Merge remote-tracking branch 'upstream/master' into sklearn_tda

12 files changed, 55 insertions, 150 deletions

diff --git a/src/Nerve_GIC/doc/COPYRIGHT b/src/Nerve_GIC/doc/COPYRIGHT
index 6b33053e..61f17f6d 100644
--- a/src/Nerve_GIC/doc/COPYRIGHT
+++ b/src/Nerve_GIC/doc/COPYRIGHT
@@ -1,19 +1,12 @@
-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.
+The files of this directory are part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
 
-Author(s):       Mathieu Carrière
+Author(s):       Vincent Rouvreau
 
-Copyright (C) 2017 Inria
+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 gives everyone the freedoms to use openFrameworks in any context:
+commercial or non-commercial, public or private, open or closed source.
 
-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/>.
+You should have received a copy of the MIT License along with this program.
+If not, see https://opensource.org/licenses/MIT.
\ No newline at end of file
diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
index e72d63dd..f9441b24 100644
--- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
+++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
@@ -1,23 +1,11 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
  *    Author(s):       Mathieu Carriere
  *
  *    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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #ifndef DOC_COVER_COMPLEX_INTRO_COVER_COMPLEX_H_
diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt
index fdecf86e..1667472f 100644
--- a/src/Nerve_GIC/example/CMakeLists.txt
+++ b/src/Nerve_GIC/example/CMakeLists.txt
@@ -1,6 +1,6 @@
 project(Nerve_GIC_examples)
 
-if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
 
   add_executable ( CoordGIC CoordGIC.cpp )
   add_executable ( FuncGIC FuncGIC.cpp )
@@ -25,4 +25,4 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   install(TARGETS CoordGIC DESTINATION bin)
   install(TARGETS FuncGIC DESTINATION bin)
 
-endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
diff --git a/src/Nerve_GIC/example/CoordGIC.cpp b/src/Nerve_GIC/example/CoordGIC.cpp
index 9889b198..fd9c224a 100644
--- a/src/Nerve_GIC/example/CoordGIC.cpp
+++ b/src/Nerve_GIC/example/CoordGIC.cpp
@@ -1,23 +1,11 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
  *    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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #include <gudhi/GIC.h>
diff --git a/src/Nerve_GIC/example/FuncGIC.cpp b/src/Nerve_GIC/example/FuncGIC.cpp
index 1f5de999..5a323795 100644
--- a/src/Nerve_GIC/example/FuncGIC.cpp
+++ b/src/Nerve_GIC/example/FuncGIC.cpp
@@ -1,23 +1,11 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
  *    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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #include <gudhi/GIC.h>
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h
index 11bb4e85..fc6a2a91 100644
--- a/src/Nerve_GIC/include/gudhi/GIC.h
+++ b/src/Nerve_GIC/include/gudhi/GIC.h
@@ -1,23 +1,12 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
  *    Author:       Mathieu Carriere
  *
  *    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/>.
+ *    Modification(s):
+ *      - 2019/08 Vincent Rouvreau: Fix issue #10 for CGAL
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #ifndef GIC_H_
@@ -46,6 +35,8 @@
 #include <boost/graph/subgraph.hpp>
 #include <boost/graph/graph_utility.hpp>
 
+#include <CGAL/version.h>  // for CGAL_VERSION_NR
+
 #include <iostream>
 #include <vector>
 #include <map>
@@ -57,6 +48,11 @@
 #include <cassert>
 #include <cmath>
 
+// Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10
+#if CGAL_VERSION_NR < 1041101000
+# error Alpha_complex_3d is only available for CGAL >= 4.11
+#endif
+
 namespace Gudhi {
 
 namespace cover_complex {
diff --git a/src/Nerve_GIC/test/CMakeLists.txt b/src/Nerve_GIC/test/CMakeLists.txt
index 99263ea0..b89c18a2 100644
--- a/src/Nerve_GIC/test/CMakeLists.txt
+++ b/src/Nerve_GIC/test/CMakeLists.txt
@@ -1,6 +1,6 @@
 project(Graph_induced_complex_tests)
 
-if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
   include(GUDHI_test_coverage)
 
   add_executable ( Nerve_GIC_test_unit test_GIC.cpp )
@@ -13,4 +13,4 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
   gudhi_add_coverage_test(Nerve_GIC_test_unit)
 
-endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
diff --git a/src/Nerve_GIC/test/test_GIC.cpp b/src/Nerve_GIC/test/test_GIC.cpp
index 0db2cce2..9d326234 100644
--- a/src/Nerve_GIC/test/test_GIC.cpp
+++ b/src/Nerve_GIC/test/test_GIC.cpp
@@ -1,23 +1,11 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
  *    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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #define BOOST_TEST_DYN_LINK
diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt
index 215f9dfd..65a08d9a 100644
--- a/src/Nerve_GIC/utilities/CMakeLists.txt
+++ b/src/Nerve_GIC/utilities/CMakeLists.txt
@@ -1,6 +1,6 @@
 project(Nerve_GIC_examples)
 
-if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
 
   add_executable ( Nerve Nerve.cpp )
   add_executable ( VoronoiGIC VoronoiGIC.cpp )
@@ -24,4 +24,4 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   install(TARGETS VoronoiGIC DESTINATION bin)
   install(FILES KeplerMapperVisuFromTxtFile.py km.py km.py.COPYRIGHT DESTINATION bin)
 
-endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
diff --git a/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py
index 701e7a52..e3101549 100755
--- a/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py
+++ b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py
@@ -5,26 +5,14 @@ import numpy as np
 from collections import defaultdict
 import argparse
 
-"""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 Carriere
+"""This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+    Author(s):       Mathieu Carriere
 
    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/>.
+   Modification(s):
+     - YYYY/MM Author: Description of the modification
 """
 
 __author__ = "Mathieu Carriere"
diff --git a/src/Nerve_GIC/utilities/Nerve.cpp b/src/Nerve_GIC/utilities/Nerve.cpp
index 667129e0..d34e922c 100644
--- a/src/Nerve_GIC/utilities/Nerve.cpp
+++ b/src/Nerve_GIC/utilities/Nerve.cpp
@@ -1,23 +1,11 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
  *    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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #include <gudhi/GIC.h>
diff --git a/src/Nerve_GIC/utilities/VoronoiGIC.cpp b/src/Nerve_GIC/utilities/VoronoiGIC.cpp
index 33deca40..0182c948 100644
--- a/src/Nerve_GIC/utilities/VoronoiGIC.cpp
+++ b/src/Nerve_GIC/utilities/VoronoiGIC.cpp
@@ -1,23 +1,11 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
  *    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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #include <gudhi/GIC.h>