Merge branch 'GUDHI:master' into const_simplex_tree

.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/doc/Intro_persistence_matrix.h

@@ -43,10 +43,10 @@ namespace persistence_matrix {
  * \subsection matrixexamples Examples
  * 
  * Here is a list of examples using the module:
- * \li \gudhi_example_link{Persistence_matrix,representative_cycles_from_matrix.cpp} - A simple example on how to
+ * \li \gudhi_example_link{Persistence_matrix,example_representative_cycles_from_matrix.cpp} - A simple example on how to
  * use the matrix to compute representative cycles.
  *
- * \li \gudhi_example_link{Persistence_matrix,simplex_tree_to_matrix.cpp} - A simplex example on how to build
+ * \li \gudhi_example_link{Persistence_matrix,example_simplex_tree_to_matrix.cpp} - A simplex example on how to build
  * a the different matrices from a simplex tree.
  * 
  * @}

src/Persistence_matrix/example/CMakeLists.txt

@@ -1,8 +1,8 @@
-add_executable_with_targets(Matrix_examples_representative_cycles representative_cycles_from_matrix.cpp TBB::tbb)
-add_test(NAME Matrix_examples_representative_cycles COMMAND $<TARGET_FILE:Matrix_examples_representative_cycles>)
+add_executable_with_targets(Persistence_matrix_example_representative_cycles_from_matrix example_representative_cycles_from_matrix.cpp TBB::tbb)
+add_test(NAME Persistence_matrix_example_representative_cycles_from_matrix COMMAND $<TARGET_FILE:Persistence_matrix_example_representative_cycles_from_matrix>)
 
-add_executable_with_targets(Matrix_examples_simplex_tree_matrix simplex_tree_to_matrix.cpp TBB::tbb)
-add_test(NAME Matrix_examples_simplex_tree_matrix COMMAND $<TARGET_FILE:Matrix_examples_simplex_tree_matrix>)
+add_executable_with_targets(Persistence_matrix_example_simplex_tree_to_matrix example_simplex_tree_to_matrix.cpp TBB::tbb)
+add_test(NAME Persistence_matrix_example_simplex_tree_to_matrix COMMAND $<TARGET_FILE:Persistence_matrix_example_simplex_tree_to_matrix>)
 
-add_executable_with_targets(Matrix_examples_field_operations example_field_operations.cpp TBB::tbb)
-add_test(NAME Matrix_examples_field_operations COMMAND $<TARGET_FILE:Matrix_examples_field_operations>)
+add_executable_with_targets(Persistence_matrix_example_field_operations example_field_operations.cpp TBB::tbb)
+add_test(NAME Persistence_matrix_example_field_operations COMMAND $<TARGET_FILE:Persistence_matrix_example_field_operations>)

src/Persistence_matrix/example/representative_cycles_from_matrix.cpp → src/Persistence_matrix/example/example_representative_cycles_from_matrix.cpp

@@ -10,7 +10,7 @@
 
 #include <iostream>
 
-#include <gudhi/matrix.h>
+#include <gudhi/Matrix.h>
 #include <gudhi/persistence_matrix_options.h>
 
 using Gudhi::persistence_matrix::Default_options;

src/Persistence_matrix/example/simplex_tree_to_matrix.cpp → src/Persistence_matrix/example/example_simplex_tree_to_matrix.cpp

@@ -10,7 +10,7 @@
 
 #include <vector>
 
-#include <gudhi/matrix.h>
+#include <gudhi/Matrix.h>
 #include <gudhi/persistence_matrix_options.h>
 #include <gudhi/Simplex_tree.h>
 

src/Persistence_matrix/include/gudhi/matrix.h → src/Persistence_matrix/include/gudhi/Matrix.h

@@ -8,7 +8,7 @@
  *      - YYYY/MM Author: Description of the modification
  */
 
-/** @file matrix.h
+/** @file Matrix.h
  * @author Hannah Schreiber
  * @brief Contains @ref Gudhi::persistence_matrix::Matrix class.
  */
@@ -31,8 +31,8 @@
 
 #include <gudhi/Fields/Z2_field_operators.h>
 
-#include <gudhi/Persistence_matrix/overlay_ididx_to_matidx.h>
-#include <gudhi/Persistence_matrix/overlay_posidx_to_matidx.h>
+#include <gudhi/Persistence_matrix/Id_to_index_overlay.h>
+#include <gudhi/Persistence_matrix/Position_to_index_overlay.h>
 
 #include <gudhi/Persistence_matrix/matrix_dimension_holders.h>
 #include <gudhi/Persistence_matrix/matrix_row_access.h>
@@ -45,11 +45,11 @@
 #include <gudhi/Persistence_matrix/chain_vine_swap.h>
 #include <gudhi/Persistence_matrix/chain_rep_cycles.h>
 
-#include <gudhi/Persistence_matrix/base_matrix.h>
-#include <gudhi/Persistence_matrix/base_matrix_with_column_compression.h>
-#include <gudhi/Persistence_matrix/boundary_matrix.h>
-#include <gudhi/Persistence_matrix/ru_matrix.h>
-#include <gudhi/Persistence_matrix/chain_matrix.h>
+#include <gudhi/Persistence_matrix/Base_matrix.h>
+#include <gudhi/Persistence_matrix/Base_matrix_with_column_compression.h>
+#include <gudhi/Persistence_matrix/Boundary_matrix.h>
+#include <gudhi/Persistence_matrix/RU_matrix.h>
+#include <gudhi/Persistence_matrix/Chain_matrix.h>
 
 #include <gudhi/Persistence_matrix/allocators/cell_constructors.h>
 #include <gudhi/Persistence_matrix/columns/cell_types.h>

src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix.h → src/Persistence_matrix/include/gudhi/Persistence_matrix/Base_matrix.h

@@ -9,7 +9,7 @@
  */
 
 /**
- * @file base_matrix.h
+ * @file Base_matrix.h
  * @author Hannah Schreiber
  * @brief Contains the @ref Gudhi::persistence_matrix::Base_matrix class.
  */
@@ -25,7 +25,7 @@ namespace Gudhi {
 namespace persistence_matrix {
 
 /**
- * @class Base_matrix base_matrix.h gudhi/Persistence_matrix/base_matrix.h
+ * @class Base_matrix Base_matrix.h gudhi/Persistence_matrix/Base_matrix.h
  * @ingroup persistence_matrix
  *
  * @brief A @ref basematrix "basic matrix" structure allowing to easily manipulate and access entire columns and rows,

src/Persistence_matrix/include/gudhi/Persistence_matrix/base_matrix_with_column_compression.h → src/Persistence_matrix/include/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h

@@ -9,7 +9,7 @@
  */
 
 /**
- * @file base_matrix_with_column_compression.h
+ * @file Base_matrix_with_column_compression.h
  * @author Hannah Schreiber
  * @brief Contains the @ref Gudhi::persistence_matrix::Base_matrix_with_column_compression class.
  */
@@ -30,8 +30,8 @@ namespace Gudhi {
 namespace persistence_matrix {
 
 /**
- * @class Base_matrix_with_column_compression base_matrix_with_column_compression.h \
- * gudhi/Persistence_matrix/base_matrix_with_column_compression.h
+ * @class Base_matrix_with_column_compression Base_matrix_with_column_compression.h \
+ * gudhi/Persistence_matrix/Base_matrix_with_column_compression.h
  * @ingroup persistence_matrix
  *
  * @brief A @ref basematrix "base matrix" (also see @ref Base_matrix), but with column compression. That is, all

src/Persistence_matrix/include/gudhi/Persistence_matrix/boundary_matrix.h → src/Persistence_matrix/include/gudhi/Persistence_matrix/Boundary_matrix.h

@@ -9,7 +9,7 @@
  */
 
 /**
- * @file boundary_matrix.h
+ * @file Boundary_matrix.h
  * @author Hannah Schreiber
  * @brief Contains the @ref Gudhi::persistence_matrix::Boundary_matrix class.
  */
@@ -25,9 +25,9 @@
 namespace Gudhi {
 namespace persistence_matrix {
 
-// TODO: factorize/inherit/compose with base matrix?
+// TODO: factorize/inherit/compose with Base_matrix?
 /**
- * @class Boundary_matrix boundary_matrix.h gudhi/Persistence_matrix/boundary_matrix.h
+ * @class Boundary_matrix Boundary_matrix.h gudhi/Persistence_matrix/Boundary_matrix.h
  * @ingroup persistence_matrix
  *
  * @brief %Matrix structure to store the ordered @ref boundarymatrix "boundary matrix" \f$ R \f$ of a filtered complex

src/Persistence_matrix/include/gudhi/Persistence_matrix/chain_matrix.h → src/Persistence_matrix/include/gudhi/Persistence_matrix/Chain_matrix.h

@@ -9,7 +9,7 @@
  */
 
 /**
- * @file chain_matrix.h
+ * @file Chain_matrix.h
  * @author Hannah Schreiber
  * @brief Contains the @ref Gudhi::persistence_matrix::Chain_matrix class.
  */
@@ -25,13 +25,13 @@
 #include <utility>    //std::swap, std::move & std::exchange
 #include <algorithm>  //std::sort
 
-#include <gudhi/Persistence_matrix/overlay_ididx_to_matidx.h> //friend
+#include <gudhi/Persistence_matrix/Id_to_index_overlay.h> //friend
 
 namespace Gudhi {
 namespace persistence_matrix {
 
 /**
- * @class Chain_matrix chain_matrix.h gudhi/Persistence_matrix/chain_matrix.h
+ * @class Chain_matrix Chain_matrix.h gudhi/Persistence_matrix/Chain_matrix.h
  * @ingroup persistence_matrix
  *
  * @brief %Matrix structure storing a compatible base of a filtered chain complex. See @cite zigzag.

src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_ididx_to_matidx.h → src/Persistence_matrix/include/gudhi/Persistence_matrix/Id_to_index_overlay.h

@@ -9,7 +9,7 @@
  */
 
 /**
- * @file overlay_ididx_to_matidx.h
+ * @file Id_to_index_overlay.h
  * @author Hannah Schreiber
  * @brief Contains the @ref Gudhi::persistence_matrix::Id_to_index_overlay class.
  */
@@ -28,7 +28,7 @@ namespace Gudhi {
 namespace persistence_matrix {
 
 /**
- * @class Id_to_index_overlay overlay_ididx_to_matidx.h gudhi/Persistence_matrix/overlay_ididx_to_matidx.h
+ * @class Id_to_index_overlay Id_to_index_overlay.h gudhi/Persistence_matrix/Id_to_index_overlay.h
  * @ingroup persistence_matrix
  *
  * @brief Overlay for @ref mp_matrices "non-basic matrices" replacing all input and output @ref MatIdx indices of

src/Persistence_matrix/include/gudhi/Persistence_matrix/overlay_posidx_to_matidx.h → src/Persistence_matrix/include/gudhi/Persistence_matrix/Position_to_index_overlay.h

@@ -9,7 +9,7 @@
  */
 
 /**
- * @file overlay_posidx_to_matidx.h
+ * @file Position_to_index_overlay.h
  * @author Hannah Schreiber
  * @brief Contains the @ref Gudhi::persistence_matrix::Position_to_index_overlay class.
  */
@@ -25,7 +25,7 @@ namespace Gudhi {
 namespace persistence_matrix {
 
 /**
- * @class Position_to_index_overlay overlay_posidx_to_matidx.h gudhi/Persistence_matrix/overlay_posidx_to_matidx.h
+ * @class Position_to_index_overlay Position_to_index_overlay.h gudhi/Persistence_matrix/Position_to_index_overlay.h
  * @ingroup persistence_matrix
  *
  * @brief Overlay for @ref chainmatrix "chain matrices" replacing all input and output @ref MatIdx indices of the

src/Persistence_matrix/include/gudhi/Persistence_matrix/ru_matrix.h → src/Persistence_matrix/include/gudhi/Persistence_matrix/RU_matrix.h

@@ -9,7 +9,7 @@
  */
 
 /**
- * @file ru_matrix.h
+ * @file RU_matrix.h
  * @author Hannah Schreiber
  * @brief Contains the @ref Gudhi::persistence_matrix::RU_matrix class.
  */
@@ -25,7 +25,7 @@ namespace Gudhi {
 namespace persistence_matrix {
 
 /**
- * @class RU_matrix ru_matrix.h gudhi/Persistence_matrix/ru_matrix.h
+ * @class RU_matrix RU_matrix.h gudhi/Persistence_matrix/RU_matrix.h
  * @ingroup persistence_matrix
  *
  * @brief %Matrix structure to store the ordered @ref boundarymatrix "boundary matrix" \f$ R \cdot U \f$ of a filtered

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. */