Seperate installation and examples from main page

Move cover complex utilities from examples
GIC.cpp example was not compiled, nor tested. It is removed.
Persistence representation : no need to link with Boost_SYSTEM


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3164 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: cf2bfa6c6de2ed359aaa165b9f80bca7e06defb1

10 files changed, 22 insertions, 136 deletions

diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
index 7578cc53..344cb031 100644
--- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
+++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
@@ -177,7 +177,6 @@ namespace cover_complex {
  * \image html "funcGICvisu.jpg" "Visualization with neato"
  *
  * \copyright GNU General Public License v3.                         
- * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
  */
 /** @} */  // end defgroup cover_complex
 
@@ -186,31 +185,3 @@ namespace cover_complex {
 }  // namespace Gudhi
 
 #endif  // DOC_COVER_COMPLEX_INTRO_COVER_COMPLEX_H_
-
-
-/* * \subsection gicexample Example with cover from function
- *
- * This example builds the GIC of a point cloud sampled on a 3D human shape (human.off).
- * The cover C comes from the preimages of intervals (with length 0.075 and gain 0)
- * covering the height function (coordinate 2),
- * and the graph G comes from a Rips complex built with threshold 0.075.
- * Note that if the gain is too big, the number of cliques increases a lot,
- * which make the computation time much larger.
- *
- * \include Nerve_GIC/GIC.cpp
- *
- * When launching:
- *
- * \code $> ./GIC ../../data/points/human.off 0.075 2 0.075 0 --v
- * \endcode
- *
- * the program outputs SC.txt, which can be visualized with python and firefox as before:
- *
- * \image html "gicvisu.jpg" "Visualization with KeplerMapper"
- * */
-
-
-/* * Using e.g.
- *
- * \code $> python KeplerMapperVisuFromTxtFile.py && firefox SC.html
- * \endcode */
diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt
index 73728dc0..434637fa 100644
--- a/src/Nerve_GIC/example/CMakeLists.txt
+++ b/src/Nerve_GIC/example/CMakeLists.txt
@@ -3,26 +3,14 @@ project(Nerve_GIC_examples)
 
 if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
-  add_executable ( Nerve Nerve.cpp )
   add_executable ( CoordGIC CoordGIC.cpp )
   add_executable ( FuncGIC FuncGIC.cpp )
-  add_executable ( VoronoiGIC VoronoiGIC.cpp )
 
   if (TBB_FOUND)
-    target_link_libraries(Nerve ${TBB_LIBRARIES})
     target_link_libraries(CoordGIC ${TBB_LIBRARIES})
     target_link_libraries(FuncGIC ${TBB_LIBRARIES})
-    target_link_libraries(VoronoiGIC ${TBB_LIBRARIES})
   endif()
 
-  file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-
-  add_test(NAME Nerve_GIC_example_nerve COMMAND $<TARGET_FILE:Nerve>
-      "${CMAKE_SOURCE_DIR}/data/points/human.off" "2" "10" "0.3")
-
-  add_test(NAME Nerve_GIC_example_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC>
-      "${CMAKE_SOURCE_DIR}/data/points/human.off" "100")
-
   add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0")
 
diff --git a/src/Nerve_GIC/example/GIC.cpp b/src/Nerve_GIC/example/GIC.cpp
deleted file mode 100644
index 2bc24a4d..00000000
--- a/src/Nerve_GIC/example/GIC.cpp
+++ /dev/null
@@ -1,95 +0,0 @@
-/*    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):       Mathieu Carrière
- *
- *    Copyright (C) 2017  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 <gudhi/GIC.h>
-
-#include <string>
-#include <vector>
-
-void usage(int nbArgs, char *const progName) {
-  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
-  std::cerr << "Usage: " << progName << " filename.off threshold coordinate resolution gain [--v] \n";
-  std::cerr << "       i.e.: " << progName << " ../../data/points/human.off 0.075 2 0.075 0 --v \n";
-  exit(-1);  // ----- >>
-}
-
-int main(int argc, char **argv) {
-  if ((argc != 6) && (argc != 7)) usage(argc, argv[0]);
-
-  using Point = std::vector<float>;
-
-  std::string off_file_name(argv[1]);
-  double threshold = atof(argv[2]);
-  int coord = atoi(argv[3]);
-  double resolution = atof(argv[4]);
-  double gain = atof(argv[5]);
-  bool verb = 0;
-  if (argc == 7) verb = 1;
-
-  // ----------------------------------------------------------------------------
-  // Init of a graph induced complex from an OFF file
-  // ----------------------------------------------------------------------------
-
-  Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
-  GIC.set_verbose(verb);
-
-  bool check = GIC.read_point_cloud(off_file_name);
-
-  if (!check) {
-    std::cout << "Incorrect OFF file." << std::endl;
-  } else {
-    GIC.set_color_from_coordinate(coord);
-    GIC.set_function_from_coordinate(coord);
-
-    GIC.set_graph_from_rips(threshold, Gudhi::Euclidean_distance());
-
-    GIC.set_resolution_with_interval_length(resolution);
-    GIC.set_gain(gain);
-    GIC.set_cover_from_function();
-
-    GIC.find_GIC_simplices();
-
-    GIC.plot_TXT_for_KeplerMapper();
-
-    Gudhi::Simplex_tree<> stree;
-    GIC.create_complex(stree);
-
-    // ----------------------------------------------------------------------------
-    // Display information about the graph induced complex
-    // ----------------------------------------------------------------------------
-
-    if (verb) {
-      std::cout << "Graph induced complex is of dimension " << stree.dimension() << " - " << stree.num_simplices()
-                << " simplices - " << stree.num_vertices() << " vertices." << std::endl;
-
-      std::cout << "Iterator on graph induced complex simplices" << std::endl;
-      for (auto f_simplex : stree.filtration_simplex_range()) {
-        for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
-          std::cout << vertex << " ";
-        }
-        std::cout << std::endl;
-      }
-    }
-  }
-
-  return 0;
-}
diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt
new file mode 100644
index 00000000..a0508dc2
--- /dev/null
+++ b/src/Nerve_GIC/utilities/CMakeLists.txt
@@ -0,0 +1,22 @@
+cmake_minimum_required(VERSION 2.6)
+project(Nerve_GIC_examples)
+
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+
+  add_executable ( Nerve Nerve.cpp )
+  add_executable ( VoronoiGIC VoronoiGIC.cpp )
+
+  if (TBB_FOUND)
+    target_link_libraries(Nerve ${TBB_LIBRARIES})
+    target_link_libraries(VoronoiGIC ${TBB_LIBRARIES})
+  endif()
+
+  file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+  add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve>
+      "${CMAKE_SOURCE_DIR}/data/points/human.off" "2" "10" "0.3")
+
+  add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC>
+      "${CMAKE_SOURCE_DIR}/data/points/human.off" "100")
+
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Nerve_GIC/example/KeplerMapperVisuFromTxtFile.py b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py
index d2897774..d2897774 100755
--- a/src/Nerve_GIC/example/KeplerMapperVisuFromTxtFile.py
+++ b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py
diff --git a/src/Nerve_GIC/example/Nerve.cpp b/src/Nerve_GIC/utilities/Nerve.cpp
index 6abdedc7..6abdedc7 100644
--- a/src/Nerve_GIC/example/Nerve.cpp
+++ b/src/Nerve_GIC/utilities/Nerve.cpp
diff --git a/src/Nerve_GIC/example/Nerve.txt b/src/Nerve_GIC/utilities/Nerve.txt
index 839ff45e..839ff45e 100644
--- a/src/Nerve_GIC/example/Nerve.txt
+++ b/src/Nerve_GIC/utilities/Nerve.txt
diff --git a/src/Nerve_GIC/example/VoronoiGIC.cpp b/src/Nerve_GIC/utilities/VoronoiGIC.cpp
index 32431cc2..32431cc2 100644
--- a/src/Nerve_GIC/example/VoronoiGIC.cpp
+++ b/src/Nerve_GIC/utilities/VoronoiGIC.cpp
diff --git a/src/Nerve_GIC/example/km.py b/src/Nerve_GIC/utilities/km.py
index 53024aab..53024aab 100755
--- a/src/Nerve_GIC/example/km.py
+++ b/src/Nerve_GIC/utilities/km.py
diff --git a/src/Nerve_GIC/example/km.py.COPYRIGHT b/src/Nerve_GIC/utilities/km.py.COPYRIGHT
index bef7b121..bef7b121 100644
--- a/src/Nerve_GIC/example/km.py.COPYRIGHT
+++ b/src/Nerve_GIC/utilities/km.py.COPYRIGHT