Merge branch 'GUDHI:master' into Multiparameter-Simplextree-C++-part

.circleci/config.yml

@@ -83,6 +83,7 @@ jobs:
   python:
     docker:
       - image: gudhi/ci_for_gudhi:2024.06.02
+    resource_class: large # Delaunay complex requires about 5 Gb of RAM to compile
     steps:
       - checkout
       - run:

.github/next_release.md

@@ -6,6 +6,12 @@ We are now using GitHub to develop the GUDHI library, do not hesitate to [fork t
 
 Below is a list of changes:
 
+- [Delaunay complex](https://gudhi.inria.fr/python/latest/delaunay_complex_user.html)
+     - The Delaunay complex can be equipped with different filtrations:
+          * Delaunay complex (no filtration values computed)
+          * Delaunay Čech complex (using minimal enclosing ball)
+          * Alpha complex (moved in this new section)
+
 - [Module](link)
      - **...**
 
@@ -29,4 +35,4 @@ For further information about downloading and installing the library ([C++](http
 ## Contributors
 
 - **...**
-- **...**
+- **...**

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

@@ -32,6 +32,7 @@ jobs:
           $PYTHON39/bin/python -m pip install numpy~=1.19.3
           $PYTHON39/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON39/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON39/bin/python -m pytest -v src/python/test/test_delaunay_complex.py
           $PYTHON39/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
           $PYTHON39/bin/python -m pytest -v src/python/test/test_cubical_complex.py
           $PYTHON39/bin/python -m pytest -v src/python/test/test_rips_complex.py

.github/workflows/pip-build-osx.yml

@@ -58,6 +58,7 @@ jobs:
           python -m pip install --user pytest build/src/python/dist/*.whl
           python -c "import gudhi; print(gudhi.__version__)"
           python -m pytest -v src/python/test/test_alpha_complex.py
+          python -m pytest -v src/python/test/test_delaunay_complex.py
           python -m pytest -v src/python/test/test_bottleneck_distance.py
           python -m pytest -v src/python/test/test_cubical_complex.py
           python -m pytest -v src/python/test/test_rips_complex.py

.github/workflows/pip-build-windows.yml

@@ -55,6 +55,7 @@ jobs:
           python -m pip install --user pytest
           python -c "import gudhi; print(gudhi.__version__)"
           python -m pytest -v ".\src\python\test\test_alpha_complex.py"
+          python -m pytest -v ".\src\python\test\test_delaunay_complex.py"
           python -m pytest -v ".\src\python\test\test_bottleneck_distance.py"
           python -m pytest -v ".\src\python\test\test_cubical_complex.py"
           python -m pytest -v ".\src\python\test\test_rips_complex.py"

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

@@ -32,6 +32,7 @@ jobs:
           $PYTHON38/bin/python -m pip install numpy --upgrade
           $PYTHON38/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON38/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON38/bin/python -m pytest -v src/python/test/test_delaunay_complex.py
           $PYTHON38/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
           $PYTHON38/bin/python -m pytest -v src/python/test/test_cubical_complex.py
           $PYTHON38/bin/python -m pytest -v src/python/test/test_rips_complex.py
@@ -54,6 +55,7 @@ jobs:
           $PYTHON39/bin/python -m pip install numpy~=1.19.3
           $PYTHON39/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON39/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON39/bin/python -m pytest -v src/python/test/test_delaunay_complex.py
           $PYTHON39/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
           $PYTHON39/bin/python -m pytest -v src/python/test/test_cubical_complex.py
           $PYTHON39/bin/python -m pytest -v src/python/test/test_rips_complex.py
@@ -72,6 +74,7 @@ jobs:
           $PYTHON310/bin/python -m pip install numpy~=1.21.6
           $PYTHON310/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON310/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON310/bin/python -m pytest -v src/python/test/test_delaunay_complex.py
           $PYTHON310/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
           $PYTHON310/bin/python -m pytest -v src/python/test/test_cubical_complex.py
           $PYTHON310/bin/python -m pytest -v src/python/test/test_rips_complex.py
@@ -90,6 +93,7 @@ jobs:
           $PYTHON311/bin/python -m pip install numpy~=1.23.2
           $PYTHON311/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON311/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON311/bin/python -m pytest -v src/python/test/test_delaunay_complex.py
           $PYTHON311/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
           $PYTHON311/bin/python -m pytest -v src/python/test/test_cubical_complex.py
           $PYTHON311/bin/python -m pytest -v src/python/test/test_rips_complex.py
@@ -108,6 +112,7 @@ jobs:
           $PYTHON312/bin/python -m pip install numpy~=1.26.0
           $PYTHON312/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON312/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON312/bin/python -m pytest -v src/python/test/test_delaunay_complex.py
           $PYTHON312/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
           $PYTHON312/bin/python -m pytest -v src/python/test/test_cubical_complex.py
           $PYTHON312/bin/python -m pytest -v src/python/test/test_rips_complex.py

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

@@ -51,6 +51,7 @@ jobs:
           python -m pip install --user pytest build/src/python/dist/*.whl
           python -c "import gudhi; print(gudhi.__version__)"
           python -m pytest -v src/python/test/test_alpha_complex.py
+          python -m pytest -v src/python/test/test_delaunay_complex.py
           python -m pytest -v src/python/test/test_bottleneck_distance.py
           python -m pytest -v src/python/test/test_cubical_complex.py
           python -m pytest -v src/python/test/test_rips_complex.py
@@ -121,6 +122,7 @@ jobs:
           python -m pip install --user pytest build/src/python/dist/*.whl
           python -c "import gudhi; print(gudhi.__version__)"
           python -m pytest -v src/python/test/test_alpha_complex.py
+          python -m pytest -v src/python/test/test_delaunay_complex.py
           python -m pytest -v src/python/test/test_bottleneck_distance.py
           python -m pytest -v src/python/test/test_cubical_complex.py
           python -m pytest -v src/python/test/test_rips_complex.py

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

@@ -49,6 +49,7 @@ jobs:
           python -m pip install --user pytest
           python -c "import gudhi; print(gudhi.__version__)"
           python -m pytest -v ".\src\python\test\test_alpha_complex.py"
+          python -m pytest -v ".\src\python\test\test_delaunay_complex.py"
           python -m pytest -v ".\src\python\test\test_bottleneck_distance.py"
           python -m pytest -v ".\src\python\test\test_cubical_complex.py"
           python -m pytest -v ".\src\python\test\test_rips_complex.py"
@@ -117,6 +118,7 @@ jobs:
           python -m pip install --user pytest
           python -c "import gudhi; print(gudhi.__version__)"
           python -m pytest -v ".\src\python\test\test_alpha_complex.py"
+          python -m pytest -v ".\src\python\test\test_delaunay_complex.py"
           python -m pytest -v ".\src\python\test\test_bottleneck_distance.py"
           python -m pytest -v ".\src\python\test\test_cubical_complex.py"
           python -m pytest -v ".\src\python\test\test_rips_complex.py"

src/Alpha_complex/include/gudhi/Alpha_complex.h

@@ -17,10 +17,6 @@
 // to construct Alpha_complex from a OFF file of points
 #include <gudhi/Points_off_io.h>
 
-#include <cmath>  // isnan, fmax
-#include <memory>  // for std::unique_ptr
-#include <cstddef>  // for std::size_t
-
 #include <CGAL/Delaunay_triangulation.h>
 #include <CGAL/Regular_triangulation.h>  // aka. Weighted Delaunay triangulation
 #include <CGAL/Epeck_d.h>  // For EXACT or SAFE version
@@ -46,6 +42,9 @@
 #include <numeric>  // for std::iota
 #include <algorithm>  // for std::sort
 #include <type_traits>  // for std::is_same_v
+#include <cmath>  // isnan, fmax
+#include <memory>  // for std::unique_ptr
+#include <cstddef>  // for std::size_t
 
 // Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10
 #if CGAL_VERSION_NR < 1041101000

src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h

@@ -48,6 +48,7 @@ class Alpha_kernel_d<Kernel, false> {
  private:
   // Kernel for functions access.
   Kernel kernel_;
+
  public:
   // Fake type for compilation to succeed (cf. std::conditional in Alpha_complex.h)
   using Weighted_point_d = void;

src/Persistence_matrix/include/gudhi/persistence_matrix_options.h

@@ -27,7 +27,7 @@ namespace persistence_matrix {
  *
  * @brief List of column types.
  */
-enum Column_types { 
+enum class Column_types { 
   LIST,           /**< @ref List_column "": Underlying container is a std::list<@ref Cell*>. */
   SET,            /**< @ref Set_column "": Underlying container is a std::set<@ref Cell*>. */
   HEAP,           /**< @ref Heap_column "": Underlying container is a std::vector<@ref Cell*> ordered as a heap.
@@ -46,7 +46,7 @@ enum Column_types {
  * @brief List if indexation schemes. See @ref mp_indexation "description of indexation schemes" for more details
  * about the meaning of the indexation types.
  */
-enum Column_indexation_types { 
+enum class Column_indexation_types { 
   CONTAINER,  /**< Default use of @ref MatIdx indices. */
   POSITION,   /**< All input and output @ref MatIdx indices are replaced with @ref PosIdx indices. */
   IDENTIFIER  /**< All input and output @ref MatIdx indices are replaced with @ref IDIdx indices. */

src/python/CMakeLists.txt

@@ -63,7 +63,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'nerve_gic', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'subsampling', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'tangential_complex', ")
-    set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'alpha_complex', ")
+    set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'delaunay_complex', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'euclidean_witness_complex', ")
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'euclidean_strong_witness_complex', ")
     # Modules that should not be auto-imported in __init__.py
@@ -182,7 +182,7 @@ if(PYTHONINTERP_FOUND)
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'tangential_complex', ")
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'euclidean_witness_complex', ")
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'euclidean_strong_witness_complex', ")
-      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'alpha_complex', ")
+      set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'delaunay_complex', ")
       set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/_points', ")
     endif ()
     set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'_pers_cub_low_dim', ")
@@ -536,6 +536,7 @@ if(PYTHONINTERP_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
       add_gudhi_py_test(test_alpha_complex)
+      add_gudhi_py_test(test_delaunay_complex)
     endif (TARGET CGAL::CGAL AND TARGET Eigen3::Eigen)
 
     if (TARGET CGAL::CGAL AND TARGET Eigen3::Eigen)