From 8cccedf070962061d7c4e28ab69f000063d2bb8b Mon Sep 17 00:00:00 2001 From: albert-github Date: Fri, 20 May 2022 17:57:29 +0200 Subject: issue #615 Documentation: references to boost Made references to boost so that they point to the last released version. --- src/Simplex_tree/include/gudhi/Simplex_tree.h | 4 ++-- src/Skeleton_blocker/concept/SkeletonBlockerDS.h | 2 +- .../include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 34bc5ace..6dce947c 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1083,8 +1083,8 @@ class Simplex_tree { * * Inserts all vertices and edges given by a OneSkeletonGraph. * OneSkeletonGraph must be a model of - * boost::VertexAndEdgeListGraph - * and boost::PropertyGraph. + * boost::VertexAndEdgeListGraph + * and boost::PropertyGraph. * * The vertex filtration value is accessible through the property tag * vertex_filtration_t. diff --git a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h index 0c2014bd..23eb3670 100644 --- a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h +++ b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h @@ -29,7 +29,7 @@ struct SkeletonBlockerDS { /** * @brief Root_vertex_handle and Vertex_handle are similar to global and local vertex descriptor - * used in boost subgraphs + * used in boost subgraphs * and allow to localize a vertex of a subcomplex on its parent root complex. * * In gross, vertices are stored in a vector diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h index 0c0cc624..d091d7dd 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h @@ -28,7 +28,7 @@ namespace skeleton_blocker { */ struct Skeleton_blocker_simple_traits { /** - * @brief Global and local handle similar to boost subgraphs. + * @brief Global and local handle similar to boost subgraphs. * Vertices are stored in a vector. * For the root simplicial complex, the local and global descriptors are the same. * For a subcomplex L and one of its vertices 'v', the local descriptor of 'v' is its position in -- cgit v1.2.3 From 5eecc6cf6dabbb41d63be60adb7cde7a07a0b27c Mon Sep 17 00:00:00 2001 From: albert-github Date: Fri, 20 May 2022 18:25:17 +0200 Subject: Documentation: Updating redirected links Updating simple links in documentation sources for which we got during link checking: ``` This is a permanent redirect. The link should be updated. ``` --- biblio/bibliography.bib | 16 ++++++++-------- src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 2 +- src/common/doc/installation.h | 12 ++++++------ src/python/doc/nerve_gic_complex_user.rst | 2 +- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index ec8772aa..8c9ee84a 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -14,7 +14,7 @@ publisher = {JMLR.org}, title = {{Statistical analysis and parameter selection for Mapper}}, volume = {19}, year = {2018}, -url = {http://jmlr.org/papers/v19/17-291.html}, +url = {https://jmlr.org/papers/v19/17-291.html}, } @inproceedings{Dey13, @@ -151,10 +151,10 @@ language={English}, %% hal-00922572, version 2 -%% http://hal.inria.fr/hal-00922572 +%% https://hal.inria.fr/hal-00922572 @techreport{boissonnat:hal-00922572, hal_id = {hal-00922572}, - url = {http://hal.inria.fr/hal-00922572}, + url = {https://hal.inria.fr/hal-00922572}, title = {Computing Persistent Homology with Various Coefficient Fields in a Single Pass}, author = {Boissonnat, Jean-Daniel and Maria, Cl{\'e}ment}, abstract = {{In this article, we introduce the multi-field persistence diagram for the persistence homology of a filtered complex. It encodes compactly the superimposition of the persistence diagrams of the complex with several field coefficients, and provides a substantially more precise description of the topology of the filtered complex. Specifically, the multi-field persistence diagram encodes the Betti numbers of integral homology and the prime divisors of the torsion coefficients of the underlying shape. Moreover, it enjoys similar stability properties as the ones of standard persistence diagrams, with the appropriate notion of distance. These properties make the multi-field persistence diagram a useful tool in computational topology.}}, @@ -167,7 +167,7 @@ language={English}, number = {RR-8436}, year = {2013}, month = Dec, - pdf = {http://hal.inria.fr/hal-00922572/PDF/RR-8436.pdf}, + pdf = {https://hal.inria.fr/hal-00922572/PDF/RR-8436.pdf}, } @@ -323,7 +323,7 @@ language={English}, %------------------------------------------------------------------ @article{rips2012, hal_id = {hal-00785072}, - url = {http://hal.archives-ouvertes.fr/hal-00785072}, + url = {https://hal.archives-ouvertes.fr/hal-00785072}, title = {{Vietoris-Rips Complexes also Provide Topologically Correct Reconstructions of Sampled Shapes}}, author = {Attali, Dominique and Lieutier, Andr{\'e} and Salinas, David}, keywords = {Shape reconstruction \sep Rips complexes \sep clique complexes \sep \v Cech complexes ; homotopy equivalence ; collapses ; high dimensions}, @@ -1115,7 +1115,7 @@ language={English} author = {Nicholas J. Cavanna and Mahmoodreza Jahanseir and Donald R. Sheehy}, booktitle = {Proceedings of the Canadian Conference on Computational Geometry}, title = {A Geometric Perspective on Sparse Filtrations}, - url = {http://research.cs.queensu.ca/cccg2015/CCCG15-papers/01.pdf}, + url = {https://research.cs.queensu.ca/cccg2015/CCCG15-papers/01.pdf}, year = {2015} } @@ -1151,7 +1151,7 @@ language={English} editor = {Lars Arge and J{\'a}nos Pach}, publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik}, address = {Dagstuhl, Germany}, - URL = {http://drops.dagstuhl.de/opus/volltexte/2015/5098}, + URL = {https://drops.dagstuhl.de/opus/volltexte/2015/5098}, URN = {urn:nbn:de:0030-drops-50981}, doi = {10.4230/LIPIcs.SOCG.2015.642}, annote = {Keywords: Simplicial complex, Compact data structures, Automaton, NP-hard} @@ -1164,7 +1164,7 @@ language={English} journal = {CoRR}, volume = {abs/1607.08449}, year = {2016}, - url = {http://arxiv.org/abs/1607.08449}, + url = {https://arxiv.org/abs/1607.08449}, archivePrefix = {arXiv}, eprint = {1607.08449}, timestamp = {Mon, 13 Aug 2018 16:46:26 +0200}, diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index a6098860..e1ab7cb3 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -24,7 +24,7 @@ namespace cover_complex { * Visualizations of the simplicial complexes can be done with either * neato (from graphviz), * geomview, - * KeplerMapper. + * KeplerMapper. * Input point clouds are assumed to be \ref FileFormatsOFF "OFF files" * * \section covers Covers diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 67d026bd..7502f394 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 Boost ≥ 1.66.0 - * and CMake ≥ 3.5. + * The library uses c++14 and requires Boost ≥ 1.66.0 + * and CMake ≥ 3.5. * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * * \subsection utilities Utilities and examples @@ -56,7 +56,7 @@ 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 GNU Multiple Precision Arithmetic + * The following example requires the GNU Multiple Precision Arithmetic * Library (GMP) and will not be built if GMP is not installed: * \li * Persistent_cohomology/rips_multifield_persistence.cpp @@ -131,10 +131,10 @@ make \endverbatim * * \subsection eigen Eigen * Some GUDHI modules (cf. \ref main_page "modules list"), and few examples require - * Eigen is a C++ template library for linear algebra: + * Eigen is a C++ template library for linear algebra: * matrices, vectors, numerical solvers, and related algorithms. * - * The following examples/utilities require the Eigen and will not be + * 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 @@ -180,7 +180,7 @@ make \endverbatim * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp * * \subsection tbb Threading Building Blocks - * Intel® TBB lets you easily write parallel + * Intel® TBB 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. * diff --git a/src/python/doc/nerve_gic_complex_user.rst b/src/python/doc/nerve_gic_complex_user.rst index 0b820abf..8633cadb 100644 --- a/src/python/doc/nerve_gic_complex_user.rst +++ b/src/python/doc/nerve_gic_complex_user.rst @@ -12,7 +12,7 @@ Definition Visualizations of the simplicial complexes can be done with either neato (from `graphviz `_), `geomview `_, -`KeplerMapper `_. +`KeplerMapper `_. Input point clouds are assumed to be OFF files (cf. `OFF file format `_). Covers -- cgit v1.2.3 From 5520a72287239a6b39d771df3b2511307709a4df Mon Sep 17 00:00:00 2001 From: albert-github Date: Sat, 21 May 2022 14:31:24 +0200 Subject: Documentation: Non persistent links During the link check we found some references to `#title..` in respect to links to CGAL, these links work at the moment but are, by CGAL, generated links during runtime based on the HTML `` tags. When a new paragraph or chapter is added these numbers will change and thus will the link point to the wrong place. All these items have also a more persistent reference anchor that is generated based on the `` of the section (e.g. `\section `). Therefore it is better to used the references based on the ``. --- src/Alpha_complex/doc/Intro_alpha_complex.h | 6 +++--- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 2 +- src/Alpha_complex/utilities/alphacomplex.md | 4 ++-- src/python/doc/alpha_complex_user.rst | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 5ab23720..ca48ebd2 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -164,11 +164,11 @@ Table of Contents * Requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 5.1.0. * * A weighted version for Alpha complex is available (cf. Alpha_complex). It is like a usual Alpha complex, but based - * on a CGAL regular triangulation instead + * on a CGAL regular triangulation instead * of Delaunay. * * This example builds the CGAL weighted alpha shapes from a small molecule, and initializes the alpha complex with - * it. This example is taken from CGAL 3d + * it. This example is taken from CGAL 3d * weighted alpha shapes. * * Then, it is asked to display information about the alpha complex. @@ -212,7 +212,7 @@ Table of Contents * Gudhi::alpha_complex::complexity::EXACT. * * This example builds the CGAL 3d weighted alpha shapes from a small molecule, and initializes the alpha complex with - * it. This example is taken from CGAL 3d + * it. This example is taken from CGAL 3d * weighted alpha shapes. * * Then, it is asked to display information about the alpha complex. diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index b3dbc9bb..562ef139 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -98,7 +98,7 @@ struct Value_from_iterator { * \tparam Periodic Boolean used to set/unset the periodic version of Alpha_complex_3d. Default value is false. * * For the weighted version, weights values are explained on CGAL - * Alpha shapes 3d and + * Alpha shapes 3d and * Regular * triangulation documentation. * diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md index 0d3c6027..1e3b8fab 100644 --- a/src/Alpha_complex/utilities/alphacomplex.md +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -64,7 +64,7 @@ N.B.: * Weights values are explained on CGAL [dD Triangulations](https://doc.cgal.org/latest/Triangulation/index.html) and -[Regular triangulation](https://doc.cgal.org/latest/Triangulation/index.html#title20) documentation. +[Regular triangulation](https://doc.cgal.org/latest/Triangulation/index.html#TriangulationSecRT) documentation. ## alpha_complex_3d_persistence ## @@ -131,6 +131,6 @@ N.B.: * `alpha_complex_3d_persistence` only accepts OFF files in dimension 3. * Filtration values are alpha square values. * Weights values are explained on CGAL -[Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0) +[Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#Alpha_shapes_3Definitions) and [Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation. diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst index b060c86e..4082cd9d 100644 --- a/src/python/doc/alpha_complex_user.rst +++ b/src/python/doc/alpha_complex_user.rst @@ -178,11 +178,11 @@ Weighted version ^^^^^^^^^^^^^^^^ A weighted version for Alpha complex is available. It is like a usual Alpha complex, but based on a -`CGAL regular triangulation `_. +`CGAL regular triangulation `_. This example builds the weighted alpha-complex of a small molecule, where atoms have different sizes. It is taken from -`CGAL 3d weighted alpha shapes `_. +`CGAL 3d weighted alpha shapes `_. Then, it is asked to display information about the alpha complex. -- cgit v1.2.3 From 5328f35be266fe2cc90512b41b654fe891e3147f Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com> Date: Mon, 23 May 2022 08:21:48 +0200 Subject: Update src/common/doc/installation.h Co-authored-by: Marc Glisse --- src/common/doc/installation.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 7502f394..6ccceca0 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -131,7 +131,7 @@ make \endverbatim * * \subsection eigen Eigen * Some GUDHI modules (cf. \ref main_page "modules list"), and few examples require - * Eigen is a C++ template library for linear algebra: + * Eigen is a C++ template library for linear algebra: * matrices, vectors, numerical solvers, and related algorithms. * * The following examples/utilities require the Eigen and will not be -- cgit v1.2.3 From 4ab108c7a45cce1e7e0a272e0577552d5d6077a8 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com> Date: Mon, 23 May 2022 08:36:44 +0200 Subject: Update biblio/bibliography.bib --- biblio/bibliography.bib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index 8c9ee84a..8462e731 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -167,7 +167,7 @@ language={English}, number = {RR-8436}, year = {2013}, month = Dec, - pdf = {https://hal.inria.fr/hal-00922572/PDF/RR-8436.pdf}, + pdf = {https://hal.inria.fr/hal-00922572v5/document}, } -- cgit v1.2.3 From e31bd798a3946e71f6f9a3b9676e286aaa623c76 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com> Date: Mon, 23 May 2022 08:36:55 +0200 Subject: Update src/common/doc/installation.h --- src/common/doc/installation.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 6ccceca0..1953c946 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -134,7 +134,7 @@ make \endverbatim * Eigen is a C++ template library for linear algebra: * matrices, vectors, numerical solvers, and related algorithms. * - * The following examples/utilities require the Eigen and will not be + * 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 -- cgit v1.2.3 From 5b3f98f85c73fa7d88606bf0f1e43734af8ffa98 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com> Date: Mon, 23 May 2022 09:23:16 +0200 Subject: [skip ci] example from a small molecule Co-authored-by: Marc Glisse --- src/Alpha_complex/doc/Intro_alpha_complex.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index ca48ebd2..d06a582c 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -168,7 +168,7 @@ Table of Contents * of Delaunay. * * This example builds the CGAL weighted alpha shapes from a small molecule, and initializes the alpha complex with - * it. This example is taken from CGAL 3d + * it. This example is taken from CGAL 3d * weighted alpha shapes. * * Then, it is asked to display information about the alpha complex. -- cgit v1.2.3 From b1a5176862ae5e3c0b52bd5d0770b0945ce85853 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com> Date: Mon, 23 May 2022 09:23:28 +0200 Subject: [skip ci] example from a small molecule --- src/Alpha_complex/doc/Intro_alpha_complex.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index d06a582c..7f14f423 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -212,7 +212,7 @@ Table of Contents * Gudhi::alpha_complex::complexity::EXACT. * * This example builds the CGAL 3d weighted alpha shapes from a small molecule, and initializes the alpha complex with - * it. This example is taken from CGAL 3d + * it. This example is taken from CGAL 3d * weighted alpha shapes. * * Then, it is asked to display information about the alpha complex. -- cgit v1.2.3 From a3a3749ac3a1d960d99ad7ce0d7f1463365ee657 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com> Date: Mon, 23 May 2022 09:23:41 +0200 Subject: [skip ci] example from a small molecule --- src/python/doc/alpha_complex_user.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst index 4082cd9d..9e67d38a 100644 --- a/src/python/doc/alpha_complex_user.rst +++ b/src/python/doc/alpha_complex_user.rst @@ -182,7 +182,7 @@ A weighted version for Alpha complex is available. It is like a usual Alpha comp This example builds the weighted alpha-complex of a small molecule, where atoms have different sizes. It is taken from -`CGAL 3d weighted alpha shapes `_. +`CGAL 3d weighted alpha shapes `_. Then, it is asked to display information about the alpha complex. -- cgit v1.2.3