Merge gudhi_doc_2.0.0 branch for GUDHI web site 2.0.0 and Copyright fixes for Debian

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2189 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0501d2d499d32b6df6c18aa273fa6f030f49ad92

16 files changed, 233 insertions, 16 deletions

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 5ca0a6bc..761168f5 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> Cl&eacute;ment 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> Cl&eacute;ment 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 &ge; 4.8.0 and \ref eigen3
     </td>
@@ -157,7 +159,7 @@
   <tr>
     <td width="25%">
       <b>Author:</b> Fran&ccedil;ois 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 &ge; 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 &ge; 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
@@ -363,7 +378,7 @@ 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.
  * 
 */
 
@@ -378,7 +393,7 @@ 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