multipers 2.6.0b1__tar.gz → 2.6.1__tar.gz

{multipers-2.6.0b1 → multipers-2.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.6.0b1
+Version: 2.6.1
 Summary: Multiparameter Topological Persistence for Machine Learning
 Keywords: TDA,Persistence,Multiparameter,sklearn,autodiff
 Author-Email: David Loiseaux <david.lapous@proton.me>, Hannah Schreiber <hannah.schreiber@inria.fr>
@@ -91,15 +91,15 @@ This library features a bunch of different functions and helpers. See below for
  - [x] [[Fast free resolutions of bifiltered chain complexes]](https://arxiv.org/abs/2512.08652) One-critical representation of multicritical filtrations, using [multi_critical](https://bitbucket.org/mkerber/multi_critical).
  - [x] [[Chunk Reduction for Multi-Parameter Persistent Homology, SoCG2019]](https://doi.org/10.4230/LIPIcs.SoCG.2019.37) Multi-filtration preprocessing algorithm for homology computations.
  - [x] [[Computing Minimal Presentations and Bigraded Betti Numbers of 2-Parameter Persistent Homology, JAAG]](https://doi.org/10.1137/20M1388425) Minimal presentation of multiparameter persistence modules, using [mpfree](https://bitbucket.org/mkerber/mpfree/src/master/). Hilbert, Rank Decomposition Signed Measures, and MMA decompositions can be computed using the mpfree backend.
- - [x] [[Hera]](https://github.com/anigmetov/hera) Matching distance between 2-parameter presentations.
- - [x] [WIP] [[Decomposing Multiparameter Persistence Modules, SoCG2025]](https://doi.org/10.4230/LIPIcs.SoCG.2025.41) Using the [AIDA](https://github.com/JanJend/AIDA) and [Persistence-Algebra](https://github.com/JanJend/Persistence-Algebra/) libraries.
+ - [x] [[Hera]](https://github.com/anigmetov/hera) Matching distance between 2-parameter presentations, 1-parameter bottleneck/wasserstein distances.
+ - [x] [[Decomposing Multiparameter Persistence Modules, SoCG2025]](https://doi.org/10.4230/LIPIcs.SoCG.2025.41) Using the [AIDA](https://github.com/JanJend/AIDA) and [Persistence-Algebra](https://github.com/JanJend/Persistence-Algebra/) libraries.
  - [x] [[Delaunay Bifiltrations of Functions on Point Clouds, SODA2024]](https://epubs.siam.org/doi/10.1137/1.9781611977912.173) Provides an alternative to function rips bifiltrations, using Delaunay complexes. Very good alternative to Rips-Density like bifiltrations.
  - [x] [[Delaunay Core Bifiltration]](https://arxiv.org/abs/2405.01214) Bifiltration for point clouds, taking into account the density. Similar to Rips-Density. 
  - [x] [[Computing the Multicover Bifiltration, SOCG2021]](https://doi.org/10.4230/LIPIcs.SoCG.2021.27) Rhomboid Tiling bifiltration. Equivalent to the multicover bifiltration, using [rhomboidtiling](https://github.com/geoo89/rhomboidtiling).
  - [x] [[Rivet]](https://github.com/rivetTDA/rivet) Interactive two parameter persistence
  - [x] [[Kernel Operations on the GPU, with Autodiff, without Memory Overflows, JMLR]](http://jmlr.org/papers/v22/20-275.html) Although not linked, at first glance, to persistence in any way, this library allows computing blazingly fast signed measures convolutions (and more!) with custom kernels. 
- - [ ] [Backend only] [[Projected distances for multi-parameter persistence modules]](https://arxiv.org/abs/2206.08818) Provides a strategy to estimate the convolution distance between multiparameter persistence module using projected barcodes. Implementation is a WIP.
- - [ ] [Partial, and experimental] [[Efficient Two-Parameter Persistence Computation via Cohomology, SoCG2023]](https://doi.org/10.4230/LIPIcs.SoCG.2023.15) Minimal presentations for 2-parameter persistence algorithm.
+ - [x] [[Projected distances for multi-parameter persistence modules]](https://arxiv.org/abs/2206.08818) Provides a strategy to estimate the convolution distance between multiparameter persistence module using projected barcodes. Implementation is a WIP.
+ - [x] [[Efficient Two-Parameter Persistence Computation via Cohomology, SoCG2023]](https://doi.org/10.4230/LIPIcs.SoCG.2023.15) Minimal presentations for 2-parameter persistence algorithm.
 
 If I missed something, or you want to add something, feel free to open an issue.
 
@@ -125,7 +125,7 @@ This is due to linked GPL/LGPL third-party components used by the build, notably
 See `THIRD_PARTY_NOTICES.md` for dependency details and pinned revisions used in this workspace.
 
 ## Citation
-Please cite this library when using it in scientific publications;
+Please cite this library and its dependencies (see above) when using it in scientific publications;
 you can use the following journal bibtex entry
 ```bib
 @article{multipers,

{multipers-2.6.0b1 → multipers-2.6.1}/README.md

@@ -52,15 +52,15 @@ This library features a bunch of different functions and helpers. See below for
  - [x] [[Fast free resolutions of bifiltered chain complexes]](https://arxiv.org/abs/2512.08652) One-critical representation of multicritical filtrations, using [multi_critical](https://bitbucket.org/mkerber/multi_critical).
  - [x] [[Chunk Reduction for Multi-Parameter Persistent Homology, SoCG2019]](https://doi.org/10.4230/LIPIcs.SoCG.2019.37) Multi-filtration preprocessing algorithm for homology computations.
  - [x] [[Computing Minimal Presentations and Bigraded Betti Numbers of 2-Parameter Persistent Homology, JAAG]](https://doi.org/10.1137/20M1388425) Minimal presentation of multiparameter persistence modules, using [mpfree](https://bitbucket.org/mkerber/mpfree/src/master/). Hilbert, Rank Decomposition Signed Measures, and MMA decompositions can be computed using the mpfree backend.
- - [x] [[Hera]](https://github.com/anigmetov/hera) Matching distance between 2-parameter presentations.
- - [x] [WIP] [[Decomposing Multiparameter Persistence Modules, SoCG2025]](https://doi.org/10.4230/LIPIcs.SoCG.2025.41) Using the [AIDA](https://github.com/JanJend/AIDA) and [Persistence-Algebra](https://github.com/JanJend/Persistence-Algebra/) libraries.
+ - [x] [[Hera]](https://github.com/anigmetov/hera) Matching distance between 2-parameter presentations, 1-parameter bottleneck/wasserstein distances.
+ - [x] [[Decomposing Multiparameter Persistence Modules, SoCG2025]](https://doi.org/10.4230/LIPIcs.SoCG.2025.41) Using the [AIDA](https://github.com/JanJend/AIDA) and [Persistence-Algebra](https://github.com/JanJend/Persistence-Algebra/) libraries.
  - [x] [[Delaunay Bifiltrations of Functions on Point Clouds, SODA2024]](https://epubs.siam.org/doi/10.1137/1.9781611977912.173) Provides an alternative to function rips bifiltrations, using Delaunay complexes. Very good alternative to Rips-Density like bifiltrations.
  - [x] [[Delaunay Core Bifiltration]](https://arxiv.org/abs/2405.01214) Bifiltration for point clouds, taking into account the density. Similar to Rips-Density. 
  - [x] [[Computing the Multicover Bifiltration, SOCG2021]](https://doi.org/10.4230/LIPIcs.SoCG.2021.27) Rhomboid Tiling bifiltration. Equivalent to the multicover bifiltration, using [rhomboidtiling](https://github.com/geoo89/rhomboidtiling).
  - [x] [[Rivet]](https://github.com/rivetTDA/rivet) Interactive two parameter persistence
  - [x] [[Kernel Operations on the GPU, with Autodiff, without Memory Overflows, JMLR]](http://jmlr.org/papers/v22/20-275.html) Although not linked, at first glance, to persistence in any way, this library allows computing blazingly fast signed measures convolutions (and more!) with custom kernels. 
- - [ ] [Backend only] [[Projected distances for multi-parameter persistence modules]](https://arxiv.org/abs/2206.08818) Provides a strategy to estimate the convolution distance between multiparameter persistence module using projected barcodes. Implementation is a WIP.
- - [ ] [Partial, and experimental] [[Efficient Two-Parameter Persistence Computation via Cohomology, SoCG2023]](https://doi.org/10.4230/LIPIcs.SoCG.2023.15) Minimal presentations for 2-parameter persistence algorithm.
+ - [x] [[Projected distances for multi-parameter persistence modules]](https://arxiv.org/abs/2206.08818) Provides a strategy to estimate the convolution distance between multiparameter persistence module using projected barcodes. Implementation is a WIP.
+ - [x] [[Efficient Two-Parameter Persistence Computation via Cohomology, SoCG2023]](https://doi.org/10.4230/LIPIcs.SoCG.2023.15) Minimal presentations for 2-parameter persistence algorithm.
 
 If I missed something, or you want to add something, feel free to open an issue.
 
@@ -86,7 +86,7 @@ This is due to linked GPL/LGPL third-party components used by the build, notably
 See `THIRD_PARTY_NOTICES.md` for dependency details and pinned revisions used in this workspace.
 
 ## Citation
-Please cite this library when using it in scientific publications;
+Please cite this library and its dependencies (see above) when using it in scientific publications;
 you can use the following journal bibtex entry
 ```bib
 @article{multipers,

{multipers-2.6.0b1 → multipers-2.6.1}/THIRD_PARTY_NOTICES.md

@@ -30,6 +30,10 @@ As a result, distributed `multipers` artifacts built with these components are l
   - Commit used in this workspace: `c414cdc60f30196ffd3ce5cda1817368655905f0`
   - License: MIT (see `ext/rhomboidtiling_newer_cgal_version/LICENSE.md`)
 
+- `CGAL Spatial_searching`
+  - Upstream: https://www.cgal.org/
+  - License: GPL-3.0-or-later OR commercial (see SPDX headers in installed CGAL Spatial_searching package)
+
 - `mpfree`
   - Upstream: https://bitbucket.org/mkerber/mpfree/
   - Header source path used at build time: `ext/mpfree`

{multipers-2.6.0b1 → multipers-2.6.1}/cmake/MultipersBuild.cmake

@@ -79,7 +79,7 @@ function(multipers_apply_common_build_flags target_name)
   )
 
   if(MSVC)
-    target_compile_options(${target_name} PRIVATE /O2 /DNDEBUG /W1 /WX- /openmp)
+    target_compile_options(${target_name} PRIVATE /O2 /DNDEBUG /W1 /WX-)
   else()
     target_compile_options(
       ${target_name}
@@ -199,6 +199,7 @@ target_include_directories(
     ${MULTIPERS_HERA_PHAT_INCLUDE_DIRS}
     ${MULTIPERS_HERA_INCLUDE_DIRS}
 )
+multipers_link_openmp(multipers_core_hera_obj)
 
 add_library(
   multipers_core_shared
@@ -345,7 +346,10 @@ multipers_add_generated_patch_file(
   "${MULTIPERS_GENERATED_EXT_PATCH_DIR}/multi_critical_runtime_logs.patch"
   MULTIPERS_MULTI_CRITICAL_LOG_PATCH_FILE
   "${CMAKE_SOURCE_DIR}/ext/multi_critical/include/multi_critical/basic.h"
+  "${CMAKE_SOURCE_DIR}/ext/multi_critical/include/multi_critical/free_resolution.h"
   "${CMAKE_SOURCE_DIR}/ext/multi_critical/mpfree_mod/include/mpfree/global.h"
+  "${CMAKE_SOURCE_DIR}/ext/multi_critical/mpp_utils_mod/include/mpp_utils/Graded_matrix.h"
+  "${CMAKE_SOURCE_DIR}/ext/multi_critical/mpp_utils_mod/include/mpp_utils/create_graded_matrices_from_pre_column_struct.h"
   "${CMAKE_SOURCE_DIR}/ext/multi_critical/multi_chunk_mod/include/multi_chunk/basic.h"
   "${CMAKE_SOURCE_DIR}/ext/multi_critical/scc_mod/include/scc/basic.h"
 )
@@ -425,6 +429,7 @@ multipers_add_generated_patch_overlay(
   MULTIPERS_MULTI_CRITICAL_PATCH_OVERLAY_ROOT
   include
   mpfree_mod/include
+  mpp_utils_mod/include
   multi_chunk_mod/include
   scc_mod/include
 )
@@ -448,7 +453,7 @@ set(MULTIPERS_FUNCTION_DELAUNAY_INCLUDE_DIRS
 set(MULTIPERS_MULTI_CRITICAL_INCLUDE_DIRS
   "${MULTIPERS_MULTI_CRITICAL_PATCH_OVERLAY_ROOT}/ext/multi_critical/include"
   "${MULTIPERS_MULTI_CRITICAL_PATCH_OVERLAY_ROOT}/ext/multi_critical/mpfree_mod/include"
-  "${CMAKE_SOURCE_DIR}/ext/multi_critical/mpp_utils_mod/include"
+  "${MULTIPERS_MULTI_CRITICAL_PATCH_OVERLAY_ROOT}/ext/multi_critical/mpp_utils_mod/include"
   "${MULTIPERS_MULTI_CRITICAL_PATCH_OVERLAY_ROOT}/ext/multi_critical/multi_chunk_mod/include"
   "${CMAKE_SOURCE_DIR}/ext/multi_critical/phat_mod/include"
   "${MULTIPERS_MULTI_CRITICAL_PATCH_OVERLAY_ROOT}/ext/multi_critical/scc_mod/include"
@@ -512,6 +517,8 @@ function(multipers_configure_module module_name target_name)
   elseif(module_name STREQUAL "_slicer_nanobind")
     multipers_link_shared_core(${target_name})
     multipers_link_tbb(${target_name})
+    # Build slicer templates in-module so import does not depend on ELF shared-core exports.
+    target_compile_definitions(${target_name} PRIVATE MULTIPERS_BUILD_CORE_TEMPLATES=1)
 
   elseif(module_name STREQUAL "_mma_nanobind")
     multipers_link_tbb(${target_name})
@@ -519,6 +526,10 @@ function(multipers_configure_module module_name target_name)
   elseif(module_name STREQUAL "_function_rips_nanobind")
     multipers_link_tbb(${target_name})
 
+  elseif(module_name STREQUAL "_core_delaunay_nanobind")
+    multipers_link_tbb(${target_name})
+    multipers_link_cgal(${target_name})
+
   elseif(module_name STREQUAL "_mpfree_interface")
     if(NOT MULTIPERS_DISABLE_MPFREE_INTERFACE)
       add_dependencies(${target_name} multipers_mpfree_log_overlay)
@@ -680,6 +691,7 @@ set(MULTIPERS_NANOBIND_MODULES
   _mma_nanobind
   _simplex_tree_multi_nanobind
   _function_rips_nanobind
+  _core_delaunay_nanobind
   _grid_helper_nanobind
   _mpfree_interface
   _function_delaunay_interface

multipers-2.6.1/ext/gudhi-devel/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h

@@ -0,0 +1,142 @@
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2020 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#ifndef ALPHA_COMPLEX_ALPHA_KERNEL_D_H_
+#define ALPHA_COMPLEX_ALPHA_KERNEL_D_H_
+
+#include <CGAL/version.h>  // for CGAL_VERSION_NR
+
+#include <Eigen/Core>  // for EIGEN_VERSION_AT_LEAST
+
+#include <utility>  // for std::make_pair
+
+// Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10
+#if CGAL_VERSION_NR < 1041101000
+# error Alpha_complex is only available for CGAL >= 4.11
+#endif
+
+#if !EIGEN_VERSION_AT_LEAST(3,1,0)
+# error Alpha_complex is only available for Eigen3 >= 3.1.0 installed with CGAL
+#endif
+
+namespace Gudhi {
+
+namespace alpha_complex {
+
+/**
+ * \class Alpha_kernel_d
+ * \brief Alpha complex kernel container.
+ * 
+ * \details
+ * The Alpha complex kernel container stores CGAL Kernel and dispatch basics computations in function of the weighted
+ * or not version of the Alpha complex.
+ */
+template < typename Kernel, bool Weighted = false >
+class Alpha_kernel_d {
+};
+
+// Unweighted Kernel_d version
+template < typename Kernel >
+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;
+  using Point_d = typename Kernel::Point_d;
+  // Numeric type of coordinates in the kernel
+  using FT = typename Kernel::FT;
+  // Sphere is a pair of point and squared radius.
+  using Sphere = typename std::pair<Point_d, FT>;
+
+  int get_dimension(const Point_d& p0) const {
+    return kernel_.point_dimension_d_object()(p0);
+  }
+
+  template<class PointIterator>
+  Sphere get_sphere(PointIterator begin, PointIterator end) const {
+    Point_d c = kernel_.construct_circumcenter_d_object()(begin, end);
+    FT r = kernel_.squared_distance_d_object()(c, *begin);
+    return std::make_pair(std::move(c), std::move(r));
+  }
+
+  template<class PointIterator>
+  FT get_squared_radius(PointIterator begin, PointIterator end) const {
+    return kernel_.compute_squared_radius_d_object()(begin, end);
+  }
+
+  FT get_squared_radius(const Sphere& sph) const {
+    return sph.second;
+  }
+
+  bool is_gabriel(const Sphere& circumcenter, const Point_d& point) {
+    return kernel_.squared_distance_d_object()(circumcenter.first, point) >= circumcenter.second;
+  }
+};
+
+// Weighted Kernel_d version
+template < typename Kernel >
+class Alpha_kernel_d<Kernel, true> {
+ private:
+  // Kernel for functions access.
+  Kernel kernel_;
+
+ public:
+  // Fake type for compilation to succeed (cf. std::conditional in Alpha_complex.h)
+  using Point_d = void;
+  using Weighted_point_d = typename Kernel::Weighted_point_d;
+  using Bare_point_d = typename Kernel::Point_d;
+  // Numeric type of coordinates in the kernel
+  using FT = typename Kernel::FT;
+  // Sphere is a weighted point (point + weight [= squared radius]).
+  using Sphere = Weighted_point_d;
+
+  int get_dimension(const Weighted_point_d& p0) const {
+    return kernel_.point_dimension_d_object()(p0.point());
+  }
+
+  template<class PointIterator>
+  Sphere get_sphere(PointIterator begin, PointIterator end) const {
+    // power_center_d_object has been renamed between CGAL 5.1 and 5.2
+#if CGAL_VERSION_NR < 1050200000
+    return kernel_.power_center_d_object()(begin, end);
+#else
+    return kernel_.construct_power_sphere_d_object()(begin, end);
+#endif
+  }
+
+  template<class PointIterator>
+  FT get_squared_radius(PointIterator begin, PointIterator end) const {
+    return kernel_.compute_squared_radius_smallest_orthogonal_sphere_d_object()(begin, end);
+  }
+
+  FT get_squared_radius(const Sphere& sph) const {
+    return sph.weight();
+  }
+
+  bool is_gabriel(const Sphere& circumcenter, const Weighted_point_d& point) {
+    // power_center_d_object has been renamed between CGAL 5.1 and 5.2
+#if CGAL_VERSION_NR < 1050200000
+    return kernel_.power_distance_d_object()(circumcenter, point) >= 0;
+#else
+    return kernel_.compute_power_product_d_object()(circumcenter, point) >= 0;
+#endif
+  }
+};
+
+}  // namespace alpha_complex
+
+namespace alphacomplex = alpha_complex;
+
+}  // namespace Gudhi
+
+#endif  // ALPHA_COMPLEX_ALPHA_KERNEL_D_H_