diff options
21 files changed, 243 insertions, 38 deletions
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index a00ae1b2..bd0c57ac 100644 --- a/CMakeGUDHIVersion.txt +++ b/CMakeGUDHIVersion.txt @@ -1,6 +1,6 @@ -set (GUDHI_MAJOR_VERSION 1) -set (GUDHI_MINOR_VERSION 3) -set (GUDHI_PATCH_VERSION 1) +set (GUDHI_MAJOR_VERSION 2) +set (GUDHI_MINOR_VERSION 0) +set (GUDHI_PATCH_VERSION 0) set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION}) message(STATUS "GUDHI version : ${GUDHI_VERSION}") diff --git a/data/meshes/min_cube3D_8.off b/data/meshes/min_cube3D_8.off deleted file mode 100644 index 7398eaea..00000000 --- a/data/meshes/min_cube3D_8.off +++ /dev/null @@ -1,16 +0,0 @@ -OFF -8 6 0 --0.500000 -0.500000 0.500000 - 0.500000 -0.500000 0.500000 --0.500000 0.500000 0.500000 - 0.500000 0.500000 0.500000 --0.500000 0.500000 -0.500000 - 0.500000 0.500000 -0.500000 --0.500000 -0.500000 -0.500000 - 0.500000 -0.500000 -0.500000 -4 0 1 3 2 -4 2 3 5 4 -4 4 5 7 6 -4 6 7 1 0 -4 1 7 5 3 -4 6 0 2 4 diff --git a/data/points/README b/data/points/README deleted file mode 100644 index 943bb2ec..00000000 --- a/data/points/README +++ /dev/null @@ -1,2 +0,0 @@ -The bunny pointset comes from the Stanford Computer Graphics Laboratory. -http://graphics.stanford.edu/data/3Dscanrep/ diff --git a/data/points/SO3.COPYRIGHT b/data/points/SO3.COPYRIGHT index 36618c9c..26bbb0ad 100644 --- a/data/points/SO3.COPYRIGHT +++ b/data/points/SO3.COPYRIGHT @@ -1,6 +1,6 @@ The SO3 points clouds have been generated from the ISOI software available at this webpage : -http://www.mitchell-lab.org/rots.php +https://mitchell-lab.biochem.wisc.edu/soi/index.php This software is an implementation of the two following papers: diff --git a/data/points/bunny.COPYRIGHT b/data/points/bunny.COPYRIGHT new file mode 100644 index 00000000..310ca5b5 --- /dev/null +++ b/data/points/bunny.COPYRIGHT @@ -0,0 +1,6 @@ +The bunny pointset comes from the Stanford Computer Graphics Laboratory. +http://graphics.stanford.edu/data/3Dscanrep/ + +Please acknowledge... + +Please be sure to acknowledge the source of the bunny data set. You are welcome to use the bunny data and models for research purposes. You are also welcome to mirror or redistribute them for free. Finally, you may publish images made using these models, or the images on this web site, in a scholarly article or book - as long as credit is given to the Stanford Computer Graphics Laboratory. However, such models or images are not to be used for commercial purposes, nor should they appear in a product for sale (with the exception of scholarly journals or books), without our permission. diff --git a/src/Alpha_complex/concept/Simplicial_complex_for_alpha.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h index 2b8bff94..2b8bff94 100644 --- a/src/Alpha_complex/concept/Simplicial_complex_for_alpha.h +++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h diff --git a/src/Alpha_complex/doc/COPYRIGHT b/src/Alpha_complex/doc/COPYRIGHT new file mode 100644 index 00000000..dbad2380 --- /dev/null +++ b/src/Alpha_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Vincent Rouvreau + +Copyright (C) 2015 INRIA + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/Bitmap_cubical_complex/doc/COPYRIGHT b/src/Bitmap_cubical_complex/doc/COPYRIGHT new file mode 100644 index 00000000..bcd46b23 --- /dev/null +++ b/src/Bitmap_cubical_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Pawel Dlotko + +Copyright (C) 2015 INRIA + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/Bottleneck_distance/doc/COPYRIGHT b/src/Bottleneck_distance/doc/COPYRIGHT new file mode 100644 index 00000000..179740a6 --- /dev/null +++ b/src/Bottleneck_distance/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): François Godi + +Copyright (C) 2015 INRIA + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/Contraction/doc/COPYRIGHT b/src/Contraction/doc/COPYRIGHT new file mode 100644 index 00000000..1de850d7 --- /dev/null +++ b/src/Contraction/doc/COPYRIGHT @@ -0,0 +1,18 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): David Salinas +Copyright (C) 2015 INRIA + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/Doxyfile b/src/Doxyfile index 3ec4ac9a..4072abbf 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -38,7 +38,7 @@ PROJECT_NAME = "GUDHI" # could be handy for archiving the generated documentation or if some version # control system is used. -PROJECT_NUMBER = "1.3.1" +PROJECT_NUMBER = "2.0.0" # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer a diff --git a/src/Persistent_cohomology/doc/COPYRIGHT b/src/Persistent_cohomology/doc/COPYRIGHT new file mode 100644 index 00000000..34345bef --- /dev/null +++ b/src/Persistent_cohomology/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Clément Maria + +Copyright (C) 2015 INRIA + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/Rips_complex/concept/Simplicial_complex_for_rips.h b/src/Rips_complex/concept/SimplicialComplexForRips.h index 7dab0615..7dab0615 100644 --- a/src/Rips_complex/concept/Simplicial_complex_for_rips.h +++ b/src/Rips_complex/concept/SimplicialComplexForRips.h diff --git a/src/Rips_complex/doc/COPYRIGHT b/src/Rips_complex/doc/COPYRIGHT new file mode 100644 index 00000000..594b7d03 --- /dev/null +++ b/src/Rips_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau + +Copyright (C) 2015 INRIA + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp index ef3a9d13..7ae8126f 100644 --- a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp +++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp @@ -1,5 +1,5 @@ #include <gudhi/Rips_complex.h> -// to construct Rips_complex from a OFF file of points +// to construct Rips_complex from a csv file representing a distance matrix #include <gudhi/reader_utils.h> #include <gudhi/Simplex_tree.h> #include <gudhi/distance_functions.h> diff --git a/src/Simplex_tree/doc/COPYRIGHT b/src/Simplex_tree/doc/COPYRIGHT new file mode 100644 index 00000000..34345bef --- /dev/null +++ b/src/Simplex_tree/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Clément Maria + +Copyright (C) 2015 INRIA + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/Skeleton_blocker/doc/COPYRIGHT b/src/Skeleton_blocker/doc/COPYRIGHT new file mode 100644 index 00000000..1de850d7 --- /dev/null +++ b/src/Skeleton_blocker/doc/COPYRIGHT @@ -0,0 +1,18 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): David Salinas +Copyright (C) 2015 INRIA + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/Tangential_complex/doc/COPYRIGHT b/src/Tangential_complex/doc/COPYRIGHT new file mode 100644 index 00000000..c4df0f64 --- /dev/null +++ b/src/Tangential_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Clement Jamin + +Copyright (C) 2015 INRIA + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/Witness_complex/doc/COPYRIGHT b/src/Witness_complex/doc/COPYRIGHT new file mode 100644 index 00000000..7d032c87 --- /dev/null +++ b/src/Witness_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are part of the Gudhi Library. The Gudhi library +(Geometric Understanding in Higher Dimensions) is a generic C++ library for +computational topology. + +Author(s): Siargey Kachanovich + +Copyright (C) 2015 INRIA + +This program is free software: you can redistribute it and/or modify it under +the terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +This program is distributed in the hope that it will be useful, but WITHOUT +ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS +FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +this program. If not, see <http://www.gnu.org/licenses/>. diff --git a/src/common/doc/header.html b/src/common/doc/header.html index a6f3ed9c..94e641b2 100644 --- a/src/common/doc/header.html +++ b/src/common/doc/header.html @@ -9,7 +9,7 @@ <!--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="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" /> +<link rel="stylesheet" type="text/css" href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/gudhi-doc-2.0.0/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> @@ -25,6 +25,13 @@ $extrastylesheet <!-- 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="http://gudhi.gforge.inria.fr" class="icon-tree"> GUDHI C++ 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> + </ul> <section class="top-bar-section"> <ul class="right"> <li class="divider"></li> @@ -37,7 +44,7 @@ $extrastylesheet <a href="#">Project</a> <ul class="dropdown"> <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li> - <li><a href="http://gudhi.gforge.inria.fr/getinvolved/">Get involved</a></li> + <li><a href="http://gudhi.gforge.inria.fr/keepintouch/">Keep in touch</a></li> <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li> <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li> <li><a href="http://gudhi.gforge.inria.fr/theyaretalkingaboutus/">They are talking about us</a></li> @@ -49,11 +56,18 @@ $extrastylesheet <ul class="dropdown"> <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li> <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li> - <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">Installation manual</a></li> </ul> </li> <li class="divider"></li> - <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">Documentation</a></li> + <li class="has-dropdown"> + <a href="#">Documentation</a> + <ul class="dropdown"> + <li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li> + <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li> + <li><a href="http://gudhi.gforge.inria.fr/cython/latest/">Cython documentation</a></li> + <li><a href="http://gudhi.gforge.inria.fr/cython/latest/installation.html">Cython installation manual</a></li> + </ul> + </li> <li class="divider"></li> <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li> <li class="divider"></li> @@ -62,7 +76,7 @@ $extrastylesheet </nav> </div><!-- /#navigation --> <!-- GUDHI website header BEGIN --> - + <div id="top"><!-- do not remove this div, it is closed by doxygen! --> <!--BEGIN TITLEAREA--> diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 0338d3b1..593faea5 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -3,7 +3,9 @@ * \image html "Gudhi_banner.png" "" width=20cm * * \section Introduction Introduction - * The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic open source C++ library for + * The GUDHI library (Geometry Understanding in Higher Dimensions) is a generic open source + * <a class="el" target="_blank" href="http://gudhi.gforge.inria.fr/doc/latest/">C++ library</a>, with a + * <a class="el" target="_blank" href="http://gudhi.gforge.inria.fr/cython/latest/">Cython interface</a>, for * Computational Topology and Topological Data Analysis * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>). * The GUDHI library intends to help the development of new algorithmic solutions in TDA and their transfer to @@ -62,7 +64,7 @@ <tr> <td width="25%"> <b>Author:</b> Clément Maria, Pawel Dlotko, Vincent Rouvreau<br> - <b>Introduced in:</b> GUDHI 1.4.0<br> + <b>Introduced in:</b> GUDHI 2.0.0<br> <b>Copyright:</b> GPL v3<br> </td> <td width="75%"> @@ -118,7 +120,7 @@ <tr> <td width="25%"> <b>Author:</b> Clément Jamin<br> - <b>Introduced in:</b> GUDHI 1.4.0<br> + <b>Introduced in:</b> GUDHI 2.0.0<br> <b>Copyright:</b> GPL v3<br> <b>Requires:</b> \ref cgal ≥ 4.8.0 and \ref eigen3 </td> @@ -157,7 +159,7 @@ <tr> <td width="25%"> <b>Author:</b> François Godi<br> - <b>Introduced in:</b> GUDHI 1.4.0<br> + <b>Introduced in:</b> GUDHI 2.0.0<br> <b>Copyright:</b> GPL v3<br> <b>Requires:</b> \ref cgal ≥ 4.8.0 and \ref eigen3 </td> @@ -213,11 +215,11 @@ </table> */ -/*! \page installation Gudhi installation +/*! \page installation GUDHI installation * \tableofcontents - * As Gudhi is a header only library, there is no need to install the library. + * As GUDHI is a header only library, there is no need to install the library. * - * Examples of Gudhi headers inclusion can be found in \ref demos. + * Examples of GUDHI headers inclusion can be found in \ref demos. * * \section compiling Compiling * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or @@ -236,6 +238,15 @@ make \endverbatim * To test your build, run the following command in a terminal: * \verbatim make test \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 + * * \section optionallibrary Optional third-party library * \subsection gmp GMP * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision @@ -251,6 +262,10 @@ make \endverbatim * \subsection cgal CGAL * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++ * library which 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> for CGAL version ≥ 4.8.0), thereafter you will be able to compile + * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE> * * Having CGAL version 4.4.0 or higher installed is recommended. The procedure to install this library according to * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html @@ -371,7 +386,7 @@ make \endverbatim * 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 * - * 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 contact us. * */ @@ -386,7 +401,7 @@ make \endverbatim * \verbinclude biblio/how_to_cite_gudhi.bib */ -// List of Gudhi examples - Doxygen needs at least a file tag to analyse comments +// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments /*! @file Examples * @example Alpha_complex/Alpha_complex_from_off.cpp * @example Alpha_complex/Alpha_complex_from_points.cpp |