Merge branch 'upstream/latest' into dfsg/latest

35 files changed, 62 insertions, 40 deletions

diff --git a/GudhUI/CMakeLists.txt b/GudhUI/CMakeLists.txt
index 2503a03e..b357b8f7 100644
--- a/GudhUI/CMakeLists.txt
+++ b/GudhUI/CMakeLists.txt
@@ -1,4 +1,3 @@
-cmake_minimum_required(VERSION 2.8)
 project(GudhUI)
 
 # Need to find OpenGL first as find_package(Qt5) tries to #include"GL/gl.h" on some platforms
@@ -38,4 +37,4 @@ if (OPENGL_FOUND)
     install(TARGETS GudhUI DESTINATION bin)
   
   endif()
-endif(OPENGL_FOUND)
\ No newline at end of file
+endif(OPENGL_FOUND)
diff --git a/GudhUI/gui/MainWindow.cpp b/GudhUI/gui/MainWindow.cpp
index 779ccd33..b11b80e9 100644
--- a/GudhUI/gui/MainWindow.cpp
+++ b/GudhUI/gui/MainWindow.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/gui/MainWindow.h b/GudhUI/gui/MainWindow.h
index 15664dcb..6076c2ee 100644
--- a/GudhUI/gui/MainWindow.h
+++ b/GudhUI/gui/MainWindow.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/gui/Menu_edge_contraction.cpp b/GudhUI/gui/Menu_edge_contraction.cpp
index a679b0bf..041bdf9e 100644
--- a/GudhUI/gui/Menu_edge_contraction.cpp
+++ b/GudhUI/gui/Menu_edge_contraction.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/gui/Menu_edge_contraction.h b/GudhUI/gui/Menu_edge_contraction.h
index 2d5640e8..0ef7b267 100644
--- a/GudhUI/gui/Menu_edge_contraction.h
+++ b/GudhUI/gui/Menu_edge_contraction.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/gui/Menu_k_nearest_neighbors.cpp b/GudhUI/gui/Menu_k_nearest_neighbors.cpp
index e24865f2..b1ad15c8 100644
--- a/GudhUI/gui/Menu_k_nearest_neighbors.cpp
+++ b/GudhUI/gui/Menu_k_nearest_neighbors.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/gui/Menu_k_nearest_neighbors.h b/GudhUI/gui/Menu_k_nearest_neighbors.h
index 77303b67..56b5b63d 100644
--- a/GudhUI/gui/Menu_k_nearest_neighbors.h
+++ b/GudhUI/gui/Menu_k_nearest_neighbors.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/gui/Menu_persistence.cpp b/GudhUI/gui/Menu_persistence.cpp
index 016c076b..ec990559 100644
--- a/GudhUI/gui/Menu_persistence.cpp
+++ b/GudhUI/gui/Menu_persistence.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/gui/Menu_persistence.h b/GudhUI/gui/Menu_persistence.h
index 1a2a2408..32f0c5ca 100644
--- a/GudhUI/gui/Menu_persistence.h
+++ b/GudhUI/gui/Menu_persistence.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/gui/Menu_uniform_neighbors.cpp b/GudhUI/gui/Menu_uniform_neighbors.cpp
index 20e4f98f..7f392b6c 100644
--- a/GudhUI/gui/Menu_uniform_neighbors.cpp
+++ b/GudhUI/gui/Menu_uniform_neighbors.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/gui/Menu_uniform_neighbors.h b/GudhUI/gui/Menu_uniform_neighbors.h
index 61316966..88a3823b 100644
--- a/GudhUI/gui/Menu_uniform_neighbors.h
+++ b/GudhUI/gui/Menu_uniform_neighbors.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/gui/gudhui.cpp b/GudhUI/gui/gudhui.cpp
index 276c4a5f..2a100fd5 100644
--- a/GudhUI/gui/gudhui.cpp
+++ b/GudhUI/gui/gudhui.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
@@ -28,7 +28,7 @@
 int main(int argc, char** argv) {
   QApplication application(argc, argv);
   application.setOrganizationDomain("inria.fr");
-  application.setOrganizationName("INRIA");
+  application.setOrganizationName("Inria");
   application.setApplicationName("GudhUI");
 
   MainWindow mw;
diff --git a/GudhUI/model/Complex_typedefs.h b/GudhUI/model/Complex_typedefs.h
index a4df2c94..347db1e3 100644
--- a/GudhUI/model/Complex_typedefs.h
+++ b/GudhUI/model/Complex_typedefs.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/model/Model.h b/GudhUI/model/Model.h
index fc284cc6..1d5cc087 100644
--- a/GudhUI/model/Model.h
+++ b/GudhUI/model/Model.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
@@ -74,7 +74,7 @@ class CGAL_geometric_flag_complex_wrapper {
       // std::cout << "size:" << vertices.size() << std::endl;
       for (std::size_t i = 0; i < vertices.size(); ++i)
         for (std::size_t j = i + 1; j < vertices.size(); ++j)
-          complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
+          complex_.add_edge_without_blockers(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
     }
   }
 
diff --git a/GudhUI/utils/Bar_code_persistence.h b/GudhUI/utils/Bar_code_persistence.h
index b527d684..49c87b3c 100644
--- a/GudhUI/utils/Bar_code_persistence.h
+++ b/GudhUI/utils/Bar_code_persistence.h
@@ -1,3 +1,26 @@
+/* This file is 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) 2014 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/>.
+ *
+ */
+
 #include <math.h>  // isfinite
 
 #include <QtGui/QApplication>
diff --git a/GudhUI/utils/Critical_points.h b/GudhUI/utils/Critical_points.h
index 2a18e079..fbd690f8 100644
--- a/GudhUI/utils/Critical_points.h
+++ b/GudhUI/utils/Critical_points.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
@@ -79,7 +79,7 @@ template<typename SkBlComplex> class Critical_points {
     unsigned pos = 0;
     for (Edge e : edges) {
       std::cout << "edge " << pos++ << "/" << edges.size() << "\n";
-      auto eh = filled_complex_.add_edge(e.first, e.second);
+      auto eh = filled_complex_.add_edge_without_blockers(e.first, e.second);
       int is_contractible(is_link_reducible(eh));
 
       switch (is_contractible) {
diff --git a/GudhUI/utils/Edge_collapsor.h b/GudhUI/utils/Edge_collapsor.h
index 151e9b01..b3cc7df7 100644
--- a/GudhUI/utils/Edge_collapsor.h
+++ b/GudhUI/utils/Edge_collapsor.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/utils/Edge_contractor.h b/GudhUI/utils/Edge_contractor.h
index 8a29ff4b..090baabe 100644
--- a/GudhUI/utils/Edge_contractor.h
+++ b/GudhUI/utils/Edge_contractor.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/utils/Furthest_point_epsilon_net.h b/GudhUI/utils/Furthest_point_epsilon_net.h
index 98346daa..dbb6661c 100644
--- a/GudhUI/utils/Furthest_point_epsilon_net.h
+++ b/GudhUI/utils/Furthest_point_epsilon_net.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/utils/Is_manifold.h b/GudhUI/utils/Is_manifold.h
index d0974463..732df607 100644
--- a/GudhUI/utils/Is_manifold.h
+++ b/GudhUI/utils/Is_manifold.h
@@ -7,7 +7,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/utils/K_nearest_builder.h b/GudhUI/utils/K_nearest_builder.h
index 7be0a4f4..14851d96 100644
--- a/GudhUI/utils/K_nearest_builder.h
+++ b/GudhUI/utils/K_nearest_builder.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
@@ -81,7 +81,7 @@ template<typename SkBlComplex> class K_nearest_builder {
       for (auto it = ++search.begin(); it != search.end(); ++it) {
         Vertex_handle q(std::get<1>(it->first));
         if (p != q && complex_.contains_vertex(p) && complex_.contains_vertex(q))
-          complex_.add_edge(p, q);
+          complex_.add_edge_without_blockers(p, q);
       }
     }
   }
diff --git a/GudhUI/utils/Lloyd_builder.h b/GudhUI/utils/Lloyd_builder.h
index 18ec9fac..67595d33 100644
--- a/GudhUI/utils/Lloyd_builder.h
+++ b/GudhUI/utils/Lloyd_builder.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/utils/MClock.h b/GudhUI/utils/MClock.h
index e8d8918a..992f6fa5 100644
--- a/GudhUI/utils/MClock.h
+++ b/GudhUI/utils/MClock.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/utils/Persistence_compute.h b/GudhUI/utils/Persistence_compute.h
index 2dc03c8e..c8afded9 100644
--- a/GudhUI/utils/Persistence_compute.h
+++ b/GudhUI/utils/Persistence_compute.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/utils/Rips_builder.h b/GudhUI/utils/Rips_builder.h
index b22f4db6..ed62c1c0 100644
--- a/GudhUI/utils/Rips_builder.h
+++ b/GudhUI/utils/Rips_builder.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
@@ -60,7 +60,7 @@ template<typename SkBlComplex> class Rips_builder {
       std::cout.flush();
       for (auto q = p; ++q != vertices.end(); /**/)
         if (squared_eucl_distance(complex_.point(*p), complex_.point(*q)) < 4 * alpha * alpha)
-          complex_.add_edge(*p, *q);
+          complex_.add_edge_without_blockers(*p, *q);
     }
     std::cout << std::endl;
   }
diff --git a/GudhUI/utils/UI_utils.h b/GudhUI/utils/UI_utils.h
index 9cc209d3..67a02869 100644
--- a/GudhUI/utils/UI_utils.h
+++ b/GudhUI/utils/UI_utils.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/utils/Vertex_collapsor.h b/GudhUI/utils/Vertex_collapsor.h
index 568dab2f..fca57f7d 100644
--- a/GudhUI/utils/Vertex_collapsor.h
+++ b/GudhUI/utils/Vertex_collapsor.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/view/Color.h b/GudhUI/view/Color.h
index ba0592e1..808dc2d8 100644
--- a/GudhUI/view/Color.h
+++ b/GudhUI/view/Color.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/view/FirstCoordProjector.h b/GudhUI/view/FirstCoordProjector.h
index 1333f5d3..3f8a6fd9 100644
--- a/GudhUI/view/FirstCoordProjector.h
+++ b/GudhUI/view/FirstCoordProjector.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/view/Projector3D.h b/GudhUI/view/Projector3D.h
index 2a756541..a1421f51 100644
--- a/GudhUI/view/Projector3D.h
+++ b/GudhUI/view/Projector3D.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/view/View_parameter.h b/GudhUI/view/View_parameter.h
index 9805abc2..578a0268 100644
--- a/GudhUI/view/View_parameter.h
+++ b/GudhUI/view/View_parameter.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/view/Viewer.cpp b/GudhUI/view/Viewer.cpp
index c6c2b345..42e35d6c 100644
--- a/GudhUI/view/Viewer.cpp
+++ b/GudhUI/view/Viewer.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/view/Viewer.h b/GudhUI/view/Viewer.h
index 797ddc53..414044ef 100644
--- a/GudhUI/view/Viewer.h
+++ b/GudhUI/view/Viewer.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/view/Viewer_instructor.cpp b/GudhUI/view/Viewer_instructor.cpp
index 1ddd4d8b..a9dc4525 100644
--- a/GudhUI/view/Viewer_instructor.cpp
+++ b/GudhUI/view/Viewer_instructor.cpp
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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
diff --git a/GudhUI/view/Viewer_instructor.h b/GudhUI/view/Viewer_instructor.h
index 05c5c1fc..4b06acb8 100644
--- a/GudhUI/view/Viewer_instructor.h
+++ b/GudhUI/view/Viewer_instructor.h
@@ -4,7 +4,7 @@
  *
  *    Author(s):       David Salinas
  *
- *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *    Copyright (C) 2014 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