multipers 2.7.0b1__tar.gz → 2.7.0b2__tar.gz

{multipers-2.7.0b1 → multipers-2.7.0b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.7.0b1
+Version: 2.7.0b2
 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>

{multipers-2.7.0b1 → multipers-2.7.0b2}/THIRD_PARTY_NOTICES.md

@@ -46,6 +46,12 @@ As a result, distributed `multipers` artifacts built with these components are l
   - Commit used in this workspace: `8a423f7e7997b744d89405ee579b4e2f1679bbb2`
   - License: LGPL-3.0-or-later (see upstream `COPYING.LESSER`)
 
+- `muphasa`
+  - Upstream: https://github.com/olivergafvert/muphasa
+  - Header/source path used at build time: `ext/muphasa`
+  - Commit used in this workspace: `c89f7a3f958c7b8222f0d0e8cbc4e8ec8dc0ca42`
+  - License: MIT (see `ext/muphasa/LICENSE`)
+
 - `multi_critical`
   - Upstream: https://bitbucket.org/mkerber/multi_critical/
   - Header source path used at build time: `ext/multi_critical`

{multipers-2.7.0b1 → multipers-2.7.0b2}/cmake/MultipersBuild.cmake

@@ -11,6 +11,7 @@ function(multipers_default_disable_flag backend_name flag_name)
 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)
 if(NOT DEFINED MULTIPERS_DISABLE_DEG_RIPS_INTERFACE)
   set(MULTIPERS_DISABLE_DEG_RIPS_INTERFACE OFF)
@@ -25,6 +26,8 @@ multipers_default_disable_flag("hera" MULTIPERS_DISABLE_HERA_INTERFACE)
 if(WIN32)
   set(MULTIPERS_DISABLE_MPFREE_INTERFACE ON)
   message(STATUS "[mpfree] Forced MULTIPERS_DISABLE_MPFREE_INTERFACE=${MULTIPERS_DISABLE_MPFREE_INTERFACE} on WIN32")
+  set(MULTIPERS_DISABLE_MUPHASA_INTERFACE ON)
+  message(STATUS "[muphasa] Forced MULTIPERS_DISABLE_MUPHASA_INTERFACE=${MULTIPERS_DISABLE_MUPHASA_INTERFACE} on WIN32")
   set(MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE ON)
   message(STATUS "[function_delaunay] Forced MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE=${MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE} on WIN32")
   set(MULTIPERS_DISABLE_DEG_RIPS_INTERFACE ON)
@@ -57,6 +60,11 @@ if(NOT EXISTS "${CMAKE_SOURCE_DIR}/ext/mpfree/include/mpfree/mpfree.h")
   message(STATUS "[mpfree] Set MULTIPERS_DISABLE_MPFREE_INTERFACE=${MULTIPERS_DISABLE_MPFREE_INTERFACE} because mpfree headers are missing")
 endif()
 
+if(NOT EXISTS "${MULTIPERS_MUPHASA_SOURCE_DIR}/mph/main.cpp")
+  set(MULTIPERS_DISABLE_MUPHASA_INTERFACE ON)
+  message(STATUS "[muphasa] Set MULTIPERS_DISABLE_MUPHASA_INTERFACE=${MULTIPERS_DISABLE_MUPHASA_INTERFACE} because Muphasa sources are missing")
+endif()
+
 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/ext/function_delaunay/include/function_delaunay/function_delaunay_with_meb.h")
   set(MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE ON)
   message(STATUS "[function_delaunay] Set MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE=${MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE} because function_delaunay headers are missing")
@@ -95,6 +103,7 @@ endif()
 
 set(MULTIPERS_INTERFACE_DISABLE_FLAGS
   MULTIPERS_DISABLE_MPFREE_INTERFACE
+  MULTIPERS_DISABLE_MUPHASA_INTERFACE
   MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE
   MULTIPERS_DISABLE_DEG_RIPS_INTERFACE
   MULTIPERS_DISABLE_2PAC_INTERFACE
@@ -299,6 +308,7 @@ set(MULTIPERS_EXT_PATCH_DIR "${CMAKE_SOURCE_DIR}/ext/patches")
 set(MULTIPERS_GENERATED_EXT_PATCH_DIR "${CMAKE_BINARY_DIR}/generated_ext_patches")
 set(MULTIPERS_EXT_PATCH_GENERATOR "${MULTIPERS_EXT_PATCH_DIR}/generate_ext_patches.py")
 set(MULTIPERS_TRACKED_MPFREE_LOG_PATCH_FILE "${MULTIPERS_EXT_PATCH_DIR}/mpfree_runtime_logs.patch")
+set(MULTIPERS_TRACKED_MUPHASA_LOG_PATCH_FILE "${MULTIPERS_EXT_PATCH_DIR}/muphasa_runtime_logs.patch")
 set(MULTIPERS_TRACKED_FUNCTION_DELAUNAY_LOG_PATCH_FILE "${MULTIPERS_EXT_PATCH_DIR}/function_delaunay_runtime_logs.patch")
 set(MULTIPERS_TRACKED_MULTI_CRITICAL_LOG_PATCH_FILE "${MULTIPERS_EXT_PATCH_DIR}/multi_critical_runtime_logs.patch")
 set(MULTIPERS_TRACKED_MULTI_CRITICAL_FEATURES_PATCH_FILE "${MULTIPERS_EXT_PATCH_DIR}/multi_critical_features.patch")
@@ -433,6 +443,13 @@ file(
   "${CMAKE_SOURCE_DIR}/ext/function_delaunay/include/function_delaunay/*.h"
 )
 
+file(
+  GLOB MULTIPERS_MUPHASA_LOG_PATCH_INPUTS
+  CONFIGURE_DEPENDS
+  "${MULTIPERS_MUPHASA_SOURCE_DIR}/mph/*.cpp"
+  "${MULTIPERS_MUPHASA_SOURCE_DIR}/mph/*.h"
+)
+
 multipers_add_optional_generated_patch(
   MULTIPERS_DISABLE_MPFREE_INTERFACE
   multipers_generate_mpfree_log_patch
@@ -443,6 +460,16 @@ multipers_add_optional_generated_patch(
   "${CMAKE_SOURCE_DIR}/ext/mpfree/include/mpfree/global.h"
 )
 
+multipers_add_optional_generated_patch(
+  MULTIPERS_DISABLE_MUPHASA_INTERFACE
+  multipers_generate_muphasa_log_patch
+  muphasa
+  muphasa_runtime_logs.patch
+  MULTIPERS_MUPHASA_LOG_PATCH_FILE
+  "${MULTIPERS_TRACKED_MUPHASA_LOG_PATCH_FILE}"
+  ${MULTIPERS_MUPHASA_LOG_PATCH_INPUTS}
+)
+
 multipers_add_optional_generated_patch(
   MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE
   multipers_generate_function_delaunay_log_patch
@@ -494,6 +521,11 @@ multipers_add_refresh_patch_target(
   mpfree
   "${MULTIPERS_TRACKED_MPFREE_LOG_PATCH_FILE}"
 )
+multipers_add_refresh_patch_target(
+  multipers_refresh_muphasa_log_patch
+  muphasa
+  "${MULTIPERS_TRACKED_MUPHASA_LOG_PATCH_FILE}"
+)
 multipers_add_refresh_patch_target(
   multipers_refresh_function_delaunay_log_patch
   function_delaunay
@@ -522,6 +554,10 @@ add_custom_target(
     "${CMAKE_COMMAND}" -E compare_files
     "${MULTIPERS_MPFREE_LOG_PATCH_FILE}"
     "${MULTIPERS_TRACKED_MPFREE_LOG_PATCH_FILE}"
+  COMMAND
+    "${CMAKE_COMMAND}" -E compare_files
+    "${MULTIPERS_MUPHASA_LOG_PATCH_FILE}"
+    "${MULTIPERS_TRACKED_MUPHASA_LOG_PATCH_FILE}"
   COMMAND
     "${CMAKE_COMMAND}" -E compare_files
     "${MULTIPERS_FUNCTION_DELAUNAY_LOG_PATCH_FILE}"
@@ -543,6 +579,7 @@ add_custom_target(
 add_dependencies(
   multipers_generate_ext_patches
   multipers_generate_mpfree_log_patch
+  multipers_generate_muphasa_log_patch
   multipers_generate_function_delaunay_log_patch
   multipers_generate_multi_critical_log_patch
   multipers_generate_multi_critical_features_patch
@@ -551,6 +588,7 @@ add_dependencies(
 add_dependencies(
   multipers_check_ext_patches
   multipers_generate_mpfree_log_patch
+  multipers_generate_muphasa_log_patch
   multipers_generate_function_delaunay_log_patch
   multipers_generate_multi_critical_log_patch
   multipers_generate_multi_critical_features_patch
@@ -567,6 +605,16 @@ multipers_add_optional_patch_overlay(
   include
 )
 
+multipers_add_optional_patch_overlay(
+  MULTIPERS_DISABLE_MUPHASA_INTERFACE
+  multipers_muphasa_log_overlay
+  muphasa
+  "${MULTIPERS_MUPHASA_LOG_PATCH_FILE}"
+  ext/muphasa
+  MULTIPERS_MUPHASA_PATCH_OVERLAY_ROOT
+  mph
+)
+
 multipers_add_optional_patch_overlay(
   MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE
   multipers_function_delaunay_log_overlay
@@ -617,6 +665,12 @@ multipers_set_optional_include_dirs(
   "${CMAKE_SOURCE_DIR}/ext/mpfree/scc_mod/include"
 )
 
+multipers_set_optional_include_dirs(
+  MULTIPERS_DISABLE_MUPHASA_INTERFACE
+  MULTIPERS_MUPHASA_INCLUDE_DIRS
+  "${MULTIPERS_MUPHASA_PATCH_OVERLAY_ROOT}/ext/muphasa/mph"
+)
+
 multipers_set_optional_include_dirs(
   MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE
   MULTIPERS_FUNCTION_DELAUNAY_INCLUDE_DIRS
@@ -666,6 +720,7 @@ target_include_directories(
     ${MULTIPERS_AIDA_INCLUDE_DIRS}
     ${MULTIPERS_2PAC_INCLUDE_DIRS}
     ${MULTIPERS_MPFREE_INCLUDE_DIRS}
+    ${MULTIPERS_MUPHASA_INCLUDE_DIRS}
     ${MULTIPERS_MULTI_CRITICAL_INCLUDE_DIRS}
     ${MULTIPERS_FUNCTION_DELAUNAY_INCLUDE_DIRS}
     ${MULTIPERS_DEG_RIPS_INCLUDE_DIRS}
@@ -678,6 +733,7 @@ endif()
 add_dependencies(
   multipers_nanobind_runtime_obj
   multipers_mpfree_log_overlay
+  multipers_muphasa_log_overlay
   multipers_function_delaunay_log_overlay
   multipers_multi_critical_log_overlay
   multipers_deg_rips_optimization_overlay
@@ -731,6 +787,22 @@ function(multipers_configure_module module_name target_name)
     endif()
     set(_use_phat_includes FALSE)
 
+  elseif(module_name STREQUAL "_muphasa_interface")
+    if(NOT MULTIPERS_DISABLE_MUPHASA_INTERFACE)
+      add_dependencies(${target_name} multipers_muphasa_log_overlay)
+      multipers_link_shared_core(${target_name})
+      multipers_link_nanobind_runtime(${target_name})
+      if(TARGET Boost::headers)
+        target_link_libraries(${target_name} PRIVATE Boost::headers)
+      elseif(TARGET Boost::boost)
+        target_link_libraries(${target_name} PRIVATE Boost::boost)
+      else()
+        target_include_directories(${target_name} PRIVATE ${Boost_INCLUDE_DIRS})
+      endif()
+      target_include_directories(${target_name} PRIVATE ${MULTIPERS_MUPHASA_INCLUDE_DIRS})
+    endif()
+    set(_use_phat_includes FALSE)
+
   elseif(module_name STREQUAL "_function_delaunay_interface")
     if(NOT MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE)
       add_dependencies(${target_name} multipers_function_delaunay_log_overlay)
@@ -894,6 +966,7 @@ set(MULTIPERS_NANOBIND_MODULES
   _core_delaunay_nanobind
   _grid_helper_nanobind
   _mpfree_interface
+  _muphasa_interface
   _function_delaunay_interface
   _deg_rips_interface
   _2pac_interface

{multipers-2.7.0b1 → multipers-2.7.0b2}/cmake/MultipersDependencies.cmake

@@ -157,6 +157,12 @@ set(MULTIPERS_FUNCTION_DELAUNAY_INCLUDE_DIRS
   "${CMAKE_SOURCE_DIR}/ext/function_delaunay/scc_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")
+  set(MULTIPERS_MUPHASA_INCLUDE_DIRS "${MULTIPERS_MUPHASA_SOURCE_DIR}/mph")
+endif()
+
 set(MULTIPERS_DEG_RIPS_SOURCE_DIR "${CMAKE_SOURCE_DIR}/ext/deg_rips" CACHE PATH "Path to a deg_rips source checkout")
 set(MULTIPERS_DEG_RIPS_INCLUDE_DIRS "")
 if(EXISTS "${MULTIPERS_DEG_RIPS_SOURCE_DIR}/include/deg_rips/build_complex.h")

multipers-2.7.0b2/ext/muphasa/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Oliver Gäfvert, Matías R. Bender, Michael Lesnick
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

multipers-2.7.0b2/ext/muphasa/README.md

@@ -0,0 +1,26 @@
+# Muphasa
+
+Muphasa is a software to compute presentations of multi-parameter persistent homology. It was devoloped by Matías R. Bender, Oliver Gäfvert, and Michael Lesnick.
+
+## Instalation
+
+To install Muphasa you need CMake. There are two options:
+
+- If you want to install Muphasa, together with its Python package and interface, you should use the script [/scripts/install_python_interface](https://github.com/olivergafvert/muphasa/blob/main/scripts/install_python_interface) . You might need additional permitions.
+
+- If you want to compile only its console version, you can use the following lines, 
+   ```
+   mkdir build; cd build
+   cmake ../mph
+   cmake --build .
+   ```
+
+## Examples
+
+- If you installed the Python interface, you can try the notebook file [/python/notebooks/examples.ipynb](https://github.com/olivergafvert/muphasa/blob/main/python/notebooks/examples.ipynb) .
+
+- If you want to test the console version, you can run the following lines
+  ```
+  ./mph ../mph/examples/example1.txt
+  ./mph --firep ../mph/examples/example2.firep
+  ```