multipers 2.5.0b1__tar.gz → 2.5.0b2__tar.gz

multipers-2.5.0b2/.clang-format

@@ -0,0 +1,90 @@
+---
+Language:        Cpp
+AccessModifierOffset: -1
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+AllowShortLoopsOnASingleLine: true
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+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
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+BinPackParameters: false
+BraceWrapping:   
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+  AfterControlStatement: false
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+CommentPragmas:  '^ IWYU pragma:'
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+ConstructorInitializerIndentWidth: 4
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+Cpp11BracedListStyle: true
+DerivePointerAlignment: true
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+IncludeCategories: 
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IndentCaseLabels: true
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
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+ObjCBlockIndentWidth: 2
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+Standard:        Auto
+TabWidth:        4
+UseTab:          Never
+SeparateDefinitionBlocks: Always
+...
+

multipers-2.5.0b2/CITATION.cff

@@ -0,0 +1,28 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Loiseaux
+  given-names: David
+- family-names: Schreiber
+  given-names: Hannah
+doi: 10.5281/zenodo.14042221
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Loiseaux
+    given-names: David
+  - family-names: Schreiber
+    given-names: Hannah
+  date-published: 2024-11-13
+  doi: 10.21105/joss.06773
+  issn: 2475-9066
+  issue: 103
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 6773
+  title: "multipers: Multiparameter Persistence for Machine Learning"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.06773"
+  volume: 9
+title: "multipers: Multiparameter Persistence for Machine Learning"

multipers-2.5.0b2/CMakeLists.txt

@@ -0,0 +1,370 @@
+cmake_minimum_required(VERSION 3.24)
+project(multipers LANGUAGES C CXX)
+
+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(CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
+  add_compile_options(
+    $<$<COMPILE_LANGUAGE:C>:-fdiagnostics-color=always>
+    $<$<COMPILE_LANGUAGE:CXX>:-fdiagnostics-color=always>
+  )
+endif()
+
+if(MSVC)
+  add_compile_options(/bigobj)
+endif()
+
+if(DEFINED ENV{CONDA_PREFIX})
+  list(PREPEND CMAKE_PREFIX_PATH "$ENV{CONDA_PREFIX}")
+endif()
+
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development.Module NumPy)
+find_package(Boost REQUIRED COMPONENTS system timer chrono)
+find_package(OpenMP REQUIRED COMPONENTS CXX)
+
+find_package(TBB CONFIG REQUIRED COMPONENTS tbb)
+
+find_library(MULTIPERS_GMP_LIBRARY REQUIRED NAMES gmp)
+
+set(MULTIPERS_BASE_INCLUDE_DIRS
+  "${CMAKE_SOURCE_DIR}/multipers/gudhi"
+  "${CMAKE_SOURCE_DIR}/multipers"
+)
+list(APPEND MULTIPERS_BASE_INCLUDE_DIRS ${Python3_INCLUDE_DIRS})
+list(APPEND MULTIPERS_BASE_INCLUDE_DIRS ${Python3_NumPy_INCLUDE_DIRS})
+
+if(DEFINED ENV{CONDA_PREFIX})
+  list(APPEND MULTIPERS_BASE_INCLUDE_DIRS
+    "$ENV{CONDA_PREFIX}/include"
+    "$ENV{CONDA_PREFIX}/include/eigen3"
+    "$ENV{CONDA_PREFIX}/Library/include"
+    "$ENV{CONDA_PREFIX}/Library/include/eigen3"
+  )
+endif()
+list(REMOVE_DUPLICATES MULTIPERS_BASE_INCLUDE_DIRS)
+
+set(MULTIPERS_TEMPLATE_FILES
+  "${CMAKE_SOURCE_DIR}/multipers/filtrations.pxd.tp"
+  "${CMAKE_SOURCE_DIR}/multipers/filtration_conversions.pxd.tp"
+  "${CMAKE_SOURCE_DIR}/multipers/slicer.pxd.tp"
+  "${CMAKE_SOURCE_DIR}/multipers/mma_structures.pyx.tp"
+  "${CMAKE_SOURCE_DIR}/multipers/simplex_tree_multi.pyx.tp"
+  "${CMAKE_SOURCE_DIR}/multipers/slicer.pyx.tp"
+)
+
+set(MULTIPERS_GENERATED_FILES
+  "${CMAKE_SOURCE_DIR}/multipers/filtrations.pxd"
+  "${CMAKE_SOURCE_DIR}/multipers/filtration_conversions.pxd"
+  "${CMAKE_SOURCE_DIR}/multipers/slicer.pxd"
+  "${CMAKE_SOURCE_DIR}/multipers/mma_structures.pyx"
+  "${CMAKE_SOURCE_DIR}/multipers/simplex_tree_multi.pyx"
+  "${CMAKE_SOURCE_DIR}/multipers/slicer.pyx"
+)
+
+add_custom_command(
+  OUTPUT ${MULTIPERS_GENERATED_FILES}
+  COMMAND "${Python3_EXECUTABLE}" "${CMAKE_SOURCE_DIR}/_tempita_grid_gen.py"
+  COMMAND "${Python3_EXECUTABLE}" "${CMAKE_SOURCE_DIR}/tools/process_tempita.py" ${MULTIPERS_TEMPLATE_FILES}
+  DEPENDS
+    "${CMAKE_SOURCE_DIR}/_tempita_grid_gen.py"
+    "${CMAKE_SOURCE_DIR}/tools/process_tempita.py"
+    ${MULTIPERS_TEMPLATE_FILES}
+  WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+  VERBATIM
+)
+
+add_custom_target(multipers_tempita DEPENDS ${MULTIPERS_GENERATED_FILES})
+
+set(MULTIPERS_CYTHON_COMMON_ARGS
+  --cplus
+  --fast-fail
+  --directive language_level=3
+  --directive embedsignature=True
+  --directive embedsignature.format=python
+  --directive binding=True
+  --directive infer_types=True
+  --directive boundscheck=False
+  --directive wraparound=True
+  --directive iterable_coroutine=True
+  --directive annotation_typing=True
+  --directive emit_code_comments=True
+  --directive initializedcheck=False
+  --directive cdivision=True
+  --directive profile=False
+  -I "${CMAKE_SOURCE_DIR}/multipers"
+)
+
+function(multipers_collect_include_dirs output_var)
+  file(GLOB_RECURSE discovered_include_dirs CONFIGURE_DEPENDS LIST_DIRECTORIES true ${ARGN})
+  list(FILTER discovered_include_dirs INCLUDE REGEX "/include$")
+  list(REMOVE_DUPLICATES discovered_include_dirs)
+  list(SORT discovered_include_dirs)
+  set(${output_var} ${discovered_include_dirs} PARENT_SCOPE)
+endfunction()
+
+multipers_collect_include_dirs(
+  MULTIPERS_AIDA_INCLUDE_DIRS
+  "${CMAKE_SOURCE_DIR}/ext/AIDA/*"
+  "${CMAKE_SOURCE_DIR}/ext/Persistence-Algebra/*"
+)
+list(APPEND MULTIPERS_AIDA_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/ext/AIDA/src")
+list(REMOVE_DUPLICATES MULTIPERS_AIDA_INCLUDE_DIRS)
+
+multipers_collect_include_dirs(
+  MULTIPERS_MPFREE_INCLUDE_DIRS
+  "${CMAKE_SOURCE_DIR}/ext/mpfree/*"
+)
+
+multipers_collect_include_dirs(
+  MULTIPERS_MULTI_CRITICAL_INCLUDE_DIRS
+  "${CMAKE_SOURCE_DIR}/ext/multi_critical/*"
+)
+
+multipers_collect_include_dirs(
+  MULTIPERS_FUNCTION_DELAUNAY_INCLUDE_DIRS
+  "${CMAKE_SOURCE_DIR}/ext/function_delaunay/*"
+)
+
+if(NOT WIN32)
+  add_library(
+    multipers_aida_static
+    STATIC
+    "${CMAKE_SOURCE_DIR}/ext/AIDA/src/aida_decompose.cpp"
+    "${CMAKE_SOURCE_DIR}/ext/AIDA/src/aida_functions.cpp"
+    "${CMAKE_SOURCE_DIR}/ext/AIDA/src/aida_helpers.cpp"
+    "${CMAKE_SOURCE_DIR}/ext/AIDA/src/aida_interface.cpp"
+    "${CMAKE_SOURCE_DIR}/ext/AIDA/src/config.cpp"
+    "${CMAKE_SOURCE_DIR}/ext/AIDA/src/option_parser.cpp"
+    "${CMAKE_SOURCE_DIR}/ext/AIDA/src/block.cpp"
+  )
+  target_include_directories(multipers_aida_static PUBLIC ${MULTIPERS_AIDA_INCLUDE_DIRS})
+  target_link_libraries(multipers_aida_static PUBLIC Boost::timer Boost::chrono)
+endif()
+
+function(multipers_apply_common_build_flags target_name)
+  target_compile_definitions(
+    ${target_name}
+    PRIVATE
+      NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+      GUDHI_USE_TBB
+      WITH_TBB=ON
+  )
+
+  if(WIN32)
+    target_compile_definitions(
+      ${target_name}
+      PRIVATE
+        MULTIPERS_DISABLE_MPFREE_INTERFACE=1
+        MULTIPERS_DISABLE_FUNCTION_DELAUNAY_INTERFACE=1
+        MULTIPERS_DISABLE_MULTI_CRITICAL_INTERFACE=1
+    )
+  endif()
+
+  if(MSVC)
+    target_compile_options(${target_name} PRIVATE /O2 /DNDEBUG /W1 /WX- /openmp)
+  else()
+    target_compile_options(
+      ${target_name}
+      PRIVATE
+        -O3
+        -fassociative-math
+        -funsafe-math-optimizations
+        -DNDEBUG
+        -Wall
+        -Wextra
+        -Wno-assume
+    )
+  endif()
+endfunction()
+
+function(multipers_link_openmp target_name)
+  target_link_libraries(${target_name} PRIVATE OpenMP::OpenMP_CXX)
+endfunction()
+
+function(multipers_link_tbb target_name)
+  if(TARGET TBB::tbb)
+    target_link_libraries(${target_name} PRIVATE TBB::tbb)
+  elseif(TARGET TBB::tbb_static)
+    target_link_libraries(${target_name} PRIVATE TBB::tbb_static)
+  else()
+    message(FATAL_ERROR "TBB target not found")
+  endif()
+endfunction()
+
+function(multipers_add_extension module_name)
+  string(REPLACE "." "/" module_path "${module_name}")
+  set(pyx_file "${CMAKE_SOURCE_DIR}/multipers/${module_path}.pyx")
+  set(pyx_template "${CMAKE_SOURCE_DIR}/multipers/${module_path}.pyx.tp")
+  if(NOT EXISTS "${pyx_file}" AND NOT EXISTS "${pyx_template}")
+    message(FATAL_ERROR "Missing Cython source/template: ${pyx_file}")
+  endif()
+
+  set(cpp_file "${CMAKE_BINARY_DIR}/cython/${module_path}.cpp")
+  set(dep_file "${cpp_file}.dep")
+  get_filename_component(cpp_dir "${cpp_file}" DIRECTORY)
+
+  add_custom_command(
+    OUTPUT "${cpp_file}"
+    COMMAND "${CMAKE_COMMAND}" -E make_directory "${cpp_dir}"
+    COMMAND "${Python3_EXECUTABLE}" -m cython ${MULTIPERS_CYTHON_COMMON_ARGS} -M "${pyx_file}" -o "${cpp_file}"
+    DEPENDS "${pyx_file}" ${MULTIPERS_GENERATED_FILES}
+    DEPFILE "${dep_file}"
+    WORKING_DIRECTORY "${CMAKE_BINARY_DIR}"
+    VERBATIM
+  )
+
+  string(REPLACE "." "_" target_name "multipers_${module_name}")
+  Python3_add_library(${target_name} MODULE WITH_SOABI "${cpp_file}")
+  add_dependencies(${target_name} multipers_tempita)
+  set_target_properties(${target_name} PROPERTIES PREFIX "")
+
+  target_include_directories(${target_name} PRIVATE ${MULTIPERS_BASE_INCLUDE_DIRS})
+  multipers_apply_common_build_flags(${target_name})
+
+  if(module_name STREQUAL "_aida_interface")
+    if(WIN32)
+      message(FATAL_ERROR "AIDA backend is not supported on Windows")
+    endif()
+    target_include_directories(${target_name} PRIVATE ${MULTIPERS_AIDA_INCLUDE_DIRS})
+    target_link_libraries(
+      ${target_name}
+      PRIVATE
+        multipers_aida_static
+        Boost::system
+        Boost::timer
+        Boost::chrono
+        "${MULTIPERS_GMP_LIBRARY}"
+    )
+    multipers_link_openmp(${target_name})
+  elseif(module_name STREQUAL "_mpfree_interface")
+    target_include_directories(${target_name} PRIVATE ${MULTIPERS_MPFREE_INCLUDE_DIRS})
+    target_link_libraries(
+      ${target_name}
+      PRIVATE
+        Boost::system
+        Boost::timer
+        Boost::chrono
+        "${MULTIPERS_GMP_LIBRARY}"
+    )
+    multipers_link_openmp(${target_name})
+  elseif(module_name STREQUAL "_multi_critical_interface")
+    target_include_directories(${target_name} PRIVATE ${MULTIPERS_MULTI_CRITICAL_INCLUDE_DIRS})
+    target_link_libraries(
+      ${target_name}
+      PRIVATE
+        Boost::system
+        Boost::timer
+        Boost::chrono
+        "${MULTIPERS_GMP_LIBRARY}"
+    )
+    multipers_link_openmp(${target_name})
+  elseif(module_name STREQUAL "_function_delaunay_interface")
+    target_include_directories(${target_name} PRIVATE ${MULTIPERS_FUNCTION_DELAUNAY_INCLUDE_DIRS})
+    target_link_libraries(
+      ${target_name}
+      PRIVATE
+        Boost::system
+        Boost::timer
+        Boost::chrono
+        "${MULTIPERS_GMP_LIBRARY}"
+    )
+    multipers_link_openmp(${target_name})
+    multipers_link_tbb(${target_name})
+  elseif(module_name STREQUAL "io" OR module_name STREQUAL "ops")
+    # No extra native libs
+  else()
+    multipers_link_tbb(${target_name})
+  endif()
+
+  set(output_name "${module_name}")
+  set(package_dir "multipers")
+
+  set_target_properties(${target_name} PROPERTIES OUTPUT_NAME "${output_name}")
+  if(WIN32)
+    install(TARGETS ${target_name}
+    LIBRARY DESTINATION "${package_dir}"
+    RUNTIME DESTINATION "${package_dir}"
+    ARCHIVE DESTINATION "${package_dir}"
+  )
+
+    install(CODE "
+      message(STATUS \"Bundling runtime deps for: $<TARGET_FILE:${target_name}>\")
+      file(GET_RUNTIME_DEPENDENCIES
+        RESOLVED_DEPENDENCIES_VAR deps
+        UNRESOLVED_DEPENDENCIES_VAR unresolved
+        CONFLICTING_DEPENDENCIES_PREFIX conflict
+        MODULES \"$<TARGET_FILE:${target_name}>\"
+        DIRECTORIES
+          \"\$ENV{CONDA_PREFIX}/Library/bin\"
+          \"\$ENV{CONDA_PREFIX}/bin\"
+        POST_EXCLUDE_REGEXES
+          \".*[Ww]indows[/\\\\][Ss]ystem32[/\\\\].*\"
+          \"api-ms-win-.*\"
+          \"ext-ms-.*\"
+      )
+
+      foreach(dep IN LISTS deps)
+        file(INSTALL
+          DESTINATION \"\${CMAKE_INSTALL_PREFIX}/${package_dir}\"
+          TYPE SHARED_LIBRARY
+          FILES \"\${dep}\"
+        )
+      endforeach()
+
+      foreach(dep IN LISTS unresolved)
+        message(WARNING \"Unresolved dependency: \${dep}\")
+      endforeach()
+    ")
+  else()
+    install(TARGETS ${target_name}
+    LIBRARY DESTINATION "${package_dir}"
+  )
+  endif()
+endfunction()
+
+set(MULTIPERS_MODULES
+  simplex_tree_multi
+  io
+  function_rips
+  mma_structures
+  multiparameter_module_approximation
+  point_measure
+  grids
+  slicer
+  ops
+  _mpfree_interface
+  _aida_interface
+  _function_delaunay_interface
+  _multi_critical_interface
+)
+
+if(WIN32)
+  list(REMOVE_ITEM MULTIPERS_MODULES
+    _aida_interface
+    # _mpfree_interface
+    # _function_delaunay_interface
+    # _multi_critical_interface
+  )
+endif()
+
+foreach(module_name IN LISTS MULTIPERS_MODULES)
+  multipers_add_extension(${module_name})
+endforeach()
+
+install(
+  DIRECTORY "${CMAKE_SOURCE_DIR}/multipers/"
+  DESTINATION multipers
+  PATTERN "__pycache__" EXCLUDE
+  PATTERN "*.pyc" EXCLUDE
+  PATTERN "*.pyo" EXCLUDE
+  PATTERN "*.pyx" EXCLUDE
+  PATTERN "*.pxd" EXCLUDE
+  PATTERN "*.tp" EXCLUDE
+  PATTERN "*.cpp" EXCLUDE
+  PATTERN "*.h" EXCLUDE
+  PATTERN "*.hpp" EXCLUDE
+)

{multipers-2.5.0b1/multipers.egg-info → multipers-2.5.0b2}/PKG-INFO

@@ -1,15 +1,14 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.5.0b1
+Version: 2.5.0b2
 Summary: Multiparameter Topological Persistence for Machine Learning
-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
-Project-URL: source, https://github.com/DavidLapous/multipers
-Project-URL: download, https://pypi.org/project/multipers/#files
-Project-URL: tracker, https://github.com/DavidLapous/multipers/issues
-Project-URL: release notes, https://github.com/DavidLapous/multipers/releases
 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-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+License-File: licenses/LGPL-3.0-or-later.txt
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -21,26 +20,11 @@ Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Classifier: Topic :: Scientific/Engineering :: Mathematics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Project-URL: source, https://github.com/DavidLapous/multipers
+Project-URL: download, https://pypi.org/project/multipers/#files
+Project-URL: tracker, https://github.com/DavidLapous/multipers/issues
+Project-URL: release notes, https://github.com/DavidLapous/multipers/releases
 Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE
-License-File: ext/AIDA/LICENSE
-License-File: ext/Persistence-Algebra/LICENSE
-License-File: ext/function_delaunay/COPYING
-License-File: ext/function_delaunay/phat/COPYING
-License-File: ext/function_delaunay/phat/COPYING.LESSER
-License-File: ext/mpfree/COPYING
-License-File: ext/mpfree/COPYING.LESSER
-License-File: ext/mpfree/phat_mod/COPYING
-License-File: ext/mpfree/phat_mod/COPYING.LESSER
-License-File: ext/multi_chunk/COPYING
-License-File: ext/multi_chunk/COPYING.LESSER
-License-File: ext/multi_critical/COPYING
-License-File: ext/multi_critical/COPYING.LESSER
-License-File: ext/multi_critical/phat_mod/COPYING
-License-File: ext/multi_critical/phat_mod/COPYING.LESSER
-License-File: licenses/LGPL-3.0-or-later.txt
-License-File: THIRD_PARTY_NOTICES.md
 Requires-Dist: numpy
 Requires-Dist: gudhi>=3.8
 Requires-Dist: tqdm
@@ -51,7 +35,7 @@ Requires-Dist: scikit-learn
 Requires-Dist: filtration-domination
 Requires-Dist: pykeops
 Requires-Dist: pot
-Dynamic: license-file
+Description-Content-Type: text/markdown
 
 # multipers : Multiparameter Persistence for Machine Learning
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.06773/status.svg)](https://doi.org/10.21105/joss.06773) [![Documentation](https://img.shields.io/badge/Documentation-website-blue)](https://davidlapous.github.io/multipers) [![Build, test](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml/badge.svg)](https://github.com/DavidLapous/multipers/actions/workflows/python_PR.yml)

{multipers-2.5.0b1 → multipers-2.5.0b2}/THIRD_PARTY_NOTICES.md

@@ -44,5 +44,5 @@ As a result, distributed `multipers` artifacts built with these components are l
 
 ## Notes
 
-- Build-time include paths for these dependencies are configured in `setup.py`.
+- Build-time include paths for these dependencies are configured in `CMakeLists.txt`.
 - If dependency revisions are updated, update the commit hashes listed here.

multipers-2.5.0b2/build_wheel_linux.sh

@@ -0,0 +1,12 @@
+##prebuild
+python setup.py build_ext -j4
+cd build
+pip wheel .. --no-build-isolation --no-deps
+## This is just a double check; should be dealt with the MANIFEST.in file
+zip -d multipers*.whl "*.cpp"  "*.tp" "*.h"
+## repairs
+pip install auditwheel --upgrade
+auditwheel show multipers*.whl
+auditwheel repair multipers*.whl --plat $(auditwheel show multipers*.whl | grep -o 'manylinux.*"' | tr -d '"')
+mv wheelhouse/multipers*.whl ..
+cd ..

multipers-2.5.0b2/build_wheel_mac.sh

@@ -0,0 +1,12 @@
+#prebuild
+python setup.py build_ext -j4
+cd build
+pip wheel .. --no-build-isolation --no-deps
+## This is just a double check; should be dealt with the MANIFEST.in file
+zip -d multipers*.whl "*.cpp"  "*.tp" "*.h"
+## repairs
+pip install delocate --upgrade
+delocate-listdeps multipers*.whl
+delocate-wheel --require-archs x86_64 -w wheelhouse -v  multipers*.whl
+mv wheelhouse/multipers*.whl ..
+cd ..