From 974a045acfdae6a9980d9473f9dc3ece716aa0e1 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Sun, 31 May 2020 09:23:14 +0200
Subject: Add some fields for PyPi nice render

---
 src/python/setup.py.in | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

(limited to 'src')

diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index b9f4e3f0..55d2b604 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -68,7 +68,17 @@ setup(
     author='GUDHI Editorial Board',
     author_email='gudhi-contact@lists.gforge.inria.fr',
     version='@GUDHI_VERSION@',
-    url='http://gudhi.gforge.inria.fr/',
+    url='https://gudhi.inria.fr/',
+    project_urls={
+        'Bug Tracker': 'https://github.com/GUDHI/gudhi-devel/issues',
+        'Documentation': 'https://gudhi.inria.fr/python/latest/',
+        'Source Code': 'https://github.com/GUDHI/gudhi-devel',
+        'License': 'https://gudhi.inria.fr/licensing/'
+        },
+    description='The Gudhi library is an open source library for Computational Topology and Topological Data ' \
+        'Analysis (TDA). It offers state-of-the-art algorithms to construct various types of simplicial complexes, ' \
+        'data structures to represent them, and algorithms to compute geometric approximations of shapes and ' \
+        'persistent homology.',
     ext_modules = ext_modules,
     install_requires = ['cython','numpy >= 1.9',],
     setup_requires = ['numpy >= 1.9','pybind11',],
-- 
cgit v1.2.3


From 433a8cdaa111ebb777450fc1ee2e316480e4b46a Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Sun, 31 May 2020 10:36:47 +0200
Subject: Add introduction to pypi description and new release version

---
 CMakeGUDHIVersion.txt     |  2 +-
 src/python/CMakeLists.txt |  3 +++
 src/python/setup.py.in    | 14 ++++++++++----
 3 files changed, 14 insertions(+), 5 deletions(-)

(limited to 'src')

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 59226274..3d8be42d 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 2)
-set (GUDHI_PATCH_VERSION 0a0)
+set (GUDHI_PATCH_VERSION 0a1)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index ab08cd6d..d4cb7477 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -235,6 +235,9 @@ if(PYTHONINTERP_FOUND)
     file(COPY "gudhi/point_cloud" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
 
+    # Other .py files
+    file(COPY "introduction.md" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
+
     add_custom_command(
         OUTPUT gudhi.so
         WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 55d2b604..ff000a2c 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -13,6 +13,7 @@ from Cython.Build import cythonize
 from numpy import get_include as numpy_get_include
 import sys
 import pybind11
+from os import path
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  Inria"
@@ -62,6 +63,11 @@ for module in pybind11_modules:
         runtime_library_dirs=runtime_library_dirs,
         ))
 
+# read the contents of introduction.md
+this_directory = path.abspath(path.dirname(__file__))
+with open(path.join(this_directory, 'introduction.md'), encoding='utf-8') as f:
+    long_description = f.read()
+
 setup(
     name = 'gudhi',
     packages=find_packages(), # find_namespace_packages(include=["gudhi*"])
@@ -75,10 +81,10 @@ setup(
         'Source Code': 'https://github.com/GUDHI/gudhi-devel',
         'License': 'https://gudhi.inria.fr/licensing/'
         },
-    description='The Gudhi library is an open source library for Computational Topology and Topological Data ' \
-        'Analysis (TDA). It offers state-of-the-art algorithms to construct various types of simplicial complexes, ' \
-        'data structures to represent them, and algorithms to compute geometric approximations of shapes and ' \
-        'persistent homology.',
+    description='The Gudhi library is an open source library for ' \
+        'Computational Topology and Topological Data Analysis (TDA).',
+    long_description=long_description,
+    long_description_content_type='text/markdown',
     ext_modules = ext_modules,
     install_requires = ['cython','numpy >= 1.9',],
     setup_requires = ['numpy >= 1.9','pybind11',],
-- 
cgit v1.2.3


From 3b91ae863718c402a991c5807579f578d266a04b Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Sun, 31 May 2020 10:43:07 +0200
Subject: add md file

---
 src/python/introduction.md | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 src/python/introduction.md

(limited to 'src')

diff --git a/src/python/introduction.md b/src/python/introduction.md
new file mode 100644
index 00000000..3277e0ac
--- /dev/null
+++ b/src/python/introduction.md
@@ -0,0 +1,30 @@
+![](https://gudhi.inria.fr/images/gudhi_architecture.png)
+
+#Introduction
+
+The Gudhi library is an open source library for Computational Topology and
+Topological Data Analysis (TDA). It offers state-of-the-art algorithms
+to construct various types of simplicial complexes, data structures to
+represent them, and algorithms to compute geometric approximations of shapes
+and persistent homology.
+
+The GUDHI library offers the following interoperable modules:
+* Complexes:
+   * Cubical
+   * Simplicial: Rips, Witness, Alpha and Čech complexes
+   * Cover: Nerve and Graph induced complexes
+* Data structures and basic operations:
+   * Simplex tree, Skeleton blockers and Toplex map
+   * Construction, update, filtration and simplification
+* Topological descriptors computation
+* Manifold reconstruction
+* Topological descriptors tools:
+   * Bottleneck distance
+   * Statistical tools
+   * Persistence diagram and barcode
+
+For more information about Topological Data Analysis and its workflow, please
+refer to the [Wikipedia TDA dedicated page][1].
+
+ [1]: https://en.wikipedia.org/wiki/Topological_data_analysis
+
-- 
cgit v1.2.3


From 5141caeff03f1e8c8c4ccae1ee7ca43fbcb2925f Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Sun, 31 May 2020 11:01:24 +0200
Subject: It was not markdown but rst...

---
 src/python/CMakeLists.txt   |  2 +-
 src/python/introduction.md  | 30 ------------------------------
 src/python/introduction.rst | 33 +++++++++++++++++++++++++++++++++
 src/python/setup.py.in      |  2 +-
 4 files changed, 35 insertions(+), 32 deletions(-)
 delete mode 100644 src/python/introduction.md
 create mode 100644 src/python/introduction.rst

(limited to 'src')

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index d4cb7477..fee6b6f5 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -236,7 +236,7 @@ if(PYTHONINTERP_FOUND)
     file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
 
     # Other .py files
-    file(COPY "introduction.md" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
+    file(COPY "introduction.rst" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
 
     add_custom_command(
         OUTPUT gudhi.so
diff --git a/src/python/introduction.md b/src/python/introduction.md
deleted file mode 100644
index 3277e0ac..00000000
--- a/src/python/introduction.md
+++ /dev/null
@@ -1,30 +0,0 @@
-![](https://gudhi.inria.fr/images/gudhi_architecture.png)
-
-#Introduction
-
-The Gudhi library is an open source library for Computational Topology and
-Topological Data Analysis (TDA). It offers state-of-the-art algorithms
-to construct various types of simplicial complexes, data structures to
-represent them, and algorithms to compute geometric approximations of shapes
-and persistent homology.
-
-The GUDHI library offers the following interoperable modules:
-* Complexes:
-   * Cubical
-   * Simplicial: Rips, Witness, Alpha and Čech complexes
-   * Cover: Nerve and Graph induced complexes
-* Data structures and basic operations:
-   * Simplex tree, Skeleton blockers and Toplex map
-   * Construction, update, filtration and simplification
-* Topological descriptors computation
-* Manifold reconstruction
-* Topological descriptors tools:
-   * Bottleneck distance
-   * Statistical tools
-   * Persistence diagram and barcode
-
-For more information about Topological Data Analysis and its workflow, please
-refer to the [Wikipedia TDA dedicated page][1].
-
- [1]: https://en.wikipedia.org/wiki/Topological_data_analysis
-
diff --git a/src/python/introduction.rst b/src/python/introduction.rst
new file mode 100644
index 00000000..2cc4642e
--- /dev/null
+++ b/src/python/introduction.rst
@@ -0,0 +1,33 @@
+.. figure::
+    https://gudhi.inria.fr/images/gudhi_architecture.png
+    :figclass: align-center
+    :width: 100 %
+    :alt: GUDHI
+
+Introduction
+============
+
+The Gudhi library is an open source library for Computational Topology and
+Topological Data Analysis (TDA). It offers state-of-the-art algorithms
+to construct various types of simplicial complexes, data structures to
+represent them, and algorithms to compute geometric approximations of shapes
+and persistent homology.
+
+The GUDHI library offers the following interoperable modules:
+
+* Complexes:
+   * Cubical
+   * Simplicial: Rips, Witness, Alpha and Čech complexes
+   * Cover: Nerve and Graph induced complexes
+* Data structures and basic operations:
+   * Simplex tree, Skeleton blockers and Toplex map
+   * Construction, update, filtration and simplification
+* Topological descriptors computation
+* Manifold reconstruction
+* Topological descriptors tools:
+   * Bottleneck distance
+   * Statistical tools
+   * Persistence diagram and barcode
+
+For more information about Topological Data Analysis and its workflow, please
+refer to the `Wikipedia TDA dedicated page <https://en.wikipedia.org/wiki/Topological_data_analysis>`_.
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index ff000a2c..4725bb44 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -65,7 +65,7 @@ for module in pybind11_modules:
 
 # read the contents of introduction.md
 this_directory = path.abspath(path.dirname(__file__))
-with open(path.join(this_directory, 'introduction.md'), encoding='utf-8') as f:
+with open(path.join(this_directory, 'introduction.rst'), encoding='utf-8') as f:
     long_description = f.read()
 
 setup(
-- 
cgit v1.2.3


From 524c5f3e8c48c25ad96d2e43634e73c18d8805c5 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Mon, 1 Jun 2020 08:26:48 +0200
Subject: try to fix pypi doc

---
 CMakeGUDHIVersion.txt       | 2 +-
 src/python/introduction.rst | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'src')

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 3ebdf68c..d344f04f 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 2)
-set (GUDHI_PATCH_VERSION 0a2)
+set (GUDHI_PATCH_VERSION 0a3)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/introduction.rst b/src/python/introduction.rst
index 2cc4642e..adfed36e 100644
--- a/src/python/introduction.rst
+++ b/src/python/introduction.rst
@@ -1,4 +1,4 @@
-.. figure::
+.. image::
     https://gudhi.inria.fr/images/gudhi_architecture.png
     :figclass: align-center
     :width: 100 %
-- 
cgit v1.2.3


From 999ca34a509f6f6222a343306b725ce0bbbce795 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Mon, 1 Jun 2020 10:12:45 +0200
Subject: Try to fix rst doc for Pypi

---
 CMakeGUDHIVersion.txt       | 2 +-
 src/python/introduction.rst | 1 -
 src/python/setup.py.in      | 4 ++--
 3 files changed, 3 insertions(+), 4 deletions(-)

(limited to 'src')

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index d344f04f..75aedb74 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 2)
-set (GUDHI_PATCH_VERSION 0a3)
+set (GUDHI_PATCH_VERSION 0a4)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/introduction.rst b/src/python/introduction.rst
index adfed36e..3e9faae9 100644
--- a/src/python/introduction.rst
+++ b/src/python/introduction.rst
@@ -1,6 +1,5 @@
 .. image::
     https://gudhi.inria.fr/images/gudhi_architecture.png
-    :figclass: align-center
     :width: 100 %
     :alt: GUDHI
 
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 4725bb44..f8eeafc4 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -63,7 +63,7 @@ for module in pybind11_modules:
         runtime_library_dirs=runtime_library_dirs,
         ))
 
-# read the contents of introduction.md
+# read the contents of introduction.rst
 this_directory = path.abspath(path.dirname(__file__))
 with open(path.join(this_directory, 'introduction.rst'), encoding='utf-8') as f:
     long_description = f.read()
@@ -83,8 +83,8 @@ setup(
         },
     description='The Gudhi library is an open source library for ' \
         'Computational Topology and Topological Data Analysis (TDA).',
+    long_description_content_type='text/x-rst',
     long_description=long_description,
-    long_description_content_type='text/markdown',
     ext_modules = ext_modules,
     install_requires = ['cython','numpy >= 1.9',],
     setup_requires = ['numpy >= 1.9','pybind11',],
-- 
cgit v1.2.3


From 6d113d120d7e07df4909a7de1ae014cfb3571f38 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Mon, 1 Jun 2020 10:30:02 +0200
Subject: Try to fix rst doc for Pypi

---
 CMakeGUDHIVersion.txt       | 2 +-
 src/python/introduction.rst | 5 +----
 2 files changed, 2 insertions(+), 5 deletions(-)

(limited to 'src')

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 75aedb74..b790b828 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 2)
-set (GUDHI_PATCH_VERSION 0a4)
+set (GUDHI_PATCH_VERSION 0a5)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/introduction.rst b/src/python/introduction.rst
index 3e9faae9..90d9a381 100644
--- a/src/python/introduction.rst
+++ b/src/python/introduction.rst
@@ -1,7 +1,4 @@
-.. image::
-    https://gudhi.inria.fr/images/gudhi_architecture.png
-    :width: 100 %
-    :alt: GUDHI
+.. image:: https://gudhi.inria.fr/images/gudhi_architecture.png
 
 Introduction
 ============
-- 
cgit v1.2.3


From 7ff9d4ceeb659cac3af10a9f9d80c7267c47363a Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Mon, 1 Jun 2020 14:46:40 +0200
Subject: Let's go like this

---
 CMakeGUDHIVersion.txt       | 2 +-
 src/python/introduction.rst | 5 -----
 2 files changed, 1 insertion(+), 6 deletions(-)

(limited to 'src')

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index b790b828..ffcbc53e 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 2)
-set (GUDHI_PATCH_VERSION 0a5)
+set (GUDHI_PATCH_VERSION 0a6)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/introduction.rst b/src/python/introduction.rst
index 90d9a381..11c06ac5 100644
--- a/src/python/introduction.rst
+++ b/src/python/introduction.rst
@@ -1,8 +1,3 @@
-.. image:: https://gudhi.inria.fr/images/gudhi_architecture.png
-
-Introduction
-============
-
 The Gudhi library is an open source library for Computational Topology and
 Topological Data Analysis (TDA). It offers state-of-the-art algorithms
 to construct various types of simplicial complexes, data structures to
-- 
cgit v1.2.3


From 4aff8dc700a0790373d82ae24076359c09ee04c8 Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Mon, 1 Jun 2020 15:24:28 +0200
Subject: Interface for hera's bottleneck_distance

---
 ext/hera                                           |  2 +-
 .../modules/GUDHI_third_party_libraries.cmake      |  1 +
 src/cmake/modules/GUDHI_user_version_target.cmake  |  2 +-
 src/python/CMakeLists.txt                          |  8 +++-
 src/python/doc/bottleneck_distance_user.rst        | 18 +++++--
 src/python/gudhi/hera.cc                           | 56 ----------------------
 src/python/gudhi/hera/__init__.py                  |  2 +
 src/python/gudhi/hera/bottleneck.cc                | 45 +++++++++++++++++
 src/python/gudhi/hera/wasserstein.cc               | 56 ++++++++++++++++++++++
 src/python/setup.py.in                             |  6 ++-
 src/python/test/test_bottleneck_distance.py        |  6 ++-
 11 files changed, 134 insertions(+), 68 deletions(-)
 delete mode 100644 src/python/gudhi/hera.cc
 create mode 100644 src/python/gudhi/hera/__init__.py
 create mode 100644 src/python/gudhi/hera/bottleneck.cc
 create mode 100644 src/python/gudhi/hera/wasserstein.cc

(limited to 'src')

diff --git a/ext/hera b/ext/hera
index 0019cae9..2c5e6c60 160000
--- a/ext/hera
+++ b/ext/hera
@@ -1 +1 @@
-Subproject commit 0019cae9dc1e9d11aa03bc59681435ba7f21eea8
+Subproject commit 2c5e6c606ee37cd68bbe9f9915dba99f7677dd87
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index f92fe93e..d80283d2 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -69,6 +69,7 @@ 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/wasserstein/include CACHE PATH "Directory where one can find Hera's wasserstein.h")
+set(HERA_BOTTLENECK_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/bottleneck/include CACHE PATH "Directory where one can find Hera's bottleneck.h")
 
 option(WITH_GUDHI_USE_TBB "Build with Intel TBB parallelization" ON)
 
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index e99bb42d..491fa459 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -68,7 +68,7 @@ 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/wasserstein/include ${GUDHI_USER_VERSION_DIR}/ext/hera/wasserstein/include)
+                   copy_directory ${CMAKE_SOURCE_DIR}/ext/hera ${GUDHI_USER_VERSION_DIR}/ext/hera)
 
 set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
 
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 96dd3f6f..1e81cac8 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -130,7 +130,8 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'reader_utils', ")
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'witness_complex', ")
     set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'strong_witness_complex', ")
-    set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera', ")
+    set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/wasserstein', ")
+    set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/bottleneck', ")
     if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
       set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'bottleneck', ")
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ")
@@ -236,6 +237,7 @@ if(PYTHONINTERP_FOUND)
     file(COPY "gudhi/point_cloud" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/dtm_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
+    file(COPY "gudhi/hera/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/hera")
 
     add_custom_command(
         OUTPUT gudhi.so
@@ -355,7 +357,9 @@ if(PYTHONINTERP_FOUND)
                COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
 
-      add_gudhi_py_test(test_bottleneck_distance)
+      if (PYBIND11_FOUND)
+        add_gudhi_py_test(test_bottleneck_distance)
+      endif()
 
       # Cover complex
       file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
diff --git a/src/python/doc/bottleneck_distance_user.rst b/src/python/doc/bottleneck_distance_user.rst
index 89da89d3..49bd3706 100644
--- a/src/python/doc/bottleneck_distance_user.rst
+++ b/src/python/doc/bottleneck_distance_user.rst
@@ -9,14 +9,22 @@ Definition
 
 .. include:: bottleneck_distance_sum.inc
 
-This implementation is based on ideas from "Geometry Helps in Bottleneck Matching and Related Problems"
-:cite:`DBLP:journals/algorithmica/EfratIK01`. Another relevant publication, although it was not used is
-"Geometry Helps to Compare Persistence Diagrams" :cite:`Kerber:2017:GHC:3047249.3064175`.
+This implementation by François Godi is based on ideas from "Geometry Helps in Bottleneck Matching and Related Problems"
+:cite:`DBLP:journals/algorithmica/EfratIK01` and requires `CGAL <installation.html#cgal>`_.
 
-Function
---------
 .. autofunction:: gudhi.bottleneck_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.
+
+Beware that its approximation allows for a multiplicative error, while the function above uses an additive error.
+
+.. autofunction:: gudhi.hera.bottleneck_distance
+
+
 Distance computation
 --------------------
 
diff --git a/src/python/gudhi/hera.cc b/src/python/gudhi/hera.cc
deleted file mode 100644
index ea80a9a8..00000000
--- a/src/python/gudhi/hera.cc
+++ /dev/null
@@ -1,56 +0,0 @@
-/*    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 <wasserstein.h> // Hera
-
-#include <pybind11_diagram_utils.h>
-
-double wasserstein_distance(
-    Dgm d1, Dgm d2,
-    double wasserstein_power, double internal_p,
-    double delta)
-{
-  // I *think* the call to request() has to be before releasing the GIL.
-  auto diag1 = numpy_to_range_of_pairs(d1);
-  auto diag2 = numpy_to_range_of_pairs(d2);
-
-  py::gil_scoped_release release;
-
-  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/hera/__init__.py b/src/python/gudhi/hera/__init__.py
new file mode 100644
index 00000000..044f81cd
--- /dev/null
+++ b/src/python/gudhi/hera/__init__.py
@@ -0,0 +1,2 @@
+from .wasserstein import wasserstein_distance
+from .bottleneck import bottleneck_distance
diff --git a/src/python/gudhi/hera/bottleneck.cc b/src/python/gudhi/hera/bottleneck.cc
new file mode 100644
index 00000000..e00b4682
--- /dev/null
+++ b/src/python/gudhi/hera/bottleneck.cc
@@ -0,0 +1,45 @@
+/*    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 <bottleneck.h> // Hera
+
+#include <pybind11_diagram_utils.h>
+
+double bottleneck_distance(Dgm d1, Dgm d2, double delta)
+{
+  // I *think* the call to request() has to be before releasing the GIL.
+  auto diag1 = numpy_to_range_of_pairs(d1);
+  auto diag2 = numpy_to_range_of_pairs(d2);
+
+  py::gil_scoped_release release;
+
+  if (delta == 0)
+    return hera::bottleneckDistExact(diag1, diag2);
+  else
+    return hera::bottleneckDistApprox(diag1, diag2, delta);
+}
+
+PYBIND11_MODULE(bottleneck, m) {
+      m.def("bottleneck_distance", &bottleneck_distance,
+          py::arg("X"), py::arg("Y"),
+          py::arg("delta") = .01,
+          R"pbdoc(
+        Compute the Bottleneck 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
+            delta (float): Relative error 1+delta
+
+        Returns:
+            float: (approximate) bottleneck distance d_B(X,Y)
+    )pbdoc");
+}
diff --git a/src/python/gudhi/hera/wasserstein.cc b/src/python/gudhi/hera/wasserstein.cc
new file mode 100644
index 00000000..1a21f02f
--- /dev/null
+++ b/src/python/gudhi/hera/wasserstein.cc
@@ -0,0 +1,56 @@
+/*    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 <wasserstein.h> // Hera
+
+#include <pybind11_diagram_utils.h>
+
+double wasserstein_distance(
+    Dgm d1, Dgm d2,
+    double wasserstein_power, double internal_p,
+    double delta)
+{
+  // I *think* the call to request() has to be before releasing the GIL.
+  auto diag1 = numpy_to_range_of_pairs(d1);
+  auto diag2 = numpy_to_range_of_pairs(d2);
+
+  py::gil_scoped_release release;
+
+  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(wasserstein, 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/setup.py.in b/src/python/setup.py.in
index b9f4e3f0..9b3c7521 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -48,10 +48,12 @@ ext_modules = cythonize(ext_modules)
 
 for module in pybind11_modules:
     my_include_dirs = include_dirs + [pybind11.get_include(False), pybind11.get_include(True)]
-    if module == 'hera':
+    if module == 'hera/wasserstein':
         my_include_dirs = ['@HERA_WASSERSTEIN_INCLUDE_DIR@'] + my_include_dirs
+    elif module == 'hera/bottleneck':
+        my_include_dirs = ['@HERA_BOTTLENECK_INCLUDE_DIR@'] + my_include_dirs
     ext_modules.append(Extension(
-        'gudhi.' + module,
+        'gudhi.' + module.replace('/', '.'),
         sources = [source_dir + module + '.cc'],
         language = 'c++',
         include_dirs = my_include_dirs,
diff --git a/src/python/test/test_bottleneck_distance.py b/src/python/test/test_bottleneck_distance.py
index 70b2abad..6915bea8 100755
--- a/src/python/test/test_bottleneck_distance.py
+++ b/src/python/test/test_bottleneck_distance.py
@@ -9,6 +9,8 @@
 """
 
 import gudhi
+import gudhi.hera
+import pytest
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016 Inria"
@@ -19,5 +21,7 @@ def test_basic_bottleneck():
     diag1 = [[2.7, 3.7], [9.6, 14.0], [34.2, 34.974], [3.0, float("Inf")]]
     diag2 = [[2.8, 4.45], [9.5, 14.1], [3.2, float("Inf")]]
 
-    assert gudhi.bottleneck_distance(diag1, diag2, 0.1) == 0.8081763781405569
     assert gudhi.bottleneck_distance(diag1, diag2) == 0.75
+    assert gudhi.bottleneck_distance(diag1, diag2, 0.1) == pytest.approx(0.75, abs=0.1)
+    assert gudhi.hera.bottleneck_distance(diag1, diag2, 0) == 0.75
+    assert gudhi.hera.bottleneck_distance(diag1, diag2, 0.1) == pytest.approx(0.75, rel=0.1)
-- 
cgit v1.2.3


From 59d3fa0aa4ed6628f0dfbe3424c1d7a5c6f9a382 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Mon, 1 Jun 2020 16:05:32 +0200
Subject: Simplify setup.py to read introduction.rst

---
 CMakeGUDHIVersion.txt  | 2 +-
 src/python/setup.py.in | 6 ++----
 2 files changed, 3 insertions(+), 5 deletions(-)

(limited to 'src')

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index ffcbc53e..95e67372 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 2)
-set (GUDHI_PATCH_VERSION 0a6)
+set (GUDHI_PATCH_VERSION 0a7)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index f8eeafc4..dc163a37 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -13,7 +13,6 @@ from Cython.Build import cythonize
 from numpy import get_include as numpy_get_include
 import sys
 import pybind11
-from os import path
 
 __author__ = "Vincent Rouvreau"
 __copyright__ = "Copyright (C) 2016  Inria"
@@ -64,9 +63,8 @@ for module in pybind11_modules:
         ))
 
 # read the contents of introduction.rst
-this_directory = path.abspath(path.dirname(__file__))
-with open(path.join(this_directory, 'introduction.rst'), encoding='utf-8') as f:
-    long_description = f.read()
+with open("introduction.rst", "r") as fh:
+    long_description = fh.read()
 
 setup(
     name = 'gudhi',
-- 
cgit v1.2.3


From 18619efce47ef7fc44ba97e9b37b7f6162f5fe1b Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Thu, 4 Jun 2020 16:41:53 +0200
Subject: Workaround for ssize_t on windows

---
 src/python/gudhi/hera/bottleneck.cc | 8 ++++++++
 1 file changed, 8 insertions(+)

(limited to 'src')

diff --git a/src/python/gudhi/hera/bottleneck.cc b/src/python/gudhi/hera/bottleneck.cc
index e00b4682..f543613e 100644
--- a/src/python/gudhi/hera/bottleneck.cc
+++ b/src/python/gudhi/hera/bottleneck.cc
@@ -8,6 +8,14 @@
  *      - YYYY/MM Author: Description of the modification
  */
 
+// https://github.com/grey-narn/hera/issues/3
+// ssize_t is a non-standard type (well, posix)
+// BaseTsd.h provides SSIZE_T on windows, this one should be the same there.
+#ifdef _MSC_VER
+#include <cstddef>
+typedef std::ptrdiff_t ssize_t;
+#endif
+
 #include <bottleneck.h> // Hera
 
 #include <pybind11_diagram_utils.h>
-- 
cgit v1.2.3


From e84f5d1b3c753147ac1601537b2be15ec118144e Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Thu, 4 Jun 2020 17:01:33 +0200
Subject: user_version: don't copy hera if an external version is specified

---
 src/cmake/modules/GUDHI_third_party_libraries.cmake | 6 ++++--
 src/cmake/modules/GUDHI_user_version_target.cmake   | 7 +++++--
 2 files changed, 9 insertions(+), 4 deletions(-)

(limited to 'src')

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index d80283d2..a56a2756 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -68,8 +68,10 @@ if(CGAL_FOUND)
 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/wasserstein/include CACHE PATH "Directory where one can find Hera's wasserstein.h")
-set(HERA_BOTTLENECK_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/bottleneck/include CACHE PATH "Directory where one can find Hera's bottleneck.h")
+set(HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include)
+set(HERA_WASSERSTEIN_INCLUDE_DIR ${HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find Hera's wasserstein.h")
+set(HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/bottleneck/include)
+set(HERA_BOTTLENECK_INCLUDE_DIR ${HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find Hera's bottleneck.h")
 
 option(WITH_GUDHI_USE_TBB "Build with Intel TBB parallelization" ON)
 
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 491fa459..e4f39aae 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -67,8 +67,11 @@ 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 ${GUDHI_USER_VERSION_DIR}/ext/hera)
+if(HERA_WASSERSTEIN_INCLUDE_DIR STREQUAL HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR OR
+    HERA_BOTTLENECK_INCLUDE_DIR STREQUAL HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR)
+  add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                     copy_directory ${CMAKE_SOURCE_DIR}/ext/hera ${GUDHI_USER_VERSION_DIR}/ext/hera)
+endif()
 
 set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
 
-- 
cgit v1.2.3


From bea81f2d7bc53876a6f071c919663261314965ab Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Thu, 4 Jun 2020 17:21:05 +0200
Subject: Use ssize_t from pybind11

---
 src/python/gudhi/hera/bottleneck.cc         | 10 ++++------
 src/python/include/pybind11_diagram_utils.h |  8 ++++----
 2 files changed, 8 insertions(+), 10 deletions(-)

(limited to 'src')

diff --git a/src/python/gudhi/hera/bottleneck.cc b/src/python/gudhi/hera/bottleneck.cc
index f543613e..846a3525 100644
--- a/src/python/gudhi/hera/bottleneck.cc
+++ b/src/python/gudhi/hera/bottleneck.cc
@@ -8,18 +8,16 @@
  *      - YYYY/MM Author: Description of the modification
  */
 
+#include <pybind11_diagram_utils.h>
+
+#ifdef _MSC_VER
 // https://github.com/grey-narn/hera/issues/3
 // ssize_t is a non-standard type (well, posix)
-// BaseTsd.h provides SSIZE_T on windows, this one should be the same there.
-#ifdef _MSC_VER
-#include <cstddef>
-typedef std::ptrdiff_t ssize_t;
+using py::ssize_t;
 #endif
 
 #include <bottleneck.h> // Hera
 
-#include <pybind11_diagram_utils.h>
-
 double bottleneck_distance(Dgm d1, Dgm d2, double delta)
 {
   // I *think* the call to request() has to be before releasing the GIL.
diff --git a/src/python/include/pybind11_diagram_utils.h b/src/python/include/pybind11_diagram_utils.h
index d9627258..2d5194f4 100644
--- a/src/python/include/pybind11_diagram_utils.h
+++ b/src/python/include/pybind11_diagram_utils.h
@@ -18,8 +18,8 @@ namespace py = pybind11;
 typedef py::array_t<double> Dgm;
 
 // Get m[i,0] and m[i,1] as a pair
-static auto pairify(void* p, ssize_t h, ssize_t w) {
-  return [=](ssize_t i){
+static auto pairify(void* p, py::ssize_t h, py::ssize_t w) {
+  return [=](py::ssize_t i){
     char* birth = (char*)p + i * h;
     char* death = birth + w;
     return std::make_pair(*(double*)birth, *(double*)death);
@@ -32,8 +32,8 @@ inline auto numpy_to_range_of_pairs(py::array_t<double> dgm) {
   if((buf.ndim!=2 || buf.shape[1]!=2) && (buf.ndim!=1 || buf.shape[0]!=0))
     throw std::runtime_error("Diagram must be an array of size n x 2");
   // In the case of shape (0), avoid reading non-existing strides[1] even if we won't use it.
-  ssize_t stride1 = buf.ndim == 2 ? buf.strides[1] : 0;
-  auto cnt = boost::counting_range<ssize_t>(0, buf.shape[0]);
+  py::ssize_t stride1 = buf.ndim == 2 ? buf.strides[1] : 0;
+  auto cnt = boost::counting_range<py::ssize_t>(0, buf.shape[0]);
   return boost::adaptors::transform(cnt, pairify(buf.ptr, buf.strides[0], stride1));
   // Be careful that the returned range cannot contain references to dead temporaries.
 }
-- 
cgit v1.2.3


From 82dc35dd749a1f388be268d7a7e3bd22f18afcf7 Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Fri, 5 Jun 2020 20:16:38 +0200
Subject: Doc changes after Vincent's review

---
 src/python/doc/bottleneck_distance_user.rst | 5 +++--
 src/python/gudhi/bottleneck.cc              | 3 ++-
 src/python/gudhi/hera/bottleneck.cc         | 3 +++
 3 files changed, 8 insertions(+), 3 deletions(-)

(limited to 'src')

diff --git a/src/python/doc/bottleneck_distance_user.rst b/src/python/doc/bottleneck_distance_user.rst
index 49bd3706..6c6e08d9 100644
--- a/src/python/doc/bottleneck_distance_user.rst
+++ b/src/python/doc/bottleneck_distance_user.rst
@@ -10,7 +10,7 @@ Definition
 .. include:: bottleneck_distance_sum.inc
 
 This implementation by François Godi is based on ideas from "Geometry Helps in Bottleneck Matching and Related Problems"
-:cite:`DBLP:journals/algorithmica/EfratIK01` and requires `CGAL <installation.html#cgal>`_.
+:cite:`DBLP:journals/algorithmica/EfratIK01` and requires `CGAL <installation.html#cgal>`_ (`GPL v3 </licensing/>`_).
 
 .. autofunction:: gudhi.bottleneck_distance
 
@@ -20,7 +20,8 @@ based on "Geometry Helps to Compare Persistence Diagrams"
 :cite:`Kerber:2017:GHC:3047249.3064175` by Michael Kerber, Dmitriy
 Morozov, and Arnur Nigmetov.
 
-Beware that its approximation allows for a multiplicative error, while the function above uses an additive error.
+.. warning::
+   Beware that its approximation allows for a multiplicative error, while the function above uses an additive error.
 
 .. autofunction:: gudhi.hera.bottleneck_distance
 
diff --git a/src/python/gudhi/bottleneck.cc b/src/python/gudhi/bottleneck.cc
index 732cb9a8..59be6088 100644
--- a/src/python/gudhi/bottleneck.cc
+++ b/src/python/gudhi/bottleneck.cc
@@ -29,7 +29,8 @@ PYBIND11_MODULE(bottleneck, m) {
           py::arg("diagram_1"), py::arg("diagram_2"),
           py::arg("e") = (std::numeric_limits<double>::min)(),
           R"pbdoc(
-    This function returns the point corresponding to a given vertex.
+    Compute the Bottleneck distance between two diagrams.
+    Points at infinity and on the diagonal are supported.
 
     :param diagram_1: The first diagram.
     :type diagram_1: numpy array of shape (m,2)
diff --git a/src/python/gudhi/hera/bottleneck.cc b/src/python/gudhi/hera/bottleneck.cc
index 846a3525..0cb562ce 100644
--- a/src/python/gudhi/hera/bottleneck.cc
+++ b/src/python/gudhi/hera/bottleneck.cc
@@ -40,6 +40,9 @@ PYBIND11_MODULE(bottleneck, m) {
         Compute the Bottleneck distance between two diagrams.
         Points at infinity are supported.
 
+        .. note::
+           Points on the diagonal are not supported and must be filtered out before calling this function.
+
         Parameters:
             X (n x 2 numpy array): First diagram
             Y (n x 2 numpy array): Second diagram
-- 
cgit v1.2.3


From dacc3e363ded8b68bb4b71c1602e2c52b10b36e5 Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Fri, 5 Jun 2020 22:29:32 +0200
Subject: author, etc

---
 src/python/gudhi/hera/__init__.py | 5 +++++
 1 file changed, 5 insertions(+)

(limited to 'src')

diff --git a/src/python/gudhi/hera/__init__.py b/src/python/gudhi/hera/__init__.py
index 044f81cd..f70b92b9 100644
--- a/src/python/gudhi/hera/__init__.py
+++ b/src/python/gudhi/hera/__init__.py
@@ -1,2 +1,7 @@
 from .wasserstein import wasserstein_distance
 from .bottleneck import bottleneck_distance
+
+
+__author__ = "Marc Glisse"
+__copyright__ = "Copyright (C) 2020 Inria"
+__license__ = "MIT"
-- 
cgit v1.2.3


From d46bfa4c50cc3bb52eaee5dffc6b798b0ae236f6 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Tue, 9 Jun 2020 07:49:45 +0200
Subject: move cython from install_requires to setup_requires

---
 CMakeGUDHIVersion.txt  | 2 +-
 src/python/setup.py.in | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

(limited to 'src')

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 857b0056..d2d98dea 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 2)
-set (GUDHI_PATCH_VERSION 0a12)
+set (GUDHI_PATCH_VERSION 0a13)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index dc163a37..875f1577 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -84,6 +84,6 @@ setup(
     long_description_content_type='text/x-rst',
     long_description=long_description,
     ext_modules = ext_modules,
-    install_requires = ['cython','numpy >= 1.9',],
-    setup_requires = ['numpy >= 1.9','pybind11',],
+    install_requires = ['numpy >= 1.9',],
+    setup_requires = ['cython','numpy >= 1.9','pybind11',],
 )
-- 
cgit v1.2.3


From e4a59f9ec6685534b03474cbcfe9395d601516e2 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Thu, 11 Jun 2020 07:23:23 +0200
Subject: Add distributor the right to add dll to the package

---
 .github/workflows/pip-packaging-windows.yml |  7 ++-----
 CMakeGUDHIVersion.txt                       |  2 +-
 src/python/CMakeLists.txt                   |  5 ++++-
 src/python/gudhi/__init__.py.in             |  3 +++
 src/python/gudhi/_distributor_init.py       | 18 ++++++++++++++++++
 5 files changed, 28 insertions(+), 7 deletions(-)
 create mode 100644 src/python/gudhi/_distributor_init.py

(limited to 'src')

diff --git a/.github/workflows/pip-packaging-windows.yml b/.github/workflows/pip-packaging-windows.yml
index 95205258..fe4d0227 100644
--- a/.github/workflows/pip-packaging-windows.yml
+++ b/.github/workflows/pip-packaging-windows.yml
@@ -35,14 +35,11 @@ jobs:
           cd build
           cmake -DCMAKE_BUILD_TYPE=Release -DGMP_INCLUDE_DIR="c:/vcpkg/installed/x64-windows/include" -DGMP_LIBRARIES="c:/vcpkg/installed/x64-windows/lib/mpir.lib" -DGMP_LIBRARIES_DIR="c:/vcpkg/installed/x64-windows/lib" -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake -DPython_ADDITIONAL_VERSIONS=3 ..
           cd src/python
+          cp c:/vcpkg/installed/x64-windows/bin/mpfr.dll .libs/
+          cp c:/vcpkg/installed/x64-windows/bin/mpir.dll .libs/
           python setup.py bdist_wheel
       - name: Publish on PyPi
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
         run: python -m twine upload --repository-url https://test.pypi.org/legacy/ build/src/python/dist/*
-      - name: Upload artifacts
-        uses: actions/upload-artifact@v1
-        with:
-          name: dependencies
-          path: c:/vcpkg/installed/x64-windows/bin/
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 4ad3921d..794b6ebf 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 2)
-set (GUDHI_PATCH_VERSION 0a16)
+set (GUDHI_PATCH_VERSION 0a17)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index fee6b6f5..b35c8de7 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -235,8 +235,11 @@ if(PYTHONINTERP_FOUND)
     file(COPY "gudhi/point_cloud" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
     file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
 
-    # Other .py files
+    # Some files for pip package
     file(COPY "introduction.rst" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
+    file(COPY "gudhi/_distributor_init.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
+    file(MAKE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/gudhi/.libs")
+    message(" o o o ${CMAKE_CURRENT_BINARY_DIR}/gudhi/.libs")
 
     add_custom_command(
         OUTPUT gudhi.so
diff --git a/src/python/gudhi/__init__.py.in b/src/python/gudhi/__init__.py.in
index 79e12fbc..e4198dcf 100644
--- a/src/python/gudhi/__init__.py.in
+++ b/src/python/gudhi/__init__.py.in
@@ -10,6 +10,9 @@
 from importlib import import_module
 from sys import exc_info
 
+# Allow distributors to run custom init code
+from . import _distributor_init
+
 __author__ = "GUDHI Editorial Board"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "https://gudhi.inria.fr/licensing/"
diff --git a/src/python/gudhi/_distributor_init.py b/src/python/gudhi/_distributor_init.py
new file mode 100644
index 00000000..0ed451f9
--- /dev/null
+++ b/src/python/gudhi/_distributor_init.py
@@ -0,0 +1,18 @@
+'''
+Helper to preload windows dlls to prevent dll not found errors.
+Once a DLL is preloaded, its namespace is made available to any subsequent DLL.
+'''
+import os
+from ctypes import WinDLL
+import glob
+if os.name == 'nt':
+    # convention for storing / loading the DLL from gudhi/.libs/, if present
+    try:
+        basedir = os.path.dirname(__file__)
+    except:
+        pass
+    else:
+        libs_dir = os.path.abspath(os.path.join(basedir, '.libs'))
+        if os.path.isdir(libs_dir):
+            for filename in glob.glob(os.path.join(libs_dir, '*dll')):
+                WinDLL(os.path.abspath(filename))
-- 
cgit v1.2.3


From 0f7cc48907e1b28e114d37e3bd30a2237d9f6c8c Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Thu, 11 Jun 2020 08:09:01 +0200
Subject: cannot import WinDLL from ctypes on non-windows systems

---
 CMakeGUDHIVersion.txt                 | 2 +-
 src/python/gudhi/_distributor_init.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

(limited to 'src')

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index fab3ee75..21f3d58c 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 2)
-set (GUDHI_PATCH_VERSION 0a18)
+set (GUDHI_PATCH_VERSION 0a19)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/gudhi/_distributor_init.py b/src/python/gudhi/_distributor_init.py
index 0ed451f9..6f3dc8a2 100644
--- a/src/python/gudhi/_distributor_init.py
+++ b/src/python/gudhi/_distributor_init.py
@@ -3,8 +3,6 @@ Helper to preload windows dlls to prevent dll not found errors.
 Once a DLL is preloaded, its namespace is made available to any subsequent DLL.
 '''
 import os
-from ctypes import WinDLL
-import glob
 if os.name == 'nt':
     # convention for storing / loading the DLL from gudhi/.libs/, if present
     try:
@@ -14,5 +12,7 @@ if os.name == 'nt':
     else:
         libs_dir = os.path.abspath(os.path.join(basedir, '.libs'))
         if os.path.isdir(libs_dir):
+            from ctypes import WinDLL
+            import glob
             for filename in glob.glob(os.path.join(libs_dir, '*dll')):
                 WinDLL(os.path.abspath(filename))
-- 
cgit v1.2.3


From aec85514aeaeac51d1589e6a24c4c393df892f91 Mon Sep 17 00:00:00 2001
From: ROUVREAU Vincent <vincent.rouvreau@inria.fr>
Date: Thu, 11 Jun 2020 12:03:49 +0200
Subject: Upload dlls from gudhi directory

---
 .github/workflows/pip-packaging-windows.yml |  4 ++--
 CMakeGUDHIVersion.txt                       |  2 +-
 src/python/CMakeLists.txt                   |  3 ---
 src/python/gudhi/__init__.py.in             |  3 ---
 src/python/gudhi/_distributor_init.py       | 18 ------------------
 src/python/setup.py.in                      |  1 +
 6 files changed, 4 insertions(+), 27 deletions(-)
 delete mode 100644 src/python/gudhi/_distributor_init.py

(limited to 'src')

diff --git a/.github/workflows/pip-packaging-windows.yml b/.github/workflows/pip-packaging-windows.yml
index f229b74f..d529d4f3 100644
--- a/.github/workflows/pip-packaging-windows.yml
+++ b/.github/workflows/pip-packaging-windows.yml
@@ -35,8 +35,8 @@ jobs:
           cd build
           cmake -DCMAKE_BUILD_TYPE=Release -DGMP_INCLUDE_DIR="c:/vcpkg/installed/x64-windows/include" -DGMP_LIBRARIES="c:/vcpkg/installed/x64-windows/lib/mpir.lib" -DGMP_LIBRARIES_DIR="c:/vcpkg/installed/x64-windows/lib" -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake -DPython_ADDITIONAL_VERSIONS=3 ..
           cd src/python
-          cp c:/vcpkg/installed/x64-windows/bin/mpfr.dll gudhi/.libs/
-          cp c:/vcpkg/installed/x64-windows/bin/mpir.dll gudhi/.libs/
+          cp c:/vcpkg/installed/x64-windows/bin/mpfr.dll gudhi/
+          cp c:/vcpkg/installed/x64-windows/bin/mpir.dll gudhi/
           python setup.py bdist_wheel
       - name: Publish on PyPi
         env:
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 21f3d58c..85d69190 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,6 +1,6 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 2)
-set (GUDHI_PATCH_VERSION 0a19)
+set (GUDHI_PATCH_VERSION 0a20)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index b35c8de7..966f5ef0 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -237,9 +237,6 @@ if(PYTHONINTERP_FOUND)
 
     # Some files for pip package
     file(COPY "introduction.rst" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
-    file(COPY "gudhi/_distributor_init.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi")
-    file(MAKE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/gudhi/.libs")
-    message(" o o o ${CMAKE_CURRENT_BINARY_DIR}/gudhi/.libs")
 
     add_custom_command(
         OUTPUT gudhi.so
diff --git a/src/python/gudhi/__init__.py.in b/src/python/gudhi/__init__.py.in
index e4198dcf..79e12fbc 100644
--- a/src/python/gudhi/__init__.py.in
+++ b/src/python/gudhi/__init__.py.in
@@ -10,9 +10,6 @@
 from importlib import import_module
 from sys import exc_info
 
-# Allow distributors to run custom init code
-from . import _distributor_init
-
 __author__ = "GUDHI Editorial Board"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "https://gudhi.inria.fr/licensing/"
diff --git a/src/python/gudhi/_distributor_init.py b/src/python/gudhi/_distributor_init.py
deleted file mode 100644
index 6f3dc8a2..00000000
--- a/src/python/gudhi/_distributor_init.py
+++ /dev/null
@@ -1,18 +0,0 @@
-'''
-Helper to preload windows dlls to prevent dll not found errors.
-Once a DLL is preloaded, its namespace is made available to any subsequent DLL.
-'''
-import os
-if os.name == 'nt':
-    # convention for storing / loading the DLL from gudhi/.libs/, if present
-    try:
-        basedir = os.path.dirname(__file__)
-    except:
-        pass
-    else:
-        libs_dir = os.path.abspath(os.path.join(basedir, '.libs'))
-        if os.path.isdir(libs_dir):
-            from ctypes import WinDLL
-            import glob
-            for filename in glob.glob(os.path.join(libs_dir, '*dll')):
-                WinDLL(os.path.abspath(filename))
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 875f1577..07ad818f 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -86,4 +86,5 @@ setup(
     ext_modules = ext_modules,
     install_requires = ['numpy >= 1.9',],
     setup_requires = ['cython','numpy >= 1.9','pybind11',],
+    package_data={"": ["*.dll"], },
 )
-- 
cgit v1.2.3


From b50a41f53af6937c6f030d08f2b969b9024e17ac Mon Sep 17 00:00:00 2001
From: Marc Glisse <marc.glisse@inria.fr>
Date: Fri, 12 Jun 2020 23:10:37 +0200
Subject: Mention pip package

---
 src/python/doc/installation.rst | 37 ++++++++++++++++++++++++++++++++-----
 1 file changed, 32 insertions(+), 5 deletions(-)

(limited to 'src')

diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst
index a66e910e..525ca84e 100644
--- a/src/python/doc/installation.rst
+++ b/src/python/doc/installation.rst
@@ -5,20 +5,47 @@
 Installation
 ############
 
-Conda
-*****
-The easiest way to install the Python version of GUDHI is using
-`conda <https://gudhi.inria.fr/conda/>`_.
+Packages
+********
+The easiest way to install the Python version of GUDHI is using pre-built packages.
+We recommend `conda <https://gudhi.inria.fr/conda/>`_
+
+.. code-block:: bash
+
+    conda install -c conda-forge gudhi
+
+Gudhi is also available on `PyPI <https://pypi.org/project/gudhi/>`_
+
+.. code-block:: bash
+
+    pip install gudhi
+
+Third party packages are also available, for instance on Debian or Ubuntu
+
+.. code-block:: bash
+
+    apt install python3-gudhi
+
+In all cases, you may still want to install some of the optional `run time dependencies`_.
 
 Compiling
 *********
+These instructions are for people who want to compile gudhi from source, they are
+unnecessary if you installed a binary package of Gudhi as above. They assume that
+you have downloaded a `release <https://github.com/GUDHI/gudhi-devel/releases>`_,
+with a name like `gudhi.3.2.0.tar.gz`, then run `tar xf gudhi.3.2.0.tar.gz`, which
+created a directory `gudhi.3.2.0`, hereinafter referred to as `/path-to-gudhi/`.
+If you are instead using a git checkout, beware that the paths are a bit
+different, and in particular the `python/` subdirectory is actually `src/python/`
+there.
+
 The library uses c++14 and requires `Boost <https://www.boost.org/>`_ :math:`\geq` 1.56.0,
 `CMake <https://www.cmake.org/>`_ :math:`\geq` 3.1  to generate makefiles,
 `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 2017.
+Studio 2017 or later.
 
 On `Windows <https://wiki.python.org/moin/WindowsCompilers>`_ , only Python
 :math:`\geq` 3.5 are available because of the required Visual Studio version.
-- 
cgit v1.2.3