Merge branch 'master' into print_warnings_to_stderr

25 files changed, 253 insertions, 86 deletions

diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index 57b92942..a3b0cc24 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -2,7 +2,7 @@ project(Alpha_complex_utilities)
 
 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})
+  target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} Boost::program_options)
 
   if (TBB_FOUND)
     target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
@@ -23,7 +23,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   install(TARGETS alpha_complex_persistence DESTINATION bin)
 
   add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
-  target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} Boost::program_options)
   if (TBB_FOUND)
     target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
   endif(TBB_FOUND)
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 3d65963a..9839c59d 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -13,7 +13,7 @@ endif (NOT CGAL_VERSION VERSION_LESS 4.11.0)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
-  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(alpha_rips_persistence_bottleneck_distance Boost::program_options)
 
   if (TBB_FOUND)
     target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
index f791e37c..e1e3522e 100644
--- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
+++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
@@ -25,7 +25,7 @@ namespace Gudhi {
 
 namespace persistence_diagram {
 
-/** \internal \brief Structure representing an euclidean bipartite graph containing
+/** \internal \brief Structure representing a Euclidean bipartite graph containing
  *  the points from the two persistence diagrams (including the projections).
  *
  * \ingroup bottleneck_distance
diff --git a/src/Cech_complex/benchmark/CMakeLists.txt b/src/Cech_complex/benchmark/CMakeLists.txt
index b7697764..c04bca53 100644
--- a/src/Cech_complex/benchmark/CMakeLists.txt
+++ b/src/Cech_complex/benchmark/CMakeLists.txt
@@ -5,7 +5,7 @@ project(Cech_complex_benchmark)
 file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
 add_executable(cech_complex_benchmark cech_complex_benchmark.cpp)
-target_link_libraries(cech_complex_benchmark ${Boost_SYSTEM_LIBRARY} ${Boost_FILESYSTEM_LIBRARY})
+target_link_libraries(cech_complex_benchmark Boost::filesystem)
 
 if (TBB_FOUND)
   target_link_libraries(cech_complex_benchmark ${TBB_LIBRARIES})
diff --git a/src/Cech_complex/example/CMakeLists.txt b/src/Cech_complex/example/CMakeLists.txt
index ab391215..98757988 100644
--- a/src/Cech_complex/example/CMakeLists.txt
+++ b/src/Cech_complex/example/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6)
 project(Cech_complex_examples)
 
 add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp )
-target_link_libraries(Cech_complex_example_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(Cech_complex_example_step_by_step Boost::program_options)
 if (TBB_FOUND)
   target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES})
 endif()
diff --git a/src/Cech_complex/utilities/CMakeLists.txt b/src/Cech_complex/utilities/CMakeLists.txt
index 30b99729..253d7304 100644
--- a/src/Cech_complex/utilities/CMakeLists.txt
+++ b/src/Cech_complex/utilities/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 2.6)
 project(Cech_complex_utilities)
 
 add_executable(cech_persistence cech_persistence.cpp)
-target_link_libraries(cech_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(cech_persistence Boost::program_options)
 
 if (TBB_FOUND)
   target_link_libraries(cech_persistence ${TBB_LIBRARIES})
diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt
index f0dc885d..c5d31aca 100644
--- a/src/Contraction/example/CMakeLists.txt
+++ b/src/Contraction/example/CMakeLists.txt
@@ -4,7 +4,6 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
   add_executable(RipsContraction Rips_contraction.cpp)
 
   add_executable(GarlandHeckbert Garland_heckbert.cpp)
-  target_link_libraries(GarlandHeckbert ${Boost_TIMER_LIBRARY})
 
   add_test(NAME Contraction_example_tore3D_0.2 COMMAND $<TARGET_FILE:RipsContraction>
     "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "0.2")
diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt
index 2bb3b0c7..f38cc543 100644
--- a/src/Persistent_cohomology/benchmark/CMakeLists.txt
+++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt
@@ -3,7 +3,7 @@ project(Persistent_cohomology_benchmark)
 if(GMP_FOUND)
    if(GMPXX_FOUND)
       add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp )
-      target_link_libraries(performance_rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+      target_link_libraries(performance_rips_persistence Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
       if (TBB_FOUND)
         target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES})
       endif(TBB_FOUND)
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 94ec13c5..4c08cd68 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -5,13 +5,13 @@ add_executable(plain_homology plain_homology.cpp)
 add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
 
 add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp)
-target_link_libraries(rips_persistence_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence_step_by_step Boost::program_options)
 
 add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp)
-target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence_via_boundary_matrix Boost::program_options)
 
 add_executable(persistence_from_file persistence_from_file.cpp)
-target_link_libraries(persistence_from_file ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(persistence_from_file Boost::program_options)
 
 if (TBB_FOUND)
   target_link_libraries(plain_homology ${TBB_LIBRARIES})
@@ -43,7 +43,7 @@ if(GMP_FOUND)
    if(GMPXX_FOUND)
       add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
       target_link_libraries(rips_multifield_persistence
-          ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
+          Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
       if (TBB_FOUND)
         target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES})
       endif(TBB_FOUND)
diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt
index 4b565628..d2448d7b 100644
--- a/src/Rips_complex/utilities/CMakeLists.txt
+++ b/src/Rips_complex/utilities/CMakeLists.txt
@@ -1,16 +1,16 @@
 project(Rips_complex_utilities)
 
 add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp)
-target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_distance_matrix_persistence Boost::program_options)
 
 add_executable(rips_persistence rips_persistence.cpp)
-target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_persistence Boost::program_options)
 
 add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp)
-target_link_libraries(rips_correlation_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(rips_correlation_matrix_persistence Boost::system Boost::program_options)
 
 add_executable(sparse_rips_persistence sparse_rips_persistence.cpp)
-target_link_libraries(sparse_rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+target_link_libraries(sparse_rips_persistence Boost::program_options)
 
 if (TBB_FOUND)
   target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES})
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index 8a8cac58..a0aabee2 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -35,7 +35,7 @@ endif()
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable ( Simplex_tree_example_cech_complex_cgal_mini_sphere_3d cech_complex_cgal_mini_sphere_3d.cpp )
-  target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${Boost_PROGRAM_OPTIONS_LIBRARY} ${CGAL_LIBRARY})
+  target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d Boost::program_options ${CGAL_LIBRARY})
   if (TBB_FOUND)
     target_link_libraries(Simplex_tree_example_cech_complex_cgal_mini_sphere_3d ${TBB_LIBRARIES})
   endif()
diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt
index 3ee0c2f6..d986d2d1 100644
--- a/src/Witness_complex/utilities/CMakeLists.txt
+++ b/src/Witness_complex/utilities/CMakeLists.txt
@@ -4,10 +4,10 @@ project(Witness_complex_utilities)
 if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   
   add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp )
-  target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(Witness_complex_strong_witness_persistence Boost::program_options)
 
   add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp )
-  target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(Witness_complex_weak_witness_persistence Boost::program_options)
 
   if (TBB_FOUND)
     target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES})
diff --git a/src/cmake/modules/GUDHI_boost_test.cmake b/src/cmake/modules/GUDHI_boost_test.cmake
index c3b29883..4a13404b 100644
--- a/src/cmake/modules/GUDHI_boost_test.cmake
+++ b/src/cmake/modules/GUDHI_boost_test.cmake
@@ -9,7 +9,6 @@ if (WITH_GUDHI_BOOST_TEST_COVERAGE)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
   endif()
   set(GUDHI_UT_LOG_FORMAT "--log_format=XML")
-  set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml")
   set(GUDHI_UT_LOG_LEVEL "--log_level=test_suite")
   set(GUDHI_UT_REPORT_LEVEL "--report_level=no")
 else (WITH_GUDHI_BOOST_TEST_COVERAGE)
@@ -19,7 +18,11 @@ else (WITH_GUDHI_BOOST_TEST_COVERAGE)
 endif(WITH_GUDHI_BOOST_TEST_COVERAGE)
 
 function(gudhi_add_boost_test unitary_test)
-  target_link_libraries(${unitary_test} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (WITH_GUDHI_BOOST_TEST_COVERAGE)
+    set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml")
+  endif(WITH_GUDHI_BOOST_TEST_COVERAGE)
+  
+  target_link_libraries(${unitary_test} Boost::unit_test_framework)
   add_test(NAME ${unitary_test} COMMAND $<TARGET_FILE:${unitary_test}>
       ${GUDHI_UT_LOG_FORMAT} ${GUDHI_UT_LOG_SINK}
       ${GUDHI_UT_LOG_LEVEL} ${GUDHI_UT_REPORT_LEVEL})
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 24a34150..6db2c76b 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -6,6 +6,38 @@ if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
 endif(NOT Boost_FOUND)
 
+# cf. https://cliutils.gitlab.io/modern-cmake/chapters/packages/Boost.html
+# This is needed if your Boost version is newer than your CMake version
+# or if you have an old version of CMake (<3.5)
+if(NOT TARGET Boost::program_options)
+    add_library(Boost::program_options IMPORTED INTERFACE)
+    set_property(TARGET Boost::program_options PROPERTY
+        INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+    set_property(TARGET Boost::program_options PROPERTY
+        INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+if(NOT TARGET Boost::filesystem)
+    add_library(Boost::filesystem IMPORTED INTERFACE)
+    set_property(TARGET Boost::filesystem PROPERTY
+        INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+    set_property(TARGET Boost::filesystem PROPERTY
+        INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+if(NOT TARGET Boost::unit_test_framework)
+    add_library(Boost::unit_test_framework IMPORTED INTERFACE)
+    set_property(TARGET Boost::unit_test_framework PROPERTY
+        INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+    set_property(TARGET Boost::unit_test_framework PROPERTY
+        INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+if(NOT TARGET Boost::system)
+    add_library(Boost::system IMPORTED INTERFACE)
+    set_property(TARGET Boost::system PROPERTY
+        INTERFACE_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIR})
+    set_property(TARGET Boost::system PROPERTY
+        INTERFACE_LINK_LIBRARIES ${Boost_LIBRARIES})
+endif()
+
 find_package(GMP)
 if(GMP_FOUND)
   INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
@@ -35,6 +67,9 @@ if(CGAL_FOUND)
   include( ${CGAL_USE_FILE} )
 endif()
 
+# For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera.
+set(HERA_WASSERSTEIN_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/geom_matching/wasserstein/include CACHE PATH "Directory where one can find Hera's wasserstein.h")
+
 option(WITH_GUDHI_USE_TBB "Build with Intel TBB parallelization" ON)
 
 # Find TBB package for parallel sort - not mandatory, just optional.
@@ -82,9 +117,6 @@ add_definitions( -DBOOST_ALL_DYN_LINK )
 # problem on Mac with boost_system and boost_thread
 add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
 
-INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
-LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-
 message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
 message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
@@ -127,6 +159,7 @@ if( PYTHONINTERP_FOUND )
   find_python_module("sphinx")
   find_python_module("sklearn")
   find_python_module("ot")
+  find_python_module("pybind11")
 endif()
 
 if(NOT GUDHI_PYTHON_PATH)
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 0b361a0f..5047252f 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -54,6 +54,9 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
 
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   copy_directory ${CMAKE_SOURCE_DIR}/ext/hera/geom_matching/wasserstein/include ${GUDHI_USER_VERSION_DIR}/ext/hera/geom_matching/wasserstein/include)
+
 set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
 
 set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi")
@@ -93,4 +96,4 @@ foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
     endforeach()
   endforeach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
 
-endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
\ No newline at end of file
+endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
index 9fdb2321..99ab6bb7 100644
--- a/src/common/doc/header.html
+++ b/src/common/doc/header.html
@@ -56,7 +56,7 @@ $extrastylesheet
                   <a href="#">Download</a>
                     <ul class="dropdown">
                         <li><a href="/licensing/">Licensing</a></li>
-                        <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5253/library-latest.zip" target="_blank">Get the latest sources</a></li>
+                        <li><a href="https://github.com/GUDHI/gudhi-devel/releases/latest" target="_blank">Get the latest sources</a></li>
                         <li><a href="/conda/">Conda package</a></li>
                         <li><a href="/dockerfile/">Dockerfile</a></li>
                     </ul>
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index b558d4c4..090a7446 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -32,6 +32,10 @@ function( add_gudhi_debug_info DEBUG_INFO )
 endfunction( add_gudhi_debug_info )
 
 if(PYTHONINTERP_FOUND)
+  if(PYBIND11_FOUND)
+    add_gudhi_debug_info("Pybind11 version ${PYBIND11_VERSION}")
+    set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'hera', ")
+  endif()
   if(CYTHON_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'simplex_tree', ")
@@ -86,6 +90,7 @@ if(PYTHONINTERP_FOUND)
     endif(MSVC)
     if(CMAKE_COMPILER_IS_GNUCXX)
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
+      set(GUDHI_PYBIND11_EXTRA_COMPILE_ARGS "${GUDHI_PYBIND11_EXTRA_COMPILE_ARGS}'-fvisibility=hidden', ")
     endif(CMAKE_COMPILER_IS_GNUCXX)
     if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
       set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
@@ -390,9 +395,9 @@ endif(CGAL_FOUND)
     add_gudhi_py_test(test_reader_utils)
 
     # Wasserstein
-    if(OT_FOUND)
+    if(OT_FOUND AND PYBIND11_FOUND)
       add_gudhi_py_test(test_wasserstein_distance)
-    endif(OT_FOUND)
+    endif()
 
     # Representations
     if(SKLEARN_FOUND AND MATPLOTLIB_FOUND)
@@ -406,32 +411,37 @@ endif(CGAL_FOUND)
           if(SCIPY_FOUND)
             if(SKLEARN_FOUND)
               if(OT_FOUND)
-                if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-                  set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
-                  # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
-                  # Images and biblio warnings because not found on developper version
-                  if (GUDHI_PYTHON_PATH STREQUAL "src/python")
-                    set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
-                  endif()
-                  # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
-                  add_custom_target(sphinx
-                      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
-                      COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                      ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
-                      DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
-                      COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
+                if(PYBIND11_FOUND)
+                  if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+                    set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
+                    # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
+                    # Images and biblio warnings because not found on developper version
+                    if (GUDHI_PYTHON_PATH STREQUAL "src/python")
+                      set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
+                    endif()
+                    # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
+                    add_custom_target(sphinx
+                        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
+                        COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                        ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
+                        DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+                        COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
   
-                  add_test(NAME sphinx_py_test
-                           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-                           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-                           ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
+                    add_test(NAME sphinx_py_test
+                             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+                             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+                             ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
   
-                  # Set missing or not modules
-                  set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
-                else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-                  message("++ Python documentation module will not be compiled because it requires a Eigen3 and CGAL version >= 4.11.0")
+                    # Set missing or not modules
+                    set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
+                  else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+                    message("++ Python documentation module will not be compiled because it requires a Eigen3 and CGAL version >= 4.11.0")
+                    set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+                  endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+                else(PYBIND11_FOUND)
+                  message("++ Python documentation module will not be compiled because pybind11 was not found")
                   set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
-                endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+                endif(PYBIND11_FOUND)
               else(OT_FOUND)
                 message("++ Python documentation module will not be compiled because POT was not found")
                 set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
diff --git a/src/python/doc/_templates/layout.html b/src/python/doc/_templates/layout.html
index 2f2d9c72..a672a281 100644
--- a/src/python/doc/_templates/layout.html
+++ b/src/python/doc/_templates/layout.html
@@ -201,7 +201,7 @@
                   <a href="#">Download</a>
                     <ul class="dropdown">
                         <li><a href="/licensing/">Licensing</a></li>
-                        <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5253/library-latest.zip" target="_blank">Get the latest sources</a></li>
+                        <li><a href="https://github.com/GUDHI/gudhi-devel/releases/latest" target="_blank">Get the latest sources</a></li>
                         <li><a href="/conda/">Conda package</a></li>
                         <li><a href="/dockerfile/">Dockerfile</a></li>
                     </ul>
diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst
index 40f3f44b..d459145b 100644
--- a/src/python/doc/installation.rst
+++ b/src/python/doc/installation.rst
@@ -14,10 +14,11 @@ Compiling
 *********
 The library uses c++14 and requires `Boost <https://www.boost.org/>`_ ≥ 1.56.0,
 `CMake <https://www.cmake.org/>`_ ≥ 3.1  to generate makefiles,
-`NumPy <http://numpy.org>`_ and `Cython <https://www.cython.org/>`_ to compile
+`NumPy <http://numpy.org>`_, `Cython <https://www.cython.org/>`_ and
+`pybind11 <https://github.com/pybind/pybind11>`_ to compile
 the GUDHI Python module.
 It is a multi-platform library and compiles on Linux, Mac OSX and Visual
-Studio 2015.
+Studio 2017.
 
 On `Windows <https://wiki.python.org/moin/WindowsCompilers>`_ , only Python
 ≥ 3.5 are available because of the required Visual Studio version.
diff --git a/src/python/doc/wasserstein_distance_user.rst b/src/python/doc/wasserstein_distance_user.rst
index 32999a0c..94b454e2 100644
--- a/src/python/doc/wasserstein_distance_user.rst
+++ b/src/python/doc/wasserstein_distance_user.rst
@@ -9,17 +9,26 @@ Definition
 
 .. include:: wasserstein_distance_sum.inc
 
-This implementation is based on ideas from "Large Scale Computation of Means and Cluster for Persistence Diagrams via Optimal Transport".
+Functions
+---------
+This implementation uses the Python Optimal Transport library and is based on
+ideas from "Large Scale Computation of Means and Cluster for Persistence
+Diagrams via Optimal Transport" :cite:`10.5555/3327546.3327645`.
 
-Function
---------
 .. autofunction:: gudhi.wasserstein.wasserstein_distance
 
+This other implementation comes from `Hera
+<https://bitbucket.org/grey_narn/hera/src/master/>`_ (BSD-3-Clause) which is
+based on "Geometry Helps to Compare Persistence Diagrams"
+:cite:`Kerber:2017:GHC:3047249.3064175` by Michael Kerber, Dmitriy
+Morozov, and Arnur Nigmetov.
+
+.. autofunction:: gudhi.hera.wasserstein_distance
 
 Basic example
 -------------
 
-This example computes the 1-Wasserstein distance from 2 persistence diagrams with euclidean ground metric.
+This example computes the 1-Wasserstein distance from 2 persistence diagrams with Euclidean ground metric.
 Note that persistence diagrams must be submitted as (n x 2) numpy arrays and must not contain inf values.
 
 .. testcode::
diff --git a/src/python/gudhi/hera.cc b/src/python/gudhi/hera.cc
new file mode 100644
index 00000000..0d562b4c
--- /dev/null
+++ b/src/python/gudhi/hera.cc
@@ -0,0 +1,71 @@
+/*    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):       Marc Glisse
+ *
+ *    Copyright (C) 2020 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+
+#include <boost/range/iterator_range.hpp>
+
+#include <wasserstein.h> // Hera
+
+#include <array>
+
+namespace py = pybind11;
+typedef py::array_t<double, py::array::c_style | py::array::forcecast> Dgm;
+
+double wasserstein_distance(
+    Dgm d1, Dgm d2,
+    double wasserstein_power, double internal_p,
+    double delta)
+{
+  py::buffer_info buf1 = d1.request();
+  py::buffer_info buf2 = d2.request();
+  // shape (n,2) or (0) for empty
+  if((buf1.ndim!=2 || buf1.shape[1]!=2) && (buf1.ndim!=1 || buf1.shape[0]!=0))
+    throw std::runtime_error("Diagram 1 must be an array of size n x 2");
+  if((buf2.ndim!=2 || buf2.shape[1]!=2) && (buf2.ndim!=1 || buf2.shape[0]!=0))
+    throw std::runtime_error("Diagram 2 must be an array of size n x 2");
+  typedef std::array<double, 2> Point;
+  auto p1 = (Point*)buf1.ptr;
+  auto p2 = (Point*)buf2.ptr;
+  auto diag1 = boost::make_iterator_range(p1, p1+buf1.shape[0]);
+  auto diag2 = boost::make_iterator_range(p2, p2+buf2.shape[0]);
+
+  hera::AuctionParams<double> params;
+  params.wasserstein_power = wasserstein_power;
+  // hera encodes infinity as -1...
+  if(std::isinf(internal_p)) internal_p = hera::get_infinity<double>();
+  params.internal_p = internal_p;
+  params.delta = delta;
+  // The extra parameters are purposedly not exposed for now.
+  return hera::wasserstein_dist(diag1, diag2, params);
+}
+
+PYBIND11_MODULE(hera, m) {
+      m.def("wasserstein_distance", &wasserstein_distance,
+          py::arg("X"), py::arg("Y"),
+          py::arg("order") = 1,
+          py::arg("internal_p") = std::numeric_limits<double>::infinity(),
+          py::arg("delta") = .01,
+          R"pbdoc(
+        Compute the Wasserstein distance between two diagrams.
+        Points at infinity are supported.
+
+        Parameters:
+            X (n x 2 numpy array): First diagram
+            Y (n x 2 numpy array): Second diagram
+            order (float): Wasserstein exponent W_q
+            internal_p (float): Internal Minkowski norm L^p in R^2
+            delta (float): Relative error 1+delta
+
+        Returns:
+            float: Approximate Wasserstein distance W_q(X,Y)
+    )pbdoc");
+}
diff --git a/src/python/gudhi/nerve_gic.pyx b/src/python/gudhi/nerve_gic.pyx
index e291579b..9c89b239 100644
--- a/src/python/gudhi/nerve_gic.pyx
+++ b/src/python/gudhi/nerve_gic.pyx
@@ -194,7 +194,7 @@ cdef class CoverComplex:
 
     def set_automatic_resolution(self):
         """Computes the optimal length of intervals (i.e. the smallest interval
-        length avoiding discretization artifacts—see :cite:`Carriere17c`) for a
+        length avoiding discretization artifacts - see :cite:`Carriere17c`) for a
         functional cover.
 
         :rtype: double
@@ -298,7 +298,7 @@ cdef class CoverComplex:
 
     def set_graph_from_automatic_rips(self, N=100):
         """Creates a graph G from a Rips complex whose threshold value is
-        automatically tuned with subsampling—see.
+        automatically tuned with subsampling - see :cite:`Carriere17c`.
 
         :param N: Number of subsampling iteration (the default reasonable value
             is 100, but there is no guarantee on how to choose it).
diff --git a/src/python/gudhi/wasserstein.py b/src/python/gudhi/wasserstein.py
index db5ddff2..13102094 100644
--- a/src/python/gudhi/wasserstein.py
+++ b/src/python/gudhi/wasserstein.py
@@ -27,8 +27,8 @@ def _build_dist_matrix(X, Y, order=2., internal_p=2.):
     '''
     :param X: (n x 2) numpy.array encoding the (points of the) first diagram.
     :param Y: (m x 2) numpy.array encoding the second diagram.
-    :param internal_p: Ground metric (i.e. norm l_p).
     :param order: exponent for the Wasserstein metric.
+    :param internal_p: Ground metric (i.e. norm L^p).
     :returns: (n+1) x (m+1) np.array encoding the cost matrix C. 
                 For 1 <= i <= n, 1 <= j <= m, C[i,j] encodes the distance between X[i] and Y[j], while C[i, m+1] (resp. C[n+1, j]) encodes the distance (to the p) between X[i] (resp Y[j]) and its orthogonal proj onto the diagonal.
                 note also that C[n+1, m+1] = 0  (it costs nothing to move from the diagonal to the diagonal).
@@ -54,8 +54,8 @@ def _build_dist_matrix(X, Y, order=2., internal_p=2.):
 def _perstot(X, order, internal_p):
     '''
     :param X: (n x 2) numpy.array (points of a given diagram).
-    :param internal_p: Ground metric on the (upper-half) plane (i.e. norm l_p in R^2); Default value is 2 (Euclidean norm).
     :param order: exponent for Wasserstein. Default value is 2.
+    :param internal_p: Ground metric on the (upper-half) plane (i.e. norm L^p in R^2); Default value is 2 (Euclidean norm).
     :returns: float, the total persistence of the diagram (that is, its distance to the empty diagram).    
     '''
     Xdiag = _proj_on_diag(X)
@@ -66,8 +66,8 @@ def wasserstein_distance(X, Y, order=2., internal_p=2.):
     '''
     :param X: (n x 2) numpy.array encoding the (finite points of the) first diagram. Must not contain essential points (i.e. with infinite coordinate).
     :param Y: (m x 2) numpy.array encoding the second diagram.
-    :param internal_p: Ground metric on the (upper-half) plane (i.e. norm l_p in R^2); Default value is 2 (euclidean norm).
     :param order: exponent for Wasserstein; Default value is 2.
+    :param internal_p: Ground metric on the (upper-half) plane (i.e. norm L^p in R^2); Default value is 2 (Euclidean norm).
     :returns: the Wasserstein distance of order q (1 <= q < infinity) between persistence diagrams with respect to the internal_p-norm as ground metric.
     :rtype: float
     '''
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 9c2124f4..f968bd59 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -8,10 +8,11 @@
      - YYYY/MM Author: Description of the modification
 """
 
-from setuptools import setup, Extension
+from setuptools import setup, Extension, find_packages
 from Cython.Build import cythonize
 from numpy import get_include as numpy_get_include
 import sys
+import pybind11
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  Inria"
@@ -42,14 +43,26 @@ for module in modules:
         runtime_library_dirs=runtime_library_dirs,
         cython_directives = {'language_level': str(sys.version_info[0])},))
 
+ext_modules = cythonize(ext_modules)
+
+ext_modules.append(Extension(
+    'gudhi.hera',
+    sources = [source_dir + 'hera.cc'],
+    language = 'c++',
+    include_dirs = include_dirs +
+        ['@HERA_WASSERSTEIN_INCLUDE_DIR@',
+        pybind11.get_include(False), pybind11.get_include(True)],
+    extra_compile_args=extra_compile_args + [@GUDHI_PYBIND11_EXTRA_COMPILE_ARGS@],
+    ))
+
 setup(
     name = 'gudhi',
-    packages=["gudhi",],
+    packages=find_packages(), # find_namespace_packages(include=["gudhi*"])
     author='GUDHI Editorial Board',
     author_email='gudhi-contact@lists.gforge.inria.fr',
     version='@GUDHI_VERSION@',
     url='http://gudhi.gforge.inria.fr/',
-    ext_modules = cythonize(ext_modules),
+    ext_modules = ext_modules,
     install_requires = ['cython','numpy >= 1.9',],
-    setup_requires = ['numpy >= 1.9',],
+    setup_requires = ['numpy >= 1.9','pybind11',],
 )
diff --git a/src/python/test/test_wasserstein_distance.py b/src/python/test/test_wasserstein_distance.py
index 43dda77e..6a6b217b 100755
--- a/src/python/test/test_wasserstein_distance.py
+++ b/src/python/test/test_wasserstein_distance.py
@@ -1,6 +1,6 @@
 """ 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):       Theo Lacombe
+    Author(s):       Theo Lacombe, Marc Glisse
 
     Copyright (C) 2019 Inria
 
@@ -8,41 +8,66 @@
       - YYYY/MM Author: Description of the modification
 """
 
-from gudhi.wasserstein import wasserstein_distance
+from gudhi.wasserstein import wasserstein_distance as pot
+from gudhi.hera import wasserstein_distance as hera
 import numpy as np
+import pytest
 
 __author__ = "Theo Lacombe"
 __copyright__ = "Copyright (C) 2019 Inria"
 __license__ = "MIT"
 
-
-def test_basic_wasserstein():
+def _basic_wasserstein(wasserstein_distance, delta, test_infinity=True):
     diag1 = np.array([[2.7, 3.7], [9.6, 14.0], [34.2, 34.974]])
     diag2 = np.array([[2.8, 4.45], [9.5, 14.1]])
     diag3 = np.array([[0, 2], [4, 6]])
     diag4 = np.array([[0, 3], [4, 8]])
-    emptydiag = np.array([[]])
+    emptydiag = np.array([])
+
+    # We just need to handle positive numbers here
+    def approx(x):
+        return pytest.approx(x, rel=delta)
 
     assert wasserstein_distance(emptydiag, emptydiag, internal_p=2.,     order=1.) == 0.
     assert wasserstein_distance(emptydiag, emptydiag, internal_p=np.inf, order=1.) == 0.
     assert wasserstein_distance(emptydiag, emptydiag, internal_p=np.inf, order=2.) == 0.
     assert wasserstein_distance(emptydiag, emptydiag, internal_p=2.,     order=2.) == 0.
 
-    assert wasserstein_distance(diag3, emptydiag, internal_p=np.inf,     order=1.) == 2.
-    assert wasserstein_distance(diag3, emptydiag, internal_p=1.,         order=1.) == 4.
+    assert wasserstein_distance(diag3, emptydiag, internal_p=np.inf,     order=1.) == approx(2.)
+    assert wasserstein_distance(diag3, emptydiag, internal_p=1.,         order=1.) == approx(4.)
+
+    assert wasserstein_distance(diag4, emptydiag, internal_p=1.,     order=2.) == approx(5.)  # thank you Pythagorician triplets
+    assert wasserstein_distance(diag4, emptydiag, internal_p=np.inf, order=2.) == approx(2.5)
+    assert wasserstein_distance(diag4, emptydiag, internal_p=2.,     order=2.) == approx(3.5355339059327378)
+
+    assert wasserstein_distance(diag1, diag2, internal_p=2.,   order=1.)   == approx(1.4453593023967701)
+    assert wasserstein_distance(diag1, diag2, internal_p=2.35, order=1.74) == approx(0.9772734057168739)
+
+    assert wasserstein_distance(diag1, emptydiag, internal_p=2.35, order=1.7863) == approx(3.141592214572228)
+
+    assert wasserstein_distance(diag3, diag4, internal_p=1.,     order=1.) == approx(3.)
+    assert wasserstein_distance(diag3, diag4, internal_p=np.inf, order=1.) == approx(3.)  # no diag matching here
+    assert wasserstein_distance(diag3, diag4, internal_p=np.inf, order=2.) == approx(np.sqrt(5))
+    assert wasserstein_distance(diag3, diag4, internal_p=1.,     order=2.) == approx(np.sqrt(5))
+    assert wasserstein_distance(diag3, diag4, internal_p=4.5,    order=2.) == approx(np.sqrt(5))
+
+    if(not test_infinity):
+        return
 
-    assert wasserstein_distance(diag4, emptydiag, internal_p=1.,     order=2.) == 5.  # thank you Pythagorician triplets
-    assert wasserstein_distance(diag4, emptydiag, internal_p=np.inf, order=2.) == 2.5
-    assert wasserstein_distance(diag4, emptydiag, internal_p=2.,     order=2.) == 3.5355339059327378
+    diag5 = np.array([[0, 3], [4, np.inf]])
+    diag6 = np.array([[7, 8], [4, 6], [3, np.inf]])
 
-    assert wasserstein_distance(diag1, diag2, internal_p=2.,   order=1.)   == 1.4453593023967701
-    assert wasserstein_distance(diag1, diag2, internal_p=2.35, order=1.74) == 0.9772734057168739
+    assert wasserstein_distance(diag4, diag5) == np.inf
+    assert wasserstein_distance(diag5, diag6, order=1, internal_p=np.inf) == approx(4.)
 
-    assert wasserstein_distance(diag1, emptydiag, internal_p=2.35, order=1.7863) == 3.141592214572228
+def hera_wrap(delta):
+    def fun(*kargs,**kwargs):
+        return hera(*kargs,**kwargs,delta=delta)
+    return fun
 
-    assert wasserstein_distance(diag3, diag4, internal_p=1.,     order=1.) == 3.
-    assert wasserstein_distance(diag3, diag4, internal_p=np.inf, order=1.) == 3.  # no diag matching here
-    assert wasserstein_distance(diag3, diag4, internal_p=np.inf, order=2.) == np.sqrt(5)
-    assert wasserstein_distance(diag3, diag4, internal_p=1.,     order=2.) == np.sqrt(5)
-    assert wasserstein_distance(diag3, diag4, internal_p=4.5,    order=2.) == np.sqrt(5)
+def test_wasserstein_distance_pot():
+    _basic_wasserstein(pot, 1e-15, test_infinity=False)
 
+def test_wasserstein_distance_hera():
+    _basic_wasserstein(hera_wrap(1e-12), 1e-12)
+    _basic_wasserstein(hera_wrap(.1), .1)