Merge pull request #675 from VincentRouvreau/release_note_3_6_0

Release note 3.6.0

9 files changed, 72 insertions, 47 deletions

diff --git a/.github/next_release.md b/.github/next_release.md
index f8085513..8e1e12da 100644
--- a/.github/next_release.md
+++ b/.github/next_release.md
@@ -1,39 +1,59 @@
-We are pleased to announce the release 3.X.X of the GUDHI library.
+We are pleased to announce the release 3.6.0.rc1 of the GUDHI library.
 
-As a major new feature, the GUDHI library now offers ...
+As a major new feature, the GUDHI library now offers automatic differentiation for the computation of
+persistence diagrams, Cubical complex persistence scikit-learn like interface, datasets fetch methods,
+and weighted version for alpha complex in any dimension D.
 
-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).
+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).
+For further information, please visit the [GUDHI web site](https://gudhi.inria.fr/).
 
+# GUDHI 3.6.0rc1 Release Notes
 Below is a list of changes made since GUDHI 3.5.0:
 
+- TensorFlow 2 models that can handle automatic differentiation for the computation of persistence diagrams:
+     - [Cubical complex](https://gudhi.inria.fr/python/latest/cubical_complex_tflow_itf_ref.html)
+     - [lower-star persistence on simplex trees](https://gudhi.inria.fr/python/latest/ls_simplex_tree_tflow_itf_ref.html)
+     - [Rips complex](https://gudhi.inria.fr/python/latest/rips_complex_tflow_itf_ref.html)
+
+- [Cubical complex](https://gudhi.inria.fr/python/latest/cubical_complex_sklearn_itf_ref.html)
+     - Cubical complex persistence scikit-learn like interface
+
+- [Datasets](https://gudhi.inria.fr/python/latest/datasets.html)
+     - `datasets.remote.fetch_bunny` and `datasets.remote.fetch_spiral_2d` allows to fetch datasets from [GUDHI-data](https://github.com/GUDHI/gudhi-data)
+
 - [Alpha complex](https://gudhi.inria.fr/python/latest/alpha_complex_user.html)
-     - the python weighted version for alpha complex is now available in any dimension D.
+     - python weighted version for alpha complex is now available in any dimension D.
      - `alpha_complex = gudhi.AlphaComplex(off_file='/data/points/tore3D_300.off')` is deprecated, please use [read_points_from_off_file](https://gudhi.inria.fr/python/latest/point_cloud.html#gudhi.read_points_from_off_file) instead.
 
+- [Edge collapse](https://gudhi.inria.fr/doc/latest/group__edge__collapse.html)
+     - rewriting of the module to improve performance
+
+- [Čech complex](https://gudhi.inria.fr/doc/latest/group__edge__collapse.html)
+     - rewriting of the module to improve performance
+
 - [Representations](https://gudhi.inria.fr/python/latest/representations.html#gudhi.representations.vector_methods.BettiCurve)
      - A more flexible Betti curve class capable of computing exact curves
 
+- [C++ documentation](https://gudhi.inria.fr/doc/latest/)
+     - upgrade and improve performance with new doxygen features
+
 - [Simplex tree](https://gudhi.inria.fr/python/latest/simplex_tree_ref.html)
-     - `__deepcopy__`, `copy` and copy constructors
+     - `__deepcopy__`, `copy` and copy constructors for python module
+     - `expansion_with_blockers` python interface
 
 - Installation
      - Boost ≥ 1.66.0 is now required (was ≥ 1.56.0).
      - Python >= 3.5 and cython >= 0.27 are now required.
 
-- [Module](link)
-     - ...
-
 - Miscellaneous
      - The [list of bugs that were solved since GUDHI-3.5.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.6.0+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/).
+## Contributors
 
+- @albert-github
+- @gspr
+- @Hind-M
+- @MathieuCarriere
+- @mglisse
+- @Soriano-Trigueros
+- @VincentRouvreau
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index b7f93799..ca2d24c1 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -2,7 +2,7 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 6)
 # GUDHI_PATCH_VERSION can be 'ZaN' for Alpha release, 'ZbN' for Beta release, 'ZrcN' for release candidate or 'Z' for a final release.
-set (GUDHI_PATCH_VERSION 0a0)
+set (GUDHI_PATCH_VERSION 0rc1)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")
diff --git a/src/python/doc/cubical_complex_sklearn_itf_ref.rst b/src/python/doc/cubical_complex_sklearn_itf_ref.rst
index 05ffdd0c..2fb8ec6a 100644
--- a/src/python/doc/cubical_complex_sklearn_itf_ref.rst
+++ b/src/python/doc/cubical_complex_sklearn_itf_ref.rst
@@ -9,7 +9,7 @@ Cubical complex persistence scikit-learn like interface
    :width: 100%
    :header-rows: 0
 
-   * - :Since: GUDHI 3.5.0
+   * - :Since: GUDHI 3.6.0
      - :License: MIT
      - :Requires: `Scikit-learn <installation.html#scikit-learn>`_
 
diff --git a/src/python/doc/cubical_complex_sum.inc b/src/python/doc/cubical_complex_sum.inc
index f1cf25d4..b27843e5 100644
--- a/src/python/doc/cubical_complex_sum.inc
+++ b/src/python/doc/cubical_complex_sum.inc
@@ -10,8 +10,10 @@
    | * :doc:`cubical_complex_user`                                            | * :doc:`cubical_complex_ref`                                                                                               |
    |                                                                          | * :doc:`periodic_cubical_complex_ref`                                                                                      |
    +--------------------------------------------------------------------------+--------------------------------------------------------------+-------------------------------------------------------------+
-   |                                                                          | * :doc:`cubical_complex_tflow_itf_ref`                       | :requires: `TensorFlow <installation.html#tensorflow>`_     |
-   |                                                                          |                                                              |                                                             |
+   | .. image::                                                               | * :doc:`cubical_complex_tflow_itf_ref`                       | :requires: `TensorFlow <installation.html#tensorflow>`_     |
+   |      img/tensorflow.png                                                  |                                                              |                                                             |
+   |      :target: https://www.tensorflow.org                                 |                                                              |                                                             |
+   |      :height: 30                                                         |                                                              |                                                             |
    +--------------------------------------------------------------------------+--------------------------------------------------------------+-------------------------------------------------------------+
    | .. image::                                                               | * :doc:`cubical_complex_sklearn_itf_ref`                     | :Requires: `Scikit-learn <installation.html#scikit-learn>`_ |
    |      img/sklearn.png                                                     |                                                              |                                                             |
diff --git a/src/python/doc/differentiation_sum.inc b/src/python/doc/differentiation_sum.inc
index 3aec33df..140cf180 100644
--- a/src/python/doc/differentiation_sum.inc
+++ b/src/python/doc/differentiation_sum.inc
@@ -1,8 +1,8 @@
 .. list-table::
-   :widths: 40 30 30
+   :width: 100%
    :header-rows: 0
 
-   * - :Since: GUDHI 3.5.0
+   * - :Since: GUDHI 3.6.0
      - :License: MIT
      - :Requires: `TensorFlow <installation.html#tensorflow>`_
 
diff --git a/src/python/doc/persistent_cohomology_user.rst b/src/python/doc/persistent_cohomology_user.rst
index a3f294b2..39744b95 100644
--- a/src/python/doc/persistent_cohomology_user.rst
+++ b/src/python/doc/persistent_cohomology_user.rst
@@ -6,19 +6,24 @@ Persistent cohomology user manual
 =================================
 Definition
 ----------
-=====================================  =====================================  =====================================
-:Author: Clément Maria                 :Since: GUDHI PYTHON 2.0.0             :License: GPL v3
-=====================================  =====================================  =====================================
-
-+-----------------------------------------------------------------+-----------------------------------------------------------------------+
-|  :doc:`persistent_cohomology_user`                              | Please refer to each data structure that contains persistence         |
-|                                                                 | feature for reference:                                                |
-|                                                                 |                                                                       |
-|                                                                 | * :doc:`simplex_tree_ref`                                             |
-|                                                                 | * :doc:`cubical_complex_ref`                                          |
-|                                                                 | * :doc:`periodic_cubical_complex_ref`                                 |
-+-----------------------------------------------------------------+-----------------------------------------------------------------------+
 
+.. list-table::
+   :width: 100%
+   :header-rows: 0
+
+   * - :Author: Clément Maria
+     - :Since: GUDHI 2.0.0
+     - :License: MIT
+
+.. list-table::
+   :width: 100%
+   :header-rows: 0
+
+   * - :doc:`persistent_cohomology_user`
+     - Please refer to each data structure that contains persistence feature for reference:
+           * :doc:`simplex_tree_ref`
+           * :doc:`cubical_complex_ref`
+           * :doc:`periodic_cubical_complex_ref`
 
 Computation of persistent cohomology using the algorithm of :cite:`DBLP:journals/dcg/SilvaMV11` and
 :cite:`DBLP:conf/compgeom/DeyFW14` and the Compressed Annotation Matrix implementation of
diff --git a/src/python/doc/rips_complex_sum.inc b/src/python/doc/rips_complex_sum.inc
index 6931ebee..2b125e54 100644
--- a/src/python/doc/rips_complex_sum.inc
+++ b/src/python/doc/rips_complex_sum.inc
@@ -12,6 +12,8 @@
    +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------------------+
    | * :doc:`rips_complex_user`                                     | * :doc:`rips_complex_ref`                                                                                                                                 |
    +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------------------+
-   |                                                                | * :doc:`rips_complex_tflow_itf_ref`                                    | :requires: `TensorFlow <installation.html#tensorflow>`_                          |
-   |                                                                |                                                                        |                                                                                  |
+   | .. image::                                                     | * :doc:`rips_complex_tflow_itf_ref`                                    | :requires: `TensorFlow <installation.html#tensorflow>`_                          |
+   |      img/tensorflow.png                                        |                                                                        |                                                                                  |
+   |      :target: https://www.tensorflow.org                       |                                                                        |                                                                                  |
+   |      :height: 30                                               |                                                                        |                                                                                  |
    +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------------------+
diff --git a/src/python/doc/rips_complex_user.rst b/src/python/doc/rips_complex_user.rst
index 27d218d4..c41a7803 100644
--- a/src/python/doc/rips_complex_user.rst
+++ b/src/python/doc/rips_complex_user.rst
@@ -7,13 +7,7 @@ Rips complex user manual
 Definition
 ----------
 
-================================================================================  ================================  ======================
-:Authors: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse, Yuichi Ike  :Since: GUDHI 2.0.0               :License: GPL v3
-================================================================================  ================================  ======================
-
-+-------------------------------------------+----------------------------------------------------------------------+
-| :doc:`rips_complex_user`                  | :doc:`rips_complex_ref`                                              |
-+-------------------------------------------+----------------------------------------------------------------------+
+.. include:: rips_complex_sum.inc
 
 The `Rips complex <https://en.wikipedia.org/wiki/Vietoris%E2%80%93Rips_complex>`_ is a simplicial complex that
 generalizes proximity (:math:`\varepsilon`-ball) graphs to higher dimensions. The vertices correspond to the input
diff --git a/src/python/doc/simplex_tree_sum.inc b/src/python/doc/simplex_tree_sum.inc
index 3ad1292c..6b534c9e 100644
--- a/src/python/doc/simplex_tree_sum.inc
+++ b/src/python/doc/simplex_tree_sum.inc
@@ -11,6 +11,8 @@
    +----------------------------------------------------------------+------------------------------------------------------------------------+---------------------------------------------------------+
    | * :doc:`simplex_tree_user`                                     | * :doc:`simplex_tree_ref`                                                                                                        |
    +----------------------------------------------------------------+------------------------------------------------------------------------+---------------------------------------------------------+
-   |                                                                | * :doc:`ls_simplex_tree_tflow_itf_ref`                                 | :requires: `TensorFlow <installation.html#tensorflow>`_ |
-   |                                                                |                                                                        |                                                         |
+   | .. image::                                                     | * :doc:`ls_simplex_tree_tflow_itf_ref`                                 | :requires: `TensorFlow <installation.html#tensorflow>`_ |
+   |      img/tensorflow.png                                        |                                                                        |                                                         |
+   |      :target: https://www.tensorflow.org                       |                                                                        |                                                         |
+   |      :height: 30                                               |                                                                        |                                                         |
    +----------------------------------------------------------------+------------------------------------------------------------------------+---------------------------------------------------------+