From f043cf8aaf676cc88e84082de49f70dd3492ecb0 Mon Sep 17 00:00:00 2001 From: albert-github Date: Sun, 22 May 2022 12:08:58 +0200 Subject: Documentation: handling references to examples in a more transparent way In case we have the files`Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp` this will be linked to `_random_bitmap_cubical_complex_8cpp-example.html` and this is now hard coded. When the setting of `CASE_SENSE_NAMES` is set to `YES` the mapping is to `Random_bitmap_cubical_complex_8cpp-example.html` but the hard coded link is still to `_random_bitmap_cubical_complex_8cpp-example.html` so the link cannot be resolved (at runtime!). Same could happen when the `CASE_SENSE_NAMES` is left blank and the the value is system dependent. It is unlikely that this happens but ... By introducing the `ALIASES` `gudhi_example_link` this can be handled by doxygen in a more transparent way. Furthermore wit 2 examples there was a double `cpp` in the text part, this has been corrected as well Notre this solution supersedes #621 and maked #621 obsolete. --- src/Doxyfile.in | 2 +- src/common/doc/installation.h | 234 ++++++++++++++---------------------------- 2 files changed, 79 insertions(+), 157 deletions(-) (limited to 'src') diff --git a/src/Doxyfile.in b/src/Doxyfile.in index f76ba2bd..b15d47a6 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in @@ -229,7 +229,7 @@ TAB_SIZE = 2 # "Side Effects:". You can put \n's in the value part of an alias to insert # newlines. -ALIASES = +ALIASES = gudhi_example_link{2}="@ref \2 \"\1/\2\"" # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources # only. Doxygen will then generate output that is more tailored for C. For diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 67d026bd..fb5ee665 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -76,58 +76,32 @@ make \endverbatim * * The following examples/utilities require the Computational Geometry Algorithms * Library (CGAL \cite cgal:eb-19b) and will not be built if CGAL version 4.11.0 or higher is not installed: - * \li - * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp - * \li - * Witness_complex/strong_witness_persistence.cpp - * \li - * Witness_complex/weak_witness_persistence.cpp - * \li - * Witness_complex/example_strong_witness_complex_off.cpp - * \li - * Witness_complex/example_witness_complex_off.cpp - * \li - * Witness_complex/example_witness_complex_sphere.cpp - * \li - * Alpha_complex/Alpha_complex_from_off.cpp - * \li - * Alpha_complex/Alpha_complex_from_points.cpp - * \li - * Alpha_complex/alpha_complex_persistence.cpp - * \li - * Persistent_cohomology/custom_persistence_sort.cpp - * \li - * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp - * \li - * Bottleneck_distance/bottleneck_basic_example.cpp - * \li - * Bottleneck_distance/bottleneck_distance.cpp - * \li - * Nerve_GIC/CoordGIC.cpp - * \li - * Nerve_GIC/FuncGIC.cpp - * \li - * Nerve_GIC/Nerve.cpp - * \li - * Nerve_GIC/VoronoiGIC.cpp - * \li - * Spatial_searching/example_spatial_searching.cpp - * \li - * Subsampling/example_choose_n_farthest_points.cpp - * \li - * Subsampling/example_pick_n_random_points.cpp - * \li - * Subsampling/example_sparsify_point_set.cpp - * \li - * Tangential_complex/example_basic.cpp - * \li - * Tangential_complex/example_with_perturb.cpp - * \li - * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp - * \li - * Alpha_complex/alpha_complex_3d_persistence.cpp - * \li - * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp + * \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 @@ -136,48 +110,27 @@ make \endverbatim * * The following examples/utilities require the Eigen and will not be * built if Eigen is not installed: - * \li - * Alpha_complex/Alpha_complex_from_off.cpp - * \li - * Alpha_complex/Alpha_complex_from_points.cpp - * \li - * Alpha_complex/alpha_complex_persistence.cpp - * \li - * Alpha_complex/alpha_complex_3d_persistence.cpp - * \li - * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp - * \li - * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp - * \li - * Persistent_cohomology/custom_persistence_sort.cpp - * \li - * Spatial_searching/example_spatial_searching.cpp - * \li - * Subsampling/example_choose_n_farthest_points.cpp - * \li - * Subsampling/example_pick_n_random_points.cpp - * \li - * Subsampling/example_sparsify_point_set.cpp - * \li - * Tangential_complex/example_basic.cpp - * \li - * Tangential_complex/example_with_perturb.cpp - * \li - * Witness_complex/strong_witness_persistence.cpp - * \li - * Witness_complex/weak_witness_persistence.cpp - * \li - * Witness_complex/example_strong_witness_complex_off.cpp - * \li - * Witness_complex/example_witness_complex_off.cpp - * \li - * Witness_complex/example_witness_complex_sphere.cpp - * \li - * Coxeter_triangulation/cell_complex_from_basic_circle_manifold.cpp - * \li - * Coxeter_triangulation/manifold_tracing_custom_function.cpp - * \li - * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.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{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 * Intel® TBB lets you easily write parallel @@ -187,68 +140,37 @@ make \endverbatim * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. * * The following examples/utilities are using Intel® TBB if installed: - * \li - * Alpha_complex/Alpha_complex_from_off.cpp - * \li - * Alpha_complex/Alpha_complex_from_points.cpp - * \li - * Alpha_complex/alpha_complex_3d_persistence.cpp - * \li - * Alpha_complex/alpha_complex_persistence.cpp - * \li - * Bitmap_cubical_complex/cubical_complex_persistence.cpp - * \li - * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp - * \li - * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * \li - * Nerve_GIC/CoordGIC.cpp - * \li - * Nerve_GIC/FuncGIC.cpp - * \li - * Nerve_GIC/Nerve.cpp - * \li - * Nerve_GIC/VoronoiGIC.cpp - * \li - * Simplex_tree/simple_simplex_tree.cpp - * \li - * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp - * \li - * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp - * \li - * Simplex_tree/graph_expansion_with_blocker.cpp - * \li - * Persistent_cohomology/alpha_complex_3d_persistence.cpp - * \li - * Persistent_cohomology/alpha_complex_persistence.cpp - * \li - * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp - * \li - * Persistent_cohomology/persistence_from_file.cpp - * \li - * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp - * \li - * Persistent_cohomology/plain_homology.cpp - * \li - * Persistent_cohomology/rips_multifield_persistence.cpp - * \li - * Persistent_cohomology/rips_persistence_step_by_step.cpp - * \li - * Persistent_cohomology/custom_persistence_sort.cpp - * \li - * Rips_complex/example_one_skeleton_rips_from_points.cpp - * \li - * Rips_complex/example_rips_complex_from_off_file.cpp - * \li - * Rips_complex/rips_distance_matrix_persistence.cpp - * \li - * Rips_complex/rips_persistence.cpp - * \li - * Witness_complex/strong_witness_persistence.cpp - * \li - * Witness_complex/weak_witness_persistence.cpp - * \li - * Witness_complex/example_nearest_landmark_table.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_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. -- cgit v1.2.3