merge upstream

.circleci/config.yml

@@ -6,7 +6,7 @@ jobs:
   examples:
     docker:
       # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_circleci_image
-      - image: gudhi/ci_for_gudhi:latest
+      - image: gudhi/ci_for_gudhi:2024.06.02
     steps:
       - checkout
       - run:
@@ -25,7 +25,7 @@ jobs:
 
   tests:
     docker:
-      - image: gudhi/ci_for_gudhi:latest
+      - image: gudhi/ci_for_gudhi:2024.06.02
     steps:
       - checkout
       - run:
@@ -42,9 +42,28 @@ jobs:
             make all
             ctest --output-on-failure
 
+  debug_tests:
+    docker:
+      - image: gudhi/ci_for_gudhi:2024.06.02
+    steps:
+      - checkout
+      - run:
+          name: Checkout submodules
+          command: |
+            git submodule sync
+            git submodule update --init
+      - run:
+          name: Build and test unitary tests
+          command: |
+            mkdir build
+            cd build
+            cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS=-fsanitize=address -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF ..
+            make all
+            ctest --output-on-failure
+
   utils:
     docker:
-      - image: gudhi/ci_for_gudhi:latest
+      - image: gudhi/ci_for_gudhi:2024.06.02
     steps:
       - checkout
       - run:
@@ -63,7 +82,8 @@ jobs:
 
   python:
     docker:
-      - image: gudhi/ci_for_gudhi:latest
+      - image: gudhi/ci_for_gudhi:2024.06.02
+    resource_class: large # Delaunay complex requires about 5 Gb of RAM to compile
     steps:
       - checkout
       - run:
@@ -80,7 +100,7 @@ jobs:
             cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version ..
             make user_version
             cd version
-            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 -DWITH_GUDHI_REMOTE_TEST=ON .
+            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DWITH_GUDHI_REMOTE_TEST=ON .
             cd python
             python3 setup.py build_ext --inplace
             ctest --output-on-failure
@@ -99,7 +119,7 @@ jobs:
 
   doxygen:
     docker:
-      - image: gudhi/doxygen_for_gudhi:latest
+      - image: gudhi/doxygen_for_gudhi:2024.06.01
     steps:
       - checkout
       - run:
@@ -129,7 +149,7 @@ jobs:
 
   bibliography:
     docker:
-      - image: gudhi/doxygen_for_gudhi:latest
+      - image: gudhi/doxygen_for_gudhi:2024.06.01
     steps:
       - checkout
       - run:
@@ -153,7 +173,7 @@ jobs:
   examples_without_cgal_eigen:
     docker:
       # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_circleci_image_without_cgal
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -172,7 +192,7 @@ jobs:
 
   tests_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -191,7 +211,7 @@ jobs:
 
   utils_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -210,7 +230,7 @@ jobs:
 
   python_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -223,7 +243,7 @@ jobs:
           command: |
             mkdir build
             cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON ..
             cd src/python
             python3 setup.py build_ext --inplace
             ctest --output-on-failure
@@ -233,7 +253,7 @@ jobs:
 
   examples_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -252,7 +272,7 @@ jobs:
 
   tests_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -271,7 +291,7 @@ jobs:
 
   utils_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -290,7 +310,7 @@ jobs:
 
   python_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -303,7 +323,7 @@ jobs:
           command: |
             mkdir build
             cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/eigen-3.3.9 -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+            cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/eigen-3.3.9 -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON ..
             cd src/python
             python3 setup.py build_ext --inplace
             ctest --output-on-failure
@@ -322,6 +342,7 @@ workflows:
       - python_without_cgal
       - examples
       - tests
+      - debug_tests
       - utils
       - python
       - doxygen

.github/changelog.md

@@ -1,15 +1,102 @@
 Release History
 ===============
 
+[Release 3.10.1](https://github.com/GUDHI/gudhi-devel/releases/tag/tags%2Fgudhi-release-3.10.1)
+-----------
+
+Release date: June 2024
+
+Below is a list of changes made since GUDHI 3.10.1:
+
+Only bug fixes have been implemented for this minor version.
+
+The [list of bugs that were solved](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.10.1+is%3Aclosed) is available on GitHub.
+
+[Release 3.10.0](https://github.com/GUDHI/gudhi-devel/releases/tag/tags%2Fgudhi-release-3.10.0)
+-----------
+
+Release date: June 2024
+
+Below is a list of changes made since GUDHI 3.9.0:
+
+- [Persistence matrix](https://gudhi.inria.fr/doc/latest/group__persistence__matrix.html)
+     > Matrix API is in a beta version and may change in incompatible ways in the near future.
+     - Matrix structure for filtered complexes with multiple functionnalities related to persistence homology, such as
+     representative cycles computation or vineyards. 
+
+- [Rips complex](https://gudhi.inria.fr/python/latest/rips_complex_sklearn_itf_ref.html)
+     - Rips complex persistence scikit-learn like interface
+
+- [Čech complex](https://gudhi.inria.fr/cechcomplex/)
+     - A new utility to compute the Delaunay-Čech filtration on a Delaunay triangulation.
+
+- Installation
+     - CGAL ≥ 5.1.0 is now required (was ≥ 4.11.0).
+     - Eigen3 ≥ 3.3.0 is now required (was ≥ 3.1.0).
+
+- Maintenance
+     - Some bug fix for CGAL ≥ 6.0, NumPy ≥ 2.0, Scikit-learn ≥ 1.4, Matplotlib ≥ 3.6 and TensorFlow ≥ 2.16.
+
+- Miscellaneous
+     - The [list of bugs that were solved since GUDHI-3.9.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.10.0+is%3Aclosed) is available on GitHub.
+
+
+[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)

.github/code_conventions.md

@@ -18,7 +18,6 @@
 * Example files should be called `example_[what_it_is].cpp`. E.g. `example_sparsify_point_set.cpp`
 
 ### In CMakeLists.txt files:
-* The name of the "project" should be in this form: `Package_[tests|examples|…]`. E.g. `project(Simplex_tree_examples)`.
 * The name if each "target" (first parameter of add_executable) should be in this form: `Package_{name of the cpp file without extension}`. E.g `add_executable(Subsampling_test_sparsify_point_set test_sparsify_point_set.cpp)`.
 
 ### Code style

.github/for_maintainers/new_gudhi_version_creation.md

@@ -25,14 +25,14 @@ nor [unlabelled closed PRs](https://github.com/GUDHI/gudhi-devel/pulls?q=is%3Apr
 **Edit the file CMakeGUDHIVersion.txt**, and increment major, minor, or patch version number, in function of the version new delivery.
 ```bash
 # cf. .gitignore - ignore this if it is a fresh clone version
-rm -rf data/points/COIL_database/lucky_cat.off_dist data/points/COIL_database/lucky_cat.off_sc.dot data/points/KleinBottle5D.off_dist data/points/KleinBottle5D.off_sc.dot data/points/human.off_dist data/points/human.off_sc.off data/points/human.off_sc.txt src/python/test/__pycache__
+rm -rf data/points/COIL_database/lucky_cat.off_dist data/points/COIL_database/lucky_cat.off_sc.dot data/points/KleinBottle5D.off_dist data/points/KleinBottle5D.off_sc.dot data/points/human.off_dist data/points/human.off_sc.off data/points/human.off_sc.txt src/python/test/__pycache__ src/python/gudhi/*.cpp
 ```
 
 Checkin the modifications, build and test the version:
 ```bash
 git submodule update --init
 rm -rf build; mkdir build; cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_REMOTE_TEST=ON -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON  -DUSER_VERSION_DIR=gudhi.@GUDHI_VERSION@ -DPython_ADDITIONAL_VERSIONS=3 ..
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_REMOTE_TEST=ON -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON  -DUSER_VERSION_DIR=gudhi.@GUDHI_VERSION@ ..
 make user_version
 date +"%d-%m-%Y-%T" > gudhi.@GUDHI_VERSION@/timestamp.txt
 tar -czvf gudhi.@GUDHI_VERSION@.tar.gz gudhi.@GUDHI_VERSION@
@@ -54,7 +54,7 @@ mkdir gudhi.doc.@GUDHI_VERSION@
 ```bash
 cd gudhi.@GUDHI_VERSION@
 rm -rf build; mkdir build; cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_EXAMPLE=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_EXAMPLE=ON ..
 make doxygen && grep warning doxygen.log
 ```
 

.github/for_maintainers/next_release_template.md

@@ -4,7 +4,7 @@ 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).
 
-Below is a list of changes made since GUDHI 3.X-1.X-1:
+Below is a list of changes:
 
 - [Module](link)
      - **...**
@@ -13,7 +13,7 @@ Below is a list of changes made since GUDHI 3.X-1.X-1:
      - **...**
 
 - 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](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.

.github/for_maintainers/switcher.json

@@ -1,9 +1,24 @@
 [
     {
-        "name": "v3.8.0 (latest)",
-        "version": "3.8.0",
+        "name": "v3.10.1 (latest)",
+        "version": "3.10.1",
         "url": "https://gudhi.inria.fr/python/latest/"
     },
+    {
+        "name": "v3.10.0",
+        "version": "3.10.0",
+        "url": "https://gudhi.inria.fr/python/3.10.0/"
+    },
+    {
+        "name": "v3.9.0",
+        "version": "3.9.0",
+        "url": "https://gudhi.inria.fr/python/3.9.0/"
+    },
+    {
+        "name": "v3.8.0",
+        "version": "3.8.0",
+        "url": "https://gudhi.inria.fr/python/3.8.0/"
+    },
     {
         "name": "v3.7.1",
         "version": "3.7.1",
@@ -69,4 +84,4 @@
         "version": "2.0.0",
         "url": "https://gudhi.inria.fr/python/2.0.0/"
     }
-]
+]