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

12 files changed, 57 insertions, 148 deletions

diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt
index f136ab27..621b0fd7 100644
--- a/src/Tangential_complex/benchmark/CMakeLists.txt
+++ b/src/Tangential_complex/benchmark/CMakeLists.txt
@@ -1,9 +1,9 @@
 project(Tangential_complex_benchmark)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable(Tangential_complex_benchmark benchmark_tc.cpp)
   target_link_libraries(Tangential_complex_benchmark ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES})
   endif(TBB_FOUND)
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
diff --git a/src/Tangential_complex/benchmark/RIB_exporter.h b/src/Tangential_complex/benchmark/RIB_exporter.h
index 59ca138a..4cec0603 100644
--- a/src/Tangential_complex/benchmark/RIB_exporter.h
+++ b/src/Tangential_complex/benchmark/RIB_exporter.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):       Clement Jamin
  *
  *    Copyright (C) 2016 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 GUDHI_TC_RIB_EXPORTER_H
diff --git a/src/Tangential_complex/benchmark/XML_exporter.h b/src/Tangential_complex/benchmark/XML_exporter.h
index 4db5687f..16b62eb6 100644
--- a/src/Tangential_complex/benchmark/XML_exporter.h
+++ b/src/Tangential_complex/benchmark/XML_exporter.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):       Clement Jamin
  *
  *    Copyright (C) 2016 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 <string>
diff --git a/src/Tangential_complex/doc/COPYRIGHT b/src/Tangential_complex/doc/COPYRIGHT
index f9f92471..61f17f6d 100644
--- a/src/Tangential_complex/doc/COPYRIGHT
+++ b/src/Tangential_complex/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):       Clement Jamin
+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 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/Tangential_complex/doc/Intro_tangential_complex.h b/src/Tangential_complex/doc/Intro_tangential_complex.h
index 501f4a8b..ce277185 100644
--- a/src/Tangential_complex/doc/Intro_tangential_complex.h
+++ b/src/Tangential_complex/doc/Intro_tangential_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):       Clement Jamin
  *
  *    Copyright (C) 2016 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_TANGENTIAL_COMPLEX_INTRO_TANGENTIAL_COMPLEX_H_
diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt
index af0dac51..cb1486a4 100644
--- a/src/Tangential_complex/example/CMakeLists.txt
+++ b/src/Tangential_complex/example/CMakeLists.txt
@@ -1,6 +1,6 @@
 project(Tangential_complex_examples)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable( Tangential_complex_example_basic example_basic.cpp )
   target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY})
   add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp )
@@ -17,4 +17,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 
   install(TARGETS Tangential_complex_example_basic DESTINATION bin)
   install(TARGETS Tangential_complex_example_with_perturb DESTINATION bin)
-endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h
index 4a78127c..f59476b1 100644
--- a/src/Tangential_complex/include/gudhi/Tangential_complex.h
+++ b/src/Tangential_complex/include/gudhi/Tangential_complex.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(s):       Clement Jamin
  *
  *    Copyright (C) 2016 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 and Eigen3
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #ifndef TANGENTIAL_COMPLEX_H_
@@ -41,9 +30,11 @@
 #include <CGAL/Delaunay_triangulation.h>
 #include <CGAL/Combination_enumerator.h>
 #include <CGAL/point_generators_d.h>
+#include <CGAL/version.h>  // for CGAL_VERSION_NR
 
 #include <Eigen/Core>
 #include <Eigen/Eigen>
+#include <Eigen/src/Core/util/Macros.h>  // for EIGEN_VERSION_AT_LEAST
 
 #include <boost/optional.hpp>
 #include <boost/iterator/transform_iterator.hpp>
@@ -74,6 +65,15 @@
 
 // #define GUDHI_TC_EXPORT_NORMALS // Only for 3D surfaces (k=2, d=3)
 
+// 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
+
+#if !EIGEN_VERSION_AT_LEAST(3,1,0)
+# error Alpha_complex_3d is only available for Eigen3 >= 3.1.0 installed with CGAL
+#endif
+
 namespace sps = Gudhi::spatial_searching;
 
 namespace Gudhi {
diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h
index f79186b0..4881bdd5 100644
--- a/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h
+++ b/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_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):       Clement Jamin
  *
  *    Copyright (C) 2016 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 TANGENTIAL_COMPLEX_SIMPLICIAL_COMPLEX_H_
diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex/config.h b/src/Tangential_complex/include/gudhi/Tangential_complex/config.h
index e1af1ea6..352531da 100644
--- a/src/Tangential_complex/include/gudhi/Tangential_complex/config.h
+++ b/src/Tangential_complex/include/gudhi/Tangential_complex/config.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):       Clement Jamin
  *
  *    Copyright (C) 2016 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 TANGENTIAL_COMPLEX_CONFIG_H_
diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h b/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h
index 2dd46118..ee6ed9ba 100644
--- a/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h
+++ b/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.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):       Clement Jamin
  *
  *    Copyright (C) 2016 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 TANGENTIAL_COMPLEX_UTILITIES_H_
diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt
index 902f19af..ae17a286 100644
--- a/src/Tangential_complex/test/CMakeLists.txt
+++ b/src/Tangential_complex/test/CMakeLists.txt
@@ -1,6 +1,6 @@
 project(Tangential_complex_tests)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   include(GUDHI_test_coverage)
 
   add_executable( Tangential_complex_test_TC test_tangential_complex.cpp )
@@ -10,4 +10,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   endif()
 
   gudhi_add_coverage_test(Tangential_complex_test_TC)
-endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
diff --git a/src/Tangential_complex/test/test_tangential_complex.cpp b/src/Tangential_complex/test/test_tangential_complex.cpp
index 103b8b30..46caec54 100644
--- a/src/Tangential_complex/test/test_tangential_complex.cpp
+++ b/src/Tangential_complex/test/test_tangential_complex.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):       Clement Jamin
  *
  *    Copyright (C) 2016 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