Merge remote-tracking branch 'upstream/master' into wbary-theo

13 files changed, 52 insertions, 12 deletions

diff --git a/.github/next_release.md b/.github/next_release.md
index 3166b0a8..83b98a1c 100644
--- a/.github/next_release.md
+++ b/.github/next_release.md
@@ -9,6 +9,7 @@ Below is a list of changes made since GUDHI 3.1.1:
 
 - [Wassertein distance](https://gudhi.inria.fr/python/latest/wasserstein_distance_user.html)
      - An another implementation comes from Hera (BSD-3-Clause) which is based on [Geometry Helps to Compare Persistence Diagrams](http://doi.acm.org/10.1145/3064175) by Michael Kerber, Dmitriy Morozov, and Arnur Nigmetov.
+     - `gudhi.wasserstein.wasserstein_distance` has now an option to return the optimal matching that achieves the distance between the two diagrams.
 
 - [Module](link)
      - ...
diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst
index 60319e84..265a82d2 100644
--- a/src/python/doc/alpha_complex_user.rst
+++ b/src/python/doc/alpha_complex_user.rst
@@ -204,8 +204,8 @@ the program output is:
    [3, 6] -> 30.25
 
 CGAL citations
-==============
+--------------
 
 .. bibliography:: ../../biblio/how_to_cite_cgal.bib
-   :filter: docnames
+   :filter: docname in docnames
    :style: unsrt
diff --git a/src/python/doc/bottleneck_distance_user.rst b/src/python/doc/bottleneck_distance_user.rst
index 9435c7f1..206fcb63 100644
--- a/src/python/doc/bottleneck_distance_user.rst
+++ b/src/python/doc/bottleneck_distance_user.rst
@@ -65,3 +65,10 @@ The output is:
 
     Bottleneck distance approximation = 0.81
     Bottleneck distance value = 0.75
+
+Bibliography
+------------
+
+.. bibliography:: ../../biblio/bibliography.bib
+   :filter: docname in docnames
+   :style: unsrt
diff --git a/src/python/doc/cubical_complex_user.rst b/src/python/doc/cubical_complex_user.rst
index 93ca6b24..e8c94bf6 100644
--- a/src/python/doc/cubical_complex_user.rst
+++ b/src/python/doc/cubical_complex_user.rst
@@ -160,8 +160,8 @@ Examples.
 End user programs are available in python/example/ folder.
 
 Bibliography
-============
+------------
 
 .. bibliography:: ../../biblio/bibliography.bib
-   :filter: docnames
+   :filter: docname in docnames
    :style: unsrt
diff --git a/src/python/doc/index.rst b/src/python/doc/index.rst
index 0e484483..c153cdfc 100644
--- a/src/python/doc/index.rst
+++ b/src/python/doc/index.rst
@@ -91,5 +91,5 @@ Bibliography
 ************
 
 .. bibliography:: ../../biblio/bibliography.bib
-   :filter: docnames
+   :filter: docname in docnames
    :style: unsrt
diff --git a/src/python/doc/nerve_gic_complex_ref.rst b/src/python/doc/nerve_gic_complex_ref.rst
index abde2e8c..6a81b7af 100644
--- a/src/python/doc/nerve_gic_complex_ref.rst
+++ b/src/python/doc/nerve_gic_complex_ref.rst
@@ -12,3 +12,10 @@ Cover complexes reference manual
    :show-inheritance:
 
    .. automethod:: gudhi.CoverComplex.__init__
+
+Bibliography
+------------
+
+.. bibliography:: ../../biblio/bibliography.bib
+   :filter: docname in docnames
+   :style: unsrt
diff --git a/src/python/doc/nerve_gic_complex_user.rst b/src/python/doc/nerve_gic_complex_user.rst
index 9101f45d..f709ce91 100644
--- a/src/python/doc/nerve_gic_complex_user.rst
+++ b/src/python/doc/nerve_gic_complex_user.rst
@@ -313,3 +313,10 @@ the program outputs again SC.dot which gives the following visualization after u
     :alt: Visualization with neato
 
     Visualization with neato
+
+Bibliography
+------------
+
+.. bibliography:: ../../biblio/bibliography.bib
+   :filter: docname in docnames
+   :style: unsrt
diff --git a/src/python/doc/persistent_cohomology_user.rst b/src/python/doc/persistent_cohomology_user.rst
index 5f931b3a..506fa3a7 100644
--- a/src/python/doc/persistent_cohomology_user.rst
+++ b/src/python/doc/persistent_cohomology_user.rst
@@ -113,8 +113,8 @@ We provide several example files: run these examples with -h for details on thei
     * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
 
 Bibliography
-============
+------------
 
 .. bibliography:: ../../biblio/bibliography.bib
-   :filter: docnames
+   :filter: docname in docnames
    :style: unsrt
diff --git a/src/python/doc/rips_complex_user.rst b/src/python/doc/rips_complex_user.rst
index 8efb12e6..c4bbcfb6 100644
--- a/src/python/doc/rips_complex_user.rst
+++ b/src/python/doc/rips_complex_user.rst
@@ -347,3 +347,10 @@ until dimension 1 - one skeleton graph in other words), the output is:
     points in the persistence diagram will be under the diagonal, and
     bottleneck distance and persistence graphical tool will not work properly,
     this is a known issue.
+
+Bibliography
+------------
+
+.. bibliography:: ../../biblio/bibliography.bib
+   :filter: docname in docnames
+   :style: unsrt
diff --git a/src/python/doc/simplex_tree_user.rst b/src/python/doc/simplex_tree_user.rst
index 3df7617f..1b272c35 100644
--- a/src/python/doc/simplex_tree_user.rst
+++ b/src/python/doc/simplex_tree_user.rst
@@ -66,3 +66,10 @@ The output is:
     ([1, 2], 4.0)
     ([1], 0.0)
     ([2], 4.0)
+
+Bibliography
+------------
+
+.. bibliography:: ../../biblio/bibliography.bib
+   :filter: docname in docnames
+   :style: unsrt
diff --git a/src/python/doc/tangential_complex_user.rst b/src/python/doc/tangential_complex_user.rst
index 852cf5b6..cf8199cc 100644
--- a/src/python/doc/tangential_complex_user.rst
+++ b/src/python/doc/tangential_complex_user.rst
@@ -197,8 +197,8 @@ The output is:
 
 
 Bibliography
-============
+------------
 
 .. bibliography:: ../../biblio/bibliography.bib
-   :filter: docnames
+   :filter: docname in docnames
    :style: unsrt
diff --git a/src/python/doc/wasserstein_distance_user.rst b/src/python/doc/wasserstein_distance_user.rst
index c5c250b5..b821b6fa 100644
--- a/src/python/doc/wasserstein_distance_user.rst
+++ b/src/python/doc/wasserstein_distance_user.rst
@@ -91,7 +91,6 @@ The output is:
     point 2 in dgm1 is matched to the diagonal
     point 1 in dgm2 is matched to the diagonal
 
-
 Barycenters
 -----------
 
@@ -166,4 +165,9 @@ The output is:
      [0.7375     0.7625    ]
      [0.2375     0.2625    ]]
 
+Bibliography
+------------
 
+.. bibliography:: ../../biblio/bibliography.bib
+   :filter: docname in docnames
+   :style: unsrt
diff --git a/src/python/doc/witness_complex_user.rst b/src/python/doc/witness_complex_user.rst
index 7087fa98..799f5444 100644
--- a/src/python/doc/witness_complex_user.rst
+++ b/src/python/doc/witness_complex_user.rst
@@ -128,8 +128,8 @@ Here is an example of constructing a strong witness complex filtration and compu
 * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
 
 Bibliography
-============
+------------
 
 .. bibliography:: ../../biblio/bibliography.bib
-   :filter: docnames
+   :filter: docname in docnames
    :style: unsrt