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-rw-r--r--src/common/doc/examples.h225
-rw-r--r--src/common/doc/footer.html13
-rw-r--r--src/common/doc/header.html124
-rw-r--r--src/common/doc/installation.h295
-rw-r--r--src/common/doc/main_page.md63
-rwxr-xr-x[-rw-r--r--]src/common/doc/stylesheet.css1371
6 files changed, 393 insertions, 1698 deletions
diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h
index c19b3444..1634b19e 100644
--- a/src/common/doc/examples.h
+++ b/src/common/doc/examples.h
@@ -1,96 +1,133 @@
-// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments
-// In user_version, `find . -name "*.cpp"` in example and utilities folders
-/*! @file Examples
- * @example Alpha_complex/Alpha_complex_from_off.cpp
- * @example Alpha_complex/Alpha_complex_from_points.cpp
- * @example Bottleneck_distance/bottleneck_basic_example.cpp
- * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
- * @example Witness_complex/example_nearest_landmark_table.cpp
- * @example Witness_complex/example_witness_complex_off.cpp
- * @example Witness_complex/example_witness_complex_sphere.cpp
- * @example Witness_complex/example_strong_witness_complex_off.cpp
- * @example Simplex_tree/mini_simplex_tree.cpp
- * @example Simplex_tree/graph_expansion_with_blocker.cpp
- * @example Simplex_tree/simple_simplex_tree.cpp
- * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
- * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
- * @example Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp
- * @example Persistent_cohomology/plain_homology.cpp
- * @example Persistent_cohomology/persistence_from_file.cpp
- * @example Persistent_cohomology/rips_persistence_step_by_step.cpp
- * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
- * @example Persistent_cohomology/custom_persistence_sort.cpp
- * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
- * @example Persistent_cohomology/rips_multifield_persistence.cpp
- * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
- * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp
- * @example Skeleton_blocker/Skeleton_blocker_link.cpp
- * @example Contraction/Garland_heckbert.cpp
- * @example Contraction/Rips_contraction.cpp
- * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
- * @example common/example_CGAL_3D_points_off_reader.cpp
- * @example common/example_vector_double_points_off_reader.cpp
- * @example common/example_CGAL_points_off_reader.cpp
- * @example Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp
- * @example Rips_complex/example_one_skeleton_rips_from_points.cpp
- * @example Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp
- * @example Rips_complex/example_rips_complex_from_off_file.cpp
- * @example Persistence_representations/persistence_intervals.cpp
- * @example Persistence_representations/persistence_vectors.cpp
- * @example Persistence_representations/persistence_heat_maps.cpp
- * @example Persistence_representations/persistence_landscape_on_grid.cpp
- * @example Persistence_representations/persistence_landscape.cpp
- * @example Tangential_complex/example_basic.cpp
- * @example Tangential_complex/example_with_perturb.cpp
- * @example Subsampling/example_custom_kernel.cpp
- * @example Subsampling/example_choose_n_farthest_points.cpp
- * @example Subsampling/example_sparsify_point_set.cpp
- * @example Subsampling/example_pick_n_random_points.cpp
- * @example Nerve_GIC/CoordGIC.cpp
- * @example Nerve_GIC/Nerve.cpp
- * @example Nerve_GIC/FuncGIC.cpp
- * @example Nerve_GIC/VoronoiGIC.cpp
- * @example Spatial_searching/example_spatial_searching.cpp
- * @example Alpha_complex/alpha_complex_3d_persistence.cpp
- * @example Alpha_complex/alpha_complex_persistence.cpp
- * @example Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp
- * @example Bottleneck_distance/bottleneck_distance.cpp
- * @example Witness_complex/weak_witness_persistence.cpp
- * @example Witness_complex/strong_witness_persistence.cpp
- * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp
- * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp
- * @example common/off_file_from_shape_generator.cpp
- * @example Rips_complex/rips_distance_matrix_persistence.cpp
- * @example Rips_complex/rips_persistence.cpp
- * @example Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
- * @example Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
- * @example Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
- * @example Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
- * @example Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
- * @example Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
- * @example Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp
- * @example Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp
- * @example Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp
- * @example Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
- * @example Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp
- * @example Persistence_representations/persistence_heat_maps/create_pssk.cpp
- * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
- * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
- * @example Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
- * @example Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
- * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
- * @example Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp
- * @example Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp
- * @example Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp
- * @example Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp
- * @example Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp
- * @example Persistence_representations/persistence_vectors/average_persistence_vectors.cpp
- * @example Persistence_representations/persistence_vectors/create_persistence_vectors.cpp
- * @example Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
- * @example Persistence_representations/persistence_landscapes/average_landscapes.cpp
- * @example Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp
- * @example Persistence_representations/persistence_landscapes/create_landscapes.cpp
- * @example Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp
- * @example Persistence_representations/persistence_landscapes/plot_landscapes.cpp
+// 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
+ * \section Witness_complex_example_section Witness_complex
+ * @example strong_witness_persistence.cpp
+ * @example weak_witness_persistence.cpp
+ * @example example_witness_complex_off.cpp
+ * @example example_strong_witness_complex_off.cpp
+ * @example example_nearest_landmark_table.cpp
+ * @example example_witness_complex_sphere.cpp
+ * \section Contraction_example_section Contraction
+ * @example Rips_contraction.cpp
+ * @example Garland_heckbert.cpp
+ * \section Simplex_tree_example_section Simplex_tree
+ * @example mini_simplex_tree.cpp
+ * @example cech_complex_cgal_mini_sphere_3d.cpp
+ * @example graph_expansion_with_blocker.cpp
+ * @example simple_simplex_tree.cpp
+ * @example simplex_tree_from_cliques_of_graph.cpp
+ * @example example_alpha_shapes_3_simplex_tree_from_off_file.cpp
+ * \section Persistent_cohomology_example_section Persistent_cohomology
+ * @example custom_persistence_sort.cpp
+ * @example rips_persistence_step_by_step.cpp
+ * @example persistence_from_file.cpp
+ * @example rips_persistence_via_boundary_matrix.cpp
+ * @example plain_homology.cpp
+ * @example rips_multifield_persistence.cpp
+ * @example persistence_from_simple_simplex_tree.cpp
+ * \section Subsampling_example_section Subsampling
+ * @example example_sparsify_point_set.cpp
+ * @example example_choose_n_farthest_points.cpp
+ * @example example_custom_distance.cpp
+ * @example example_pick_n_random_points.cpp
+ * \section Toplex_map_example_section Toplex_map
+ * @example simple_toplex_map.cpp
+ * \section Collapse_example_section Collapse
+ * @example distance_matrix_edge_collapse_rips_persistence.cpp
+ * @example point_cloud_edge_collapse_rips_persistence.cpp
+ * @example edge_collapse_conserve_persistence.cpp
+ * @example edge_collapse_basic_example.cpp
+ * \section Cech_complex_example_section Cech_complex
+ * @example cech_persistence.cpp
+ * @example cech_complex_example_from_points.cpp
+ * \section Bitmap_cubical_complex_example_section Bitmap_cubical_complex
+ * @example periodic_cubical_complex_persistence.cpp
+ * @example cubical_complex_persistence.cpp
+ * @example Random_bitmap_cubical_complex.cpp
+ * \section Coxeter_triangulation_example_section Coxeter_triangulation
+ * @example cell_complex_from_basic_circle_manifold.cpp
+ * @example manifold_tracing_flat_torus_with_boundary.cpp
+ * @example manifold_tracing_custom_function.cpp
+ * \section Nerve_GIC_example_section Nerve_GIC
+ * @example VoronoiGIC.cpp
+ * @example Nerve.cpp
+ * @example CoordGIC.cpp
+ * @example FuncGIC.cpp
+ * \section Tangential_complex_example_section Tangential_complex
+ * @example example_basic.cpp
+ * @example example_with_perturb.cpp
+ * \section Persistence_representations_example_section Persistence_representations
+ * @example persistence_vectors/create_persistence_vectors.cpp
+ * @example persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
+ * @example persistence_vectors/plot_persistence_vectors.cpp
+ * @example persistence_vectors/average_persistence_vectors.cpp
+ * @example persistence_vectors/compute_distance_of_persistence_vectors.cpp
+ * @example persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
+ * @example persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
+ * @example persistence_intervals/plot_persistence_Betti_numbers.cpp
+ * @example persistence_intervals/compute_bottleneck_distance.cpp
+ * @example persistence_intervals/compute_number_of_dominant_intervals.cpp
+ * @example persistence_intervals/plot_histogram_of_intervals_lengths.cpp
+ * @example persistence_intervals/plot_persistence_intervals.cpp
+ * @example persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
+ * @example persistence_heat_maps/create_pssk.cpp
+ * @example persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
+ * @example persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
+ * @example persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
+ * @example persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
+ * @example persistence_heat_maps/plot_persistence_heat_map.cpp
+ * @example persistence_heat_maps/create_persistence_heat_maps.cpp
+ * @example persistence_heat_maps/average_persistence_heat_maps.cpp
+ * @example persistence_landscapes/compute_distance_of_landscapes.cpp
+ * @example persistence_landscapes/compute_scalar_product_of_landscapes.cpp
+ * @example persistence_landscapes/average_landscapes.cpp
+ * @example persistence_landscapes/plot_landscapes.cpp
+ * @example persistence_landscapes/create_landscapes.cpp
+ * @example persistence_landscape_on_grid.cpp
+ * @example persistence_intervals.cpp
+ * @example persistence_landscape.cpp
+ * @example persistence_vectors.cpp
+ * @example sliced_wasserstein.cpp
+ * @example persistence_heat_maps.cpp
+ * \section Spatial_searching_example_section Spatial_searching
+ * @example example_spatial_searching.cpp
+ * \section Bottleneck_distance_example_section Bottleneck_distance
+ * @example bottleneck_distance.cpp
+ * @example bottleneck_basic_example.cpp
+ * @example alpha_rips_persistence_bottleneck_distance.cpp
+ * \section common_example_section common
+ * @example off_file_from_shape_generator.cpp
+ * @example example_vector_double_points_off_reader.cpp
+ * @example example_CGAL_points_off_reader.cpp
+ * @example example_CGAL_3D_points_off_reader.cpp
+ * \section Alpha_complex_example_section Alpha_complex
+ * @example alpha_complex_3d_persistence.cpp
+ * @example alpha_complex_persistence.cpp
+ * @example Fast_alpha_complex_from_off.cpp
+ * @example Alpha_complex_3d_from_points.cpp
+ * @example Alpha_complex_from_off.cpp
+ * @example Weighted_alpha_complex_3d_from_points.cpp
+ * @example Weighted_alpha_complex_from_points.cpp
+ * @example Alpha_complex_from_points.cpp
+ * \section Skeleton_blocker_example_section Skeleton_blocker
+ * @example Skeleton_blocker_from_simplices.cpp
+ * @example Skeleton_blocker_link.cpp
+ * @example Skeleton_blocker_iteration.cpp
+ * \section Rips_complex_example_section Rips_complex
+ * @example rips_persistence.cpp
+ * @example rips_correlation_matrix_persistence.cpp
+ * @example sparse_rips_persistence.cpp
+ * @example rips_distance_matrix_persistence.cpp
+ * @example example_sparse_rips.cpp
+ * @example example_rips_complex_from_csv_distance_matrix_file.cpp
+ * @example example_one_skeleton_rips_from_correlation_matrix.cpp
+ * @example example_one_skeleton_rips_from_distance_matrix.cpp
+ * @example example_one_skeleton_rips_from_points.cpp
+ * @example example_rips_complex_from_off_file.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 99ab6bb7..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>
@@ -18,72 +15,77 @@ $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>
- <ul class="title-area">
- <li class="name">
- <h1 class="show-for-small-only"><a href="" class="icon-tree"> GUDHI library</a></h1>
- </li>
- <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone -->
- <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li>
+ <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>
+ </li>
+ <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone -->
+ <li class="toggle-topbar menu-icon"><a href="#"><span>Nav</span></a></li>
+ </ul>
+ <section class="top-bar-section">
+ <ul class="right">
+ <li class="divider"></li>
+ <li><a href="/contact/">Contact</a></li>
</ul>
- <section class="top-bar-section">
- <ul class="right">
- <li class="divider"></li>
- <li><a href="/contact/">Contact</a></li>
- </ul>
- <ul class="left">
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- </ul>
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- <a href="#">Download</a>
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- <li><a href="/conda/">Conda package</a></li>
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- <li><a href="https://gudhi.inria.fr/python/latest/installation.html">Python installation manual</a></li>
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- </ul>
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- <li class="divider"></li>
- </ul>
- </section>
- </nav>
- </div><!-- /#navigation -->
- <!-- GUDHI website header BEGIN -->
+ <ul class="left">
+ <li><a href="/"> <img src="/assets/img/home.png" alt=" GUDHI"/> GUDHI </a></li>
+ <li class="divider"></li>
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+ <ul class="dropdown">
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+ <li><a href="/relatedprojects/">Related projects</a></li>
+ <li><a href="/theyaretalkingaboutus/">They are talking about us</a></li>
+ <li><a href="/inaction/">GUDHI in action</a></li>
+ <li><a href="/etymology/">Etymology</a></li>
+ </ul>
+ </li>
+ <li class="divider"></li>
+ <li class="has-dropdown">
+ <a href="#">Download</a>
+ <ul class="dropdown">
+ <li><a href="/licensing/">Licensing</a></li>
+ <li><a href="https://github.com/GUDHI/gudhi-devel/releases/latest" target="_blank">Get the latest sources</a></li>
+ <li><a href="/conda/">Conda package</a></li>
+ <li><a href="https://pypi.org/project/gudhi/" target="_blank">Pip package</a></li>
+ <li><a href="/dockerfile/">Dockerfile</a></li>
+ </ul>
+ </li>
+ <li class="divider"></li>
+ <li class="has-dropdown">
+ <a href="#">Documentation</a>
+ <ul class="dropdown">
+ <li><a href="/introduction/">Introduction</a></li>
+ <li><a href="/doc/latest/installation.html">C++ installation manual</a></li>
+ <li><a href="/doc/latest/">C++ documentation</a></li>
+ <li><a href="/python/latest/installation.html">Python installation manual</a></li>
+ <li><a href="/python/latest/">Python documentation</a></li>
+ <li><a href="/utils/">Utilities</a></li>
+ <li><a href="/tutorials/">Tutorials</a></li>
+ </ul>
+ </li>
+ <li class="divider"></li>
+ <li><a href="/interfaces/">Interfaces</a></li>
+ <li class="divider"></li>
+ </ul>
+ </section>
+ </nav>
+</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 ce2c5448..f2f8a476 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -5,22 +5,22 @@
* 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; 3.1.
- * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
+ * The library uses c++17 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 2017.
*
* \subsection utilities Utilities and examples
* To build the utilities, run the following commands in a terminal:
\verbatim cd /path-to-gudhi/
mkdir build
cd build/
-cmake ..
+cmake -DCMAKE_BUILD_TYPE=Release ..
make \endverbatim
* By default, examples are disabled. You can activate their compilation with
- * <a href="https://cmake.org/cmake/help/v3.0/manual/ccmake.1.html">ccmake</a> (on Linux and Mac OSX),
- * <a href="https://cmake.org/cmake/help/v3.0/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or by modifying the
+ * <a href="https://cmake.org/cmake/help/latest/manual/ccmake.1.html">ccmake</a> (on Linux and Mac OSX),
+ * <a href="https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or by modifying the
* cmake command as follows :
-\verbatim cmake -DWITH_GUDHI_EXAMPLE=ON ..
+\verbatim cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=ON ..
make \endverbatim
* A list of utilities and examples is available <a href="examples.html">here</a>.
*
@@ -28,23 +28,31 @@ make \endverbatim
* To install the library (headers and activated utilities), run the following command in a terminal:
* \verbatim make install \endverbatim
* This action may require to be in the sudoer or administrator of the machine in function of the operating system and
- * of <a href="https://cmake.org/cmake/help/v3.0/variable/CMAKE_INSTALL_PREFIX.html">CMAKE_INSTALL_PREFIX</a>.
+ * of <a href="https://cmake.org/cmake/help/latest/variable/CMAKE_INSTALL_PREFIX.html">CMAKE_INSTALL_PREFIX</a>.
*
+ * \note Python module will be compiled by the `make` command, but `make install` will not install it. Please refer to
+ * the <a href="https://gudhi.inria.fr/python/latest/installation.html#gudhi-python-module-installation">Python
+ * module installation documentation</a>.
+ *
* \subsection testsuites Test suites
* To test your build, run the following command in a terminal:
* \verbatim make test \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:
-\verbatim
-make doxygen
-# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/
-# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder`
-\endverbatim
+ * \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; 1.9.5 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>
@@ -55,10 +63,9 @@ make doxygen
* 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="_persistent_cohomology_2rips_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.
*
@@ -66,190 +73,118 @@ make doxygen
* Some GUDHI modules (cf. \ref main_page "modules list"), and few examples require CGAL, a C++ library that provides
* easy access to efficient and reliable geometric algorithms.
*
- * \note There is no need to install CGAL, you can just <CODE>cmake . && make</CODE> CGAL (or even
- * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE>), thereafter you will be able to compile
- * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE>
+ * \note There is no need to install CGAL, you can just <CODE>cmake -DCMAKE_BUILD_TYPE=Release . && make</CODE> CGAL
+ * (or even <CODE>cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_HEADER_ONLY=ON .</CODE>), thereafter you will be able to
+ * compile GUDHI by calling <CODE>cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE>
*
* The procedure to install this library according to
* your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
*
* The following examples/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="_simplex_tree_2example_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="_witness_complex_2strong_witness_persistence_8cpp-example.html">
- * Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
- * Witness_complex/weak_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html">
- * Witness_complex/example_strong_witness_complex_off.cpp</a>
- * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html">
- * Witness_complex/example_witness_complex_off.cpp</a>
- * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html">
- * Witness_complex/example_witness_complex_sphere.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_off.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
- * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
- * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
- * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html">
- * Bottleneck_distance/bottleneck_basic_example.cpp</a>
- * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html">
- * Bottleneck_distance/bottleneck_distance.cpp</a>
- * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html">
- * Nerve_GIC/CoordGIC.cpp</a>
- * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html">
- * Nerve_GIC/FuncGIC.cpp</a>
- * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html">
- * Nerve_GIC/Nerve.cpp</a>
- * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html">
- * Nerve_GIC/VoronoiGIC.cpp</a>
- * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
- * Spatial_searching/example_spatial_searching.cpp</a>
- * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
- * Subsampling/example_choose_n_farthest_points.cpp</a>
- * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
- * Subsampling/example_custom_kernel.cpp</a>
- * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
- * Subsampling/example_pick_n_random_points.cpp</a>
- * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
- * Subsampling/example_sparsify_point_set.cpp</a>
- * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
- * Tangential_complex/example_basic.cpp</a>
- * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
- * Tangential_complex/example_with_perturb.cpp</a>
- * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html">
- * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_3d_persistence.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_2_alpha_complex_from_off_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_off.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html">
- * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
- * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
- * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
- * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
- * Spatial_searching/example_spatial_searching.cpp</a>
- * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
- * Subsampling/example_choose_n_farthest_points.cpp</a>
- * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
- * Subsampling/example_custom_kernel.cpp</a>
- * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
- * Subsampling/example_pick_n_random_points.cpp</a>
- * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
- * Subsampling/example_sparsify_point_set.cpp</a>
- * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
- * Tangential_complex/example_basic.cpp</a>
- * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
- * Tangential_complex/example_with_perturb.cpp</a>
- * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
- * Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
- * Witness_complex/weak_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html">
- * Witness_complex/example_strong_witness_complex_off.cpp</a>
- * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html">
- * Witness_complex/example_witness_complex_off.cpp</a>
- * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html">
- * Witness_complex/example_witness_complex_sphere.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_2_alpha_complex_from_off_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_off.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
- * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
- * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a>
- * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
- * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp</a>
- * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html">
- * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a>
- * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html">
- * Nerve_GIC/CoordGIC.cpp</a>
- * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html">
- * Nerve_GIC/FuncGIC.cpp</a>
- * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html">
- * Nerve_GIC/Nerve.cpp</a>
- * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html">
- * Nerve_GIC/VoronoiGIC.cpp</a>
- * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
- * Simplex_tree/simple_simplex_tree.cpp</a>
- * \li <a href="_simplex_tree_2example_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_2simplex_tree_from_cliques_of_graph_8cpp-example.html">
- * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a>
- * \li <a href="_simplex_tree_2graph_expansion_with_blocker_8cpp-example.html">
- * Simplex_tree/graph_expansion_with_blocker.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_complex_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html">
- * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a>
- * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html">
- * Persistent_cohomology/persistence_from_file.cpp</a>
- * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html">
- * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a>
- * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html">
- * Persistent_cohomology/plain_homology.cpp</a>
- * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
- * Persistent_cohomology/rips_multifield_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html">
- * Persistent_cohomology/rips_persistence_step_by_step.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
- * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html">
- * Rips_complex/example_one_skeleton_rips_from_points.cpp</a>
- * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html">
- * Rips_complex/example_rips_complex_from_off_file.cpp</a>
- * \li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html">
- * Rips_complex/rips_distance_matrix_persistence.cpp</a>
- * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html">
- * Rips_complex/rips_persistence.cpp</a>
- * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
- * Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
- * Witness_complex/weak_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2example_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. You may report bugs or suggestions to:
- * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+ * Please help us improving the quality of the GUDHI library.
+ * You may <a href="https://github.com/GUDHI/gudhi-devel/issues">report bugs</a> or
+ * <a href="https://gudhi.inria.fr/contact/">contact us</a> for any suggestions.
*
- * GUDHI is open to external contributions. If you want to join our development team, please contact us.
+ * GUDHI is open to external contributions. If you want to join our development team, please take some time to read our
+ * <a href="https://github.com/GUDHI/gudhi-devel/blob/master/.github/CONTRIBUTING.md">contributing guide</a>.
*
*/
diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md
index a33d98cd..9b7c2853 100644
--- a/src/common/doc/main_page.md
+++ b/src/common/doc/main_page.md
@@ -135,7 +135,7 @@
</tr>
</table>
-## Filtrations and reconstructions {#FiltrationsReconstructions}
+## Filtrations
### Alpha complex
<table>
@@ -178,10 +178,10 @@
The set of all simplices is filtered by the radius of their minimal enclosing ball.
</td>
<td width="15%">
- <b>Author:</b> Vincent Rouvreau<br>
+ <b>Author:</b> Vincent Rouvreau, Hind Montassif<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>
@@ -217,6 +217,35 @@
</tr>
</table>
+### Edge collapse
+
+<table>
+ <tr>
+ <td width="35%" rowspan=2>
+ \image html "dominated_edge.png"
+ </td>
+ <td width="50%">
+ Edge collapse is able to reduce any flag filtration to a smaller flag filtration with the same persistence, using
+ only the 1-skeletons of a simplicial complex.
+ The reduction is exact and the persistence homology of the reduced sequence is identical to the persistence
+ 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 edgecollapsearxiv.
+ </td>
+ <td width="15%">
+ <b>Author:</b> Siddharth Pritam, Marc Glisse<br>
+ <b>Introduced in:</b> GUDHI 3.3.0<br>
+ <b>Copyright:</b> MIT
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 height="25">
+ <b>User manual:</b> \ref edge_collapse
+ </td>
+ </tr>
+</table>
+
### Witness complex
<table>
@@ -268,6 +297,32 @@
</tr>
</table>
+## Manifold reconstructions
+### Coxeter triangulation
+
+<table>
+ <tr>
+ <td width="35%" rowspan=2>
+ \image html "manifold_tracing_on_custom_function_example.png"
+ </td>
+ <td width="50%">
+ Coxeter triangulation module is designed to provide tools for constructing a piecewise-linear approximation of an
+ \f$m\f$-dimensional smooth manifold embedded in \f$ \mathbb{R}^d \f$ using an ambient triangulation.
+ </td>
+ <td width="15%">
+ <b>Author:</b> Siargey Kachanovich<br>
+ <b>Introduced in:</b> GUDHI 3.4.0<br>
+ <b>Copyright:</b> MIT [(LGPL v3)](../../licensing/)<br>
+ <b>Requires:</b> \ref eigen &ge; 3.1.0
+ </td>
+ </tr>
+ <tr>
+ <td colspan=2 height="25">
+ <b>User manual:</b> \ref coxeter_triangulation
+ </td>
+ </tr>
+</table>
+
### Tangential complex
<table>
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+ border: 0px none;
}
-
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{
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+ font: 60% Tahoma, Arial,sans-serif;
}
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}
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- #doc-content
- {
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- width:auto !important;
- overflow:inherit;
- display:inline;
- }
+// 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;
}
-
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-18 06:25:47 +0000