multipers 2.5.0b4__tar.gz → 2.6.0__tar.gz

{multipers-2.5.0b4 → multipers-2.6.0}/CMakeLists.txt

@@ -1,20 +1,33 @@
-cmake_minimum_required(VERSION 3.24)
+cmake_minimum_required(VERSION 3.27)
 project(multipers LANGUAGES C CXX)
 
 if(POLICY CMP0167)
   cmake_policy(SET CMP0167 NEW)
 endif()
 
+
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 set(CMAKE_COLOR_DIAGNOSTICS ON)
 
+if(NOT CMAKE_SOURCE_DIR STREQUAL CMAKE_BINARY_DIR)
+  file(REMOVE "${CMAKE_SOURCE_DIR}/compile_commands.json")
+  file(
+    CREATE_LINK
+    "${CMAKE_BINARY_DIR}/compile_commands.json"
+    "${CMAKE_SOURCE_DIR}/compile_commands.json"
+    SYMBOLIC
+    COPY_ON_ERROR
+  )
+endif()
+
 if(CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
   add_compile_options(
     $<$<COMPILE_LANGUAGE:C>:-fdiagnostics-color=always>
     $<$<COMPILE_LANGUAGE:CXX>:-fdiagnostics-color=always>
+    -g0
   )
 endif()
 

{multipers-2.5.0b4 → multipers-2.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.5.0b4
+Version: 2.6.0
 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>
@@ -91,14 +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] [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.
 
@@ -109,7 +110,7 @@ If I missed something, or you want to add something, feel free to open an issue.
 (Möbius inversion in python, degree-rips using [persistable](https://github.com/LuisScoccola/persistable) and [RIVET](https://github.com/rivetTDA/rivet/)),<br>
 [Mathieu Carrière](https://www-sop.inria.fr/members/Mathieu.Carriere/) (Sliced Wasserstein),<br>
 [Odin Hoff Gardå](https://odinhg.github.io/) (Delaunay Core bifiltration),<br>
-[Michael Kerber](https://www.geometrie.tugraz.at/kerber/) ([mpfree](https://bitbucket.org/mkerber/mpfree/src/master/), [function_delaunay](https://bitbucket.org/mkerber/function_delaunay), [multi_critical](https://bitbucket.org/mkerber/multi_critical) [multi_chunck](https://bitbucket.org/mkerber/multi_chunk) backends),<br>
+[Michael Kerber](https://www.geometrie.tugraz.at/kerber/) ([mpfree](https://bitbucket.org/mkerber/mpfree/src/master/), [function_delaunay](https://bitbucket.org/mkerber/function_delaunay), [multi_critical](https://bitbucket.org/mkerber/multi_critical), [multi_chunk](https://bitbucket.org/mkerber/multi_chunk) backends),<br>
 [Jan Jendrysiak](https://github.com/JanJend) ([Module Decomposition (AIDA)](https://github.com/JanJend/AIDA), [Persistence Algebra](https://github.com/JanJend/Persistence-Algebra)).<br>
 
 ## Licensing
@@ -124,7 +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-2.5.0b4 → multipers-2.6.0}/README.md

@@ -52,14 +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] [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.
 
@@ -70,7 +71,7 @@ If I missed something, or you want to add something, feel free to open an issue.
 (Möbius inversion in python, degree-rips using [persistable](https://github.com/LuisScoccola/persistable) and [RIVET](https://github.com/rivetTDA/rivet/)),<br>
 [Mathieu Carrière](https://www-sop.inria.fr/members/Mathieu.Carriere/) (Sliced Wasserstein),<br>
 [Odin Hoff Gardå](https://odinhg.github.io/) (Delaunay Core bifiltration),<br>
-[Michael Kerber](https://www.geometrie.tugraz.at/kerber/) ([mpfree](https://bitbucket.org/mkerber/mpfree/src/master/), [function_delaunay](https://bitbucket.org/mkerber/function_delaunay), [multi_critical](https://bitbucket.org/mkerber/multi_critical) [multi_chunck](https://bitbucket.org/mkerber/multi_chunk) backends),<br>
+[Michael Kerber](https://www.geometrie.tugraz.at/kerber/) ([mpfree](https://bitbucket.org/mkerber/mpfree/src/master/), [function_delaunay](https://bitbucket.org/mkerber/function_delaunay), [multi_critical](https://bitbucket.org/mkerber/multi_critical), [multi_chunk](https://bitbucket.org/mkerber/multi_chunk) backends),<br>
 [Jan Jendrysiak](https://github.com/JanJend) ([Module Decomposition (AIDA)](https://github.com/JanJend/AIDA), [Persistence Algebra](https://github.com/JanJend/Persistence-Algebra)).<br>
 
 ## Licensing
@@ -85,7 +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-2.5.0b4 → multipers-2.6.0}/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-2.6.0/cmake/ApplyExtPatchOverlay.cmake

@@ -0,0 +1,55 @@
+if(NOT DEFINED REPO_ROOT)
+  message(FATAL_ERROR "ApplyExtPatchOverlay.cmake needs REPO_ROOT")
+endif()
+if(NOT DEFINED OVERLAY_ROOT)
+  message(FATAL_ERROR "ApplyExtPatchOverlay.cmake needs OVERLAY_ROOT")
+endif()
+if(NOT DEFINED LIBRARY_NAME)
+  message(FATAL_ERROR "ApplyExtPatchOverlay.cmake needs LIBRARY_NAME")
+endif()
+if(NOT DEFINED LIBRARY_RELATIVE_ROOT)
+  message(FATAL_ERROR "ApplyExtPatchOverlay.cmake needs LIBRARY_RELATIVE_ROOT")
+endif()
+if(NOT DEFINED SUBDIRS)
+  message(FATAL_ERROR "ApplyExtPatchOverlay.cmake needs SUBDIRS")
+endif()
+if(NOT DEFINED PATCH_FILE)
+  message(FATAL_ERROR "ApplyExtPatchOverlay.cmake needs PATCH_FILE")
+endif()
+if(NOT DEFINED PATCH_EXECUTABLE)
+  message(FATAL_ERROR "ApplyExtPatchOverlay.cmake needs PATCH_EXECUTABLE")
+endif()
+if(NOT DEFINED STAMP_FILE)
+  message(FATAL_ERROR "ApplyExtPatchOverlay.cmake needs STAMP_FILE")
+endif()
+
+file(REMOVE_RECURSE "${OVERLAY_ROOT}")
+
+foreach(subdir IN LISTS SUBDIRS)
+  set(_src "${REPO_ROOT}/${LIBRARY_RELATIVE_ROOT}/${subdir}")
+  if(NOT EXISTS "${_src}")
+    message(FATAL_ERROR "Failed to copy ${LIBRARY_NAME} subtree ${subdir} into patch overlay: source path ${_src} is missing")
+  endif()
+
+  get_filename_component(_subdir_parent "${subdir}" DIRECTORY)
+  set(_dst_parent "${OVERLAY_ROOT}/${LIBRARY_RELATIVE_ROOT}")
+  if(NOT "${_subdir_parent}" STREQUAL "")
+    set(_dst_parent "${_dst_parent}/${_subdir_parent}")
+  endif()
+  file(MAKE_DIRECTORY "${_dst_parent}")
+  file(COPY "${_src}" DESTINATION "${_dst_parent}")
+endforeach()
+
+execute_process(
+  COMMAND "${PATCH_EXECUTABLE}" -p1 -i "${PATCH_FILE}"
+  WORKING_DIRECTORY "${OVERLAY_ROOT}"
+  RESULT_VARIABLE patch_result
+  OUTPUT_VARIABLE patch_stdout
+  ERROR_VARIABLE patch_stderr
+)
+if(NOT patch_result EQUAL 0)
+  message(FATAL_ERROR
+    "Failed to apply ${LIBRARY_NAME} runtime log patch.\nstdout:\n${patch_stdout}\nstderr:\n${patch_stderr}")
+endif()
+
+file(WRITE "${STAMP_FILE}" "${LIBRARY_NAME} runtime log overlay ready\n")