Merge branch 'master' of https://github.com/GUDHI/gudhi-devel into perslay

15 files changed, 199 insertions, 98 deletions

diff --git a/.circleci/config.yml b/.circleci/config.yml
index e2df5c87..958ec994 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -10,6 +10,11 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test examples
           command: |
             mkdir build
@@ -24,6 +29,11 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test unitary tests
           command: |
             mkdir build
@@ -38,6 +48,11 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test utilities
           command: |
             mkdir build
@@ -52,10 +67,13 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test python module. Generates and tests the python documentation
           command: |
-            git submodule init
-            git submodule update
             mkdir build
             cd build
             cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version ..
@@ -64,6 +82,7 @@ jobs:
             cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 -DWITH_GUDHI_REMOTE_TEST=ON .
             cd python
             python3 setup.py build_ext --inplace
+            ctest --output-on-failure
             make sphinx
             cp -R sphinx /tmp/sphinx
             python3 setup.py install
@@ -83,10 +102,13 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Generates the C++ documentation with doxygen
           command: |
-            git submodule init
-            git submodule update
             mkdir build
             cd build
             cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version ..
@@ -104,6 +126,26 @@ jobs:
           path: /tmp/doxygen
           destination: doxygen
 
+  bibliography:
+    docker:
+      - image: gudhi/doxygen_for_gudhi:latest
+    steps:
+      - checkout
+      - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
+          name: Test the LaTeX bibliography files
+          command: |
+            mkdir build
+            cd build
+            cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version ..
+            cd biblio/test
+            latexmk -pdf -interaction=nonstopmode test_biblio.tex
+            latexmk -pdf -interaction=nonstopmode test_gudhi_citation.tex
+
 
 ### With all third parties, except CGAL and Eigen
 
@@ -114,6 +156,11 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test examples without cgal and eigen
           command: |
             mkdir build
@@ -128,6 +175,11 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test unitary tests without cgal and eigen
           command: |
             mkdir build
@@ -142,6 +194,11 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test utilities without cgal and eigen
           command: |
             mkdir build
@@ -156,10 +213,13 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test python module without cgal and eigen
           command: |
-            git submodule init
-            git submodule update
             mkdir build
             cd build
             cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..
@@ -176,6 +236,11 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test examples without cgal
           command: |
             mkdir build
@@ -190,6 +255,11 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test unitary tests without cgal
           command: |
             mkdir build
@@ -204,6 +274,11 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test utilities without cgal
           command: |
             mkdir build
@@ -218,10 +293,13 @@ jobs:
     steps:
       - checkout
       - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
           name: Build and test python module without cgal
           command: |
-            git submodule init
-            git submodule update
             mkdir build
             cd build
             cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/eigen-3.3.9 -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..
diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib
index 0a3ef43d..d8472ad0 100644
--- a/biblio/bibliography.bib
+++ b/biblio/bibliography.bib
@@ -1090,7 +1090,7 @@ language={English}
 @ARTICLE{Reininghaus_Huber_ALL_PSSK,
     author = {J. Reininghaus and S. Huber and U. Bauer and R. Kwitt},
     title = {A Stable Multi-Scale Kernel for Topological Machine Learning.},
-    journal = {Proc. 2015 IEEE Conf. Comp. Vision & Pat. Rec. (CVPR '15)},
+    journal = {Proc. 2015 IEEE Conf. Comp. Vision \& Pat. Rec. (CVPR '15)},
     year = {2015}
 }
 
diff --git a/biblio/test/test_biblio.tex b/biblio/test/test_biblio.tex
new file mode 100644
index 00000000..97dee9ed
--- /dev/null
+++ b/biblio/test/test_biblio.tex
@@ -0,0 +1,7 @@
+\documentclass{article}
+\usepackage{hyperref}
+\bibliographystyle{plainurl}
+\begin{document}
+\nocite{*}
+\bibliography{../bibliography}
+\end{document}
\ No newline at end of file
diff --git a/biblio/test/test_gudhi_citation.tex b/biblio/test/test_gudhi_citation.tex
new file mode 100644
index 00000000..5fb2d33d
--- /dev/null
+++ b/biblio/test/test_gudhi_citation.tex
@@ -0,0 +1,7 @@
+\documentclass{article}
+\usepackage{hyperref}
+\bibliographystyle{plainurl}
+\begin{document}
+\nocite{*}
+\bibliography{../how_to_cite_gudhi}
+\end{document}
\ No newline at end of file
diff --git a/src/Doxyfile.in b/src/Doxyfile.in
index 1ec190d9..d5664a49 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -700,7 +700,6 @@ LAYOUT_FILE            =
 # search path. See also \cite for info how to create references.
 
 CITE_BIB_FILES         = @CMAKE_SOURCE_DIR@/biblio/bibliography.bib \
-                         @CMAKE_SOURCE_DIR@/biblio/how_to_cite_cgal.bib \
                          @CMAKE_SOURCE_DIR@/biblio/how_to_cite_gudhi.bib
 
 #---------------------------------------------------------------------------
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/cmake/modules/GUDHI_submodules.cmake b/src/cmake/modules/GUDHI_submodules.cmake
index c844386d..9ede852d 100644
--- a/src/cmake/modules/GUDHI_submodules.cmake
+++ b/src/cmake/modules/GUDHI_submodules.cmake
@@ -1,3 +1,5 @@
 # For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera.
 set(HERA_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/include)
 set(HERA_INCLUDE_DIR ${HERA_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find hera/{wasserstein.h,bottleneck.h}")
+# since everything is cleanly under include/hera/, there is no harm always including it
+include_directories(${HERA_INCLUDE_DIR})
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 2144ff6f..b9bf1414 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -18,14 +18,17 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
 string(TIMESTAMP GUDHI_VERSION_YEAR "%Y")
 configure_file(${CMAKE_SOURCE_DIR}/biblio/how_to_cite_gudhi.bib.in "${CMAKE_CURRENT_BINARY_DIR}/biblio/how_to_cite_gudhi.bib" @ONLY)
 file(COPY "${CMAKE_SOURCE_DIR}/biblio/bibliography.bib" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/biblio/")
+file(COPY "${CMAKE_SOURCE_DIR}/biblio/test" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/biblio")
 
 # append cgal citation inside bibliography - sphinx cannot deal with more than one bib file
 file(READ "${CMAKE_SOURCE_DIR}/biblio/how_to_cite_cgal.bib" CGAL_CITATION_CONTENT)
 file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/biblio/bibliography.bib" "${CGAL_CITATION_CONTENT}")
 
-# Copy biblio directory for user version
+# Copy biblio files for user version
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                   copy_directory ${CMAKE_CURRENT_BINARY_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio)
+                   copy ${CMAKE_CURRENT_BINARY_DIR}/biblio/bibliography.bib ${GUDHI_USER_VERSION_DIR}/biblio/bibliography.bib)
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   copy ${CMAKE_CURRENT_BINARY_DIR}/biblio/how_to_cite_gudhi.bib ${GUDHI_USER_VERSION_DIR}/biblio/how_to_cite_gudhi.bib)
 
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy ${CMAKE_SOURCE_DIR}/README.md ${GUDHI_USER_VERSION_DIR}/README.md)
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 0b86f1bb..198d0c65 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -163,10 +163,10 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'clustering/_tomato', ")
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/wasserstein', ")
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/bottleneck', ")
+    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ")
     if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
       set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/_points', ")
       set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'bottleneck', ")
-      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ")
     endif ()
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'subsampling', ")
@@ -432,38 +432,38 @@ if(PYTHONINTERP_FOUND)
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 
       add_gudhi_py_test(test_bottleneck_distance)
+    endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
 
-      # Cover complex
-      file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.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 cover_complex_nerve_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
-               -f human.off -c 2 -r 10 -g 0.3)
+    # Cover complex
+    file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.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 cover_complex_nerve_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
+             -f human.off -c 2 -r 10 -g 0.3)
 
-      add_test(NAME cover_complex_coordinate_gic_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
-               -f human.off -c 0 -v)
+    add_test(NAME cover_complex_coordinate_gic_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
+             -f human.off -c 0 -v)
 
-      add_test(NAME cover_complex_functional_gic_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
-               -o lucky_cat.off
-               -f lucky_cat_PCA1 -v)
+    add_test(NAME cover_complex_functional_gic_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
+             -o lucky_cat.off
+             -f lucky_cat_PCA1 -v)
 
-      add_test(NAME cover_complex_voronoi_gic_example_py_test
-               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
-               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
-               -f human.off -n 700 -v)
+    add_test(NAME cover_complex_voronoi_gic_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
+             -f human.off -n 700 -v)
 
-      add_gudhi_py_test(test_cover_complex)
-    endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
+    add_gudhi_py_test(test_cover_complex)
 
     if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
       # Alpha
diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd
index f86f1232..5309c6fa 100644
--- a/src/python/gudhi/simplex_tree.pxd
+++ b/src/python/gudhi/simplex_tree.pxd
@@ -56,7 +56,8 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi":
         int upper_bound_dimension() nogil
         bool find_simplex(vector[int] simplex) nogil
         bool insert(vector[int] simplex, double filtration) nogil
-        void insert_matrix(double* filtrations, int n, int stride0, int stride1, double max_filtration) nogil
+        void insert_matrix(double* filtrations, int n, int stride0, int stride1, double max_filtration) nogil except +
+        void insert_batch_vertices(vector[int] v, double f) nogil except +
         vector[pair[vector[int], double]] get_star(vector[int] simplex) nogil
         vector[pair[vector[int], double]] get_cofaces(vector[int] simplex, int dimension) nogil
         void expansion(int max_dim) nogil except +
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 18215d2f..4cf176f5 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -12,6 +12,7 @@ from libc.stdint cimport intptr_t, int32_t, int64_t
 import numpy as np
 cimport gudhi.simplex_tree
 cimport cython
+from numpy.math cimport INFINITY
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
@@ -239,7 +240,7 @@ cdef class SimplexTree:
 
     @staticmethod
     @cython.boundscheck(False)
-    def create_from_array(filtrations, double max_filtration=np.inf):
+    def create_from_array(filtrations, double max_filtration=INFINITY):
         """Creates a new, empty complex and inserts vertices and edges. The vertices are numbered from 0 to n-1, and
         the filtration values are encoded in the array, with the diagonal representing the vertices. It is the
         caller's responsibility to ensure that this defines a filtration, which can be achieved with either::
@@ -281,6 +282,8 @@ cdef class SimplexTree:
 
         .. seealso:: :func:`insert_batch`
         """
+        # Without this, it could be slow if we end up inserting vertices in a bad order (flat_map).
+        self.get_ptr().insert_batch_vertices(np.unique(np.stack((edges.row, edges.col))), INFINITY)
         # TODO: optimize this?
         for edge in zip(edges.row, edges.col, edges.data):
             self.get_ptr().insert((edge[0], edge[1]), edge[2])
@@ -303,8 +306,7 @@ cdef class SimplexTree:
         :param filtrations: the filtration values.
         :type filtrations: numpy.array of shape (n,)
         """
-        # This may be slow if we end up inserting vertices in a bad order (flat_map).
-        # We could first insert the vertices from np.unique(vertex_array), or leave it to the caller.
+        cdef vector[int] vertices = np.unique(vertex_array)
         cdef Py_ssize_t k = vertex_array.shape[0]
         cdef Py_ssize_t n = vertex_array.shape[1]
         assert filtrations.shape[0] == n, 'inconsistent sizes for vertex_array and filtrations'
@@ -312,6 +314,9 @@ cdef class SimplexTree:
         cdef Py_ssize_t j
         cdef vector[int] v
         with nogil:
+            # Without this, it could be slow if we end up inserting vertices in a bad order (flat_map).
+            # NaN currently does the wrong thing
+            self.get_ptr().insert_batch_vertices(vertices, INFINITY)
             for i in range(n):
                 for j in range(k):
                     v.push_back(vertex_array[j, i])
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 1ecbe985..6eb0db42 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -48,8 +48,6 @@ ext_modules = cythonize(ext_modules, compiler_directives={'language_level': '3'}
 
 for module in pybind11_modules:
     my_include_dirs = include_dirs + [pybind11.get_include(False), pybind11.get_include(True)]
-    if module.startswith('hera/'):
-        my_include_dirs = ['@HERA_INCLUDE_DIR@'] + my_include_dirs
     ext_modules.append(Extension(
         'gudhi.' + module.replace('/', '.'),
         sources = [source_dir + module + '.cc'],