Merge remote-tracking branch 'upstream/patch-1' into coxeter-integration

18 files changed, 88 insertions, 237 deletions

diff --git a/src/Alpha_complex/concept/SimplicialComplexForAlpha.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h
index ba97c802..1c6c3b0c 100644
--- a/src/Alpha_complex/concept/SimplicialComplexForAlpha.h
+++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha.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):       Vincent Rouvreau
  *
  *    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 CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_
diff --git a/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.h
index 7acdf105..3a6830ff 100644
--- a/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.h
+++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha3d.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):       Vincent Rouvreau
  *
  *    Copyright (C) 2018 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 CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_3D_H_
diff --git a/src/Alpha_complex/doc/COPYRIGHT b/src/Alpha_complex/doc/COPYRIGHT
index 5f1d97cc..61f17f6d 100644
--- a/src/Alpha_complex/doc/COPYRIGHT
+++ b/src/Alpha_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):       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/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index ab7c4794..b075d1fc 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_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):       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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #ifndef DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index c62a220c..b069b443 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -1,6 +1,6 @@
 project(Alpha_complex_examples)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable ( Alpha_complex_example_from_points Alpha_complex_from_points.cpp )
   target_link_libraries(Alpha_complex_example_from_points  ${CGAL_LIBRARY})
   add_executable ( Alpha_complex_example_from_off Alpha_complex_from_off.cpp )
@@ -26,9 +26,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     add_test(Alpha_complex_example_from_off_32_diff_files ${DIFF_PATH}
         ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
   endif()
-endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp )
   target_link_libraries(Alpha_complex_example_weighted_3d_from_points  ${CGAL_LIBRARY})
   if (TBB_FOUND)
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index af9f59ea..8919cdb9 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_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):       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/>.
+ *    Modification(s):
+ *      - 2019/08 Vincent Rouvreau: Fix issue #10 for CGAL and Eigen3
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #ifndef ALPHA_COMPLEX_H_
@@ -35,6 +24,9 @@
 #include <CGAL/Spatial_sort_traits_adapter_d.h>
 #include <CGAL/property_map.h>  // for CGAL::Identity_property_map
 #include <CGAL/NT_converter.h>
+#include <CGAL/version.h>  // for CGAL_VERSION_NR
+
+#include <Eigen/src/Core/util/Macros.h>  // for EIGEN_VERSION_AT_LEAST
 
 #include <iostream>
 #include <vector>
@@ -45,6 +37,15 @@
 #include <stdexcept>
 #include <numeric>  // for std::iota
 
+// 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 Gudhi {
 
 namespace alpha_complex {
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
index 32dfcc16..13ebb9c1 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.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):       Vincent Rouvreau
  *
  *    Copyright (C) 2018 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 ALPHA_COMPLEX_3D_H_
@@ -44,7 +33,9 @@
 #include <CGAL/Object.h>
 #include <CGAL/tuple.h>
 #include <CGAL/iterator.h>
-#include <CGAL/version.h>
+#include <CGAL/version.h>  // for CGAL_VERSION_NR
+
+#include <Eigen/src/Core/util/Macros.h>  // for EIGEN_VERSION_AT_LEAST
 
 #include <boost/container/static_vector.hpp>
 
@@ -57,11 +48,15 @@
 #include <type_traits>  // for std::conditional and std::enable_if
 #include <limits>  // for numeric_limits<>
 
+// Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10
 #if CGAL_VERSION_NR < 1041101000
-// Make compilation fail - required for external projects - https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/10
 # 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 Gudhi {
 
 namespace alpha_complex {
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_options.h b/src/Alpha_complex/include/gudhi/Alpha_complex_options.h
index 7a555fa1..85c83672 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex_options.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex_options.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):       Vincent Rouvreau
  *
  *    Copyright (C) 2018 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 ALPHA_COMPLEX_OPTIONS_H_
diff --git a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp
index ec905d5b..1102838a 100644
--- a/src/Alpha_complex/test/Alpha_complex_3d_unit_test.cpp
+++ b/src/Alpha_complex/test/Alpha_complex_3d_unit_test.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):       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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #define BOOST_TEST_DYN_LINK
diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
index 622fcae8..01e4cee3 100644
--- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.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):       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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #define BOOST_TEST_DYN_LINK
@@ -42,7 +30,7 @@
 // Use dynamic_dimension_tag for the user to be able to set dimension
 typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d;
 // Use static dimension_tag for the user not to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel_s;
+typedef CGAL::Epick_d< CGAL::Dimension_tag<3> > Kernel_s;
 // The triangulation uses the default instantiation of the TriangulationDataStructure template parameter
 
 typedef boost::mpl::list<Kernel_d, Kernel_s> list_of_kernel_variants;
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index 7c6bf9aa..ad5b6314 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -1,7 +1,7 @@
 project(Alpha_complex_tests)
 
 include(GUDHI_test_coverage)
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
 
   # Do not forget to copy test files in current binary dir
   file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
@@ -14,9 +14,6 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 
   gudhi_add_coverage_test(Alpha_complex_test_unit)
 
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable ( Alpha_complex_3d_test_unit Alpha_complex_3d_unit_test.cpp )
   target_link_libraries(Alpha_complex_3d_test_unit ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
   add_executable ( Weighted_alpha_complex_3d_test_unit Weighted_alpha_complex_3d_unit_test.cpp )
diff --git a/src/Alpha_complex/test/Periodic_alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Periodic_alpha_complex_3d_unit_test.cpp
index ed4cbff0..ac3791a4 100644
--- a/src/Alpha_complex/test/Periodic_alpha_complex_3d_unit_test.cpp
+++ b/src/Alpha_complex/test/Periodic_alpha_complex_3d_unit_test.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):       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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #define BOOST_TEST_DYN_LINK
diff --git a/src/Alpha_complex/test/Weighted_alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Weighted_alpha_complex_3d_unit_test.cpp
index c16b3718..44deb930 100644
--- a/src/Alpha_complex/test/Weighted_alpha_complex_3d_unit_test.cpp
+++ b/src/Alpha_complex/test/Weighted_alpha_complex_3d_unit_test.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):       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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #define BOOST_TEST_DYN_LINK
diff --git a/src/Alpha_complex/test/Weighted_periodic_alpha_complex_3d_unit_test.cpp b/src/Alpha_complex/test/Weighted_periodic_alpha_complex_3d_unit_test.cpp
index e8ac83e5..670c7799 100644
--- a/src/Alpha_complex/test/Weighted_periodic_alpha_complex_3d_unit_test.cpp
+++ b/src/Alpha_complex/test/Weighted_periodic_alpha_complex_3d_unit_test.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):       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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #define BOOST_TEST_DYN_LINK
diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index e76edc5f..5295f3cd 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -1,6 +1,6 @@
 project(Alpha_complex_utilities)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
   target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
@@ -12,9 +12,6 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 
   install(TARGETS alpha_complex_persistence DESTINATION bin)
 
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
-
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
   target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
   if (TBB_FOUND)
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
index 09c84eb3..2272576e 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.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):       Vincent Rouvreau
  *
  *    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/>.
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
  */
 
 #include <boost/program_options.hpp>
diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
index 8e6c40b7..fab7bd30 100644
--- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_persistence.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):       Vincent Rouvreau
  *
  *    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 <boost/program_options.hpp>
diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md
index 50a39d32..fcd16a3b 100644
--- a/src/Alpha_complex/utilities/alphacomplex.md
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -33,7 +33,7 @@ a prime number).
 

 where

 `<input OFF file>` is the path to the input point cloud in

-[nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

+[nOFF ASCII format]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsOFF).

 

 **Allowed options**

 

@@ -87,7 +87,7 @@ a prime number).
 ```

 

 where `<input OFF file>` is the path to the input point cloud in

-[nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

+[nOFF ASCII format]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsOFF).

 

 **Allowed options**

 

@@ -103,8 +103,10 @@ to be recorded. Enter a negative value to see zero length intervals.
 * `-c [ --cuboid-file ]` is the path to the file describing the periodic domain.

 It must be in the format described

 [here]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsIsoCuboid).

+Default version is not periodic.

 * `-w [ --weight-file ]` is the path to the file containing the weights of the

 points (one value per line).

+Default version is not weighted.

 * `-e [ --exact ]` for the exact computation version (not compatible with

 weight and periodic version).

 * `-f [ --fast ]` for the fast computation version.