6 files changed, 60 insertions, 59 deletions
diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
index f9441b24..e1ab7cb3 100644
--- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
+++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
@@ -24,7 +24,7 @@ namespace cover_complex {
  * Visualizations of the simplicial complexes can be done with either
  * neato (from <a target="_blank" href="http://www.graphviz.org/">graphviz</a>),
  * <a target="_blank" href="http://www.geomview.org/">geomview</a>,
- * <a target="_blank" href="https://github.com/MLWave/kepler-mapper">KeplerMapper</a>.
+ * <a target="_blank" href="https://github.com/scikit-tda/kepler-mapper">KeplerMapper</a>.
  * Input point clouds are assumed to be \ref FileFormatsOFF "OFF files"
  *
  * \section covers Covers
@@ -53,7 +53,7 @@ namespace cover_complex {
  * covering the height function (coordinate 2),
  * which are then refined into their connected components using the triangulation of the .OFF file.
  *
- * \include Nerve_GIC/Nerve.cpp
+ * \include Nerve.cpp
  *
  * When launching:
  *
@@ -62,7 +62,7 @@ namespace cover_complex {
  *
  * the program output is:
  *
- * \include Nerve_GIC/Nerve.txt
+ * \include Nerve.txt
  *
  * The program also writes a file ../../data/points/human_sc.txt. The first three lines in this file are the location
  * of the input point cloud and the function used to compute the cover.
@@ -96,7 +96,7 @@ namespace cover_complex {
  * comes from the triangulation of the human shape. Note that the resulting simplicial complex is in dimension 3
  * in this example.
  *
- * \include Nerve_GIC/VoronoiGIC.cpp
+ * \include VoronoiGIC.cpp
  *
  * When launching:
  *
@@ -129,7 +129,7 @@ namespace cover_complex {
  * with automatic resolution and gain. Note that automatic threshold, resolution and gain
  * can be computed as well for the Nerve.
  *
- * \include Nerve_GIC/CoordGIC.cpp
+ * \include CoordGIC.cpp
  *
  * When launching:
  *
@@ -152,7 +152,7 @@ namespace cover_complex {
  * The function is now the first eigenfunction given by PCA, whose values
  * are written in a file (lucky_cat_PCA1). Threshold, resolution and gain are automatically selected as before.
  *
- * \include Nerve_GIC/FuncGIC.cpp
+ * \include FuncGIC.cpp
  *
  * When launching:
  *
diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt
index 4b0f4677..9faf1f3b 100644
--- a/src/Nerve_GIC/example/CMakeLists.txt
+++ b/src/Nerve_GIC/example/CMakeLists.txt
@@ -1,25 +1,21 @@
 project(Nerve_GIC_examples)
 
-if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+add_executable ( CoordGIC CoordGIC.cpp )
+add_executable ( FuncGIC FuncGIC.cpp )
 
-  add_executable ( CoordGIC CoordGIC.cpp )
-  add_executable ( FuncGIC FuncGIC.cpp )
+if (TBB_FOUND)
+  target_link_libraries(CoordGIC ${TBB_LIBRARIES})
+  target_link_libraries(FuncGIC ${TBB_LIBRARIES})
+endif()
 
-  if (TBB_FOUND)
-    target_link_libraries(CoordGIC ${TBB_LIBRARIES})
-    target_link_libraries(FuncGIC ${TBB_LIBRARIES})
-  endif()
+# Copy files for not to pollute sources when testing
+file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-  # Copy files for not to pollute sources when testing
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC>
+    "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0")
 
-  add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC>
-      "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0")
-
-  add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC>
-      "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off"
-      "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1")
-
-endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC>
+    "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off"
+    "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1")
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h
index 1b1f9323..047fba61 100644
--- a/src/Nerve_GIC/include/gudhi/GIC.h
+++ b/src/Nerve_GIC/include/gudhi/GIC.h
@@ -17,6 +17,14 @@
 #include <mutex>
 #endif
 
+#if __has_include(<CGAL/version.h>)
+# define GUDHI_GIC_USE_CGAL 1
+# include <gudhi/Bottleneck.h>
+#elif __has_include(<hera/bottleneck.h>)
+# define GUDHI_GIC_USE_HERA 1
+# include <hera/bottleneck.h>
+#endif
+
 #include <gudhi/Debug_utils.h>
 #include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/reader_utils.h>
@@ -25,7 +33,6 @@
 #include <gudhi/Points_off_io.h>
 #include <gudhi/distance_functions.h>
 #include <gudhi/Persistent_cohomology.h>
-#include <gudhi/Bottleneck.h>
 
 #include <boost/config.hpp>
 #include <boost/graph/graph_traits.hpp>
@@ -35,8 +42,6 @@
 #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>
@@ -1228,7 +1233,14 @@ class Cover_complex {
         Cboot.set_cover_from_function();
         Cboot.find_simplices();
         Cboot.compute_PD();
+#ifdef GUDHI_GIC_USE_CGAL
         double db = Gudhi::persistence_diagram::bottleneck_distance(this->PD, Cboot.PD);
+#elif defined GUDHI_GIC_USE_HERA
+        double db = hera::bottleneckDistExact(this->PD, Cboot.PD);
+#else
+        double db;
+        throw std::logic_error("This function requires CGAL or Hera for the bottleneck distance.");
+#endif
         if (verbose)  std::clog << db << std::endl;
         distribution.push_back(db);
       }
diff --git a/src/Nerve_GIC/test/CMakeLists.txt b/src/Nerve_GIC/test/CMakeLists.txt
index 567bf43f..e012a178 100644
--- a/src/Nerve_GIC/test/CMakeLists.txt
+++ b/src/Nerve_GIC/test/CMakeLists.txt
@@ -1,15 +1,12 @@
 project(Graph_induced_complex_tests)
 
-if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
-  include(GUDHI_boost_test)
+include(GUDHI_boost_test)
 
-  add_executable ( Nerve_GIC_test_unit test_GIC.cpp )
-  if (TBB_FOUND)
-    target_link_libraries(Nerve_GIC_test_unit ${TBB_LIBRARIES})
-  endif()
+add_executable ( Nerve_GIC_test_unit test_GIC.cpp )
+if (TBB_FOUND)
+  target_link_libraries(Nerve_GIC_test_unit ${TBB_LIBRARIES})
+endif()
 
-  file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-  gudhi_add_boost_test(Nerve_GIC_test_unit)
-
-endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+gudhi_add_boost_test(Nerve_GIC_test_unit)
diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt
index 65a08d9a..4521a992 100644
--- a/src/Nerve_GIC/utilities/CMakeLists.txt
+++ b/src/Nerve_GIC/utilities/CMakeLists.txt
@@ -1,27 +1,23 @@
 project(Nerve_GIC_examples)
 
-if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+add_executable ( Nerve Nerve.cpp )
+add_executable ( VoronoiGIC VoronoiGIC.cpp )
 
-  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()
 
-  if (TBB_FOUND)
-    target_link_libraries(Nerve ${TBB_LIBRARIES})
-    target_link_libraries(VoronoiGIC ${TBB_LIBRARIES})
-  endif()
+file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+# Copy files for not to pollute sources when testing
+file(COPY "${CMAKE_SOURCE_DIR}/data/points/human.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-  file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-  # Copy files for not to pollute sources when testing
-  file(COPY "${CMAKE_SOURCE_DIR}/data/points/human.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve>
+    "human.off" "2" "10" "0.3")
 
-  add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve>
-      "human.off" "2" "10" "0.3")
+add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC>
+    "human.off" "100")
 
-  add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC>
-      "human.off" "100")
-
-  install(TARGETS Nerve DESTINATION bin)
-  install(TARGETS VoronoiGIC DESTINATION bin)
-  install(FILES KeplerMapperVisuFromTxtFile.py km.py km.py.COPYRIGHT DESTINATION bin)
-
-endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+install(TARGETS Nerve DESTINATION bin)
+install(TARGETS VoronoiGIC DESTINATION bin)
+install(FILES KeplerMapperVisuFromTxtFile.py km.py km.py.COPYRIGHT DESTINATION bin)
diff --git a/src/Nerve_GIC/utilities/km.py.COPYRIGHT b/src/Nerve_GIC/utilities/km.py.COPYRIGHT
index bef7b121..5358d287 100644
--- a/src/Nerve_GIC/utilities/km.py.COPYRIGHT
+++ b/src/Nerve_GIC/utilities/km.py.COPYRIGHT
@@ -1,7 +1,7 @@
 km.py is a fork of https://github.com/MLWave/kepler-mapper.
 Only the visualization part has been kept (Mapper part has been removed).
 
-This file has te following Copyright :
+This file has the following Copyright :
 
 The MIT License (MIT)