Merge branch 'master' into optimize_silhouettes

23 files changed, 325 insertions, 294 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/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index 6c0f4c78..58d627c2 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -26,6 +26,7 @@ namespace contraction {
 
 
 /** \defgroup contr Edge contraction
+@{
 
 \author David Salinas
 
@@ -195,7 +196,6 @@ int main (int argc, char *argv[])
 
 	return EXIT_SUCCESS;
 }
-}
   \endcode
 
 \verbatim
diff --git a/src/Doxyfile.in b/src/Doxyfile.in
index ae8db1a3..54ec9078 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -229,13 +229,7 @@ TAB_SIZE               = 2
 # "Side Effects:". You can put \n's in the value part of an alias to insert
 # newlines.
 
-ALIASES                =
-
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding "class=itcl::class"
-# will allow you to use the command class in the itcl::class meaning.
-
-TCL_SUBST              =
+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
@@ -874,7 +868,7 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = @CMAKE_SOURCE_DIR@/biblio/ \
+EXAMPLE_PATH           = @CMAKE_SOURCE_DIR@ \
                          @CMAKE_SOURCE_DIR@/data/ \
                          @GUDHI_DOXYGEN_EXAMPLE_PATH@
 
@@ -1040,25 +1034,6 @@ USE_HTAGS              = NO
 
 VERBATIM_HEADERS       = YES
 
-# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
-# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
-# cost of reduced performance. This can be particularly helpful with template
-# rich C++ code for which doxygen's built-in parser lacks the necessary type
-# information.
-# Note: The availability of this option depends on whether or not doxygen was
-# generated with the -Duse-libclang=ON option for CMake.
-# The default value is: NO.
-
-CLANG_ASSISTED_PARSING = NO
-
-# If clang assisted parsing is enabled you can provide the compiler with command
-# line options that you would normally use when invoking the compiler. Note that
-# the include paths will already be set by doxygen for the files and directories
-# specified with INPUT and INCLUDE_PATH.
-# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
-
-CLANG_OPTIONS          =
-
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
@@ -1070,13 +1045,6 @@ CLANG_OPTIONS          =
 
 ALPHABETICAL_INDEX     = YES
 
-# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
-# which the alphabetical index list will be split.
-# Minimum value: 1, maximum value: 20, default value: 5.
-# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
-
-COLS_IN_ALPHA_INDEX    = 5
-
 # In case all classes in a project start with a common prefix, all classes will
 # be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
 # can be used to specify a prefix (or a list of prefixes) that should be ignored
@@ -1505,6 +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.
@@ -1526,15 +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
@@ -1775,16 +1753,6 @@ LATEX_BATCHMODE        = NO
 
 LATEX_HIDE_INDICES     = NO
 
-# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
-# code with syntax highlighting in the LaTeX output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_SOURCE_CODE      = NO
-
 # The LATEX_BIB_STYLE tag can be used to specify the style to use for the
 # bibliography, e.g. plainnat, or ieeetr. See
 # http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
@@ -1857,16 +1825,6 @@ RTF_STYLESHEET_FILE    =
 
 RTF_EXTENSIONS_FILE    =
 
-# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
-# with syntax highlighting in the RTF output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_SOURCE_CODE        = NO
-
 #---------------------------------------------------------------------------
 # Configuration options related to the man page output
 #---------------------------------------------------------------------------
@@ -1956,15 +1914,6 @@ GENERATE_DOCBOOK       = NO
 
 DOCBOOK_OUTPUT         = docbook
 
-# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
-# program listings (including syntax highlighting and cross-referencing
-# information) to the DOCBOOK output. Note that enabling this will significantly
-# increase the size of the DOCBOOK output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-
-DOCBOOK_PROGRAMLISTING = NO
-
 #---------------------------------------------------------------------------
 # Configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
@@ -2139,12 +2088,6 @@ EXTERNAL_GROUPS        = YES
 
 EXTERNAL_PAGES         = YES
 
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of 'which perl').
-# The default file (with absolute path) is: /usr/bin/perl.
-
-PERL_PATH              = /usr/bin/perl
-
 #---------------------------------------------------------------------------
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
@@ -2158,15 +2101,6 @@ PERL_PATH              = /usr/bin/perl
 
 CLASS_DIAGRAMS         = NO
 
-# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see:
-# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where
-# the mscgen tool resides. If left empty the tool is assumed to be found in the
-# default search path.
-
-MSCGEN_PATH            =
-
 # You can include diagrams made with dia in doxygen documentation. Doxygen will
 # then run dia to produce the diagram and insert it in the documentation. The
 # DIA_PATH tag allows you to specify the directory where the dia binary resides.
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 d48f6616..6dce947c 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -187,6 +187,12 @@ class Simplex_tree {
   typedef Simplex_tree_boundary_simplex_iterator<Simplex_tree> Boundary_simplex_iterator;
   /** \brief Range over the simplices of the boundary of a simplex. */
   typedef boost::iterator_range<Boundary_simplex_iterator> Boundary_simplex_range;
+  /** \brief Iterator over the simplices of the boundary of a simplex and their opposite vertices.
+   *
+   * 'value_type' is std::pair<Simplex_handle, Vertex_handle>. */
+  typedef Simplex_tree_boundary_opposite_vertex_simplex_iterator<Simplex_tree> Boundary_opposite_vertex_simplex_iterator;
+  /** \brief Range over the simplices of the boundary of a simplex and their opposite vertices. */
+  typedef boost::iterator_range<Boundary_opposite_vertex_simplex_iterator> Boundary_opposite_vertex_simplex_range;
   /** \brief Iterator over the simplices of the simplicial complex.
    *
    * 'value_type' is Simplex_handle. */
@@ -296,6 +302,23 @@ class Simplex_tree {
                                   Boundary_simplex_iterator(this));
   }
 
+  /** \brief Given a simplex, returns a range over the simplices of its boundary and their opposite vertices.
+   *
+   * The boundary of a simplex is the set of codimension \f$1\f$ subsimplices of the simplex.
+   * If the simplex is \f$[v_0, \cdots ,v_d]\f$, with canonical orientation induced by \f$ v_0 < \cdots < v_d \f$, the
+   * iterator enumerates the simplices of the boundary in the order:
+   * \f$[v_0,\cdots,\widehat{v_i},\cdots,v_d]\f$ for \f$i\f$ from \f$d\f$ to \f$0\f$, where \f$\widehat{v_i}\f$ means
+   * that the vertex \f$v_i\f$, known as the opposite vertex, is omitted from boundary, but returned as the second
+   * element of a pair.
+   *
+   * @param[in] sh Simplex for which the boundary is computed.
+   */
+  template<class SimplexHandle>
+  Boundary_opposite_vertex_simplex_range boundary_opposite_vertex_simplex_range(SimplexHandle sh) {
+    return Boundary_opposite_vertex_simplex_range(Boundary_opposite_vertex_simplex_iterator(this, sh),
+                                                  Boundary_opposite_vertex_simplex_iterator(this));
+  }
+
   /** @} */  // end range and iterator methods
   /** \name Constructor/Destructor
    * @{ */
@@ -1060,8 +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/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
index e5522cc7..394c6ee1 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
@@ -5,6 +5,7 @@
  *    Copyright (C) 2014 Inria
  *
  *    Modification(s):
+ *      - 2022/04 Vincent Rouvreau: Add Simplex_tree_boundary_opposite_vertex_simplex_iterator for alpha and cech purpose
  *      - YYYY/MM Author: Description of the modification
  */
 
@@ -17,6 +18,7 @@
 #include <boost/container/static_vector.hpp>
 
 #include <vector>
+#include <utility>  // for std::pair
 
 namespace Gudhi {
 
@@ -123,7 +125,7 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
 
  private:
   friend class boost::iterator_core_access;
-// valid when iterating along the SAME boundary.
+  // valid when iterating along the SAME boundary.
   bool equal(Simplex_tree_boundary_simplex_iterator const& other) const {
     return sh_ == other.sh_;
   }
@@ -178,6 +180,116 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
   Simplex_handle sh_;  // current Simplex_handle in the boundary
   SimplexTree * st_;  // simplex containing the simplicial complex
 };
+
+/* \brief Iterator over the simplices of the boundary of a simplex and their opposite vertices.
+ *
+ * Forward iterator, value_type is std::pair<SimplexTree::Simplex_handle, SimplexTree::Vertex_handle>.*/
+template<class SimplexTree>
+class Simplex_tree_boundary_opposite_vertex_simplex_iterator : public boost::iterator_facade<
+    Simplex_tree_boundary_opposite_vertex_simplex_iterator<SimplexTree>,
+    std::pair<typename SimplexTree::Simplex_handle, typename SimplexTree::Vertex_handle> const, boost::forward_traversal_tag> {
+ public:
+  using Simplex_handle = typename SimplexTree::Simplex_handle;
+  using Vertex_handle = typename SimplexTree::Vertex_handle;
+  using Siblings = typename SimplexTree::Siblings;
+
+  // For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is
+  // overwritten.
+  Simplex_tree_boundary_opposite_vertex_simplex_iterator()
+      : sib_(nullptr),
+        st_(nullptr)  {
+  }
+
+  // any end() iterator
+  explicit Simplex_tree_boundary_opposite_vertex_simplex_iterator(SimplexTree * st)
+      : last_(st->null_vertex()),
+        next_(st->null_vertex()),
+        sib_(nullptr),
+        baov_(st->null_simplex(), st->null_vertex()),
+        st_(st)  {
+  }
+
+  template<class SimplexHandle>
+  Simplex_tree_boundary_opposite_vertex_simplex_iterator(SimplexTree * st, SimplexHandle sh)
+      : last_(sh->first),
+        next_(st->null_vertex()),
+        sib_(nullptr),
+        baov_(st->null_simplex(), sh->first),
+        st_(st) {
+    // Only check once at the beginning instead of for every increment, as this is expensive.
+    if (SimplexTree::Options::contiguous_vertices)
+      GUDHI_CHECK(st_->contiguous_vertices(), "The set of vertices is not { 0, ..., n } without holes");
+    Siblings * sib = st->self_siblings(sh);
+    next_ = sib->parent();
+    sib_ = sib->oncles();
+    if (sib_ != nullptr) {
+      if (SimplexTree::Options::contiguous_vertices && sib_->oncles() == nullptr)
+        // Only relevant for edges
+        baov_.first = sib_->members_.begin()+next_;
+      else
+        baov_.first = sib_->find(next_);
+    }
+  }
+
+ private:
+  friend class boost::iterator_core_access;
+
+  // valid when iterating along the SAME boundary.
+  bool equal(Simplex_tree_boundary_opposite_vertex_simplex_iterator const& other) const {
+    return (baov_.first == other.baov_.first);
+  }
+
+  std::pair<Simplex_handle, Vertex_handle> const& dereference() const {
+   return baov_;
+  }
+
+  void increment() {
+    if (sib_ == nullptr) {
+      baov_.first = st_->null_simplex();
+      return;  // ------>>
+    }
+    Siblings * for_sib = sib_;
+    Siblings * new_sib = sib_->oncles();
+    auto rit = suffix_.rbegin();
+    if (SimplexTree::Options::contiguous_vertices && new_sib == nullptr) {
+      // We reached the root, use a short-cut to find a vertex.
+      if (rit == suffix_.rend()) {
+        baov_.second = baov_.first->first;
+        // Segment, this vertex is the last boundary simplex
+        baov_.first = for_sib->members_.begin()+last_;
+        sib_ = nullptr;
+        return;
+      } else {
+        // Dim >= 2, initial step of the descent
+        baov_.first = for_sib->members_.begin()+*rit;
+        for_sib = baov_.first->second.children();
+        ++rit;
+      }
+    }
+    for (; rit != suffix_.rend(); ++rit) {
+      baov_.first = for_sib->find(*rit);
+      for_sib = baov_.first->second.children();
+    }
+    baov_.first = for_sib->find(last_);  // baov_.first points to the right simplex now
+    suffix_.push_back(next_);
+    next_ = sib_->parent();
+    sib_ = new_sib;
+    baov_.second = suffix_.back();
+  }
+
+  // Most of the storage should be moved to the range, iterators should be light.
+  Vertex_handle last_;  // last vertex of the simplex
+  Vertex_handle next_;  // next vertex to push in suffix_
+  // 40 seems a conservative bound on the dimension of a Simplex_tree for now,
+  // as it would not fit on the biggest hard-drive.
+  boost::container::static_vector<Vertex_handle, 40> suffix_;
+  // static_vector still has some overhead compared to a trivial hand-made
+  // version using std::aligned_storage, or compared to making suffix_ static.
+  Siblings * sib_;  // where the next search will start from
+  std::pair<Simplex_handle, Vertex_handle> baov_;  // a pair containing the current Simplex_handle in the boundary and its opposite vertex
+  SimplexTree * st_;  // simplex containing the simplicial complex
+};
+
 /*---------------------------------------------------------------------------*/
 /* \brief Iterator over the simplices of a simplicial complex.
  *
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
index b53bad29..ae25d290 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
@@ -36,6 +36,7 @@ class Simplex_tree_siblings {
   template<class T> friend class Simplex_tree_boundary_simplex_iterator;
   template<class T> friend class Simplex_tree_complex_simplex_iterator;
   template<class T> friend class Simplex_tree_skeleton_simplex_iterator;
+  template<class T> friend class Simplex_tree_boundary_opposite_vertex_simplex_iterator;
 
   typedef typename SimplexTree::Vertex_handle Vertex_handle;
   typedef typename SimplexTree::Filtration_value Filtration_value;
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index bdd41d34..b18e2ec4 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -17,6 +17,8 @@
 #include <limits>
 #include <functional>  // greater
 #include <tuple>  // std::tie
+#include <iterator>  // for std::distance
+#include <cstddef>  // for std::size_t
 
 #define BOOST_TEST_DYN_LINK
 #define BOOST_TEST_MODULE "simplex_tree"
@@ -991,3 +993,48 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_reset_filtration, typeST, list_of_tes
 
 }
 
+BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_boundaries_and_opposite_vertex_iterator, typeST, list_of_tested_variants) {
+  std::clog << "********************************************************************" << std::endl;
+  std::clog << "TEST OF BOUNDARIES AND OPPOSITE VERTEX ITERATORS" << std::endl;
+  typeST st;
+
+  st.insert_simplex_and_subfaces({2, 1, 0}, 3.);
+  st.insert_simplex_and_subfaces({3, 0}, 2.);
+  st.insert_simplex_and_subfaces({3, 4, 5}, 3.);
+  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 4.);
+
+  /* Inserted simplex:        */
+  /*    1   6                 */
+  /*    o---o                 */
+  /*   /X\7/                  */
+  /*  o---o---o---o           */
+  /*  2   0   3\X/4           */
+  /*            o             */
+  /*            5             */
+  using Simplex = std::vector<typename typeST::Vertex_handle>;
+  // simplices must be kept sorted by vertex number for std::vector to use operator== - cf. last BOOST_CHECK
+  std::vector<Simplex> simplices = {{0, 1, 2}, {0, 3}, {0, 1, 6, 7}, {3, 4, 5}, {3, 5}, {2}};
+  for (auto simplex : simplices) {
+    Simplex opposite_vertices;
+    for(auto boundary_and_opposite_vertex : st.boundary_opposite_vertex_simplex_range(st.find(simplex))) {
+      Simplex output;
+      for (auto vertex : st.simplex_vertex_range(boundary_and_opposite_vertex.first)) {
+        std::clog << vertex << " ";
+        output.emplace_back(vertex);
+      }
+      std::clog << " - opposite vertex = " << boundary_and_opposite_vertex.second << std::endl;
+      // Check that boundary simplex + opposite vertex = simplex given as input
+      output.emplace_back(boundary_and_opposite_vertex.second);
+      std::sort(output.begin(), output.end());
+      BOOST_CHECK(simplex == output);
+      opposite_vertices.emplace_back(boundary_and_opposite_vertex.second);
+    }
+    // Check that the list of all opposite vertices = simplex given as input
+    // no opposite vertices if simplex given as input is of dimension 1
+    std::sort(opposite_vertices.begin(), opposite_vertices.end());
+    if (simplex.size() > 1)
+      BOOST_CHECK(simplex == opposite_vertices);
+    else
+      BOOST_CHECK(opposite_vertices.size() == 0);
+  }
+}
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/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
index 125c6387..031bcb9c 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
@@ -1071,7 +1071,6 @@ class Skeleton_blocker_complex {
 
   /**
    * Removes all the popable blockers of the complex and delete them.
-   * @returns the number of popable blockers deleted
    */
   void remove_popable_blockers();
 
@@ -1103,7 +1102,6 @@ class Skeleton_blocker_complex {
  public:
   /**
    * Remove the star of the edge connecting vertices a and b.
-   * @returns the number of blocker that have been removed
    */
   void remove_star(Vertex_handle a, Vertex_handle b);
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
index 404f04f9..5db9c2fd 100644..100755
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
@@ -39,7 +39,6 @@ bool Skeleton_blocker_complex<SkeletonBlockerDS>::is_popable_blocker(Blocker_han
 
 /**
  * Removes all the popable blockers of the complex and delete them.
- * @returns the number of popable blockers deleted
  */
 template<typename SkeletonBlockerDS>
 void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_popable_blockers() {
@@ -160,7 +159,6 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::update_blockers_after_remove_s
 
 /**
  * Remove the star of the edge connecting vertices a and b.
- * @returns the number of blocker that have been removed
  */
 template<typename SkeletonBlockerDS>
 void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(Vertex_handle a, Vertex_handle b) {
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/examples.h b/src/common/doc/examples.h
index 879fb96a..556a24f1 100644
--- a/src/common/doc/examples.h
+++ b/src/common/doc/examples.h
@@ -1,6 +1,6 @@
 // List of GUDHI examples and utils - Doxygen needs at least a file tag to analyse comments
 // Generated from scripts/cpp_examples_for_doxygen.py
-/*! @file Examples
+/*! @file
  * \section Witness_complex_example_section Witness_complex
  * @example strong_witness_persistence.cpp
  * @example weak_witness_persistence.cpp
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