From bfb5b9c373454c62f5ff5be3b4a69428ce6708b0 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau Date: Wed, 20 Dec 2023 10:54:04 +0100 Subject: [PATCH] Version 3.9.0rc1 --- .github/changelog.md | 52 +++++++++++++++++++++++++++++++++++++++++-- CMakeGUDHIVersion.txt | 2 +- 2 files changed, 51 insertions(+), 3 deletions(-) diff --git a/.github/changelog.md b/.github/changelog.md index 7b459d3f4f..6375375830 100644 --- a/.github/changelog.md +++ b/.github/changelog.md @@ -1,6 +1,56 @@ 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) ----------- @@ -8,8 +58,6 @@ 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) diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index a4b081117b..6d048a5db8 100644 --- a/CMakeGUDHIVersion.txt +++ b/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}")