From a19368075090f5409dc12081df944f90353eb5df Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 2 Oct 2015 16:00:28 +0000 Subject: Doxygen to be made from user version. Hypergenerator fix. Add definitions for debug traces. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@821 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5625aaab792264df86d7d442a2e6ff9886cf5d24 --- src/Doxyfile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'src/Doxyfile') diff --git a/src/Doxyfile b/src/Doxyfile index 62412627..85c496a8 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -672,7 +672,7 @@ LAYOUT_FILE = # search path. Do not use file names with spaces, bibtex cannot handle them. See # also \cite for info how to create references. -CITE_BIB_FILES = ../biblio/bibliography.bib +CITE_BIB_FILES = biblio/bibliography.bib #--------------------------------------------------------------------------- # Configuration options related to warning and progress messages @@ -831,9 +831,9 @@ EXAMPLE_RECURSIVE = NO # that contain images that are to be included in the documentation (see the # \image command). -IMAGE_PATH = Skeleton_blocker/doc/ \ - common/doc/ \ - Contraction/doc/ +IMAGE_PATH = doc/Skeleton_blocker/ \ + doc/common/ \ + doc/Contraction/ # The INPUT_FILTER tag can be used to specify a program that doxygen should -- cgit v1.2.3 From 3b22ae31478387efd64ae5f185128857f17ca9ee Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 23 Oct 2015 09:40:36 +0000 Subject: generate_version excludes bottleneck for version 1.2.0 - to be removed for 1.3.0 generate_version copies concept for doxygen purpose Contact gudhi-users on skbl and contraction page Doxygen warning fixes Doxygen Software section git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@871 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: bd7e252c2d0528f4bbc40c33a9221e1d6b386510 --- scripts/generate_version.sh | 10 ++++- src/Contraction/include/gudhi/Edge_contraction.h | 2 +- src/Doxyfile | 6 +-- src/Simplex_tree/concept/SimplexTreeOptions.h | 6 +-- .../include/gudhi/Skeleton_blocker.h | 2 +- .../include/gudhi/Skeleton_blocker_complex.h | 4 +- src/common/doc/main_page.h | 51 +++++++++++++++++++++- 7 files changed, 68 insertions(+), 13 deletions(-) (limited to 'src/Doxyfile') diff --git a/scripts/generate_version.sh b/scripts/generate_version.sh index 43a54c1c..323396dc 100755 --- a/scripts/generate_version.sh +++ b/scripts/generate_version.sh @@ -61,12 +61,13 @@ cp $ROOT_DIR/GUDHIVersion.cmake.in $VERSION_DIR PACKAGE_INC_DIR="/include" #PACKAGE_SRC_DIR="/source" PACKAGE_EX_DIR="/example" +PACKAGE_CONCEPT_DIR="/concept" PACKAGE_DOC_DIR="/doc" for package in `ls $ROOT_DIR/src/` do - echo $package - if [ -d "$ROOT_DIR/src/$package" ] + if [ -d "$ROOT_DIR/src/$package" ] && [ $package != "Bottleneck" ] then + echo $package if [ "$package" == "cmake" ] then # SPECIFIC FOR CMAKE MODULES @@ -91,6 +92,11 @@ do mkdir -p $VERSION_DIR$PACKAGE_EX_DIR/$package cp -R $ROOT_DIR/src/$package$PACKAGE_EX_DIR/* $VERSION_DIR$PACKAGE_EX_DIR/$package fi + if [ -d "$ROOT_DIR/src/$package$PACKAGE_CONCEPT_DIR" ] + then + mkdir -p $VERSION_DIR$PACKAGE_CONCEPT_DIR/$package + cp -R $ROOT_DIR/src/$package$PACKAGE_CONCEPT_DIR/* $VERSION_DIR$PACKAGE_CONCEPT_DIR/$package + fi if [ -d "$ROOT_DIR/src/$package$PACKAGE_DOC_DIR" ] then mkdir -p $VERSION_DIR$PACKAGE_DOC_DIR/$package diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h index dfce8d1b..f3076057 100644 --- a/src/Contraction/include/gudhi/Edge_contraction.h +++ b/src/Contraction/include/gudhi/Edge_contraction.h @@ -226,7 +226,7 @@ Time to simplify and enumerate simplices: \copyright GNU General Public License v3. -\verbatim Contact: David Salinas, david.salinas@inria.fr \endverbatim +\verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup } // namespace contraction diff --git a/src/Doxyfile b/src/Doxyfile index 85c496a8..084a9abb 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 = "1.1.0" +PROJECT_NUMBER = "1.2.0" # 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 @@ -1338,7 +1338,7 @@ ECLIPSE_DOC_ID = org.doxygen.Project # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. -DISABLE_INDEX = NO +DISABLE_INDEX = YES # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index # structure should be generated to display hierarchical information. If the tag @@ -1355,7 +1355,7 @@ DISABLE_INDEX = NO # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. -GENERATE_TREEVIEW = NO +GENERATE_TREEVIEW = YES # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that # doxygen will group on one line in the generated HTML documentation. diff --git a/src/Simplex_tree/concept/SimplexTreeOptions.h b/src/Simplex_tree/concept/SimplexTreeOptions.h index a50a2bf1..add3ebdd 100644 --- a/src/Simplex_tree/concept/SimplexTreeOptions.h +++ b/src/Simplex_tree/concept/SimplexTreeOptions.h @@ -34,8 +34,8 @@ struct SimplexTreeOptions { /// Must be a signed integer type. typedef SimplexKey Simplex_key; /// If true, each simplex has extra storage for one `Simplex_key`. Necessary for `Persistent_cohomology`. - static constexpr bool store_key; - /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology. - static constexpr bool store_filtration; + static const bool store_key; + /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology. + static const bool store_filtration; }; diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h index 792a7994..3be480fd 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h @@ -241,7 +241,7 @@ their collaboration to write the two initial papers \copyright GNU General Public License v3. -\verbatim Contact: David Salinas, david.salinas@inria.fr \endverbatim +\verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h index 07f371a2..d26d12b0 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h @@ -1018,7 +1018,7 @@ class Skeleton_blocker_complex { } //@} - /** @Simplification operations + /** @name Simplification operations */ //@{ @@ -1131,7 +1131,7 @@ class Skeleton_blocker_complex { } //@} - /** @Edge contraction operations + /** @name Edge contraction operations */ //@{ diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 315aa0ac..d1060740 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -7,7 +7,7 @@ The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C+ topological analysis of high-dimensional data whose goal is to provide robust, efficient, flexible and easy to use implementations of state-of-the-art algorithms and data structures for computational topology. -This library is part of the Gudhi project. +This library is part of the Gudhi project. The current release of the library allows to use several data-structures for simplicial complexes : simplex tree, Hasse diagram or skeleton-blocker. Several operations can then be done on top of these @@ -70,3 +70,52 @@ make \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ + +/*! \page Software Software + * \tableofcontents + * \section SoftwareIntroduction Introduction + * The GUDHI open source library will provide the central data structures and algorithms that underly applications in geometry understanding in higher dimensions. It is intended to both help the development of new algorithmic solutions inside and outside the project, and to facilitate the transfer of results in applied fields. + * + * The current release of the GUDHI library includes: + * + * – Data structures to represent, construct and manipulate simplicial complexes. + * + * – Algorithms to compute persistent homology and multi-field persistent homology. + * + * – Simplification methods via implicit representations. + * + * + * The library is available here and the documentation is + * available at this webpage. + * + * \section ReleaseHistory Release history + * + * – ??-??-2015; release v.1.2.0, Skeleton-Blocker simplex insertion, GudhUI (Gudhi Qt demo), Simplex tree coface function, Clang build issue fix. + * + * – 12-18-2014; release v.1.1, Skeleton-Blocker data-structure, simplification package, additional examples for topological persistence. + * + * – 08-12-2014; release v. 1.0.2, initialize simplex keys in initialize_filtration in Simplex_tree + * + * – 07-11-2014: release v. 1.0.1, bug fix in summing columns in Persistent_cohomology + * + * – 06-23-2014: release v. 1.0 + * + * \section Citation How to cite Gudhi + * Each Gudhi module (either data structures or algorithms) has an author section. + * + * Thank you to refer to this section, and to cite the author(s) of all the module you are using. + * + * \section Soon Coming soon + * + * – Alpha complex. + * + * – Bottleneck distance. + * + * – Zig zag persistence. + * + * – Witness complex. + * + * – Tangential complex. + * + * – Hard clustering. +*/ -- cgit v1.2.3 From 6b9fa936e42bd0c48f9320716937294dbcd7a21b Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 3 Nov 2015 10:50:47 +0000 Subject: Fix doxygen after doc review for 1.2.0 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@881 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: cffd514dde3fd716bac3768c4af56d3ff5777931 --- biblio/how_to_cite_gudhi.bib | 44 +++++++++++++++++ src/Doxyfile | 5 +- src/common/doc/main_page.h | 109 ++++++++++++++++++++++++++----------------- 3 files changed, 112 insertions(+), 46 deletions(-) create mode 100644 biblio/how_to_cite_gudhi.bib (limited to 'src/Doxyfile') diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib new file mode 100644 index 00000000..851dd5d9 --- /dev/null +++ b/biblio/how_to_cite_gudhi.bib @@ -0,0 +1,44 @@ +@book{gudhi:urm +, title = "{GUDHI} User and Reference Manual" +, author = "{The GUDHI Project}" +, publisher = "{GUDHI Editorial Board}" +, year = 2015 +, url = "http://gudhi.gforge.inria.fr/doc/latest/" +} + +@incollection{gudhi:FilteredComplexes +, author = "Cl\'ement Maria" +, title = "Filtered Complexes" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/doc/latest/group__simplex__tree.html" +, year = 2015 +} + +@incollection{gudhi:PersistentCohomology +, author = "Cl\'ement Maria" +, title = "Persistent Cohomology" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/doc/latest/group__persistent__cohomology.html" +, year = 2015 +} + +@incollection{gudhi:Contraction +, author = "David Salinas" +, title = "Contraction" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/doc/latest/group__contr.html" +, year = 2015 +} + +@incollection{gudhi:Skeleton-Blocker +, author = "David Salinas" +, title = "Skeleton-Blocker" +, publisher = "{GUDHI Editorial Board}" +, booktitle = "{GUDHI} User and Reference Manual" +, url = "http://gudhi.gforge.inria.fr/doc/latest/group__skbl.html" +, year = 2015 +} + diff --git a/src/Doxyfile b/src/Doxyfile index 084a9abb..faa0d3fe 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -672,7 +672,8 @@ LAYOUT_FILE = # search path. Do not use file names with spaces, bibtex cannot handle them. See # also \cite for info how to create references. -CITE_BIB_FILES = biblio/bibliography.bib +CITE_BIB_FILES = biblio/bibliography.bib \ + biblio/how_to_cite_gudhi.bib #--------------------------------------------------------------------------- # Configuration options related to warning and progress messages @@ -811,7 +812,7 @@ EXCLUDE_SYMBOLS = # that contain example code fragments that are included (see the \include # command). -EXAMPLE_PATH = +EXAMPLE_PATH = biblio/ # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index ce6ef96a..43297b45 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -65,6 +65,14 @@ cmake .. make \endverbatim +\subsection testsuites Test suites + +To test your build, run the following command in a terminal: + +\verbatim +make test +\endverbatim + \details \copyright GNU General Public License v3. @@ -75,60 +83,73 @@ make /*! \page Software Software * \tableofcontents * \section SoftwareIntroduction Introduction - * The GUDHI open source library will provide the central data structures and algorithms that underly applications in geometry understanding in higher dimensions. It is intended to both help the development of new algorithmic solutions inside and outside the project, and to facilitate the transfer of results in applied fields. - * - * The current release of the GUDHI library includes: + * The GUDHI library is a C++ open source library **intended to provide** the central data structures and algorithms + * that underly applications in Geometric and Topological Data Analysis + * (TDA). The GUDHI + * library is developed as part of the GUDHI + * project supported by the European Research Council. The GUDHI library can both help the development of new + * algorithmic solutions and to facilitate the transfer of state of the art results and new applications of TDA. * - * – Data structures to represent, construct and manipulate simplicial complexes. - * - * – Algorithms to compute persistent homology and multi-field persistent homology. + * The current release of the GUDHI library includes: * - * – Simplification methods via implicit representations. + * \li Data structures to represent, construct and manipulate simplicial complexes. + * \li Algorithms to compute persistent homology and multi-field persistent homology. + * \li Simplification methods via implicit representations. * * - * The library is available here and the documentation is - * available at this webpage. + * The library is available here + * and the documentation is available at this + * webpage. * - * \section ReleaseHistory Release history - * - * – 24-10-2015; release v.1.2.0, GudhUI (Gudhi Qt demo), Simplex tree coface function, Clang build issue fix. - * - * – 12-18-2014; release v.1.1, Skeleton-Blocker data-structure, simplification package, additional examples for topological persistence. - * - * – 08-12-2014; release v. 1.0.2, initialize simplex keys in initialize_filtration in Simplex_tree - * - * – 07-11-2014: release v. 1.0.1, bug fix in summing columns in Persistent_cohomology - * - * – 06-23-2014: release v. 1.0 + * The library comes with data sets, \ref demos and \ref testsuites. * - * \section Citation How to cite Gudhi - * Each Gudhi module (either data structures or algorithms) has an author section. + * \subsection People People * - * Thank you to refer to this section, and to cite the author(s) of all the module you are using. + * The development of the GUDHI library is steered by an Editorial Board, which is responsible for guiding the + * development of the library, developers, and the user community. * - * \section Upcoming Upcoming - * - * – Alpha complex. - * - * – Bottleneck distance. - * - * – Zig zag persistence. - * - * – Witness complex. - * - * – Tangential complex. - * - * – Clustering. + * The Editorial board is composed of: + * + * \li + * Jean-Daniel Boissonnat | INRIA Sophia Antipolis - Méditerranée + * \li Marc Glisse | INRIA Saclay - Ile de France + * \li Clément Jamin | INRIA Sophia Antipolis - Méditerranée + * \li Vincent Rouvreau | INRIA Saclay - Ile de France * - * \section Contributions Contributions - * Gudhi is opened to external contributions. If you just want to report bugs, feel free to contact us. + * \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 * - * If you want to join our development team, you will have to create an accout on the - * INRIA forge and ask to join the GUDHI project. + * Gudhi is **open** to external contributions. If you want to join our development team, please contact us. + * + * + * \section ReleaseHistory Release history + * + * \li 24-10-2015; release v.1.2.0, GudhUI (Gudhi Qt demo), Simplex tree coface function, Clang build issue fix. + * \li 18-12-2014; release v.1.1, Skeleton-Blocker data-structure, simplification package, additional examples for topological persistence. + * \li 08-12-2014; release v. 1.0.2, initialize simplex keys in initialize_filtration in Simplex_tree + * \li 07-11-2014: release v. 1.0.1, bug fix in summing columns in Persistent_cohomology + * \li 23-06-2014: release v. 1.0 + * + * \section Upcoming Upcoming + * + * The library is under active development. New packages to be released next include: + * \li Alpha complex. + * \li Bottleneck distance. + * \li Zig zag persistence. + * \li Witness complex. + * \li Tangential complex. + * \li Clustering. +*/ + +/*! \page Citation Acknowledging the GUDHI library + * We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use + * of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages. + * Feel free to contact us in case you have any question or remark on this topic. * - * Your development will have to follow our - * submitting - * process (code, documentation, and unitary tests review) and not to break the existing - * test suite. + * We provide \ref GudhiBibtex entries for the modules of the User and Reference Manual, as well as for publications + * directly related to the GUDHI library. + * \section GudhiBibtex GUDHI bibtex + * \verbinclude biblio/how_to_cite_gudhi.bib */ + -- cgit v1.2.3