From a08971af8be1405c91429cf52e4c3301ffd50945 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 11 Aug 2020 17:13:22 +0200 Subject: Next release + version creation improvement --- .github/next_release.md | 47 +++++++++-------------------------------------- 1 file changed, 9 insertions(+), 38 deletions(-) (limited to '.github/next_release.md') diff --git a/.github/next_release.md b/.github/next_release.md index 14546066..cd2376eb 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -1,47 +1,19 @@ -We are pleased to announce the release 3.3.0 of the GUDHI library. +We are pleased to announce the release 3.4.0 of the GUDHI library. -As a major new feature, the GUDHI library now offers a persistence-based clustering algorithm, weighted Rips complex using DTM -and edge collapse. +As a major new feature, the GUDHI library now offers ... -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). +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.3.4.0.tar.gz). -Below is a list of changes made since GUDHI 3.2.0: +Below is a list of changes made since GUDHI 3.3.0: -- [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 - -- [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 - -- 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 +- [Module](link) + - ... - Miscellaneous - - The [list of bugs that were solved since GUDHI-3.2.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.3.0+is%3Aclosed) - is available on GitHub. + - The [list of bugs that were solved since GUDHI-3.3.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.4.0+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. @@ -53,4 +25,3 @@ 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 c6619e0207abf0fb5198b66a8d8f00f975c3da84 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 18 Sep 2020 16:27:49 +0200 Subject: Use CGAL 5.1 by default on dockers. Update next release --- .github/next_release.md | 6 +++--- Dockerfile_for_circleci_image | 10 +++++++++- Dockerfile_for_pip | 8 ++++---- Dockerfile_gudhi_installation | 12 ++++++++++++ 4 files changed, 28 insertions(+), 8 deletions(-) (limited to '.github/next_release.md') diff --git a/.github/next_release.md b/.github/next_release.md index cd2376eb..190f8408 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -1,13 +1,13 @@ We are pleased to announce the release 3.4.0 of the GUDHI library. -As a major new feature, the GUDHI library now offers ... +As a major new feature, the GUDHI library now offers dD weighted alpha complex, ... 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.3.4.0.tar.gz). Below is a list of changes made since GUDHI 3.3.0: -- [Module](link) - - ... +- [Alpha complex](https://gudhi.inria.fr/doc/latest/group__alpha__complex.html) + - the C++ weighted version for alpha complex is now available in dimension D. - [Module](link) - ... diff --git a/Dockerfile_for_circleci_image b/Dockerfile_for_circleci_image index 87f57071..ec1b8ff8 100644 --- a/Dockerfile_for_circleci_image +++ b/Dockerfile_for_circleci_image @@ -41,7 +41,6 @@ RUN apt-get install -y make \ libgmp3-dev \ libmpfr-dev \ libtbb-dev \ - libcgal-dev \ locales \ python3 \ python3-pip \ @@ -51,6 +50,15 @@ RUN apt-get install -y make \ pkg-config \ curl +RUN curl -LO "https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz" \ + && tar xf CGAL-5.1.tar.xz \ + && mkdir build \ + && cd build \ + && cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \ + && make install \ + && cd .. \ + && rm -rf build CGAL-5.1 + ADD .github/build-requirements.txt / ADD .github/test-requirements.txt / diff --git a/Dockerfile_for_pip b/Dockerfile_for_pip index 8f60e37c..83c6d684 100644 --- a/Dockerfile_for_pip +++ b/Dockerfile_for_pip @@ -23,14 +23,14 @@ RUN git clone -b boost-1.73.0 --depth 1 https://github.com/boostorg/boost.git \ && cd .. \ && rm -rf boost -RUN wget https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-5.0.2/CGAL-5.0.2.tar.xz \ - && tar xf CGAL-5.0.2.tar.xz \ +RUN wget https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz \ + && tar xf CGAL-5.1.tar.xz \ && mkdir build \ && cd build \ - && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.0.2/ \ + && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \ && make install \ && cd .. \ - && rm -rf build CGAL-5.0.2 + && rm -rf build CGAL-5.1 ADD .github/build-requirements.txt / diff --git a/Dockerfile_gudhi_installation b/Dockerfile_gudhi_installation index 92430fce..ebd21f8d 100644 --- a/Dockerfile_gudhi_installation +++ b/Dockerfile_gudhi_installation @@ -23,6 +23,9 @@ ENV LANG en_US.UTF-8 ENV LANGUAGE en_US:en ENV LC_ALL en_US.UTF-8 +# Update again +RUN apt-get update + # Required for Gudhi compilation RUN apt-get install -y make \ g++ \ @@ -47,6 +50,15 @@ RUN apt-get install -y make \ pkg-config \ curl +RUN curl -LO "https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz" \ + && tar xf CGAL-5.1.tar.xz \ + && mkdir build \ + && cd build \ + && cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \ + && make install \ + && cd .. \ + && rm -rf build CGAL-5.1 + RUN pip3 install \ numpy \ matplotlib \ -- cgit v1.2.3 From c1579e92d6cc78958522604769b0bc595c5f0eae Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Sun, 1 Nov 2020 00:13:10 +0100 Subject: release notes --- .github/next_release.md | 3 +++ 1 file changed, 3 insertions(+) (limited to '.github/next_release.md') diff --git a/.github/next_release.md b/.github/next_release.md index cd2376eb..54f389d1 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -12,6 +12,9 @@ Below is a list of changes made since GUDHI 3.3.0: - [Module](link) - ... +- [Subsampling](https://gudhi.inria.fr/doc/latest/group__subsampling.html) + - The C++ function `choose_n_farthest_points()` now takes a distance function instead of a kernel as first argument, users can replace `k` with `k.squared_distance_d_object()` in each call in their code. + - Miscellaneous - The [list of bugs that were solved since GUDHI-3.3.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.4.0+is%3Aclosed) is available on GitHub. -- cgit v1.2.3 From ed925ed2068623ea4bacc539084deda1ebf95344 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 14 Dec 2020 11:27:14 +0100 Subject: Release note 3.4.0 --- .github/next_release.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to '.github/next_release.md') diff --git a/.github/next_release.md b/.github/next_release.md index 7e7fe03b..96886627 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -9,8 +9,9 @@ Below is a list of changes made since GUDHI 3.3.0: - [Alpha complex](https://gudhi.inria.fr/doc/latest/group__alpha__complex.html) - the C++ weighted version for alpha complex is now available in dimension D. -- [Module](link) - - ... +- Simplex tree [C++](https://gudhi.inria.fr/doc/latest/class_gudhi_1_1_simplex__tree.html) [Python](http://gudhi.gforge.inria.fr/python/latest/simplex_tree_ref.html) + - A new method to reset the filtrations + - A new method to get the boundaries of a simplex - [Subsampling](https://gudhi.inria.fr/doc/latest/group__subsampling.html) - The C++ function `choose_n_farthest_points()` now takes a distance function instead of a kernel as first argument, users can replace `k` with `k.squared_distance_d_object()` in each call in their code. -- cgit v1.2.3 From 8a6f8fab73050a540b8b21e580b697f172165399 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 14 Dec 2020 11:31:36 +0100 Subject: teasing --- .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 96886627..d8f53f0f 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -1,6 +1,6 @@ We are pleased to announce the release 3.4.0 of the GUDHI library. -As a major new feature, the GUDHI library now offers dD weighted alpha complex, ... +As a major new feature, the GUDHI library now offers dD weighted alpha complex, pip and conda packages for Python 3.9. 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.3.4.0.tar.gz). -- cgit v1.2.3 From 0ef1266a5357f85322ceb1b0aedb431efadd7b6c Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 15 Dec 2020 15:33:15 +0100 Subject: release note review: 'in any dimension' --- .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 d8f53f0f..5a74966d 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -7,7 +7,7 @@ We are now using GitHub to develop the GUDHI library, do not hesitate to [fork t Below is a list of changes made since GUDHI 3.3.0: - [Alpha complex](https://gudhi.inria.fr/doc/latest/group__alpha__complex.html) - - the C++ weighted version for alpha complex is now available in dimension D. + - the C++ weighted version for alpha complex is now available in any dimension D. - Simplex tree [C++](https://gudhi.inria.fr/doc/latest/class_gudhi_1_1_simplex__tree.html) [Python](http://gudhi.gforge.inria.fr/python/latest/simplex_tree_ref.html) - A new method to reset the filtrations -- cgit v1.2.3