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

27 files changed, 367 insertions, 73 deletions

diff --git a/.appveyor.yml b/.appveyor.yml
index 4a76ea0a..34f42dea 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -39,6 +39,7 @@ init:
 
 
 install:
+  - git submodule update --init
   - vcpkg install tbb:x64-windows boost-disjoint-sets:x64-windows boost-serialization:x64-windows boost-date-time:x64-windows boost-system:x64-windows boost-filesystem:x64-windows boost-units:x64-windows boost-thread:x64-windows boost-program-options:x64-windows eigen3:x64-windows mpfr:x64-windows mpir:x64-windows cgal:x64-windows
   - SET PATH=c:\Tools\vcpkg\installed\x64-windows\bin;%PATH%
   - SET PATH=%PYTHON%;%PYTHON%\Scripts;%PYTHON%\Library\bin;%PATH%
@@ -48,7 +49,7 @@ install:
   - pip --version
   - python -m pip install --upgrade pip
   - pip install -U setuptools numpy matplotlib scipy Cython pytest
-  - pip install -U POT
+  - pip install -U POT pybind11
 
 build_script:
   - mkdir build
diff --git a/.circleci/config.yml b/.circleci/config.yml
index f4073746..4f86cb12 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -51,6 +51,8 @@ jobs:
       - 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 -DUSER_VERSION_DIR=version ..;
@@ -78,6 +80,8 @@ jobs:
       - run:
           name: Generates the C++ documentation with doxygen
           command: |
+            git submodule init
+            git submodule update
             mkdir build;
             cd build;
             cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF -DUSER_VERSION_DIR=version ..;
@@ -97,4 +101,4 @@ workflows:
       - tests
       - utils
       - python
-      - doxygen
\ No newline at end of file
+      - doxygen
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 00000000..6e8b3ab1
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "ext/hera"]
+	path = ext/hera
+	url = https://bitbucket.org/grey_narn/hera.git
diff --git a/.travis.yml b/.travis.yml
index 60d32ef8..8980be10 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -61,7 +61,7 @@ before_cache:
 install: 
   - python3 -m pip install --upgrade pip setuptools wheel
   - python3 -m pip install --user pytest Cython sphinx sphinxcontrib-bibtex sphinx-paramlinks matplotlib numpy scipy scikit-learn
-  - python3 -m pip install --user POT
+  - python3 -m pip install --user POT pybind11
 
 script: 
   - rm -rf build
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index ed19ecfb..0f827b9e 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 1)
-set (GUDHI_PATCH_VERSION 0)
+set (GUDHI_PATCH_VERSION 1)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5dcc6803..d9244dc0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -65,5 +65,7 @@ include(GUDHI_user_version_target)
 # For "make doxygen" - Requires GUDHI_USER_VERSION_DIR to be set - Done in GUDHI_user_version_target for dev version
 include(GUDHI_doxygen_target)
 
+configure_file(${CMAKE_SOURCE_DIR}/for_dev/for_maintainers/new_gudhi_version_creation.md "${CMAKE_CURRENT_BINARY_DIR}/" @ONLY)
+
 message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
 message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"")
diff --git a/Dockerfile_for_circleci_image b/Dockerfile_for_circleci_image
index b7d0dcca..ebd2f366 100644
--- a/Dockerfile_for_circleci_image
+++ b/Dockerfile_for_circleci_image
@@ -58,7 +58,8 @@ RUN pip3 install \
     scikit-learn \
     sphinx \
     sphinx-paramlinks \
-    sphinxcontrib-bibtex
+    sphinxcontrib-bibtex \
+    tensorflow
 
 # apt clean up
 RUN apt autoremove && rm -rf /var/lib/apt/lists/*
diff --git a/Dockerfile_gudhi_installation b/Dockerfile_gudhi_installation
index d5d86338..f9e8813b 100644
--- a/Dockerfile_gudhi_installation
+++ b/Dockerfile_gudhi_installation
@@ -42,6 +42,7 @@ RUN apt-get install -y make \
     python3-pip \
     python3-pytest \
     python3-tk \
+    python3-pybind11 \
     libfreetype6-dev \
     pkg-config \
     curl
@@ -57,11 +58,11 @@ RUN pip3 install \
 # apt clean up
 RUN apt autoremove && rm -rf /var/lib/apt/lists/*
 
-RUN curl -LO "https://github.com/GUDHI/gudhi-devel/releases/download/tags%2Fgudhi-release-3.1.0/gudhi.3.1.0.tar.gz" \
-&& tar xf gudhi.3.1.0.tar.gz \
-&& cd gudhi.3.1.0 \
+RUN curl -LO "https://github.com/GUDHI/gudhi-devel/releases/download/tags%2Fgudhi-release-3.1.1/gudhi.3.1.1.tar.gz" \
+&& tar xf gudhi.3.1.1.tar.gz \
+&& cd gudhi.3.1.1 \
 && mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_PYTHON=OFF -DPython_ADDITIONAL_VERSIONS=3 ..  \
 && make all test install \
 && cmake -DWITH_GUDHI_PYTHON=ON . \
 && cd python \
-&& python3 setup.py install
\ No newline at end of file
+&& python3 setup.py install
diff --git a/README.md b/README.md
index 167a38b3..f7e3d70c 100644
--- a/README.md
+++ b/README.md
@@ -10,6 +10,15 @@
 
 The GUDHI library is a generic open source C++ library, with a Python interface, for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding. The library offers state-of-the-art data structures and algorithms to construct simplicial complexes and compute persistent homology.
 
+# Source code
+
+We recommend that users get official releases from [the GUDHI website](https://gudhi.inria.fr/).
+
+For potential contributors, to fully checkout GUDHI, after cloning the git repository, you may also need to checkout its submodules using
+```sh
+git submodule update --init
+```
+
 # Compilation and installation
 
 To install GUDHI, you can follow the [C++ compilation procedure](https://gudhi.inria.fr/doc/latest/installation.html), the [Python compilation procedure](https://gudhi.inria.fr/python/latest/installation.html), use our [conda-forge package](https://gudhi.inria.fr/conda/), or [go with Docker](https://gudhi.inria.fr/dockerfile/).
diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib
index a1b951e0..3bbe7960 100644
--- a/biblio/bibliography.bib
+++ b/biblio/bibliography.bib
@@ -1180,3 +1180,15 @@ language={English}
     booktitle = {In Neural Information Processing Systems},
     year = {2007}
 }
+@inproceedings{10.5555/3327546.3327645,
+author = {Lacombe, Th\'{e}o and Cuturi, Marco and Oudot, Steve},
+title = {Large Scale Computation of Means and Clusters for Persistence Diagrams Using Optimal Transport},
+year = {2018},
+publisher = {Curran Associates Inc.},
+address = {Red Hook, NY, USA},
+booktitle = {Proceedings of the 32nd International Conference on Neural Information Processing Systems},
+pages = {9792–9802},
+numpages = {11},
+location = {Montr\'{e}al, Canada},
+series = {NIPS’18}
+}
diff --git a/ext/hera b/ext/hera
new file mode 160000
+Subproject 9a89971855acefe39dce0e2adadf53b88ca8f68
diff --git a/code_conventions.md b/for_dev/code_conventions.md
index 5882f78e..5882f78e 100644
--- a/code_conventions.md
+++ b/for_dev/code_conventions.md
diff --git a/for_dev/for_maintainers/new_gudhi_version_creation.md b/for_dev/for_maintainers/new_gudhi_version_creation.md
new file mode 100644
index 00000000..4a40f373
--- /dev/null
+++ b/for_dev/for_maintainers/new_gudhi_version_creation.md
@@ -0,0 +1,97 @@
+# Create a new GUDHI version
+
+We will consider that all operations will be performed in a brand new clone of the main project:
+```bash
+git clone https://github.com/GUDHI/gudhi-devel.git
+cd gudhi-devel
+```
+
+## Version file modification
+
+**Edit the file CMakeGUDHIVersion.txt**, and increment major, minor, or patch version number, in function of the version new delivery.
+```bash
+# cf. .gitignore - ignore this if it is a fresh clone version
+rm -rf data/points/COIL_database/lucky_cat.off_dist data/points/COIL_database/lucky_cat.off_sc.dot data/points/KleinBottle5D.off_dist data/points/KleinBottle5D.off_sc.dot data/points/human.off_dist data/points/human.off_sc.off data/points/human.off_sc.txt
+```
+
+Checkin the modifications, build and test the version:
+```bash
+mkdir build
+cd build
+cmake -DCGAL_DIR=/your/path/to/CGAL -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON  -DUSER_VERSION_DIR=gudhi.@GUDHI_VERSION@ -DPython_ADDITIONAL_VERSIONS=3 ..
+make user_version
+date +"%d-%m-%Y-%T" > gudhi.@GUDHI_VERSION@/timestamp.txt
+tar -czvf gudhi.@GUDHI_VERSION@.tar.gz gudhi.@GUDHI_VERSION@
+md5sum gudhi.@GUDHI_VERSION@.tar.gz > md5sum.txt
+sha256sum gudhi.@GUDHI_VERSION@.tar.gz > sha256sum.txt
+sha512sum gudhi.@GUDHI_VERSION@.tar.gz > sha512sum.txt
+
+make -j all test
+```
+
+***[Check there are no error]***
+
+## Create the documentation
+```bash
+mkdir gudhi.doc.@GUDHI_VERSION@
+make doxygen  2>&1 | tee dox.log && grep warning dox.log
+```
+
+***[Check there are no error and the warnings]***
+
+```bash
+cp -R gudhi.@GUDHI_VERSION@/doc/html gudhi.doc.@GUDHI_VERSION@/cpp
+cd gudhi.@GUDHI_VERSION@
+rm -rf build; mkdir build; cd build; cmake -DCGAL_DIR=/your/path/to/CGAL -DWITH_GUDHI_EXAMPLE=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+export LC_ALL=en_US.UTF-8  # cf. bug
+make sphinx
+```
+
+***[Check there are no error]***
+
+```bash
+cp -R python/sphinx ../../gudhi.doc.@GUDHI_VERSION@/python
+cd ../..
+tar -czvf gudhi.doc.@GUDHI_VERSION@.tar.gz gudhi.doc.@GUDHI_VERSION@
+
+cd gudhi.@GUDHI_VERSION@/build
+make all test
+```
+
+***[Check there are no error]***
+
+## Upload the documentation
+
+Upload by ftp the content of the directory gudhi.doc.@GUDHI_VERSION@/cpp in a new directory on ForgeLogin@scm.gforge.inria.fr:/home/groups/gudhi/htdocs/doc/@GUDHI_VERSION@
+
+Upload by ftp the content of the directory gudhi.doc.@GUDHI_VERSION@/python in a new directory on ForgeLogin@scm.gforge.inria.fr:/home/groups/gudhi/htdocs/python/@GUDHI_VERSION@
+
+Through ssh, make the **latest** link to your new version of the documentation:
+```bash
+ssh ForgeLogin@scm.gforge.inria.fr
+cd /home/groups/gudhi/htdocs/doc
+rm latest
+ln -s @GUDHI_VERSION@ latest
+cd /home/groups/gudhi/htdocs/python
+rm latest
+ln -s @GUDHI_VERSION@ latest
+```
+
+## Put a version label on files
+
+* Go on page https://github.com/GUDHI/gudhi-devel/releases/new
+* Name the tag: tags/gudhi-release-@GUDHI_VERSION@
+* Name the release GUDHI @GUDHI_VERSION@
+* Write the release note
+* Drag'n drop *gudhi.@GUDHI_VERSION@.tar.gz*, *md5sum.txt*, *sha256sum.txt*, *sha512sum.txt* files
+* Tick the *This is a pre-release* check button if this is a release candidate (untick if this is an official version)
+* Click the *Publish the release* button
+
+***[Where X, Y and Z corresponds respectively to the major, minor, and patch version number]***
+
+
+## Mail sending
+Send version mail to the following lists :
+* gudhi-devel@lists.gforge.inria.fr
+* gudhi-users@lists.gforge.inria.fr (not for release candidate)
+
diff --git a/for_dev/for_maintainers/next_release_template.md b/for_dev/for_maintainers/next_release_template.md
new file mode 100644
index 00000000..a2805a55
--- /dev/null
+++ b/for_dev/for_maintainers/next_release_template.md
@@ -0,0 +1,28 @@
+We are pleased to announce the release 3.X.X of the GUDHI library.
+
+As a major new feature, the GUDHI library now offers ...
+
+We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz).
+
+Below is a list of changes made since GUDHI 3.X-1.X-1:
+
+- [Module](link)
+     - ...
+
+- [Module](link)
+     - ...
+
+- Miscellaneous
+     - The [list of bugs that were solved since GUDHI-3.X-1.X-1](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.1.1+is%3Aclosed) is available on GitHub.
+
+All modules are distributed under the terms of the MIT license.
+However, there are still GPL dependencies for many modules. We invite you to check our [license dedicated web page](https://gudhi.inria.fr/licensing/) for further details.
+
+We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages.
+
+We provide [bibtex entries](https://gudhi.inria.fr/doc/latest/_citation.html) for the modules of the User and Reference Manual, as well as for publications directly related to the GUDHI library. 
+
+Feel free to [contact us](https://gudhi.inria.fr/contact/) in case you have any questions or remarks.
+
+For further information about downloading and installing the library ([C++](https://gudhi.inria.fr/doc/latest/installation.html) or [Python](https://gudhi.inria.fr/python/latest/installation.html)), please visit the [GUDHI web site](https://gudhi.inria.fr/).
+
diff --git a/next_release.md b/for_dev/next_release.md
index 26d4fca5..a2805a55 100644
--- a/next_release.md
+++ b/for_dev/next_release.md
@@ -4,7 +4,7 @@ As a major new feature, the GUDHI library now offers ...
 
 We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz).
 
-Below is a list of changes made since Gudhi 3.1.0:
+Below is a list of changes made since GUDHI 3.X-1.X-1:
 
 - [Module](link)
      - ...
@@ -13,8 +13,7 @@ Below is a list of changes made since Gudhi 3.1.0:
      - ...
 
 - Miscellaneous
-     - See the list of [bug fixes](https://github.com/GUDHI/gudhi-devel/issues?utf8=%E2%9C%93&q=is%3Aissue+label%3A3.X.X+).
-
+     - The [list of bugs that were solved since GUDHI-3.X-1.X-1](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.1.1+is%3Aclosed) is available on GitHub.
 
 All modules are distributed under the terms of the MIT license.
 However, there are still GPL dependencies for many modules. We invite you to check our [license dedicated web page](https://gudhi.inria.fr/licensing/) for further details.
@@ -25,4 +24,5 @@ We provide [bibtex entries](https://gudhi.inria.fr/doc/latest/_citation.html) fo
 
 Feel free to [contact us](https://gudhi.inria.fr/contact/) in case you have any questions or remarks.
 
-For further information about downloading and installing the library ([C++](https://gudhi.inria.fr/doc/3.1.0.rc1/installation.html) or [Python](https://gudhi.inria.fr/python/3.1.0.rc1/installation.html)), please visit the [GUDHI web site](https://gudhi.inria.fr/).
+For further information about downloading and installing the library ([C++](https://gudhi.inria.fr/doc/latest/installation.html) or [Python](https://gudhi.inria.fr/python/latest/installation.html)), please visit the [GUDHI web site](https://gudhi.inria.fr/).
+
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/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 24a34150..359d1c12 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -35,6 +35,9 @@ 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.
@@ -127,6 +130,7 @@ 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/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 f993165c..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","gudhi.representations"],
+    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)