1ab7cb3 100644
--- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
+++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
@@ -24,7 +24,7 @@ namespace cover_complex {
  * Visualizations of the simplicial complexes can be done with either
  * neato (from <a target="_blank" href="http://www.graphviz.org/">graphviz</a>),
  * <a target="_blank" href="http://www.geomview.org/">geomview</a>,
- * <a target="_blank" href="https://github.com/MLWave/kepler-mapper">KeplerMapper</a>.
+ * <a target="_blank" href="https://github.com/scikit-tda/kepler-mapper">KeplerMapper</a>.
  * Input point clouds are assumed to be \ref FileFormatsOFF "OFF files"
  *
  * \section covers Covers
diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
index a3613d0d..94579564 100644
--- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
+++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h
@@ -131,8 +131,7 @@ namespace persistent_cohomology {
 
 We provide several example files: run these examples with -h for details on their use, and read the README file.
 
-\li <a href="rips_persistence_8cpp-example.html">
-Rips_complex/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence
+\li \gudhi_example_link{Rips_complex,rips_persistence.cpp} computes the Rips complex of a point cloud and outputs its persistence
 diagram.
 \code $> ./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 \endcode
 \code The complex contains 177838 simplices 
@@ -144,12 +143,10 @@ diagram.
 
 More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page.
 
-\li <a href="rips_multifield_persistence_8cpp-example.html">
-Persistent_cohomology/rips_multifield_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its
+\li \gudhi_example_link{Persistent_cohomology,rips_multifield_persistence.cpp} computes the Rips complex of a point cloud and outputs its
 persistence diagram with a family of field coefficients.
 
-\li <a href="rips_distance_matrix_persistence_8cpp-example.html">
-Rips_complex/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and
+\li \gudhi_example_link{Rips_complex,rips_distance_matrix_persistence.cpp} computes the Rips complex of a distance matrix and
 outputs its persistence diagram.
 
 The file should contain square or lower triangular distance matrix with semicolons as separators.
@@ -158,8 +155,7 @@ Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an
 
 More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page.
 
-\li <a href="rips_correlation_matrix_persistence_8cpp-example.html">
-Rips_complex/rips_correlation_matrix_persistence.cpp</a>
+\li \gudhi_example_link{Rips_complex,rips_correlation_matrix_persistence.cpp}
 computes the Rips complex of a correlation matrix and outputs its persistence diagram.
 
 Note that no check is performed if the matrix given as the input is a correlation matrix.
@@ -169,8 +165,7 @@ Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv
 
 More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page.
 
-\li <a href="alpha_complex_3d_persistence_8cpp-example.html">
-Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with
+\li \gudhi_example_link{Alpha_complex,alpha_complex_3d_persistence.cpp} computes the persistent homology with
 \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file.
 \code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45 \endcode
 \code Simplex_tree dim: 3
@@ -235,8 +230,7 @@ Note that the lengths of the sides of the periodic cuboid have to be the same.<b
 3  2 36.8838 inf
 3  3 58.6783 inf  \endcode
 
-\li <a href="alpha_complex_persistence_8cpp-example.html">
-Alpha_complex/alpha_complex_persistence.cpp</a> computes the persistent homology with
+\li \gudhi_example_link{Alpha_complex,alpha_complex_persistence.cpp} computes the persistent homology with
 \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file.
 \code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode
 \code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices.
@@ -248,8 +242,7 @@ Simplex_tree dim: 3
 
 More details on the <a href="../../alphacomplex/">Alpha complex utilities</a> dedicated page.
 
-\li <a href="plain_homology_8cpp-example.html">
-Persistent_cohomology/plain_homology.cpp</a> computes the plain homology of a simple simplicial complex without
+\li \gudhi_example_link{Persistent_cohomology,plain_homology.cpp} computes the plain homology of a simple simplicial complex without
 filtration values.
 
  */
diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index 3888ec8f..cd77b327 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -63,9 +63,8 @@ namespace rips_complex {
  * value set with \f$max(filtration(4,5), filtration(4,6), filtration(5,6))\f$.
  * And so on for simplex (0,1,2,3).
  * 
- * If the Rips_complex interfaces are not detailed enough for your need, please refer to
- * <a href="rips_persistence_step_by_step_8cpp-example.html">
- * rips_persistence_step_by_step.cpp</a> example, where the constructions of the graph and
+ * If the Rips_complex interfaces are not detailed enough for your need, please refer to the example
+ * \gudhi_example_link{Persistent_cohomology,rips_persistence_step_by_step.cpp} , where the constructions of the graph and
  * the Simplex_tree are more detailed.
  *
  * \section sparserips Sparse Rips complex
diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h
index ef8dec91..2d3ecdec 100644
--- a/src/Simplex_tree/doc/Intro_simplex_tree.h
+++ b/src/Simplex_tree/doc/Intro_simplex_tree.h
@@ -39,11 +39,9 @@ namespace Gudhi {
  * \subsubsection filteredcomplexessimplextreeexamples Examples
  * 
  * Here is a list of simplex tree examples :
- * \li <a href="simple_simplex_tree_8cpp-example.html">
- * Simplex_tree/simple_simplex_tree.cpp</a> - Simple simplex tree construction and basic function use.
+ * \li \gudhi_example_link{Simplex_tree,simple_simplex_tree.cpp} - Simple simplex tree construction and basic function use.
  *
- * \li <a href="simplex_tree_from_cliques_of_graph_8cpp-example.html">
- * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - Simplex tree construction from cliques of graph read in
+ * \li \gudhi_example_link{Simplex_tree,simplex_tree_from_cliques_of_graph.cpp} - Simplex tree construction from cliques of graph read in
  * a file.
  * 
  * Simplex tree construction with \f$\mathbb{Z}/3\mathbb{Z}\f$ coefficients on weighted graph Klein bottle file:
@@ -54,12 +52,10 @@ Expand the simplex tree in 3.8e-05 s.
 Information of the Simplex Tree: 
 Number of vertices = 10   Number of simplices = 98 \endcode
  * 
- * \li <a href="example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
- * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> - Simplex tree is computed and displayed
+ * \li \gudhi_example_link{Simplex_tree,example_alpha_shapes_3_simplex_tree_from_off_file.cpp} - Simplex tree is computed and displayed
  * from a 3D alpha complex (Requires CGAL, GMP and GMPXX to be installed).
  * 
- * \li <a href="graph_expansion_with_blocker_8cpp-example.html">
- * Simplex_tree/graph_expansion_with_blocker.cpp</a> - Simple simplex tree construction from a one-skeleton graph with
+ * \li \gudhi_example_link{Simplex_tree,graph_expansion_with_blocker.cpp} - Simple simplex tree construction from a one-skeleton graph with
  * a simple blocker expansion method.
  *
  * \subsection filteredcomplexeshassecomplex Hasse complex
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 629a1f9c..4d94c037 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1083,8 +1083,8 @@ class Simplex_tree {
    *
    * Inserts all vertices and edges given by a OneSkeletonGraph.
    * OneSkeletonGraph must be a model of
-   * <a href="http://www.boost.org/doc/libs/1_76_0/libs/graph/doc/VertexAndEdgeListGraph.html">boost::VertexAndEdgeListGraph</a>
-   * and <a href="http://www.boost.org/doc/libs/1_76_0/libs/graph/doc/PropertyGraph.html">boost::PropertyGraph</a>.
+   * <a href="https://www.boost.org/doc/libs/release/libs/graph/doc/VertexAndEdgeListGraph.html">boost::VertexAndEdgeListGraph</a>
+   * and <a href="https://www.boost.org/doc/libs/release/libs/graph/doc/PropertyGraph.html">boost::PropertyGraph</a>.
    *
    * The vertex filtration value is accessible through the property tag
    * vertex_filtration_t.
diff --git a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h
index 0c2014bd..23eb3670 100644
--- a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h
+++ b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h
@@ -29,7 +29,7 @@ struct SkeletonBlockerDS {
 
   /**
    * @brief Root_vertex_handle and Vertex_handle are similar to global and local vertex descriptor
-   * used in <a href="http://www.boost.org/doc/libs/1_38_0/libs/graph/doc/subgraph.html">boost subgraphs</a>
+   * used in <a href="https://www.boost.org/doc/libs/release/libs/graph/doc/subgraph.html">boost subgraphs</a>
    * and allow to localize a vertex of a subcomplex on its parent root complex.
    *
    * In gross, vertices are stored in a vector
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
index 0c0cc624..d091d7dd 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h
@@ -28,7 +28,7 @@ namespace skeleton_blocker {
  */
 struct Skeleton_blocker_simple_traits {
   /**
-   * @brief Global and local handle similar to <a href="http://www.boost.org/doc/libs/1_38_0/libs/graph/doc/subgraph.html">boost subgraphs</a>.
+   * @brief Global and local handle similar to <a href="https://www.boost.org/doc/libs/release/libs/graph/doc/subgraph.html">boost subgraphs</a>.
    * Vertices are stored in a vector.
    * For the root simplicial complex, the local and global descriptors are the same.
    * For a subcomplex L and one of its vertices 'v', the local descriptor of 'v' is its position in
diff --git a/src/cmake/modules/GUDHI_doxygen_target.cmake b/src/cmake/modules/GUDHI_doxygen_target.cmake
index 0f80b187..6b9514de 100644
--- a/src/cmake/modules/GUDHI_doxygen_target.cmake
+++ b/src/cmake/modules/GUDHI_doxygen_target.cmake
@@ -44,6 +44,14 @@ if(DOXYGEN_FOUND)
     set(GUDHI_DOXYGEN_UTILS_PATH "utilities/*")
   endif()
 
+  message("++ Doxygen version ${DOXYGEN_VERSION}")
+  if (DOXYGEN_VERSION VERSION_LESS 1.9.2)
+    set(GUDHI_DOXYGEN_MATHJAX_VERSION "MATHJAX_VERSION = MathJax_2")
+    set(GUDHI_DOXYGEN_MATHJAX_EXTENSIONS "TeX/AMSmath TeX/AMSsymbols")
+  else()
+    set(GUDHI_DOXYGEN_MATHJAX_VERSION "MATHJAX_VERSION = MathJax_3")
+    set(GUDHI_DOXYGEN_MATHJAX_EXTENSIONS "ams")
+  endif()
   configure_file(${GUDHI_DOXYGEN_SOURCE_PREFIX}/Doxyfile.in "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile" @ONLY)
 
   add_custom_target(doxygen ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index 67d026bd..24a7fc7a 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -5,8 +5,8 @@
  * Examples of GUDHI headers inclusion can be found in \ref utilities.
  * 
  * \section compiling Compiling
- * The library uses c++14 and requires <a target="_blank" href="http://www.boost.org/">Boost</a>  &ge; 1.66.0
- * and <a target="_blank" href="https://www.cmake.org/">CMake</a> &ge; 3.5.
+ * The library uses c++14 and requires <a target="_blank" href="https://www.boost.org/">Boost</a>  &ge; 1.66.0
+ * and <a target="_blank" href="https://cmake.org/">CMake</a> &ge; 3.5.
  * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
  * 
  * \subsection utilities Utilities and examples
@@ -56,10 +56,9 @@ make \endverbatim
  * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
  * arithmetic, operating on signed integers, rational numbers, and floating point numbers.
  * 
- * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic
+ * The following example requires the <a target="_blank" href="https://gmplib.org/">GNU Multiple Precision Arithmetic
  * Library</a> (GMP) and will not be built if GMP is not installed:
- * \li <a href="rips_multifield_persistence_8cpp-example.html">
- * Persistent_cohomology/rips_multifield_persistence.cpp</a>
+ * \li \gudhi_example_link{Persistent_cohomology,rips_multifield_persistence.cpp}
  *
  * Having GMP version 4.2 or higher installed is recommended.
  * 
@@ -76,179 +75,101 @@ make \endverbatim
  * 
  * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
  * Library</a> (CGAL \cite cgal:eb-19b) and will not be built if CGAL version 4.11.0 or higher is not installed:
- * \li <a href="example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
- * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
- * \li <a href="strong_witness_persistence_8cpp-example.html">
- * Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="weak_witness_persistence_8cpp-example.html">
- * Witness_complex/weak_witness_persistence.cpp</a>
- * \li <a href="example_strong_witness_complex_off_8cpp-example.html">
- * Witness_complex/example_strong_witness_complex_off.cpp</a>
- * \li <a href="example_witness_complex_off_8cpp-example.html">
- * Witness_complex/example_witness_complex_off.cpp</a>
- * \li <a href="example_witness_complex_sphere_8cpp-example.html">
- * Witness_complex/example_witness_complex_sphere.cpp</a>
- * \li <a href="_alpha_complex_from_off_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_off.cpp</a>
- * \li <a href="_alpha_complex_from_points_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="alpha_complex_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="custom_persistence_sort_8cpp-example.html">
- * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
- * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
- * \li <a href="bottleneck_basic_example_8cpp-example.html">
- * Bottleneck_distance/bottleneck_basic_example.cpp</a>
- * \li <a href="bottleneck_distance_8cpp-example.html">
- * Bottleneck_distance/bottleneck_distance.cpp</a>
- * \li <a href="_coord_g_i_c_8cpp-example.html">
- * Nerve_GIC/CoordGIC.cpp</a>
- * \li <a href="_func_g_i_c_8cpp-example.html">
- * Nerve_GIC/FuncGIC.cpp</a>
- * \li <a href="_nerve_8cpp-example.html">
- * Nerve_GIC/Nerve.cpp</a>
- * \li <a href="_voronoi_g_i_c_8cpp-example.html">
- * Nerve_GIC/VoronoiGIC.cpp</a>
- * \li <a href="example_spatial_searching_8cpp-example.html">
- * Spatial_searching/example_spatial_searching.cpp</a>
- * \li <a href="example_choose_n_farthest_points_8cpp-example.html">
- * Subsampling/example_choose_n_farthest_points.cpp</a>
- * \li <a href="example_pick_n_random_points_8cpp-example.html">
- * Subsampling/example_pick_n_random_points.cpp</a>
- * \li <a href="example_sparsify_point_set_8cpp-example.html">
- * Subsampling/example_sparsify_point_set.cpp</a>
- * \li <a href="example_basic_8cpp-example.html">
- * Tangential_complex/example_basic.cpp</a>
- * \li <a href="example_with_perturb_8cpp-example.html">
- * Tangential_complex/example_with_perturb.cpp</a>
- * \li <a href="_weighted_alpha_complex_3d_from_points_8cpp-example.html">
- * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
- * \li <a href="alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_coxeter_triangulation_2manifold_tracing_flat_torus_with_boundary_8cpp-example.html">
- * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp</a>
+ * \li \gudhi_example_link{Simplex_tree,example_alpha_shapes_3_simplex_tree_from_off_file.cpp}
+ * \li \gudhi_example_link{Witness_complex,strong_witness_persistence.cpp}
+ * \li \gudhi_example_link{Witness_complex,weak_witness_persistence.cpp}
+ * \li \gudhi_example_link{Witness_complex,example_strong_witness_complex_off.cpp}
+ * \li \gudhi_example_link{Witness_complex,example_witness_complex_off.cpp}
+ * \li \gudhi_example_link{Witness_complex,example_witness_complex_sphere.cpp}
+ * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_off.cpp}
+ * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_points.cpp}
+ * \li \gudhi_example_link{Alpha_complex,alpha_complex_persistence.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,custom_persistence_sort.cpp}
+ * \li \gudhi_example_link{Bottleneck_distance,alpha_rips_persistence_bottleneck_distance.cpp}
+ * \li \gudhi_example_link{Bottleneck_distance,bottleneck_basic_example.cpp}
+ * \li \gudhi_example_link{Bottleneck_distance,bottleneck_distance.cpp}
+ * \li \gudhi_example_link{Nerve_GIC,CoordGIC.cpp}
+ * \li \gudhi_example_link{Nerve_GIC,FuncGIC.cpp}
+ * \li \gudhi_example_link{Nerve_GIC,Nerve.cpp}
+ * \li \gudhi_example_link{Nerve_GIC,VoronoiGIC.cpp}
+ * \li \gudhi_example_link{Spatial_searching,example_spatial_searching.cpp}
+ * \li \gudhi_example_link{Subsampling,example_choose_n_farthest_points.cpp}
+ * \li \gudhi_example_link{Subsampling,example_pick_n_random_points.cpp}
+ * \li \gudhi_example_link{Subsampling,example_sparsify_point_set.cpp}
+ * \li \gudhi_example_link{Tangential_complex,example_basic.cpp}
+ * \li \gudhi_example_link{Tangential_complex,example_with_perturb.cpp}
+ * \li \gudhi_example_link{Alpha_complex,Weighted_alpha_complex_3d_from_points.cpp}
+ * \li \gudhi_example_link{Alpha_complex,alpha_complex_3d_persistence.cpp}
+ * \li \gudhi_example_link{Coxeter_triangulation,manifold_tracing_flat_torus_with_boundary.cpp}
  *
  * \subsection eigen Eigen
  * Some GUDHI modules (cf. \ref main_page "modules list"), and few examples require
- * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen</a> is a C++ template library for linear algebra:
+ * <a target="_blank" href="https://eigen.tuxfamily.org">Eigen</a> is a C++ template library for linear algebra:
  * matrices, vectors, numerical solvers, and related algorithms.
  * 
- * The following examples/utilities require the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen</a> and will not be
+ * The following examples/utilities require the <a target="_blank" href="https://eigen.tuxfamily.org">Eigen</a> and will not be
  * built if Eigen is not installed:
- * \li <a href="_alpha_complex_from_off_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_off.cpp</a>
- * \li <a href="_alpha_complex_from_points_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="alpha_complex_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_weighted_alpha_complex_3d_from_points_8cpp-example.html">
- * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
- * \li <a href="alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
- * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
- * \li <a href="custom_persistence_sort_8cpp-example.html">
- * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="example_spatial_searching_8cpp-example.html">
- * Spatial_searching/example_spatial_searching.cpp</a>
- * \li <a href="example_choose_n_farthest_points_8cpp-example.html">
- * Subsampling/example_choose_n_farthest_points.cpp</a>
- * \li <a href="example_pick_n_random_points_8cpp-example.html">
- * Subsampling/example_pick_n_random_points.cpp</a>
- * \li <a href="example_sparsify_point_set_8cpp-example.html">
- * Subsampling/example_sparsify_point_set.cpp</a>
- * \li <a href="example_basic_8cpp-example.html">
- * Tangential_complex/example_basic.cpp</a>
- * \li <a href="example_with_perturb_8cpp-example.html">
- * Tangential_complex/example_with_perturb.cpp</a>
- * \li <a href="strong_witness_persistence_8cpp-example.html">
- * Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="weak_witness_persistence_8cpp-example.html">
- * Witness_complex/weak_witness_persistence.cpp</a>
- * \li <a href="example_strong_witness_complex_off_8cpp-example.html">
- * Witness_complex/example_strong_witness_complex_off.cpp</a>
- * \li <a href="example_witness_complex_off_8cpp-example.html">
- * Witness_complex/example_witness_complex_off.cpp</a>
- * \li <a href="example_witness_complex_sphere_8cpp-example.html">
- * Witness_complex/example_witness_complex_sphere.cpp</a>
- * \li <a href="_coxeter_triangulation_2cell_complex_from_basic_circle_manifold_8cpp-example.html">
- * Coxeter_triangulation/cell_complex_from_basic_circle_manifold.cpp</a>
- * \li <a href="_coxeter_triangulation_2manifold_tracing_custom_function_8cpp-example.html">
- * Coxeter_triangulation/manifold_tracing_custom_function.cpp</a>
- * \li <a href="_coxeter_triangulation_2manifold_tracing_flat_torus_with_boundary_8cpp-example.html">
- * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp</a>
+ * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_off.cpp}
+ * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_points.cpp}
+ * \li \gudhi_example_link{Alpha_complex,alpha_complex_persistence.cpp}
+ * \li \gudhi_example_link{Alpha_complex,alpha_complex_3d_persistence.cpp}
+ * \li \gudhi_example_link{Alpha_complex,Weighted_alpha_complex_3d_from_points.cpp}
+ * \li \gudhi_example_link{Bottleneck_distance,alpha_rips_persistence_bottleneck_distance.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,custom_persistence_sort.cpp}
+ * \li \gudhi_example_link{Spatial_searching,example_spatial_searching.cpp}
+ * \li \gudhi_example_link{Subsampling,example_choose_n_farthest_points.cpp}
+ * \li \gudhi_example_link{Subsampling,example_pick_n_random_points.cpp}
+ * \li \gudhi_example_link{Subsampling,example_sparsify_point_set.cpp}
+ * \li \gudhi_example_link{Tangential_complex,example_basic.cpp}
+ * \li \gudhi_example_link{Tangential_complex,example_with_perturb.cpp}
+ * \li \gudhi_example_link{Witness_complex,strong_witness_persistence.cpp}
+ * \li \gudhi_example_link{Witness_complex,weak_witness_persistence.cpp}
+ * \li \gudhi_example_link{Witness_complex,example_strong_witness_complex_off.cpp}
+ * \li \gudhi_example_link{Witness_complex,example_witness_complex_off.cpp}
+ * \li \gudhi_example_link{Witness_complex,example_witness_complex_sphere.cpp}
+ * \li \gudhi_example_link{Coxeter_triangulation,cell_complex_from_basic_circle_manifold.cpp}
+ * \li \gudhi_example_link{Coxeter_triangulation,manifold_tracing_custom_function.cpp}
+ * \li \gudhi_example_link{Coxeter_triangulation,manifold_tracing_flat_torus_with_boundary.cpp}
  *
  * \subsection tbb Threading Building Blocks
- * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel&reg; TBB</a> lets you easily write parallel
+ * <a target="_blank" href="https://github.com/oneapi-src/oneTBB">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/utilities are using Intel&reg; TBB if installed:
- * \li <a href="_alpha_complex_from_off_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_off.cpp</a>
- * \li <a href="_alpha_complex_from_points_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="alpha_complex_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="cubical_complex_persistence_8cpp-example.html">
- * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a>
- * \li <a href="periodic_cubical_complex_persistence_8cpp-example.html">
- * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp</a>
- * \li <a href="_random_bitmap_cubical_complex_8cpp-example.html">
- * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a>
- * \li <a href="_coord_g_i_c_8cpp-example.html">
- * Nerve_GIC/CoordGIC.cpp</a>
- * \li <a href="_func_g_i_c_8cpp-example.html">
- * Nerve_GIC/FuncGIC.cpp</a>
- * \li <a href="_nerve_8cpp-example.html">
- * Nerve_GIC/Nerve.cpp</a>
- * \li <a href="_voronoi_g_i_c_8cpp-example.html">
- * Nerve_GIC/VoronoiGIC.cpp</a>
- * \li <a href="simple_simplex_tree_8cpp-example.html">
- * Simplex_tree/simple_simplex_tree.cpp</a>
- * \li <a href="example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
- * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
- * \li <a href="simplex_tree_from_cliques_of_graph_8cpp-example.html">
- * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a>
- * \li <a href="graph_expansion_with_blocker_8cpp-example.html">
- * Simplex_tree/graph_expansion_with_blocker.cpp</a>
- * \li <a href="alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="alpha_complex_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_persistence.cpp</a>
- * \li <a href="rips_persistence_via_boundary_matrix_8cpp-example.html">
- * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a>
- * \li <a href="persistence_from_file_8cpp-example.html">
- * Persistent_cohomology/persistence_from_file.cpp</a>
- * \li <a href="persistence_from_simple_simplex_tree_8cpp-example.html">
- * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a>
- * \li <a href="plain_homology_8cpp-example.html">
- * Persistent_cohomology/plain_homology.cpp</a>
- * \li <a href="rips_multifield_persistence_8cpp-example.html">
- * Persistent_cohomology/rips_multifield_persistence.cpp</a>
- * \li <a href="rips_persistence_step_by_step_8cpp-example.html">
- * Persistent_cohomology/rips_persistence_step_by_step.cpp</a>
- * \li <a href="custom_persistence_sort_8cpp-example.html">
- * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="example_one_skeleton_rips_from_points_8cpp-example.html">
- * Rips_complex/example_one_skeleton_rips_from_points.cpp</a>
- * \li <a href="example_rips_complex_from_off_file_8cpp-example.html">
- * Rips_complex/example_rips_complex_from_off_file.cpp</a>
- * \li <a href="rips_distance_matrix_persistence_8cpp-example.html">
- * Rips_complex/rips_distance_matrix_persistence.cpp</a>
- * \li <a href="rips_persistence_8cpp-example.html">
- * Rips_complex/rips_persistence.cpp</a>
- * \li <a href="strong_witness_persistence_8cpp-example.html">
- * Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="weak_witness_persistence_8cpp-example.html">
- * Witness_complex/weak_witness_persistence.cpp</a>
- * \li <a href="example_nearest_landmark_table_8cpp-example.html">
- * Witness_complex/example_nearest_landmark_table.cpp</a>
+ * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_off.cpp}
+ * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_points.cpp}
+ * \li \gudhi_example_link{Alpha_complex,alpha_complex_3d_persistence.cpp}
+ * \li \gudhi_example_link{Alpha_complex,alpha_complex_persistence.cpp}
+ * \li \gudhi_example_link{Bitmap_cubical_complex,cubical_complex_persistence.cpp}
+ * \li \gudhi_example_link{Bitmap_cubical_complex,periodic_cubical_complex_persistence.cpp}
+ * \li \gudhi_example_link{Bitmap_cubical_complex,Random_bitmap_cubical_complex.cpp}
+ * \li \gudhi_example_link{Nerve_GIC,CoordGIC.cpp}
+ * \li \gudhi_example_link{Nerve_GIC,FuncGIC.cpp}
+ * \li \gudhi_example_link{Nerve_GIC,Nerve.cpp}
+ * \li \gudhi_example_link{Nerve_GIC,VoronoiGIC.cpp}
+ * \li \gudhi_example_link{Simplex_tree,simple_simplex_tree.cpp}
+ * \li \gudhi_example_link{Simplex_tree,example_alpha_shapes_3_simplex_tree_from_off_file.cpp}
+ * \li \gudhi_example_link{Simplex_tree,simplex_tree_from_cliques_of_graph.cpp}
+ * \li \gudhi_example_link{Simplex_tree,graph_expansion_with_blocker.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,alpha_complex_3d_persistence.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,alpha_complex_persistence.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,rips_persistence_via_boundary_matrix.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,persistence_from_file.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,persistence_from_simple_simplex_tree.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,plain_homology.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,rips_multifield_persistence.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,rips_persistence_step_by_step.cpp}
+ * \li \gudhi_example_link{Persistent_cohomology,custom_persistence_sort.cpp}
+ * \li \gudhi_example_link{Rips_complex,example_one_skeleton_rips_from_points.cpp}
+ * \li \gudhi_example_link{Rips_complex,example_rips_complex_from_off_file.cpp}
+ * \li \gudhi_example_link{Rips_complex,rips_distance_matrix_persistence.cpp}
+ * \li \gudhi_example_link{Rips_complex,rips_persistence.cpp}
+ * \li \gudhi_example_link{Witness_complex,strong_witness_persistence.cpp}
+ * \li \gudhi_example_link{Witness_complex,weak_witness_persistence.cpp}
+ * \li \gudhi_example_link{Witness_complex,example_nearest_landmark_table.cpp}
  *
  * \section Contributions Bug reports and contributions
  * Please help us improving the quality of the GUDHI library.
diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst
index b060c86e..9e67d38a 100644
--- a/src/python/doc/alpha_complex_user.rst
+++ b/src/python/doc/alpha_complex_user.rst
@@ -178,11 +178,11 @@ Weighted version
 ^^^^^^^^^^^^^^^^
 
 A weighted version for Alpha complex is available. It is like a usual Alpha complex, but based on a
-`CGAL regular triangulation <https://doc.cgal.org/latest/Triangulation/index.html#title20>`_.
+`CGAL regular triangulation <https://doc.cgal.org/latest/Triangulation/index.html#TriangulationSecRT>`_.
 
 This example builds the weighted alpha-complex of a small molecule, where atoms have different sizes.
 It is taken from
-`CGAL 3d weighted alpha shapes <https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title13>`_.
+`CGAL 3d weighted alpha shapes <https://doc.cgal.org/latest/Alpha_shapes_3/index.html#AlphaShape_3DExampleforWeightedAlphaShapes>`_.
 
 Then, it is asked to display information about the alpha complex.
 
diff --git a/src/python/doc/nerve_gic_complex_user.rst b/src/python/doc/nerve_gic_complex_user.rst
index 0b820abf..8633cadb 100644
--- a/src/python/doc/nerve_gic_complex_user.rst
+++ b/src/python/doc/nerve_gic_complex_user.rst
@@ -12,7 +12,7 @@ Definition
 Visualizations of the simplicial complexes can be done with either
 neato (from `graphviz <http://www.graphviz.org/>`_),
 `geomview <http://www.geomview.org/>`_,
-`KeplerMapper <https://github.com/MLWave/kepler-mapper>`_.
+`KeplerMapper <https://github.com/scikit-tda/kepler-mapper>`_.
 Input point clouds are assumed to be OFF files (cf. `OFF file format <fileformats.html#off-file-format>`_).
 
 Covers