Doxygen fix after doc review

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@882 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: e702746a6f8bdc7bb06bee2710ebe60dff504c69

2 files changed, 71 insertions, 106 deletions

diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index f3076057..349bb7d8 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -37,7 +37,7 @@ namespace Gudhi {
 namespace contraction {
 
 
-/** \defgroup contr Contraction
+/** \defgroup contr Edge contraction
 
 \author David Salinas
 
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 43297b45..730b74df 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -1,101 +1,24 @@
-/**
-\mainpage 
-
-\image html "Gudhi_banner.jpg" "" width=20cm
-
-The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C++ library for 
-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 <a class="el" href="https://project.inria.fr/gudhi/">Gudhi project</a>.
-
-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
-representations such as persistent homology computation or simplification. 
-All data-structures are generic and several of their aspects (such as stored elements, policies) 
-can be parameterized via template classes.
-We refer to 
-\cite gudhilibrary_ICMS14
-for a detailed description of the design of the library.
-
-\section installation Gudhi installation
-
-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.
-
-
-\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 more recent.
-It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013. 
-
-
-\subsection gmp GMP:
-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 examples require the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic Library</a> (GMP) 
-and will not be built if GMP is not installed:
-  - Persistent_cohomology/rips_multifield_persistence
-
-Having GMP version 4.2 or higher installed is recommended.
-
-\subsection cgal CGAL:
-CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms.
-
-The following example requires the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms Library</a> (CGAL) 
-and will not be built if CGAL is not installed:
-  - GudhUI
-  - Persistent_cohomology/alpha_shapes_persistence
-  - Simplex_tree/simplex_tree_from_alpha_shapes_3
-
-Having CGAL version 4.4 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
-
-\subsection demos Demos and examples
-
-To build the demos and libraries, run the following commands in a terminal:
-
-\verbatim
-cd /path-to-gudhi/
-mkdir build
-cd build/
-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.                         
-\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
-
-*/
-
-/*! \page Software Software
- * \tableofcontents
- * \section SoftwareIntroduction Introduction
- * 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
- * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>). The GUDHI
- * library is developed as part of the <a class="el" target="_blank" href="https://project.inria.fr/gudhi/">GUDHI
- * project</a> 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.
+/*! \mainpage
+ * \image html "Gudhi_banner.jpg" "" width=20cm
+ * 
+ * \section Introduction Introduction
+ * The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic open source C++ library 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 is developed as part of the
+ * <a class="el" target="_blank" href="https://project.inria.fr/gudhi/">GUDHI project</a> supported by the European
+ * Research Council. The GUDHI library intends  to help the development of new algorithmic solutions in TDA and their
+ * transfer to applications. It provides robust, efficient, flexible and easy to use implementations of
+ * state-of-the-art algorithms and data structures.
  * 
  * The current release of the GUDHI library includes:
  * 
  * \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.
+ * \li Simplication of simplicial complexes by edge contraction.
  * 
+ * All data-structures are generic and several of their aspects can be parameterized via template classes.
+ * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library.
  *
  * The library is available <a class="el" target="_blank" href="https://gforge.inria.fr/frs/?group_id=3865">here</a>
  * and the documentation is available at this <a class="el" href="http://gudhi.gforge.inria.fr/doc/latest/">
@@ -103,9 +26,11 @@ make test
  * 
  * The library comes with data sets, \ref demos and \ref testsuites.
  * 
- * \subsection People People
+ * Gudhi is also accessible though the
+ * <a class="el" target="_blank" href="https://cran.r-project.org/web/packages/TDA/index.html">R package TDA</a>
+ * (Statistical Tools for Topological Data Analysis).
  * 
- * The development of the GUDHI library is steered by an Editorial Board, which is responsible for guiding the
+ * The development of the GUDHI library is steered by an Editorial Board, who is responsible for guiding the
  * development of the library, developers, and the user community.
  * 
  * The Editorial board is composed of:
@@ -116,22 +41,62 @@ make test
  * \li Clément Jamin | INRIA Sophia Antipolis - Méditerranée
  * \li Vincent Rouvreau | INRIA Saclay - Ile de France
  * 
+*/
+
+/*! \page installation Gudhi installation
+ * 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.
+ * 
+ * \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
+ * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013.
+ * 
+ * \subsection gmp GMP:
+ * 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
+ * Library</a> (GMP) and will not be built if GMP is not installed:
+ * \li Persistent_cohomology/rips_multifield_persistence
+ * Having GMP version 4.2 or higher installed is recommended.
+ * 
+ * \subsection cgal CGAL:
+ * CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms.
+ * 
+ * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
+ * Library</a> (CGAL) and will not be built if CGAL is not installed:
+ * \li GudhUI
+ * \li Persistent_cohomology/alpha_shapes_persistence
+ * \li Simplex_tree/simplex_tree_from_alpha_shapes_3
+ * Having CGAL version 4.4 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
+ * 
+ * \subsection demos Demos and examples
+ * To build the demos and libraries, run the following commands in a terminal:
+ * \verbatim
+ * cd /path-to-gudhi/
+ * mkdir build
+ * cd build/
+ * cmake ..
+ * make
+ * \endverbatim
+ * 
+ * \subsection testsuites Test suites
+ * To test your build, run the following command in a terminal:
+ * \verbatim
+ * make test
+ * \endverbatim
+ * 
  * \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
  * 
- * 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.
  * 
- * 
- * \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
+*/
+
+/*! \page Upcoming Upcoming
  *
  * The library is under active development. New packages to be released next include:
  * \li Alpha complex.