Merge pull request #1010 from VincentRouvreau/gudhi_3.9.0rc1

Version 3.9.0rc1

.github/changelog.md

@@ -1,15 +1,63 @@
 Release History
 ===============
 
+
+[Release 3.9.0](https://github.com/GUDHI/gudhi-devel/releases/tag/tags%2Fgudhi-release-3.9.0)
+-----------
+
+Release date: December 2023
+
+Below is a list of changes made since GUDHI 3.8.0:
+
+- [CubicalPersistence](https://gudhi.inria.fr/python/latest/cubical_complex_sklearn_itf_ref.html)
+     - Much faster implementation for the 2d case with input from top-dimensional cells.
+
+- [Simplex_tree](https://gudhi.inria.fr/doc/latest/group__simplex__tree.html)
+     - A helper `for_each_simplex` that applies a given function object on each simplex
+     - A new method `num_simplices_by_dimension` is now available thanks to this helper.
+     - A `clear` method to empty the data stucture.
+     - A new argument `ignore_infinite_values` for `initialize_filtration` method to skip infinite values. As a side effect, this change enhances the persistence computation.
+     - `Simplex_tree_options_full_featured` has been renamed `Simplex_tree_options_default` and `Simplex_tree_options_python`.
+     These are respectively the default options used by the `Simplex_tree` and by the python interface of the `SimplexTree` (as before this version).
+     - From GUDHI 3.9.0, `Simplex_tree_options_full_featured` now activates `link_nodes_by_label` and `stable_simplex_handles` (making it slower, except for browsing cofaces).
+
+     | Simplex_tree_options_*  | :warning: full_featured | default | python | minimal |
+     | ---- | ---- | ---- | ---- | ---- |
+     | store_key              | 1       | 1      | 1      | 0 |
+     | store_filtration       | 1       | 1      | 1      | 0 |
+     | contiguous_vertices    | 0       | 0      | 0      | 0 |
+     | link_nodes_by_label    | ***1*** | 0      | 0      | 0 |
+     | stable_simplex_handles | ***1*** | 0      | 0      | 0 |
+     | Filtration_value       | double  | double | double |   |
+
+- [Simplex_tree options](https://gudhi.inria.fr/doc/latest/struct_simplex_tree_options.html)
+     - A new option `link_nodes_by_label` to speed up cofaces and stars access, when set to true.
+     - A new option `stable_simplex_handles` to keep Simplex handles valid even after insertions or removals, when set to true.
+
+- [Čech complex](https://gudhi.inria.fr/doc/latest/group__cech__complex.html)
+     - A function `assign_MEB_filtration` that assigns to each simplex a filtration value equal to the squared radius of its minimal enclosing ball (MEB), given a simplicial complex and an embedding of its vertices. Applied on a Delaunay triangulation, it computes the Delaunay-Čech filtration.
+
+- [Edge collapse](https://gudhi.inria.fr/python/latest/edge_collapse.html)
+     - A Python function `reduce_graph` to simplify a clique filtration (represented as a sparse weighted graph), while preserving its persistent homology.
+
+- [Mapper/GIC/Nerve complexes](https://gudhi.inria.fr/python/latest/cover_complex_sklearn_isk_ref.html)
+     - A new method `save_to_html` to ease the Keppler Mapper visualization
+
+- Installation
+     - Boost ≥ 1.71.0 is now required (was ≥ 1.66.0).
+     - cython >= 3.0.0 is now supported.
+     - Python 3.12 pip package.
+
+- Miscellaneous
+     - The [list of bugs that were solved since GUDHI-3.8.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.9.0+is%3Aclosed) is available on GitHub.
+
 [Release 3.8.0](https://github.com/GUDHI/gudhi-devel/releases/tag/tags%2Fgudhi-release-3.8.0)
 -----------
 
 Release date: April 2023
 
 As a major new feature, the GUDHI library now offers Perslay, a Tensorflow model for the representations module, scikit-learn like interfaces for Cover Complexes, a new function to compute persistence of a function on ℝ and the possibility to build a Cubical Complex as a lower-star filtration from vertices.
 
-We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz).
-
 Below is a list of changes made since GUDHI 3.7.1:
 
 - [Perslay](https://gudhi.inria.fr/python/latest/representations_tflow_itf_ref.html)

CMakeGUDHIVersion.txt

@@ -2,7 +2,7 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 9)
 # 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 0a1)
+set (GUDHI_PATCH_VERSION 0rc1)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")