From 82befbd4731b7e12f9e09a9c3bb1277b71044273 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 21 May 2020 08:15:43 +0200 Subject: Next release --- .github/next_release.md | 50 ++++++++++--------------------------------------- 1 file changed, 10 insertions(+), 40 deletions(-) (limited to '.github/next_release.md') diff --git a/.github/next_release.md b/.github/next_release.md index d3c9ce68..a2805a55 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -1,50 +1,19 @@ -We are pleased to announce the release 3.2.0 of the GUDHI library. +We are pleased to announce the release 3.X.X of the GUDHI library. -As a major new feature, the GUDHI library now offers a Python interface to [Hera](https://bitbucket.org/grey_narn/hera/src/master/) to compute the Wasserstein distance. -[PyBind11](https://github.com/pybind/pybind11) is now required to build the Python module. +As a major new feature, the GUDHI library now offers ... -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.3.2.0.tar.gz). +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 3.1.1: +Below is a list of changes made since GUDHI 3.X-1.X-1: -- Point cloud utilities - - A new module [Time Delay Embedding](https://gudhi.inria.fr/python/latest/point_cloud.html#time-delay-embedding) - to embed time-series data in the R^d according to [Takens' Embedding Theorem](https://en.wikipedia.org/wiki/Takens%27s_theorem) - and obtain the coordinates of each point. - - A new module [K Nearest Neighbors](https://gudhi.inria.fr/python/latest/point_cloud.html#k-nearest-neighbors) - that wraps several implementations for computing the k nearest neighbors in a point set. - - A new module [Distance To Measure](https://gudhi.inria.fr/python/latest/point_cloud.html#distance-to-measure) - to compute the distance to the empirical measure defined by a point set +- [Module](link) + - ... -- [Persistence representations](https://gudhi.inria.fr/python/latest/representations.html) - - Interface to Wasserstein distances. - -- Rips complex - - A new module [Weighted Rips Complex](https://gudhi.inria.fr/python/latest/rips_complex_user.html#weighted-rips-complex) - to construct a simplicial complex from a distance matrix and weights on vertices. - -- [Wassertein distance](https://gudhi.inria.fr/python/latest/wasserstein_distance_user.html) - - An [another implementation](https://gudhi.inria.fr/python/latest/wasserstein_distance_user.html#hera) - 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. - - A new module [Barycenters](https://gudhi.inria.fr/python/latest/wasserstein_distance_user.html#barycenters) - to estimate the Frechet mean (aka Wasserstein barycenter) between persistence diagrams. - -- [Simplex tree](https://gudhi.inria.fr/python/latest/simplex_tree_ref.html) - - Extend filtration method to compute extended persistence - - Flag and lower star persistence pairs generators - - A new interface to filtration, simplices and skeleton getters to return an iterator - -- [Alpha complex](https://gudhi.inria.fr/doc/latest/group__alpha__complex.html) - - Improve computations (cache circumcenters computation and point comparison improvement) - -- [Persistence graphical tools](https://gudhi.inria.fr/python/latest/persistence_graphical_tools_user.html) - - New rendering option proposed (use LaTeX style, add grey block, improved positioning of labels, etc.). - - Can now handle (N x 2) numpy arrays as input +- [Module](link) + - ... - Miscellaneous - - The [list of bugs that were solved since GUDHI-3.2.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.2.0+is%3Aclosed) is available on GitHub. + - The [list of bugs that were solved since GUDHI-3.X-1.X-1](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.1.1+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. @@ -56,3 +25,4 @@ We provide [bibtex entries](https://gudhi.inria.fr/doc/latest/_citation.html) fo 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/). + -- cgit v1.2.3 From f7f856de8bc1cf861645f8c8c8a72a7392ef543e Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 2 Jul 2020 11:24:47 +0200 Subject: Update next_release --- .github/next_release.md | 35 ++++++++++++++++++++++++++--------- CMakeGUDHIVersion.txt | 4 +++- 2 files changed, 29 insertions(+), 10 deletions(-) (limited to '.github/next_release.md') diff --git a/.github/next_release.md b/.github/next_release.md index a2805a55..188dd87f 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -1,19 +1,36 @@ -We are pleased to announce the release 3.X.X of the GUDHI library. +We are pleased to announce the release 3.3.0 of the GUDHI library. -As a major new feature, the GUDHI library now offers ... +As a major new feature, the GUDHI library now offers -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). +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.3.3.0.tar.gz). -Below is a list of changes made since GUDHI 3.X-1.X-1: +Below is a list of changes made since GUDHI 3.2.0: -- [Module](link) - - ... +- [DTM density estimator](https://gudhi.inria.fr/python/latest/point_cloud.html#module-gudhi.point_cloud.dtm) + - Python implementation of a density estimator based on the distance to the empirical measure defined by a point set. -- [Module](link) - - ... +- [DTM Rips complex](https://gudhi.inria.fr/python/latest/rips_complex_user.html#dtm-rips-complex) + - This Python implementation constructs a weighted Rips complex giving larger weights to outliers, + which reduces their impact on the persistence diagram + +- [Alpha complex](https://gudhi.inria.fr/python/latest/alpha_complex_user.html) - Python interface improvements + - 'fast' and 'exact' computations + - Delaunay complex construction by not setting filtration values + - Use the specific 3d alpha complex automatically to make the computations faster + +- [Clustering](https://gudhi.inria.fr/python/latest/clustering.html) + - Python implementation of [ToMATo](https://doi.org/10.1145/2535927), a persistence-based clustering algorithm + +- [Bottleneck distance](https://gudhi.inria.fr/python/latest/bottleneck_distance_user.html) + - Python interface to [hera](https://github.com/grey-narn/hera)'s bottleneck distance + +- Representations - Python interface change + - [Wasserstein metrics](https://gudhi.inria.fr/python/latest/representations.html#gudhi.representations.metrics.WassersteinDistance) + is now [hera](https://github.com/grey-narn/hera) by default - Miscellaneous - - The [list of bugs that were solved since GUDHI-3.X-1.X-1](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.1.1+is%3Aclosed) is available on GitHub. + - The [list of bugs that were solved since GUDHI-3.2.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.3.0+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. diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt index b9895bb1..a78b8adc 100644 --- a/CMakeGUDHIVersion.txt +++ b/CMakeGUDHIVersion.txt @@ -1,6 +1,8 @@ +# Must be conform to pep440 - https://www.python.org/dev/peps/pep-0440/#pre-releases set (GUDHI_MAJOR_VERSION 3) set (GUDHI_MINOR_VERSION 3) -set (GUDHI_PATCH_VERSION 0.rc1) +# 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 0rc1) set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION}) message(STATUS "GUDHI version : ${GUDHI_VERSION}") -- cgit v1.2.3 From 8a7d277a60a44c2bda62a4e57a6c29304b1c81c0 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 2 Jul 2020 13:31:01 +0200 Subject: Missing sentence end --- .github/next_release.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.github/next_release.md') diff --git a/.github/next_release.md b/.github/next_release.md index 188dd87f..cc868db7 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -1,6 +1,6 @@ We are pleased to announce the release 3.3.0 of the GUDHI library. -As a major new feature, the GUDHI library now offers +As a major new feature, the GUDHI library now offers a persistence-based clustering algorithm and weighted Rips complex using DTM. 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.3.3.0.tar.gz). -- cgit v1.2.3 From e44b0a88e2241f81b51b9060f73ac86f53c9cfc1 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 2 Jul 2020 21:23:50 +0200 Subject: [skip ci] modify release note --- .github/next_release.md | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) (limited to '.github/next_release.md') diff --git a/.github/next_release.md b/.github/next_release.md index cc868db7..e73f7c96 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -1,8 +1,10 @@ We are pleased to announce the release 3.3.0 of the GUDHI library. -As a major new feature, the GUDHI library now offers a persistence-based clustering algorithm and weighted Rips complex using DTM. +As a major new feature, the GUDHI library now offers a persistence-based clustering algorithm, weighted Rips complex using DTM +and edge collapse. -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.3.3.0.tar.gz). +The GUDHI library is hosted on GitHub, 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.3.3.0.tar.gz). Below is a list of changes made since GUDHI 3.2.0: @@ -21,6 +23,10 @@ Below is a list of changes made since GUDHI 3.2.0: - [Clustering](https://gudhi.inria.fr/python/latest/clustering.html) - Python implementation of [ToMATo](https://doi.org/10.1145/2535927), a persistence-based clustering algorithm +- [Edge Collapse](https://gudhi.inria.fr/doc/latest/group__edge__collapse.html) of a filtered flag complex + - This C++ implementation reduces a filtration of Vietoris-Rips complex from its graph to another smaller + flag filtration with the same persistence. + - [Bottleneck distance](https://gudhi.inria.fr/python/latest/bottleneck_distance_user.html) - Python interface to [hera](https://github.com/grey-narn/hera)'s bottleneck distance -- cgit v1.2.3 From 5fc667a7cbc61649801074f884752bbc33e47b0d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 4 Aug 2020 05:47:38 +0200 Subject: Add Atol to next release --- .github/next_release.md | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) (limited to '.github/next_release.md') diff --git a/.github/next_release.md b/.github/next_release.md index e73f7c96..14546066 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -30,8 +30,13 @@ Below is a list of changes made since GUDHI 3.2.0: - [Bottleneck distance](https://gudhi.inria.fr/python/latest/bottleneck_distance_user.html) - Python interface to [hera](https://github.com/grey-narn/hera)'s bottleneck distance -- Representations - Python interface change - - [Wasserstein metrics](https://gudhi.inria.fr/python/latest/representations.html#gudhi.representations.metrics.WassersteinDistance) +- Persistence representations + - [Atol](https://gudhi.inria.fr/python/latest/representations.html#gudhi.representations.vector_methods.Atol) + is integrated in finite vectorisation methods. This + [article](https://www.fujitsu.com/global/about/resources/news/press-releases/2020/0316-01.html) talks about + applications using Atol. This module was originally available at + [https://github.com/martinroyer/atol](https://github.com/martinroyer/atol) + - Python interface change: [Wasserstein metrics](https://gudhi.inria.fr/python/latest/representations.html#gudhi.representations.metrics.WassersteinDistance) is now [hera](https://github.com/grey-narn/hera) by default - Miscellaneous -- cgit v1.2.3