merge upstream

Author: hschreiber

.circleci/config.yml

@@ -1,12 +1,11 @@
 version: 2.0
 jobs:
-
-### With all third parties
+  ### With all third parties
 
   examples:
     docker:
       # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_circleci_image
-      - image: gudhi/ci_for_gudhi:2024.06.02
+      - image: gudhi/ci_for_gudhi:2024.09.01
     steps:
       - checkout
       - run:
@@ -25,7 +24,7 @@ jobs:
 
   tests:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.06.02
+      - image: gudhi/ci_for_gudhi:2024.09.01
     steps:
       - checkout
       - run:
@@ -44,7 +43,7 @@ jobs:
 
   debug_tests:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.06.02
+      - image: gudhi/ci_for_gudhi:2024.09.01
     steps:
       - checkout
       - run:
@@ -63,7 +62,7 @@ jobs:
 
   utils:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.06.02
+      - image: gudhi/ci_for_gudhi:2024.09.01
     steps:
       - checkout
       - run:
@@ -82,7 +81,7 @@ jobs:
 
   python:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.06.02
+      - image: gudhi/ci_for_gudhi:2024.09.01
     resource_class: large # Delaunay complex requires about 5 Gb of RAM to compile
     steps:
       - checkout
@@ -94,7 +93,6 @@ jobs:
       - run:
           name: Build and test python module. Generates and tests the python documentation
           command: |
-            pip3 install pydata-sphinx-theme
             mkdir build
             cd build
             cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version ..
@@ -167,8 +165,7 @@ jobs:
             latexmk -pdf -interaction=nonstopmode test_biblio.tex
             latexmk -pdf -interaction=nonstopmode test_gudhi_citation.tex
 
-
-### With all third parties, except CGAL and Eigen
+  ### With all third parties, except CGAL and Eigen
 
   examples_without_cgal_eigen:
     docker:
@@ -248,8 +245,7 @@ jobs:
             python3 setup.py build_ext --inplace
             ctest --output-on-failure
 
-
-### With all third parties, except CGAL
+  ### With all third parties, except CGAL
 
   examples_without_cgal:
     docker:

.github/for_maintainers/new_gudhi_version_creation.md

@@ -25,7 +25,7 @@ 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__ src/python/gudhi/*.cpp
+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__
 ```
 
 Checkin the modifications, build and test the version:
@@ -154,4 +154,4 @@ Send version mail to the following lists :
 
 **Edit the file CMakeGUDHIVersion.txt**, and increment major, minor, or patch version number, in function of the future version (something like `3.X+1.0a0`).
 
-Reset [.github/next_release.md](.github/next_release.md) with [.github/for_maintainers/next_release_template.md](.github/for_maintainers/next_release_template.md).
+Reset [.github/next_release.md](.github/next_release.md) with [.github/for_maintainers/next_release_template.md](.github/for_maintainers/next_release_template.md).

.github/next_release.md

@@ -20,6 +20,7 @@ Below is a list of changes:
 
 - Installation
      - CMake ≥ 3.15 is now required (was ≥ 3.8).
+     - Python ≥ 3.8 is now required (was ≥ 3.5), because of `importlib.metadata`.
 
 - Miscellaneous
      - The [list of bugs that were solved](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.11.0+is%3Aclosed) is available on GitHub.
@@ -29,7 +30,7 @@ However, there are still GPL dependencies for many modules. We invite you to che
 
 We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages.
 
-We provide [bibtex entries](https://gudhi.inria.fr/doc/latest/_citation.html) for the modules of the User and Reference Manual, as well as for publications directly related to the GUDHI library. 
+We provide [bibtex entries](https://gudhi.inria.fr/doc/latest/_citation.html) for the modules of the User and Reference Manual, as well as for publications directly related to the GUDHI library.
 
 Feel free to [contact us](https://gudhi.inria.fr/contact/) in case you have any questions or remarks.
 

.github/workflows/pip-packaging-linux.yml

@@ -19,7 +19,6 @@ jobs:
       # numpy~=1.21.4 means any numpy=1.21.*, but also numpy>=1.21.4 (numpy~=1.21 do not work as it means any numpy==1.*)
       - name: Build wheel for Python 3.8
         run: |
-          rm -rf src/python/gudhi/*.cpp
           mkdir build_38
           cd build_38
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON38/bin/python ..
@@ -38,7 +37,6 @@ jobs:
           $PYTHON38/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.9
         run: |
-          rm -rf src/python/gudhi/*.cpp
           mkdir build_39
           cd build_39
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON39/bin/python ..
@@ -61,7 +59,6 @@ jobs:
           $PYTHON39/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.10
         run: |
-          rm -rf src/python/gudhi/*.cpp
           mkdir build_310
           cd build_310
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON310/bin/python ..
@@ -80,7 +77,6 @@ jobs:
           $PYTHON310/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.11
         run: |
-          rm -rf src/python/gudhi/*.cpp
           mkdir build_311
           cd build_311
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON311/bin/python ..
@@ -99,7 +95,6 @@ jobs:
           $PYTHON311/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.12
         run: |
-          rm -rf src/python/gudhi/*.cpp
           mkdir build_312
           cd build_312
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON312/bin/python ..

.gitignore

@@ -1,9 +1,6 @@
 # Classical CMake build directory
 /*build*
 
-# Generated by Cython
-src/python/gudhi/*.cpp
-
 # Generated by tests
 data/points/COIL_database/lucky_cat.off_dist
 data/points/COIL_database/lucky_cat.off_sc.dot

CMakeLists.txt

@@ -37,6 +37,7 @@ add_gudhi_module(Hasse_complex)
 add_gudhi_module(Persistence_representations)
 add_gudhi_module(Persistent_cohomology)
 add_gudhi_module(Rips_complex)
+add_gudhi_module(Ripser)
 add_gudhi_module(Simplex_tree)
 add_gudhi_module(Skeleton_blocker)
 add_gudhi_module(Spatial_searching)
@@ -46,6 +47,7 @@ add_gudhi_module(Toplex_map)
 add_gudhi_module(Witness_complex)
 add_gudhi_module(Nerve_GIC)
 add_gudhi_module(Persistence_matrix)
+add_gudhi_module(Zigzag_persistence)
 add_gudhi_module(Multi_persistence)
 add_gudhi_module(Multi_filtration)
 

data/distance_matrix/tore3D_1307_distance_matrix.csv

@@ -12,6 +12,7 @@
 #define BOOST_TEST_MODULE "incremental_delaunay"
 #include <boost/test/unit_test.hpp>
 #include <boost/range/adaptor/sliced.hpp>
+#include <boost/mpl/list.hpp>
 
 #include <CGAL/Epick_d.h>
 #include <CGAL/Epeck_d.h>

src/Alpha_complex/test/Incremental_delaunay_test.cpp

@@ -36,6 +36,7 @@ add_gudhi_module(Hasse_complex)
 add_gudhi_module(Persistence_representations)
 add_gudhi_module(Persistent_cohomology)
 add_gudhi_module(Rips_complex)
+add_gudhi_module(Ripser)
 add_gudhi_module(Simplex_tree)
 add_gudhi_module(Skeleton_blocker)
 add_gudhi_module(Spatial_searching)
@@ -45,6 +46,7 @@ add_gudhi_module(Toplex_map)
 add_gudhi_module(Witness_complex)
 add_gudhi_module(Nerve_GIC)
 add_gudhi_module(Persistence_matrix)
+add_gudhi_module(Zigzag_persistence)
 add_gudhi_module(Multi_persistence)
 add_gudhi_module(Multi_filtration)