Merge tag 'tags/gudhi-release-3.6.0' into dfsg/latest

author: Gard Spreemann <gspr@nonempty.org> 2022-08-17 14:31:07 +0200
committer: Gard Spreemann <gspr@nonempty.org> 2022-08-17 14:31:07 +0200
commit: e65c2f6750eca50a2333801a25f401b318e49ef7 (patch)
tree: ea24364b96a3dafe237d21d836a0857675d257b1 /src/common
parent: dbc404626955aee632fa47ee7a4d4c3add7d6188 (diff)
parent: de8bd5109fcdc6d4d200c74685bab031d953d2af (diff)
9 files changed, 135 insertions, 1596 deletions
diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h
index 879fb96a..1634b19e 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
@@ -40,7 +40,6 @@
  * @example edge_collapse_basic_example.cpp
  * \section Cech_complex_example_section Cech_complex
  * @example cech_persistence.cpp
- * @example cech_complex_step_by_step.cpp
  * @example cech_complex_example_from_points.cpp
  * \section Bitmap_cubical_complex_example_section Bitmap_cubical_complex
  * @example periodic_cubical_complex_persistence.cpp
diff --git a/src/common/doc/footer.html b/src/common/doc/footer.html
index 4168c6bc..08a2cbd0 100644
--- a/src/common/doc/footer.html
+++ b/src/common/doc/footer.html
@@ -1,5 +1,9 @@
-<!-- HTML footer for doxygen 1.8.6-->
+<!-- HTML footer for doxygen 1.9.4-->
 <!-- start footer part -->
+<!--BEGIN GENERATE_TREEVIEW-->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+<!--END GENERATE_TREEVIEW-->
+<ul>
 <table style="width:100%">
   <tr class="no-bullet shadow-black">
       <td class="network-entypo">
@@ -10,14 +14,15 @@
 <!--END PROJECT_NAME-->
       </td>
       <td class="network-entypo">
-<!--BEGIN GENERATE_TREEVIEW-->
         $generatedby
         <a href="http://www.doxygen.org/index.html">
         Doxygen</a> $doxygenversion
-<!--END GENERATE_TREEVIEW-->
       </td>
   </tr>
 </table>
-
+</ul>
+<!--BEGIN GENERATE_TREEVIEW-->
+</div>
+<!--END GENERATE_TREEVIEW-->
 </body>
 </html>
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
index 7c20478b..a97e1b2f 100644
--- a/src/common/doc/header.html
+++ b/src/common/doc/header.html
@@ -8,9 +8,6 @@
 <meta name="generator" content="Doxygen $doxygenversion"/>
 <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
 <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
-<!-- GUDHI website css for header BEGIN -->
-<link rel="stylesheet" type="text/css" href="https://gudhi.inria.fr/assets/css/styles_feeling_responsive.css" />
-<!-- GUDHI website css for header END -->
 <link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="$relpath^jquery.js"></script>
 <script type="text/javascript" src="$relpath^dynsections.js"></script>
@@ -18,13 +15,17 @@ $treeview
 $search
 $mathjax
 <link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
+<!-- GUDHI website css for header BEGIN -->
+<link rel="stylesheet" type="text/css" href="https://gudhi.inria.fr/assets/css/styles_feeling_responsive.css" />
+<!-- GUDHI website css for header END -->
 $extrastylesheet
 </head>
 <body>
 
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
 <!-- GUDHI website header BEGIN -->
 <div id="navigation" class="sticky">
-  <nav class="top-bar" role="navigation" data-topbar>
+  <nav class="top-bar" role="navigation" data-topbar="true">
     <ul class="title-area">
       <li class="name">
       <h1 class="show-for-small-only"><a href="" class="icon-tree"> GUDHI library</a></h1>
@@ -38,7 +39,7 @@ $extrastylesheet
               <li><a  href="/contact/">Contact</a></li>
       </ul>
       <ul class="left">
-              <li><a  href="/"> <img src="/assets/img/home.png" alt="  GUDHI">  GUDHI </a></li>
+              <li><a  href="/"> <img src="/assets/img/home.png" alt="  GUDHI"/>  GUDHI </a></li>
               <li class="divider"></li>
               <li class="has-dropdown">
                 <a  href="#">Project</a>
@@ -85,7 +86,6 @@ $extrastylesheet
 </div><!-- /#navigation -->
 <!-- GUDHI website header END -->
 
-<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
 
 <!--BEGIN TITLEAREA-->
 <div id="titlearea">
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index ef668dfb..28526498 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; 1.56.0
- * 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
@@ -40,13 +40,20 @@ make \endverbatim
  * `make test` is using <a href="https://cmake.org/cmake/help/latest/manual/ctest.1.html">Ctest</a> (CMake test driver
  * program). If some of the tests are failing, please send us the result of the following command:
  * \verbatim ctest --output-on-failure \endverbatim
+ * Testing fetching datasets feature requires the use of the internet and is disabled by default. If you want to include this test, set WITH_GUDHI_REMOTE_TEST to ON when building in the previous step (note that this test is included in the python module):
+ * \verbatim cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_REMOTE_TEST=ON --DWITH_GUDHI_PYTHON=ON .. \endverbatim
  * 
- * \subsection documentationgeneration Documentation
- * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required.
- * Run the following command in a terminal:
+ * \subsection documentationgeneration C++ documentation
+ * To generate the C++ documentation, the <a target="_blank" href="http://www.doxygen.org/">doxygen</a> program
+ * is required (version &ge; 1.9.3 is advised). Run the following command in a terminal:
  * \verbatim make doxygen \endverbatim
  * Documentation will be generated in a folder named <code>html</code>.
  *
+ * In case there is not a full setup present and only the documentation should be build the following command sequence
+ * can be used:
+\verbatim  cmake -DWITH_GUDHI_THIRD_PARTY=OFF ..
+make doxygen\endverbatim
+ *
  * \subsection helloworld Hello world !
  * The <a target="_blank" href="https://github.com/GUDHI/hello-gudhi-world">Hello world for GUDHI</a>
  * project is an example to help developers to make their own C++ project on top of the GUDHI library.
@@ -56,10 +63,9 @@ 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 +82,101 @@ 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/common/doc/main_page.md b/src/common/doc/main_page.md
index 17354179..ce903405 100644
--- a/src/common/doc/main_page.md
+++ b/src/common/doc/main_page.md
@@ -180,8 +180,8 @@
     <td width="15%">
       <b>Author:</b> Vincent Rouvreau<br>
       <b>Introduced in:</b> GUDHI 2.2.0<br>
-      <b>Copyright:</b> MIT [(GPL v3)](../../licensing/)<br>
-      <b>Includes:</b> [Miniball](https://people.inf.ethz.ch/gaertner/subdir/software/miniball.html)<br>
+      <b>Copyright:</b> MIT [(LGPL v3)](../../licensing/)<br>
+      <b>Requires:</b> \ref cgal
     </td>
  </tr>
  <tr>
@@ -231,13 +231,12 @@
     homology of the input sequence. The resulting method is simple and extremely efficient.
 
     Computation of edge collapse and persistent homology of a filtered flag complex via edge collapse as described in
-    \cite edgecollapsesocg2020.
+    \cite edgecollapsearxiv.
     </td>
     <td width="15%">
-      <b>Author:</b> Siddharth Pritam<br>
+      <b>Author:</b> Siddharth Pritam, Marc Glisse<br>
       <b>Introduced in:</b> GUDHI 3.3.0<br>
-      <b>Copyright:</b> MIT<br>
-      <b>Requires:</b> \ref eigen
+      <b>Copyright:</b> MIT
     </td>
  </tr>
  <tr>
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-{
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-{
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-{
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-{
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-{
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-{ 
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- 
 #projectname
 {
-	border: 0px none;
-	font: 300% Tahoma, Arial,sans-serif;
-	margin: 0px;
-	padding: 2px 0px;
+  border: 0px none;
 }
-    
 #projectbrief
 {
-	font: 60% Tahoma, Arial,sans-serif;
-	margin: 0px;
-	padding: 0px;
+  font: 60% Tahoma, Arial,sans-serif;
 }
-
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 {
-	font: 80% Tahoma, Arial,sans-serif;
-	margin: 0px;
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-{
-        text-align: center;
-}
-
-.dotgraph
-{
-        text-align: center;
+  font: 80% Tahoma, Arial,sans-serif;
 }
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+.arrow
 {
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-	opacity: 0.9;
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+    width: auto;
+    height: auto;
+    padding-left: 16px;
 }
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-@media print
-{
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-  #side-nav { display: none; }
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-  .summary { display: none; }
-  .memitem { page-break-inside: avoid; }
-  #doc-content
-  {
-    margin-left:0 !important;
-    height:auto !important;
-    width:auto !important;
-    overflow:inherit;
-    display:inline;
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+// With the doxygen versions <= 1.9.2 the default setting 'overflow: hidden;' causes problems.
+// With the commit:
+//   Commit: 590198b416cd53313d150428d2f912586065ea0d [590198b]
+//   Date: Wednesday, December 1, 2021 1:37:26 PM
+//   issue #8924 Horizontal scroll bar missing in HTML for wide class="dotgraph" objects
+// for the doxygen 1.9.3 version this has already been corrected but to run properly with the <= 1.9.2 version
+// this setting is required
+ul {
+  overflow: visible;
 }
-
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index 9bbc62b7..5e5a1e31 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -13,8 +13,6 @@
 
 #include <gudhi/Debug_utils.h>
 
-#include <gudhi/Miniball.hpp>
-
 #include <boost/range/metafunctions.hpp>
 #include <boost/range/size.hpp>
 
@@ -59,53 +57,6 @@ class Euclidean_distance {
   }
 };
 
-/** @brief Compute the radius of the minimal enclosing ball between Points given by a range of coordinates.
- * The points are assumed to have the same dimension. */
-class Minimal_enclosing_ball_radius {
- public:
-  /** \brief Minimal_enclosing_ball_radius from two points.
-   *
-   * @param[in] point_1 First point.
-   * @param[in] point_2 second point.
-   * @return The minimal enclosing ball radius for the two points (aka. Euclidean distance / 2.).
-   *
-   * \tparam Point must be a range of Cartesian coordinates.
-   *
-   */
-  template< typename Point >
-  typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type
-  operator()(const Point& point_1, const Point& point_2) const {
-    return Euclidean_distance()(point_1, point_2) / 2.;
-  }
-  /** \brief Minimal_enclosing_ball_radius from a point cloud.
-   *
-   * @param[in] point_cloud The points.
-   * @return The minimal enclosing ball radius for the points.
-   *
-   * \tparam Point_cloud must be a range of points with Cartesian coordinates.
-   * Point_cloud is a range over a range of Coordinate.
-   *
-   */
-  template< typename Point_cloud,
-            typename Point_iterator = typename boost::range_const_iterator<Point_cloud>::type,
-            typename Point = typename std::iterator_traits<Point_iterator>::value_type,
-            typename Coordinate_iterator = typename boost::range_const_iterator<Point>::type,
-            typename Coordinate = typename std::iterator_traits<Coordinate_iterator>::value_type>
-  Coordinate
-  operator()(const Point_cloud& point_cloud) const {
-    using Min_sphere = Miniball::Miniball<Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>;
-
-    Min_sphere ms(boost::size(*point_cloud.begin()), point_cloud.begin(), point_cloud.end());
-#ifdef DEBUG_TRACES
-    std::clog << "Minimal_enclosing_ball_radius = " << std::sqrt(ms.squared_radius()) << " | nb points = "
-              << boost::size(point_cloud) << " | dimension = "
-              << boost::size(*point_cloud.begin()) << std::endl;
-#endif  // DEBUG_TRACES
-
-    return std::sqrt(ms.squared_radius());
-  }
-};
-
 }  // namespace Gudhi
 
 #endif  // DISTANCE_FUNCTIONS_H_
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index a1b104e2..a7d82541 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -14,11 +14,7 @@
 #include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/Debug_utils.h>
 
-#if BOOST_VERSION < 106600
-# include <boost/function_output_iterator.hpp>
-#else
 # include <boost/iterator/function_output_iterator.hpp>
-#endif
 #include <boost/graph/adjacency_list.hpp>
 
 #include <iostream>
@@ -235,7 +231,7 @@ std::vector<std::vector<Filtration_value>> read_lower_triangular_matrix_from_csv
 
   std::string line;
 
-  // the first line is emtpy, so we ignore it:
+  // the first line is empty, so we ignore it:
   std::getline(in, line);
   std::vector<Filtration_value> values_in_this_line;
   result.push_back(values_in_this_line);
diff --git a/src/common/include/gudhi/writing_persistence_to_file.h b/src/common/include/gudhi/writing_persistence_to_file.h
index 2e36b831..3a0df1a8 100644
--- a/src/common/include/gudhi/writing_persistence_to_file.h
+++ b/src/common/include/gudhi/writing_persistence_to_file.h
@@ -48,7 +48,7 @@ class Persistence_interval_common {
       : birth_(birth), death_(death), dimension_(dim), arith_element_(field) {}
 
   /**
-   * Operator to compare two persistence pairs. During the comparision all the
+   * Operator to compare two persistence pairs. During the comparison all the
    * fields: birth, death, dimensiona and arith_element_ are taken into account
    * and they all have to be equal for two pairs to be equal.
   **/
@@ -65,7 +65,7 @@ class Persistence_interval_common {
   /**
    * Operator to compare objects of a type Persistence_interval_common.
    * One intervals is smaller than the other if it has lower persistence.
-   * Note that this operator do not take Arith_element into account when doing comparisions.
+   * Note that this operator do not take Arith_element into account when doing comparisons.
   **/
   bool operator<(const Persistence_interval_common& i2) const {
     return fabs(this->death_ - this->birth_) < fabs(i2.death_ - i2.birth_);
author	Gard Spreemann <gspr@nonempty.org>	2022-08-17 14:31:07 +0200
committer	Gard Spreemann <gspr@nonempty.org>	2022-08-17 14:31:07 +0200
commit	e65c2f6750eca50a2333801a25f401b318e49ef7 (patch)
tree	ea24364b96a3dafe237d21d836a0857675d257b1 /src/common
parent	dbc404626955aee632fa47ee7a4d4c3add7d6188 (diff)
parent	de8bd5109fcdc6d4d200c74685bab031d953d2af (diff)