multipers 2.7.0b5__tar.gz → 2.7.0b7__tar.gz

{multipers-2.7.0b5 → multipers-2.7.0b7}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.7.0b5
+Version: 2.7.0b7
 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>
 Maintainer-Email: David Loiseaux <david.lapous@proton.me>
-License-Expression: GPL-3.0-or-later
+License-Expression: GPL-3.0-only
 License-File: LICENSE
 License-File: THIRD_PARTY_NOTICES.md
 License-File: licenses/LGPL-3.0-or-later.txt
@@ -26,7 +26,7 @@ Project-URL: tracker, https://github.com/DavidLapous/multipers/issues
 Project-URL: release notes, https://github.com/DavidLapous/multipers/releases
 Requires-Python: >=3.10
 Requires-Dist: numpy
-Requires-Dist: gudhi>=3.8
+Requires-Dist: gudhi>=3.13
 Requires-Dist: tqdm
 Requires-Dist: scipy
 Requires-Dist: joblib
@@ -99,9 +99,12 @@ This library features a bunch of different functions and helpers. See below for
  - [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. 
  - [x] [[Projected distances for multi-parameter persistence modules, Institut Fourier]](https://aif.centre-mersenne.org/articles/10.5802/aif.3752/) and [[Computation of $\gamma$-linear projected barcodes, JACT]](https://doi.org/10.1007/s41468-025-00209-9) Provides a strategy to estimate the convolution distance between multiparameter persistence module using projected barcodes.
- - [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.
+ - [x] [[Efficient Two-Parameter Persistence Computation via Cohomology, SoCG2023]](https://doi.org/10.4230/LIPIcs.SoCG.2023.15) Minimal presentations for 2-parameter persistence using the [2pac](https://gitlab.com/flenzen/2pac) cohomology and homology backends.
  - [x] [[deg_rips]](https://bitbucket.org/mkerber/deg_rips) Efficient implementation of the DegreeRips bifiltration. Alternative to the multipers-native one.
- - [ ] [[Multiscale Clusterings BiFiltration, ICLR2026]](https://openreview.net/forum?id=E7D6uybODJ) WIP implementation. 
+ - [ ] [[Multiscale Clusterings BiFiltration, ICLR2026]](https://openreview.net/forum?id=E7D6uybODJ) Native MCbiF constructor with standard and nerve filtrations.
+ - [ ] [[Muphasa]](https://github.com/olivergafvert/muphasa) Minimal presentations for $(3+)$-parameter persistence modules.
+ - [ ] [[Graphcode: Learning from multiparameter persistent homology using graph neural networks, NeurIPS2024]](https://neurips.cc/virtual/2024/poster/95396) Graphcodes for 2-parameter persistence modules, using [graphcode](https://bitbucket.org/mkerber/graphcode).
+ - [ ] [[Computing the Skyscraper Invariant, SoCG2026]](https://doi.org/10.4230/LIPIcs.SoCG.2026.47) Skyscraper invariants and filtered landscapes for 2-parameter persistence modules, using [Skyscraper-Invariant](https://github.com/JanJend/Skyscraper-Invariant).
 
 
 If I missed something, or you want to add something, feel free to open an issue.
@@ -113,22 +116,22 @@ 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_chunk](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), [[deg_rips]](https://bitbucket.org/mkerber/deg_rips) 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
 
 `multipers` distributions that include the compiled external interfaces are provided under
-**GPL-3.0-or-later**.
+**GPL-3.0-only** when they contain the Skyscraper-Invariant backend.
 
 This is due to linked GPL/LGPL third-party components used by the build, notably
-`AIDA`, `Persistence-Algebra`, `function_delaunay`, `mpfree`, `multi_critical`, and
+`AIDA`, `Persistence-Algebra`, `Skyscraper-Invariant`, `function_delaunay`, `mpfree`, `multi_critical`, and
 `multi_chunk`.
 
 See `THIRD_PARTY_NOTICES.md` for dependency details and pinned revisions used in this workspace.
 
 ## Citation
-Please cite this library and its dependencies (see above) when using it in scientific publications;
+Please cite this library and its dependencies (see above or [in the biblio](https://davidlapous.github.io/multipers/bibliography.html)) when using it in scientific publications;
 you can use the following journal bibtex entry
 ```bib
 @article{multipers,
@@ -147,5 +150,9 @@ you can use the following journal bibtex entry
 }
 ```
 ## Contributions
-Feel free to contribute, report a bug on a pipeline, or ask for documentation by opening an issue.<br>
-In particular, if you have a nice example or application that is not taken care in the documentation (see the `./docs/notebooks/` folder), please contact me to add it there.
+Feel free to contribute, report a bug on a pipeline, or ask for documentation
+by opening an issue.<br>
+A good amount of doc pages are empty notebooks that just need to be filled!  
+In particular, if you have a nice example or application that is not taken care
+in the documentation (see the `./docs/notebooks/` folder), please open a PR or
+contact me to add it there.

{multipers-2.7.0b5 → multipers-2.7.0b7}/README.md

@@ -60,9 +60,12 @@ This library features a bunch of different functions and helpers. See below for
  - [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. 
  - [x] [[Projected distances for multi-parameter persistence modules, Institut Fourier]](https://aif.centre-mersenne.org/articles/10.5802/aif.3752/) and [[Computation of $\gamma$-linear projected barcodes, JACT]](https://doi.org/10.1007/s41468-025-00209-9) Provides a strategy to estimate the convolution distance between multiparameter persistence module using projected barcodes.
- - [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.
+ - [x] [[Efficient Two-Parameter Persistence Computation via Cohomology, SoCG2023]](https://doi.org/10.4230/LIPIcs.SoCG.2023.15) Minimal presentations for 2-parameter persistence using the [2pac](https://gitlab.com/flenzen/2pac) cohomology and homology backends.
  - [x] [[deg_rips]](https://bitbucket.org/mkerber/deg_rips) Efficient implementation of the DegreeRips bifiltration. Alternative to the multipers-native one.
- - [ ] [[Multiscale Clusterings BiFiltration, ICLR2026]](https://openreview.net/forum?id=E7D6uybODJ) WIP implementation. 
+ - [ ] [[Multiscale Clusterings BiFiltration, ICLR2026]](https://openreview.net/forum?id=E7D6uybODJ) Native MCbiF constructor with standard and nerve filtrations.
+ - [ ] [[Muphasa]](https://github.com/olivergafvert/muphasa) Minimal presentations for $(3+)$-parameter persistence modules.
+ - [ ] [[Graphcode: Learning from multiparameter persistent homology using graph neural networks, NeurIPS2024]](https://neurips.cc/virtual/2024/poster/95396) Graphcodes for 2-parameter persistence modules, using [graphcode](https://bitbucket.org/mkerber/graphcode).
+ - [ ] [[Computing the Skyscraper Invariant, SoCG2026]](https://doi.org/10.4230/LIPIcs.SoCG.2026.47) Skyscraper invariants and filtered landscapes for 2-parameter persistence modules, using [Skyscraper-Invariant](https://github.com/JanJend/Skyscraper-Invariant).
 
 
 If I missed something, or you want to add something, feel free to open an issue.
@@ -74,22 +77,22 @@ 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_chunk](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), [[deg_rips]](https://bitbucket.org/mkerber/deg_rips) 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
 
 `multipers` distributions that include the compiled external interfaces are provided under
-**GPL-3.0-or-later**.
+**GPL-3.0-only** when they contain the Skyscraper-Invariant backend.
 
 This is due to linked GPL/LGPL third-party components used by the build, notably
-`AIDA`, `Persistence-Algebra`, `function_delaunay`, `mpfree`, `multi_critical`, and
+`AIDA`, `Persistence-Algebra`, `Skyscraper-Invariant`, `function_delaunay`, `mpfree`, `multi_critical`, and
 `multi_chunk`.
 
 See `THIRD_PARTY_NOTICES.md` for dependency details and pinned revisions used in this workspace.
 
 ## Citation
-Please cite this library and its dependencies (see above) when using it in scientific publications;
+Please cite this library and its dependencies (see above or [in the biblio](https://davidlapous.github.io/multipers/bibliography.html)) when using it in scientific publications;
 you can use the following journal bibtex entry
 ```bib
 @article{multipers,
@@ -108,5 +111,9 @@ you can use the following journal bibtex entry
 }
 ```
 ## Contributions
-Feel free to contribute, report a bug on a pipeline, or ask for documentation by opening an issue.<br>
-In particular, if you have a nice example or application that is not taken care in the documentation (see the `./docs/notebooks/` folder), please contact me to add it there.
+Feel free to contribute, report a bug on a pipeline, or ask for documentation
+by opening an issue.<br>
+A good amount of doc pages are empty notebooks that just need to be filled!  
+In particular, if you have a nice example or application that is not taken care
+in the documentation (see the `./docs/notebooks/` folder), please open a PR or
+contact me to add it there.

{multipers-2.7.0b5 → multipers-2.7.0b7}/THIRD_PARTY_NOTICES.md

@@ -1,8 +1,8 @@
 # Third-Party Notices
 
 This distribution includes and/or links against third-party components with GPL/LGPL licenses.
-As a result, distributed `multipers` artifacts built with these components are licensed under
-`GPL-3.0-or-later`.
+Distributed `multipers` artifacts containing the Skyscraper-Invariant backend are licensed under
+`GPL-3.0-only`; builds without that backend remain `GPL-3.0-or-later`.
 
 ## Components
 
@@ -18,6 +18,13 @@ As a result, distributed `multipers` artifacts built with these components are l
   - Commit used in this workspace: `07e2c0d0bd7b6b48f6a584eee42d4c6ad583e078`
   - License: GPL-3.0-or-later (see `ext/Persistence-Algebra/LICENSE`)
 
+- `Skyscraper-Invariant`
+  - Upstream: https://github.com/JanJend/Skyscraper-Invariant
+  - Fork: https://github.com/DavidLapous/Skyscraper-Invariant
+  - Source in this repository: `ext/Skyscraper-Invariant/`
+  - Commit used in this workspace: `cea2ef8fd7dcdba24bd3c53820b18287de1308fe`
+  - License: GPL-3.0-only (see upstream `README.md` and `ext/Skyscraper-Invariant/LICENSE`)
+
 - `function_delaunay`
   - Upstream: https://bitbucket.org/mkerber/function_delaunay/
   - Header source path used at build time: `ext/function_delaunay`

{multipers-2.7.0b5 → multipers-2.7.0b7}/cmake/MultipersBuild.cmake

@@ -13,6 +13,7 @@ endfunction()
 multipers_default_disable_flag("mpfree" MULTIPERS_DISABLE_MPFREE_INTERFACE)
 multipers_default_disable_flag("muphasa" MULTIPERS_DISABLE_MUPHASA_INTERFACE)
 multipers_default_disable_flag("function_delaunay" MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE)
+multipers_default_disable_flag("graphcode" MULTIPERS_DISABLE_GRAPHCODE_INTERFACE)
 if(NOT DEFINED MULTIPERS_DISABLE_DEG_RIPS_INTERFACE)
   set(MULTIPERS_DISABLE_DEG_RIPS_INTERFACE OFF)
   message(STATUS "[deg_rips] Defaulted MULTIPERS_DISABLE_DEG_RIPS_INTERFACE=${MULTIPERS_DISABLE_DEG_RIPS_INTERFACE}")
@@ -22,6 +23,8 @@ endif()
 multipers_default_disable_flag("multi_critical" MULTIPERS_DISABLE_MULTI_CRITICAL_INTERFACE)
 multipers_default_disable_flag("rhomboid" MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE)
 multipers_default_disable_flag("hera" MULTIPERS_DISABLE_HERA_INTERFACE)
+multipers_default_disable_flag("persistence_algebra" MULTIPERS_DISABLE_PERSISTENCE_ALGEBRA_INTERFACE)
+multipers_default_disable_flag("skyscraper" MULTIPERS_DISABLE_SKYSCRAPER_INTERFACE)
 
 if(WIN32)
   set(MULTIPERS_DISABLE_MPFREE_INTERFACE ON)
@@ -30,6 +33,8 @@ if(WIN32)
   message(STATUS "[muphasa] Forced MULTIPERS_DISABLE_MUPHASA_INTERFACE=${MULTIPERS_DISABLE_MUPHASA_INTERFACE} on WIN32")
   set(MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE ON)
   message(STATUS "[function_delaunay] Forced MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE=${MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE} on WIN32")
+  set(MULTIPERS_DISABLE_GRAPHCODE_INTERFACE ON)
+  message(STATUS "[graphcode] Forced MULTIPERS_DISABLE_GRAPHCODE_INTERFACE=${MULTIPERS_DISABLE_GRAPHCODE_INTERFACE} on WIN32")
   set(MULTIPERS_DISABLE_DEG_RIPS_INTERFACE ON)
   message(STATUS "[deg_rips] Forced MULTIPERS_DISABLE_DEG_RIPS_INTERFACE=${MULTIPERS_DISABLE_DEG_RIPS_INTERFACE} on WIN32")
   set(MULTIPERS_DISABLE_MULTI_CRITICAL_INTERFACE ON)
@@ -38,6 +43,10 @@ if(WIN32)
   message(STATUS "[rhomboid] Forced MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE=${MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE} on WIN32")
   set(MULTIPERS_DISABLE_HERA_INTERFACE ON)
   message(STATUS "[hera] Forced MULTIPERS_DISABLE_HERA_INTERFACE=${MULTIPERS_DISABLE_HERA_INTERFACE} on WIN32")
+  set(MULTIPERS_DISABLE_PERSISTENCE_ALGEBRA_INTERFACE ON)
+  message(STATUS "[persistence_algebra] Forced MULTIPERS_DISABLE_PERSISTENCE_ALGEBRA_INTERFACE=${MULTIPERS_DISABLE_PERSISTENCE_ALGEBRA_INTERFACE} on WIN32")
+  set(MULTIPERS_DISABLE_SKYSCRAPER_INTERFACE ON)
+  message(STATUS "[skyscraper] Forced MULTIPERS_DISABLE_SKYSCRAPER_INTERFACE=ON on WIN32")
 endif()
 
 if(NOT MULTIPERS_HAS_FLAT_FILTRATION_CONTAINER)
@@ -70,6 +79,11 @@ if(NOT EXISTS "${CMAKE_SOURCE_DIR}/ext/function_delaunay/include/function_delaun
   message(STATUS "[function_delaunay] Set MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE=${MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE} because function_delaunay headers are missing")
 endif()
 
+if(NOT EXISTS "${MULTIPERS_GRAPHCODE_SOURCE_DIR}/include/graphcode/Graphcode.h")
+  set(MULTIPERS_DISABLE_GRAPHCODE_INTERFACE ON)
+  message(STATUS "[graphcode] Set MULTIPERS_DISABLE_GRAPHCODE_INTERFACE=${MULTIPERS_DISABLE_GRAPHCODE_INTERFACE} because graphcode headers are missing")
+endif()
+
 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/ext/multi_critical/include/multi_critical/basic.h")
   set(MULTIPERS_DISABLE_MULTI_CRITICAL_INTERFACE ON)
   message(STATUS "[multi_critical] Set MULTIPERS_DISABLE_MULTI_CRITICAL_INTERFACE=${MULTIPERS_DISABLE_MULTI_CRITICAL_INTERFACE} because multi_critical headers are missing")
@@ -94,6 +108,31 @@ else()
   message(STATUS "[aida] multipers_aida_static target is available")
 endif()
 
+if(MULTIPERS_DISABLE_AIDA_INTERFACE OR MULTIPERS_DISABLE_PERSISTENCE_ALGEBRA_INTERFACE
+   OR NOT TARGET multipers_aida_static
+   OR NOT EXISTS "${CMAKE_SOURCE_DIR}/ext/Persistence-Algebra/include/grlina/graded_linalg.hpp"
+   OR NOT EXISTS "${MULTIPERS_SKYSCRAPER_SOURCE_DIR}/include/skyscraper_core.hpp")
+  set(MULTIPERS_DISABLE_SKYSCRAPER_INTERFACE ON)
+  message(STATUS "[skyscraper] Disabled because AIDA, Persistence-Algebra, or core is unavailable")
+endif()
+
+if(NOT MULTIPERS_DISABLE_SKYSCRAPER_INTERFACE)
+  add_library(multipers_skyscraper_core STATIC
+    "${MULTIPERS_SKYSCRAPER_SOURCE_DIR}/src/skyscraper_core.cpp"
+    "${MULTIPERS_SKYSCRAPER_SOURCE_DIR}/src/uni_b1.cpp"
+    "${MULTIPERS_SKYSCRAPER_SOURCE_DIR}/src/hnf_at.cpp"
+  )
+  target_include_directories(multipers_skyscraper_core PUBLIC ${MULTIPERS_SKYSCRAPER_INCLUDE_DIRS})
+  if(TARGET Boost::headers)
+    target_link_libraries(multipers_skyscraper_core PUBLIC Boost::headers)
+  elseif(TARGET Boost::boost)
+    target_link_libraries(multipers_skyscraper_core PUBLIC Boost::boost)
+  else()
+    target_include_directories(multipers_skyscraper_core PUBLIC ${Boost_INCLUDE_DIRS})
+  endif()
+  set_target_properties(multipers_skyscraper_core PROPERTIES CXX_VISIBILITY_PRESET hidden VISIBILITY_INLINES_HIDDEN ON)
+endif()
+
 if(NOT TARGET multipers_rhomboid_tiling_static)
   set(MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE ON)
   message(STATUS "[rhomboid] Set MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE=${MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE} because multipers_rhomboid_tiling_static is missing")
@@ -105,12 +144,15 @@ set(MULTIPERS_INTERFACE_DISABLE_FLAGS
   MULTIPERS_DISABLE_MPFREE_INTERFACE
   MULTIPERS_DISABLE_MUPHASA_INTERFACE
   MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE
+  MULTIPERS_DISABLE_GRAPHCODE_INTERFACE
   MULTIPERS_DISABLE_DEG_RIPS_INTERFACE
   MULTIPERS_DISABLE_2PAC_INTERFACE
   MULTIPERS_DISABLE_AIDA_INTERFACE
   MULTIPERS_DISABLE_MULTI_CRITICAL_INTERFACE
   MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE
   MULTIPERS_DISABLE_HERA_INTERFACE
+  MULTIPERS_DISABLE_PERSISTENCE_ALGEBRA_INTERFACE
+  MULTIPERS_DISABLE_SKYSCRAPER_INTERFACE
 )
 
 set(MULTIPERS_INTERFACE_DISABLE_DEFINITIONS "")
@@ -175,8 +217,7 @@ set(MULTIPERS_GENERATED_INCLUDE_DIRS
 
 set(MULTIPERS_COMPILED_MODULES_DIR "${CMAKE_BINARY_DIR}/compiled_modules/multipers")
 
-if(WIN32 AND NOT SKBUILD AND NOT DEFINED ENV{MULTIPERS_INTERNAL_WHEEL_BUILD})
-  # Only collect runtime deps for local installs, not wheel builds
+if(WIN32)
   set(MULTIPERS_WINDOWS_RUNTIME_DEP_SET multipers_windows_runtime_deps)
   set(MULTIPERS_WINDOWS_RUNTIME_DEP_DIRECTORIES "")
   if(DEFINED ENV{CONDA_PREFIX} AND NOT "$ENV{CONDA_PREFIX}" STREQUAL "")
@@ -247,6 +288,11 @@ multipers_add_core_object_library(
   multipers_core_hera_obj
   "${CMAKE_SOURCE_DIR}/tools/core/hera_monte_carlo_core.cc"
 )
+
+multipers_add_core_object_library(
+  multipers_core_graph_mph0_obj
+  "${CMAKE_SOURCE_DIR}/multipers/graph_mph0/graph_mph0.cpp"
+)
 target_include_directories(
   multipers_core_hera_obj
   BEFORE
@@ -264,6 +310,7 @@ add_library(
   $<TARGET_OBJECTS:multipers_core_simplextree_obj>
   $<TARGET_OBJECTS:multipers_core_slicer_obj>
   $<TARGET_OBJECTS:multipers_core_hera_obj>
+  $<TARGET_OBJECTS:multipers_core_graph_mph0_obj>
 )
 add_dependencies(multipers_core_shared multipers_codegen)
 multipers_link_tbb(multipers_core_shared)
@@ -723,6 +770,7 @@ target_include_directories(
     ${MULTIPERS_MUPHASA_INCLUDE_DIRS}
     ${MULTIPERS_MULTI_CRITICAL_INCLUDE_DIRS}
     ${MULTIPERS_FUNCTION_DELAUNAY_INCLUDE_DIRS}
+    ${MULTIPERS_GRAPHCODE_INCLUDE_DIRS}
     ${MULTIPERS_DEG_RIPS_INCLUDE_DIRS}
     ${MULTIPERS_RHOMBOID_TILING_INCLUDE_DIRS}
     ${MULTIPERS_HERA_INCLUDE_DIRS}
@@ -759,6 +807,7 @@ function(multipers_configure_module module_name target_name)
     multipers_link_tbb(${target_name})
 
   elseif(module_name STREQUAL "_slicer_nanobind")
+    target_sources(${target_name} PRIVATE "${CMAKE_SOURCE_DIR}/multipers/graph_mph0/nanobind_interface.cpp")
     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.
@@ -782,7 +831,7 @@ function(multipers_configure_module module_name target_name)
       add_dependencies(${target_name} multipers_mpfree_log_overlay)
       multipers_link_shared_core(${target_name})
       multipers_link_nanobind_runtime(${target_name})
-      target_link_libraries(${target_name} PRIVATE Boost::system Boost::timer Boost::chrono)
+      target_link_libraries(${target_name} PRIVATE Boost::timer Boost::chrono)
       target_link_libraries(${target_name} PRIVATE "${MULTIPERS_GMP_LIBRARY}")
       multipers_link_openmp(${target_name})
       multipers_link_tbb(${target_name})
@@ -811,7 +860,7 @@ function(multipers_configure_module module_name target_name)
       add_dependencies(${target_name} multipers_function_delaunay_log_overlay)
       multipers_link_shared_core(${target_name})
       multipers_link_nanobind_runtime(${target_name})
-      target_link_libraries(${target_name} PRIVATE Boost::system Boost::timer Boost::chrono)
+      target_link_libraries(${target_name} PRIVATE Boost::timer Boost::chrono)
       target_link_libraries(${target_name} PRIVATE "${MULTIPERS_GMP_LIBRARY}")
       multipers_link_openmp(${target_name})
       multipers_link_tbb(${target_name})
@@ -819,12 +868,21 @@ function(multipers_configure_module module_name target_name)
     endif()
     set(_use_phat_includes FALSE)
 
+  elseif(module_name STREQUAL "_graphcode_interface")
+    if(NOT MULTIPERS_DISABLE_GRAPHCODE_INTERFACE)
+      multipers_link_shared_core(${target_name})
+      multipers_link_nanobind_runtime(${target_name})
+      target_link_libraries(${target_name} PRIVATE Boost::timer Boost::chrono)
+      target_include_directories(${target_name} PRIVATE ${MULTIPERS_GRAPHCODE_INCLUDE_DIRS})
+    endif()
+    set(_use_phat_includes FALSE)
+
   elseif(module_name STREQUAL "_deg_rips_interface")
     if(NOT MULTIPERS_DISABLE_DEG_RIPS_INTERFACE)
       add_dependencies(${target_name} multipers_deg_rips_optimization_overlay)
       multipers_link_shared_core(${target_name})
       multipers_link_nanobind_runtime(${target_name})
-      target_link_libraries(${target_name} PRIVATE Boost::system Boost::timer Boost::chrono)
+      target_link_libraries(${target_name} PRIVATE Boost::timer Boost::chrono)
       multipers_link_tbb(${target_name})
       target_include_directories(${target_name} PRIVATE ${MULTIPERS_DEG_RIPS_INCLUDE_DIRS})
     endif()
@@ -835,7 +893,7 @@ function(multipers_configure_module module_name target_name)
       add_dependencies(${target_name} multipers_multi_critical_log_overlay)
       multipers_link_shared_core(${target_name})
       multipers_link_nanobind_runtime(${target_name})
-      target_link_libraries(${target_name} PRIVATE Boost::system Boost::timer Boost::chrono)
+      target_link_libraries(${target_name} PRIVATE Boost::timer Boost::chrono)
       target_link_libraries(${target_name} PRIVATE "${MULTIPERS_GMP_LIBRARY}")
       multipers_link_openmp(${target_name})
       multipers_link_tbb(${target_name})
@@ -867,7 +925,7 @@ function(multipers_configure_module module_name target_name)
     if(NOT MULTIPERS_DISABLE_AIDA_INTERFACE)
       multipers_link_shared_core(${target_name})
       multipers_link_nanobind_runtime(${target_name})
-      target_link_libraries(${target_name} PRIVATE Boost::system Boost::timer Boost::chrono)
+      target_link_libraries(${target_name} PRIVATE Boost::timer Boost::chrono)
       target_link_libraries(${target_name} PRIVATE "${MULTIPERS_GMP_LIBRARY}")
       multipers_link_openmp(${target_name})
       multipers_link_tbb(${target_name})
@@ -875,6 +933,35 @@ function(multipers_configure_module module_name target_name)
       target_include_directories(${target_name} PRIVATE ${MULTIPERS_AIDA_INCLUDE_DIRS})
     endif()
 
+  elseif(module_name STREQUAL "_end_curves_interface")
+    if(NOT MULTIPERS_DISABLE_PERSISTENCE_ALGEBRA_INTERFACE)
+      target_include_directories(${target_name} PRIVATE "${CMAKE_SOURCE_DIR}/ext/Persistence-Algebra/include")
+    endif()
+    if(NOT MULTIPERS_DISABLE_AIDA_INTERFACE)
+      multipers_link_nanobind_runtime(${target_name})
+      target_link_libraries(${target_name} PRIVATE Boost::timer Boost::chrono)
+      target_link_libraries(${target_name} PRIVATE "${MULTIPERS_GMP_LIBRARY}")
+      multipers_link_openmp(${target_name})
+      multipers_link_tbb(${target_name})
+      target_link_libraries(${target_name} PRIVATE multipers_aida_static)
+      target_include_directories(${target_name} PRIVATE ${MULTIPERS_AIDA_INCLUDE_DIRS})
+    endif()
+
+  elseif(module_name STREQUAL "_persistence_algebra_interface")
+    if(NOT MULTIPERS_DISABLE_PERSISTENCE_ALGEBRA_INTERFACE)
+      multipers_link_nanobind_runtime(${target_name})
+      multipers_link_openmp(${target_name})
+      multipers_link_tbb(${target_name})
+      target_include_directories(${target_name} PRIVATE "${CMAKE_SOURCE_DIR}/ext/Persistence-Algebra/include")
+    endif()
+
+  elseif(module_name STREQUAL "_skyscraper_interface")
+    if(NOT MULTIPERS_DISABLE_SKYSCRAPER_INTERFACE)
+      multipers_link_nanobind_runtime(${target_name})
+      target_link_libraries(${target_name} PRIVATE multipers_skyscraper_core)
+      target_include_directories(${target_name} PRIVATE ${MULTIPERS_SKYSCRAPER_INCLUDE_DIRS})
+    endif()
+
   elseif(module_name STREQUAL "_hera_interface")
     if(NOT MULTIPERS_DISABLE_HERA_INTERFACE)
       multipers_link_shared_core(${target_name})
@@ -972,14 +1059,22 @@ set(MULTIPERS_NANOBIND_MODULES
   _mpfree_interface
   _muphasa_interface
   _function_delaunay_interface
+  _graphcode_interface
   _deg_rips_interface
   _2pac_interface
   _hera_interface
   _multi_critical_interface
   _rhomboid_tiling_interface
   _aida_interface
+  _end_curves_interface
+  _persistence_algebra_interface
+  _skyscraper_interface
 )
 
+if(NOT CGAL_FOUND)
+  list(REMOVE_ITEM MULTIPERS_NANOBIND_MODULES _core_delaunay_nanobind)
+endif()
+
 foreach(module_name IN LISTS MULTIPERS_NANOBIND_MODULES)
   multipers_add_nanobind_module(${module_name})
   string(REPLACE "." "_" module_target_name "multipers_${module_name}")

{multipers-2.7.0b5 → multipers-2.7.0b7}/cmake/MultipersDependencies.cmake

@@ -43,7 +43,7 @@ set(MULTIPERS_NANOBIND_ROBIN_MAP_INCLUDE_DIR "${MULTIPERS_NANOBIND_PACKAGE_DIR}/
 list(PREPEND CMAKE_PREFIX_PATH "${MULTIPERS_NANOBIND_CMAKE_DIR}")
 find_package(nanobind CONFIG REQUIRED)
 
-find_package(Boost REQUIRED COMPONENTS system timer chrono)
+find_package(Boost REQUIRED COMPONENTS timer chrono)
 find_package(OpenMP REQUIRED COMPONENTS CXX)
 find_package(TBB CONFIG REQUIRED COMPONENTS tbb)
 if(POLICY CMP0167)
@@ -74,6 +74,8 @@ if(WIN32)
   message(STATUS "[2pac] Forced MULTIPERS_DISABLE_2PAC_INTERFACE=${MULTIPERS_DISABLE_2PAC_INTERFACE} on WIN32")
   set(MULTIPERS_DISABLE_AIDA_INTERFACE ON)
   message(STATUS "[aida] Forced MULTIPERS_DISABLE_AIDA_INTERFACE=${MULTIPERS_DISABLE_AIDA_INTERFACE} on WIN32")
+  set(MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE ON)
+  message(STATUS "[rhomboid] Forced MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE=${MULTIPERS_DISABLE_RHOMBOID_TILING_INTERFACE} on WIN32")
 endif()
 
 set(
@@ -124,6 +126,12 @@ set(MULTIPERS_AIDA_INCLUDE_DIRS
   "${CMAKE_SOURCE_DIR}/ext/Persistence-Algebra/include"
 )
 
+set(MULTIPERS_SKYSCRAPER_SOURCE_DIR "${CMAKE_SOURCE_DIR}/ext/Skyscraper-Invariant" CACHE PATH "Path to Skyscraper-Invariant")
+set(MULTIPERS_SKYSCRAPER_INCLUDE_DIRS
+  "${MULTIPERS_SKYSCRAPER_SOURCE_DIR}/include"
+  "${CMAKE_SOURCE_DIR}/ext/Persistence-Algebra/include"
+)
+
 set(MULTIPERS_MPFREE_INCLUDE_DIRS
   "${CMAKE_SOURCE_DIR}/ext/mpfree/include"
   "${CMAKE_SOURCE_DIR}/ext/mpfree/mpp_utils_mod/include"
@@ -157,6 +165,13 @@ set(MULTIPERS_FUNCTION_DELAUNAY_INCLUDE_DIRS
   "${CMAKE_SOURCE_DIR}/ext/function_delaunay/scc_mod/include"
 )
 
+set(MULTIPERS_GRAPHCODE_SOURCE_DIR "${CMAKE_SOURCE_DIR}/ext/graphcode" CACHE PATH "Path to a graphcode source checkout")
+set(MULTIPERS_GRAPHCODE_INCLUDE_DIRS
+  "${MULTIPERS_GRAPHCODE_SOURCE_DIR}/include"
+  "${MULTIPERS_GRAPHCODE_SOURCE_DIR}/mpp_utils_mod/include"
+  "${MULTIPERS_GRAPHCODE_SOURCE_DIR}/phat_mod/include"
+)
+
 set(MULTIPERS_MUPHASA_SOURCE_DIR "${CMAKE_SOURCE_DIR}/ext/muphasa" CACHE PATH "Path to a Muphasa source checkout")
 set(MULTIPERS_MUPHASA_INCLUDE_DIRS "")
 if(EXISTS "${MULTIPERS_MUPHASA_SOURCE_DIR}/mph/main.cpp")

multipers-2.7.0b7/ext/2pac/CMakeLists.txt

@@ -0,0 +1,63 @@
+cmake_minimum_required(VERSION 3.28.0)
+project(2pac)
+
+# Make produced makefile show full commands.
+set(CMAKE_VERBOSE_MAKEFILE ON)
+# Set details for release and debug mode. Use release by default.
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE Release)
+endif()
+# set(CMAKE_DEBUG_POSTFIX _debug)
+# Specify flags
+set(CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+set(CMAKE_CXX_FLAGS "-Wall")
+set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O3 -flto")
+set(CMAKE_CXX_FLAGS_DEBUG "-D_LIBCPP_ENABLE_ASSERTIONS=1 -g")
+# Build variant for vector-matrices
+option(VECTORS "Build with sorted vectors as spase matrix implementatiton")
+if(VECTORS)
+   message("Building with vectors")
+   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DARRAY_MATRICES")
+endif()
+
+set(SRC_FILES
+    minimize.cpp factor.cpp chunk.cpp reductions.cpp bireductions.cpp 
+    lw.cpp complexes.cpp matrices.cpp ArrayColumn.cpp HeapColumn.cpp 
+    time_measurement.cpp block_column_matrix.cpp Cone.cpp 
+    relative_cohomology.cpp computation.cpp CliqueComplex.cpp
+)
+
+
+add_executable(2pac 2pac.cpp ${SRC_FILES})
+# set_target_properties(2pac PROPERTIES DEBUG_POSTFIX ${CMAKE_DEBUG_POSTFIX})
+
+find_package(Boost REQUIRED COMPONENTS program_options)
+include_directories(${Boost_INCLUDE_DIRS})
+link_directories(${Boost_LIBRARY_DIR_RELEASE})
+target_link_libraries(2pac ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+find_package(OpenMP COMPONENTS CXX)
+if(OpenMP_CXX_FOUND)
+    message("Will compile with multiprocessing.")
+    target_compile_options(2pac PRIVATE ${OpenMP_CXX_FLAGS})
+    target_link_libraries(2pac ${OpenMP_CXX_FLAGS})
+else()
+    message("Will compile WITHOUT multiprocessing.")
+endif()
+
+set(PYBIND11_FINDPYTHON ON)
+find_package(pybind11)
+if(pybind11_FOUND)
+    message("Will build python bindings.")
+    pybind11_add_module(2pacpy bindings.cpp ${SRC_FILES})
+    if(OpenMP_XXX_FOUND)
+        target_compile_options(2pacpy PRIVATE ${OpenMP_CXX_FLAGS})
+        target_link_libraries(2pacpy ${OpenMP_CXX_FLAGS})
+    endif()
+    set_target_properties(2pacpy PROPERTIES OUTPUT_NAME twopac)
+    # set_target_properties(2pacpy PROPERTIES DEBUG_POSTFIX ${CMAKE_DEBUG_POSTFIX})
+else()
+	message(WARNING "Could not find pybind11; will compile without python bindings.")
+endif()

{multipers-2.7.0b5 → multipers-2.7.0b7}/ext/2pac/complexes.cpp

@@ -157,7 +157,7 @@ void save_complex_scc(std::ostream &str, std::shared_ptr<Complex> complex, uint
             str << matrices[d].columns() << " ";
         }
     str << matrices.back().rows() << " # Ranks of the free modules." << std::endl;
-    str << "--field GF(2)" << std::endl;
+    // str << "--field GF(2)" << std::endl;
     for(int d = matrices.size()-1; d >= 0; --d){
         auto &m = matrices[d];
         m.data.consolidate();
@@ -167,10 +167,12 @@ void save_complex_scc(std::ostream &str, std::shared_ptr<Complex> complex, uint
         for(uint j = 0; j < m.columns(); ++j){
             str << m.column_grades[j].x << " " << m.column_grades[j].y << " ; ";
             for(auto i : m.data[j].data)
-                str << i+1 << " ";
+                // str << i+1 << " "; for one-based indexing
+                str << i << " ";
             str << std::endl;
         }
     }
+		str << std::endl;
 }
 
 #include <boost/spirit/home/x3.hpp>
@@ -236,7 +238,8 @@ MatricesFromSccFile::MatricesFromSccFile(std::ifstream& iss)
                = *pair_[(
                     [&](auto& ctx) {
                         if (_attr(ctx).second % 2){
-                            int r = _attr(ctx).first-1; // switch from 1-based indexing to 0-based indexing
+                            // int r = _attr(ctx).first-1; // switch from 1-based indexing (scc2020) to 0-based indexing (internal)
+                            int r = _attr(ctx).first;
                             if(r < 0)
                                 throw std::invalid_argument("Row indices must be positive (line " + std::to_string(line_no) + ")");
                             _val(ctx).push_back(r);
@@ -250,7 +253,8 @@ MatricesFromSccFile::MatricesFromSccFile(std::ifstream& iss)
     int last_block_begin, last_block_end;
 
     // parse blocks of rows of grade -- boundary information
-    for(int j = 0; j < ranks.size() - 1; j++){
+    for(unsigned int j = 0; j < ranks.size() - 1; j++){
+        std::cout << "Reading " << j << "th boundary matrix" << std::endl;
         int block_begin = line_no, block_end;
         std::vector<grade> grades;
         std::vector<std::vector<uint>> columns;
@@ -298,7 +302,7 @@ MatricesFromSccFile::MatricesFromSccFile(std::ifstream& iss)
     else {
         // last block given
         std::vector<grade> grades;
-        for(uint i = 0; i < ranks.back(); i++){
+        for(int i = 0; i < ranks.back(); i++){
             std::pair<double, double> result;
             if(!x3::phrase_parse(f, l,
                 *empty >> grade_ >> comment >> x3::eol[increment_line_no],
@@ -329,4 +333,4 @@ GradedMatrix MatricesFromSccFile::next_matrix(){
     auto result = std::move(matrices.back());
     matrices.pop_back();
     return result.D();
-}
+}

{multipers-2.7.0b5 → multipers-2.7.0b7}/ext/2pac/computation.hpp

@@ -3,6 +3,7 @@
 #include "block_column_matrix.hpp"
 #include "matrices.hpp"
 #include <optional>
+#include <array>
 
 typedef std::pair<GradedMatrix, GradedMatrix> resolution_t;
 typedef std::array<std::vector<grade>, 3> betti_numbers_t;

{multipers-2.7.0b5 → multipers-2.7.0b7}/ext/2pac/indirect.hpp

@@ -3,6 +3,7 @@
 #include "typedefs.hpp"
 #include "matrices.hpp"
 #include <algorithm>
+#include <optional>
 #ifdef ARRAY_MATRICES
 #include <boost/heap/priority_queue.hpp>
 

{multipers-2.7.0b5 → multipers-2.7.0b7}/ext/2pac/relative_cohomology.cpp

@@ -310,7 +310,7 @@ GradedMatrix cohomology_kernel(const GradedMatrix& Dg){
                 p.set(i, j);
                 break;
             }
-            if(!(p.get(i) < j && M_grades[p.get(i)] <= z)){
+            if(!(p.get(i) < int(j) && M_grades[p.get(i)] <= z)){
                 Q.push({M_grades[p[i]] | z, p[i]});
                 p.set(i, j);
                 break;