Merge pull request #700 from VincentRouvreau/cite_gudhi_biblio

Proposal for how_to_cite_gudhi update

5 files changed, 151 insertions, 56 deletions

diff --git a/biblio/how_to_cite_gudhi.bib.in b/biblio/how_to_cite_gudhi.bib.in
index 579dbf41..a1a971fc 100644
--- a/biblio/how_to_cite_gudhi.bib.in
+++ b/biblio/how_to_cite_gudhi.bib.in
@@ -7,6 +7,16 @@
 , url =    "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/"
 }
 
+@incollection{gudhi:CubicalComplex
+, author =  "Pawel Dlotko"
+, title =   "Cubical complex"
+, publisher =  "{GUDHI Editorial Board}"
+, edition =     "{@GUDHI_VERSION@}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cubical__complex.html"
+, year =        @GUDHI_VERSION_YEAR@
+}
+
 @incollection{gudhi:FilteredComplexes
 , author =  "Cl\'ement Maria"
 , title =   "Filtered Complexes"
@@ -17,33 +27,33 @@
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:PersistentCohomology
-, author =  "Cl\'ement Maria"
-, title =   "Persistent Cohomology"
+@incollection{gudhi:ToplexMap
+, author =  "Fran{{\c{c}}ois Godi"
+, title =   "Toplex map"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__persistent__cohomology.html"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__toplex__map.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:Contraction
+@incollection{gudhi:SkeletonBlocker
 , author =  "David Salinas"
-, title =   "Contraction"
+, title =   "Skeleton-Blocker"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__contr.html"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__skbl.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:SkeletonBlocker
+@incollection{gudhi:Contraction
 , author =  "David Salinas"
-, title =   "Skeleton-Blocker"
+, title =   "Contraction"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__skbl.html"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__contr.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
 
@@ -57,13 +67,33 @@
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:CubicalComplex
-, author =  "Pawel Dlotko"
-, title =   "Cubical complex"
+@incollection{gudhi:CechComplex
+, author =  "Vincent Rouvreau, Hind Montassif"
+, title =   "\v{C}ech complex"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cubical__complex.html"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cech__complex.html"
+, year =        @GUDHI_VERSION_YEAR@
+}
+
+@incollection{gudhi:RipsComplex
+, author =  "Cl\'ement Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse"
+, title =   "Rips complex"
+, publisher =  "{GUDHI Editorial Board}"
+, edition =     "{@GUDHI_VERSION@}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__rips__complex.html"
+, year =        @GUDHI_VERSION_YEAR@
+}
+
+@incollection{gudhi:Collapse
+, author =  "Siddharth Pritam, Marc Glisse"
+, title =   "Edge collapse"
+, publisher =  "{GUDHI Editorial Board}"
+, edition =     "{@GUDHI_VERSION@}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__edge__collapse.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
 
@@ -77,23 +107,23 @@
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:SubSampling
-, author =  "Cl\'ement Jamin and Siargey Kachanovich"
-, title =   "Subsampling"
+@incollection{gudhi:CoverComplex
+, author =  "Mathieu Carri\`ere"
+, title =   "Cover complex"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__subsampling.html"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cover__complex.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:SpatialSearching
-, author =  "Cl\'ement Jamin"
-, title =   "Spatial searching"
+@incollection{gudhi:CoxeterTriangulation
+, author =  "Siargey Kachanovich"
+, title =   "Coxeter triangulation"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__spatial__searching.html"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cover__complex.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
 
@@ -107,13 +137,13 @@
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:RipsComplex
-, author =  "Cl\'ement Maria and Pawel Dlotko and Vincent Rouvreau and Marc Glisse"
-, title =   "Rips complex"
+@incollection{gudhi:PersistentCohomology
+, author =  "Cl\'ement Maria"
+, title =   "Persistent Cohomology"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__rips__complex.html"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__persistent__cohomology.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
 
@@ -127,42 +157,106 @@
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:cython
-, author =  "Vincent Rouvreau"
-, title =   "Cython interface"
+@incollection{gudhi:PersistenceRepresentations
+, author =  "Pawel Dlotko"
+, title =   "Persistence representations"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group___persistence__representations.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:CoverComplex
-, author =  "Mathieu Carri\`ere"
-, title =   "Cover complex"
+@incollection{gudhi:SubSampling
+, author =  "Cl\'ement Jamin, Siargey Kachanovich"
+, title =   "Subsampling"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cover__complex.html"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__subsampling.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:PersistenceRepresentations
-, author =  "Pawel Dlotko"
-, title =   "Persistence representations"
+@incollection{gudhi:SpatialSearching
+, author =  "Cl\'ement Jamin"
+, title =   "Spatial searching"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group___persistence__representations.html"
+, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__spatial__searching.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
 
-@incollection{gudhi:Collapse
-, author =  "Siddharth Pritam and Marc Glisse"
-, title =   "Edge collapse"
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Python specific gudhi modules
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+@incollection{gudhi:WeightedRipsComplex
+, author =  "Rapha\"el Tinarrage, Yuichi Ike, Masatoshi Takenouchi"
+, title =   "Weighted Rips Complex"
 , publisher =  "{GUDHI Editorial Board}"
 , edition =     "{@GUDHI_VERSION@}"
 , booktitle =   "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__edge__collapse.html"
+, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/rips_complex_user.html#weighted-rips-complex"
+, year =        @GUDHI_VERSION_YEAR@
+}
+
+@incollection{gudhi:DTMRipsComplex
+, author =  "Yuichi Ike"
+, title =   "DTM Rips Complex"
+, publisher =  "{GUDHI Editorial Board}"
+, edition =     "{@GUDHI_VERSION@}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/rips_complex_user.html#dtm-rips-complex"
+, year =        @GUDHI_VERSION_YEAR@
+}
+
+@incollection{gudhi:WassersteinDistance
+, author =  "Theo Lacombe, Marc Glisse"
+, title =   "Wasserstein distance"
+, publisher =  "{GUDHI Editorial Board}"
+, edition =     "{@GUDHI_VERSION@}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/wasserstein_distance_user.html"
+, year =        @GUDHI_VERSION_YEAR@
+}
+
+@incollection{gudhi:PersistenceRepresentationsScikitlearnInterface
+, author =  "Mathieu Carri\`ere, Gard Spreemann, Wojciech Reise"
+, title =   "Persistence representations scikit-learn like interface"
+, publisher =  "{GUDHI Editorial Board}"
+, edition =     "{@GUDHI_VERSION@}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/representations.html"
+, year =        @GUDHI_VERSION_YEAR@
+}
+
+@incollection{gudhi:Atol
+, author =  "Martin Royer"
+, title =   "Measure Vectorization for Automatic Topologically-Oriented Learning"
+, publisher =  "{GUDHI Editorial Board}"
+, edition =     "{@GUDHI_VERSION@}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/representations.html#gudhi.representations.vector_methods.Atol"
+, year =        @GUDHI_VERSION_YEAR@
+}
+
+@incollection{gudhi:DistanceToMeasure
+, author =  "Marc Glisse"
+, title =   "Distance to measure"
+, publisher =  "{GUDHI Editorial Board}"
+, edition =     "{@GUDHI_VERSION@}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/point_cloud.html#module-gudhi.point_cloud.knn"
+, year =        @GUDHI_VERSION_YEAR@
+}
+
+@incollection{gudhi:PersistenceBasedClustering
+, author =  "Marc Glisse"
+, title =   "persistence-based clustering"
+, publisher =  "{GUDHI Editorial Board}"
+, edition =     "{@GUDHI_VERSION@}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/clustering.html"
 , year =        @GUDHI_VERSION_YEAR@
 }
diff --git a/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h
index 595fb64b..73093c07 100644
--- a/src/Cech_complex/doc/Intro_cech_complex.h
+++ b/src/Cech_complex/doc/Intro_cech_complex.h
@@ -17,7 +17,7 @@ namespace cech_complex {
 
 /**  \defgroup cech_complex Čech complex
  * 
- * \author    Vincent Rouvreau
+ * \author    Vincent Rouvreau, Hind montassif
  * 
  * @{
  * 
diff --git a/src/Cech_complex/include/gudhi/Cech_complex.h b/src/Cech_complex/include/gudhi/Cech_complex.h
index 625f7c9c..dbdf5e93 100644
--- a/src/Cech_complex/include/gudhi/Cech_complex.h
+++ b/src/Cech_complex/include/gudhi/Cech_complex.h
@@ -1,11 +1,12 @@
 /*    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):       Vincent Rouvreau
+ *    Author(s):       Vincent Rouvreau, Hind Montassif
  *
  *    Copyright (C) 2018 Inria
  *
  *    Modification(s):
  *      - YYYY/MM Author: Description of the modification
+ *      - 2022/02 Hind Montassif : Replace MiniBall with Sphere_circumradius
  */
 
 #ifndef CECH_COMPLEX_H_
diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md
index ce903405..9b7c2853 100644
--- a/src/common/doc/main_page.md
+++ b/src/common/doc/main_page.md
@@ -178,7 +178,7 @@
     The set of all simplices is filtered by the radius of their minimal enclosing ball.
     </td>
     <td width="15%">
-      <b>Author:</b> Vincent Rouvreau<br>
+      <b>Author:</b> Vincent Rouvreau, Hind Montassif<br>
       <b>Introduced in:</b> GUDHI 2.2.0<br>
       <b>Copyright:</b> MIT [(LGPL v3)](../../licensing/)<br>
       <b>Requires:</b> \ref cgal
diff --git a/src/python/doc/representations_sum.inc b/src/python/doc/representations_sum.inc
index 4298aea9..9515f044 100644
--- a/src/python/doc/representations_sum.inc
+++ b/src/python/doc/representations_sum.inc
@@ -1,14 +1,14 @@
 .. table::
    :widths: 30 40 30
 
-   +------------------------------------------------------------------+----------------------------------------------------------------+-------------------------------------------------------------+
-   | .. figure::                                                      | Vectorizations, distances and kernels that work on persistence | :Author: Mathieu Carrière, Martin Royer                     |
-   |      img/sklearn-tda.png                                         | diagrams, compatible with scikit-learn.                        |                                                             |
-   |                                                                  |                                                                | :Since: GUDHI 3.1.0                                         |
-   |                                                                  |                                                                |                                                             |
-   |                                                                  |                                                                | :License: MIT                                               |
-   |                                                                  |                                                                |                                                             |
-   |                                                                  |                                                                | :Requires: `Scikit-learn <installation.html#scikit-learn>`_ |
-   +------------------------------------------------------------------+----------------------------------------------------------------+-------------------------------------------------------------+
-   | * :doc:`representations`                                                                                                                                                                        |
-   +------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------+
+   +------------------------------------------------------------------+----------------------------------------------------------------+-------------------------------------------------------------------------+
+   | .. figure::                                                      | Vectorizations, distances and kernels that work on persistence | :Author: Mathieu Carrière, Martin Royer, Gard Spreemann, Wojciech Reise |
+   |      img/sklearn-tda.png                                         | diagrams, compatible with scikit-learn.                        |                                                                         |
+   |                                                                  |                                                                | :Since: GUDHI 3.1.0                                                     |
+   |                                                                  |                                                                |                                                                         |
+   |                                                                  |                                                                | :License: MIT                                                           |
+   |                                                                  |                                                                |                                                                         |
+   |                                                                  |                                                                | :Requires: `Scikit-learn <installation.html#scikit-learn>`_             |
+   +------------------------------------------------------------------+----------------------------------------------------------------+-------------------------------------------------------------------------+
+   | * :doc:`representations`                                                                                                                                                                                    |
+   +------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+