Documentation: handling references to examples in a more transparent way

Adding the other examples also with `gudhi_example_link`.

5 files changed, 16 insertions, 30 deletions

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/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/common/doc/installation.h b/src/common/doc/installation.h
index fb5ee665..e786f53a 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -58,8 +58,7 @@ make \endverbatim
  * 
  * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic
  * Library</a> (GMP) and will not be built if GMP is not installed:
- * \li <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.
  *