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-rw-r--r--biblio/bibliography.bib16
-rw-r--r--src/Alpha_complex/doc/Intro_alpha_complex.h6
-rw-r--r--src/Alpha_complex/include/gudhi/Alpha_complex_3d.h2
-rw-r--r--src/Alpha_complex/utilities/alphacomplex.md4
-rw-r--r--src/Nerve_GIC/doc/Intro_graph_induced_complex.h2
-rw-r--r--src/Simplex_tree/include/gudhi/Simplex_tree.h4
-rw-r--r--src/Skeleton_blocker/concept/SkeletonBlockerDS.h2
-rw-r--r--src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h2
-rw-r--r--src/common/doc/installation.h12
-rw-r--r--src/python/doc/alpha_complex_user.rst4
-rw-r--r--src/python/doc/nerve_gic_complex_user.rst2
11 files changed, 28 insertions, 28 deletions
diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib
index ec8772aa..8462e731 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-00922572v5/document},
}
@@ -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/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index 5ab23720..7f14f423 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
* <b>Requires:</b> \ref eigen &ge; 3.1.0 and \ref cgal &ge; 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 <a href="https://doc.cgal.org/latest/Triangulation/index.html#title20">CGAL regular triangulation</a> instead
+ * on a <a href="https://doc.cgal.org/latest/Triangulation/index.html#TriangulationSecRT">CGAL regular triangulation</a> 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 <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title13">CGAL 3d
+ * it. This example is taken from <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#AlphaShape_3DExampleforWeightedAlphaShapes">CGAL 3d
* weighted alpha shapes</a>.
*
* 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 <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title13">CGAL 3d
+ * it. This example is taken from <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#AlphaShape_3DExampleforWeightedAlphaShapes">CGAL 3d
* weighted alpha shapes</a>.
*
* 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<complexity::EXACT> {
* \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
- * <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0">Alpha shapes 3d</a> and
+ * <a href="https://doc.cgal.org/latest/Alpha_shapes_3/index.html#Alpha_shapes_3Definitions">Alpha shapes 3d</a> and
* <a href="https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation">Regular
* triangulation</a> 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/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 <a target="_blank" href="http://www.graphviz.org/">graphviz</a>),
* <a target="_blank" href="http://www.geomview.org/">geomview</a>,
- * <a target="_blank" href="https://github.com/MLWave/kepler-mapper">KeplerMapper</a>.
+ * <a target="_blank" href="https://github.com/scikit-tda/kepler-mapper">KeplerMapper</a>.
* Input point clouds are assumed to be \ref FileFormatsOFF "OFF files"
*
* \section covers Covers
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
- * <a href="http://www.boost.org/doc/libs/1_76_0/libs/graph/doc/VertexAndEdgeListGraph.html">boost::VertexAndEdgeListGraph</a>
- * and <a href="http://www.boost.org/doc/libs/1_76_0/libs/graph/doc/PropertyGraph.html">boost::PropertyGraph</a>.
+ * <a href="https://www.boost.org/doc/libs/release/libs/graph/doc/VertexAndEdgeListGraph.html">boost::VertexAndEdgeListGraph</a>
+ * and <a href="https://www.boost.org/doc/libs/release/libs/graph/doc/PropertyGraph.html">boost::PropertyGraph</a>.
*
* 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 <a href="http://www.boost.org/doc/libs/1_38_0/libs/graph/doc/subgraph.html">boost subgraphs</a>
+ * used in <a href="https://www.boost.org/doc/libs/release/libs/graph/doc/subgraph.html">boost subgraphs</a>
* 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 <a href="http://www.boost.org/doc/libs/1_38_0/libs/graph/doc/subgraph.html">boost subgraphs</a>.
+ * @brief Global and local handle similar to <a href="https://www.boost.org/doc/libs/release/libs/graph/doc/subgraph.html">boost subgraphs</a>.
* 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
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index 67d026bd..1953c946 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; 1.66.0
- * 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
@@ -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 <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>
@@ -131,10 +131,10 @@ make \endverbatim
*
* \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>
@@ -180,7 +180,7 @@ make \endverbatim
* Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp</a>
*
* \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.
*
diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst
index b060c86e..9e67d38a 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 <https://doc.cgal.org/latest/Triangulation/index.html#title20>`_.
+`CGAL regular triangulation <https://doc.cgal.org/latest/Triangulation/index.html#TriangulationSecRT>`_.
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 <https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title13>`_.
+`CGAL 3d weighted alpha shapes <https://doc.cgal.org/latest/Alpha_shapes_3/index.html#AlphaShape_3DExampleforWeightedAlphaShapes>`_.
Then, it is asked to display information about the alpha complex.
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 <http://www.graphviz.org/>`_),
`geomview <http://www.geomview.org/>`_,
-`KeplerMapper <https://github.com/MLWave/kepler-mapper>`_.
+`KeplerMapper <https://github.com/scikit-tda/kepler-mapper>`_.
Input point clouds are assumed to be OFF files (cf. `OFF file format <fileformats.html#off-file-format>`_).
Covers
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-01 09:47:05 +0000