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Add Apple Silicon support#2

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Aero-Ex merged 5 commits intoAero-Ex:mainfrom
trK54Ylmz:main
Apr 27, 2026
Merged

Add Apple Silicon support#2
Aero-Ex merged 5 commits intoAero-Ex:mainfrom
trK54Ylmz:main

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@trK54Ylmz trK54Ylmz commented Apr 24, 2026 •
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This PR intends to add Apple Silicon support.

Which features are tested?

  • Generate without constraints
  • Generate with constraints
  • Export model

What are the results of these changes?

1. Add Apple Silicon support to Motion correction 

$ python setup.py bdist_wheel
running bdist_wheel
running build
running build_py
creating build/lib.macosx-26.0-arm64-cpython-313/motion_correction
copying python/motion_correction/__init__.py -> build/lib.macosx-26.0-arm64-cpython-313/motion_correction
copying python/motion_correction/motion_postprocess.py -> build/lib.macosx-26.0-arm64-cpython-313/motion_correction
running build_ext
-- The C compiler identification is AppleClang 17.0.0.17000603
-- The CXX compiler identification is AppleClang 17.0.0.17000603
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- pybind11 not found, fetching from GitHub...
CMake Deprecation Warning at build/temp.macosx-26.0-arm64-cpython-313/_deps/pybind11-src/CMakeLists.txt:8 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- pybind11 v2.11.1
CMake Warning (dev) at build/temp.macosx-26.0-arm64-cpython-313/_deps/pybind11-src/tools/FindPythonLibsNew.cmake:98 (find_package):
  Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
  are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
  the cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  build/temp.macosx-26.0-arm64-cpython-313/_deps/pybind11-src/tools/pybind11Tools.cmake:50 (find_package)
  build/temp.macosx-26.0-arm64-cpython-313/_deps/pybind11-src/tools/pybind11Common.cmake:188 (include)
  build/temp.macosx-26.0-arm64-cpython-313/_deps/pybind11-src/CMakeLists.txt:210 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PythonInterp: /Users/tarik/External/python/kimodo/.venv/bin/python (found suitable version "3.13.13", minimum required is "3.6")
-- Found PythonLibs: /opt/homebrew/opt/python@3.13/Frameworks/Python.framework/Versions/3.13/lib/libpython3.13.dylib
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Performing Test HAS_FLTO_THIN
-- Performing Test HAS_FLTO_THIN - Success
-- Eigen3 not found, fetching from GitLab...
CMake Deprecation Warning at build/temp.macosx-26.0-arm64-cpython-313/_deps/eigen-src/CMakeLists.txt:2 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- Performing Test EIGEN_COMPILER_SUPPORT_CPP11
-- Performing Test EIGEN_COMPILER_SUPPORT_CPP11 - Success
-- Performing Test COMPILER_SUPPORT_std=cpp03
-- Performing Test COMPILER_SUPPORT_std=cpp03 - Success
-- Performing Test standard_math_library_linked_to_automatically
-- Performing Test standard_math_library_linked_to_automatically - Success
-- Standard libraries to link to explicitly: none
-- Performing Test COMPILER_SUPPORT_WERROR
-- Performing Test COMPILER_SUPPORT_WERROR - Success
-- Performing Test COMPILER_SUPPORT_pedantic
-- Performing Test COMPILER_SUPPORT_pedantic - Success
-- Performing Test COMPILER_SUPPORT_Wall
-- Performing Test COMPILER_SUPPORT_Wall - Success
-- Performing Test COMPILER_SUPPORT_Wextra
-- Performing Test COMPILER_SUPPORT_Wextra - Success
-- Performing Test COMPILER_SUPPORT_Wundef
-- Performing Test COMPILER_SUPPORT_Wundef - Success
-- Performing Test COMPILER_SUPPORT_Wcastalign
-- Performing Test COMPILER_SUPPORT_Wcastalign - Success
-- Performing Test COMPILER_SUPPORT_Wcharsubscripts
-- Performing Test COMPILER_SUPPORT_Wcharsubscripts - Success
-- Performing Test COMPILER_SUPPORT_Wnonvirtualdtor
-- Performing Test COMPILER_SUPPORT_Wnonvirtualdtor - Success
-- Performing Test COMPILER_SUPPORT_Wunusedlocaltypedefs
-- Performing Test COMPILER_SUPPORT_Wunusedlocaltypedefs - Success
-- Performing Test COMPILER_SUPPORT_Wpointerarith
-- Performing Test COMPILER_SUPPORT_Wpointerarith - Success
-- Performing Test COMPILER_SUPPORT_Wwritestrings
-- Performing Test COMPILER_SUPPORT_Wwritestrings - Success
-- Performing Test COMPILER_SUPPORT_Wformatsecurity
-- Performing Test COMPILER_SUPPORT_Wformatsecurity - Success
-- Performing Test COMPILER_SUPPORT_Wshorten64to32
-- Performing Test COMPILER_SUPPORT_Wshorten64to32 - Success
-- Performing Test COMPILER_SUPPORT_Wlogicalop
-- Performing Test COMPILER_SUPPORT_Wlogicalop - Failed
-- Performing Test COMPILER_SUPPORT_Wenumconversion
-- Performing Test COMPILER_SUPPORT_Wenumconversion - Success
-- Performing Test COMPILER_SUPPORT_Wcpp11extensions
-- Performing Test COMPILER_SUPPORT_Wcpp11extensions - Success
-- Performing Test COMPILER_SUPPORT_Wdoublepromotion
-- Performing Test COMPILER_SUPPORT_Wdoublepromotion - Success
-- Performing Test COMPILER_SUPPORT_Wshadow
-- Performing Test COMPILER_SUPPORT_Wshadow - Success
-- Performing Test COMPILER_SUPPORT_Wnopsabi
-- Performing Test COMPILER_SUPPORT_Wnopsabi - Success
-- Performing Test COMPILER_SUPPORT_Wnovariadicmacros
-- Performing Test COMPILER_SUPPORT_Wnovariadicmacros - Success
-- Performing Test COMPILER_SUPPORT_Wnolonglong
-- Performing Test COMPILER_SUPPORT_Wnolonglong - Success
-- Performing Test COMPILER_SUPPORT_fnochecknew
-- Performing Test COMPILER_SUPPORT_fnochecknew - Success
-- Performing Test COMPILER_SUPPORT_fnocommon
-- Performing Test COMPILER_SUPPORT_fnocommon - Failed
-- Performing Test COMPILER_SUPPORT_fstrictaliasing
-- Performing Test COMPILER_SUPPORT_fstrictaliasing - Failed
-- Performing Test COMPILER_SUPPORT_wd981
-- Performing Test COMPILER_SUPPORT_wd981 - Failed
-- Performing Test COMPILER_SUPPORT_wd2304
-- Performing Test COMPILER_SUPPORT_wd2304 - Failed
-- Performing Test COMPILER_SUPPORT_STRICTANSI
-- Performing Test COMPILER_SUPPORT_STRICTANSI - Failed
-- Performing Test COMPILER_SUPPORT_Qunusedarguments
-- Performing Test COMPILER_SUPPORT_Qunusedarguments - Failed
-- Performing Test COMPILER_SUPPORT_ansi
-- Performing Test COMPILER_SUPPORT_ansi - Failed
-- Performing Test COMPILER_SUPPORT_OPENMP
-- Performing Test COMPILER_SUPPORT_OPENMP - Failed
-- Looking for a Fortran compiler
-- Looking for a Fortran compiler - /opt/homebrew/bin/gfortran
-- The Fortran compiler identification is GNU 15.2.0
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /opt/homebrew/bin/gfortran - skipped
-- Found unsuitable Qt version "6.11.0" from /opt/homebrew/bin/qmake
-- Qt4 not found, so disabling the mandelbrot and opengl demos
-- Could NOT find CHOLMOD (missing: CHOLMOD_INCLUDES CHOLMOD_LIBRARIES)
-- Could NOT find UMFPACK (missing: UMFPACK_INCLUDES UMFPACK_LIBRARIES)
-- Could NOT find KLU (missing: KLU_INCLUDES KLU_LIBRARIES)
-- Could NOT find SuperLU (missing: SUPERLU_INCLUDES SUPERLU_LIBRARIES SUPERLU_VERSION_OK) (Required is at least version "4.0")
-- Checking for one of the modules 'hwloc'
-- Performing Test HAVE_HWLOC_PARENT_MEMBER
-- Performing Test HAVE_HWLOC_PARENT_MEMBER - Success
-- Performing Test HAVE_HWLOC_CACHE_ATTR
-- Performing Test HAVE_HWLOC_CACHE_ATTR - Success
-- Performing Test HAVE_HWLOC_OBJ_PU
-- Performing Test HAVE_HWLOC_OBJ_PU - Success
-- Looking for hwloc_bitmap_free in hwloc
-- Looking for hwloc_bitmap_free in hwloc - not found
-- A version of Pastix has been found but pastix_nompi.h does not exist in the include directory. Because Eigen tests require a version without MPI, we disable the Pastix backend.
--
-- Configured Eigen 3.4.0
--
-- Available targets (use: make TARGET):
-- ---------+--------------------------------------------------------------
-- Target   |   Description
-- ---------+--------------------------------------------------------------
-- install  | Install Eigen. Headers will be installed to:
--          |     <CMAKE_INSTALL_PREFIX>/<INCLUDE_INSTALL_DIR>
--          |   Using the following values:
--          |     CMAKE_INSTALL_PREFIX: /usr/local
--          |     INCLUDE_INSTALL_DIR:  include/eigen3
--          |   Change the install location of Eigen headers using:
--          |     cmake . -DCMAKE_INSTALL_PREFIX=yourprefix
--          |   Or:
--          |     cmake . -DINCLUDE_INSTALL_DIR=yourdir
-- doc      | Generate the API documentation, requires Doxygen & LaTeX
-- blas     | Build BLAS library (not the same thing as Eigen)
-- uninstall| Remove files installed by the install target
-- ---------+--------------------------------------------------------------
--
-- SSE2Neon not found; fetching from GitHub...
-- Resolved SSE2Neon_SOURCE_DIR -> /Users/tarik/External/python/kimodo/MotionCorrection/build/temp.macosx-26.0-arm64-cpython-313/_deps/sse2neon-src
-- Adding SSE2Neon include dir: /Users/tarik/External/python/kimodo/MotionCorrection/build/temp.macosx-26.0-arm64-cpython-313/_deps/sse2neon-src
-- Configuring done (24.5s)
-- Generating done (0.1s)
CMake Warning:
  Manually-specified variables were not used by the project:

    Python3_EXECUTABLE


-- Build files have been written to: /Users/tarik/External/python/kimodo/MotionCorrection/build/temp.macosx-26.0-arm64-cpython-313
[  0%] Building CXX object CMakeFiles/motion_correction_cpp_base.dir/src/cpp/Math/Types.cpp.o
[  0%] Building CXX object CMakeFiles/motion_correction_cpp_base.dir/src/cpp/Math/Quaternion.cpp.o
[ 28%] Building CXX object CMakeFiles/motion_correction_cpp_base.dir/src/cpp/Math/Matrix.cpp.o
[ 28%] Building CXX object CMakeFiles/motion_correction_cpp_base.dir/src/cpp/Math/Transform.cpp.o
[ 42%] Building CXX object CMakeFiles/motion_correction_cpp_base.dir/src/cpp/Math/Vector.cpp.o
[ 57%] Building CXX object CMakeFiles/motion_correction_cpp_base.dir/src/cpp/AnimProcessing/InverseKinematics.cpp.o
[ 57%] Building CXX object CMakeFiles/motion_correction_cpp_base.dir/src/cpp/AnimProcessing/TrajectoryCorrector.cpp.o
[ 71%] Building CXX object CMakeFiles/motion_correction_cpp_base.dir/src/cpp/AnimProcessing/Utility.cpp.o
[ 85%] Linking CXX static library libmotion_correction_cpp_base.a
[ 85%] Built target motion_correction_cpp_base
[ 85%] Building CXX object CMakeFiles/_motion_correction.dir/src/cpp/BindingsPython.cpp.o
[100%] Linking CXX shared module /Users/tarik/External/python/kimodo/MotionCorrection/build/lib.macosx-26.0-arm64-cpython-313/motion_correction/_motion_correction.cpython-313-darwin.so
[100%] Built target _motion_correction
/Users/tarik/External/python/kimodo/.venv/lib/python3.13/site-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        This deprecation is overdue, please update your project and remove deprecated
        calls to avoid build errors in the future.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
installing to build/bdist.macosx-26.0-arm64/wheel
running install
running install_lib
creating build/bdist.macosx-26.0-arm64/wheel
creating build/bdist.macosx-26.0-arm64/wheel/motion_correction
copying build/lib.macosx-26.0-arm64-cpython-313/motion_correction/_motion_correction.cpython-313-darwin.so -> build/bdist.macosx-26.0-arm64/wheel/./motion_correction
copying build/lib.macosx-26.0-arm64-cpython-313/motion_correction/__init__.py -> build/bdist.macosx-26.0-arm64/wheel/./motion_correction
copying build/lib.macosx-26.0-arm64-cpython-313/motion_correction/motion_postprocess.py -> build/bdist.macosx-26.0-arm64/wheel/./motion_correction
running install_egg_info
running egg_info
writing python/motion_correction.egg-info/PKG-INFO
writing dependency_links to python/motion_correction.egg-info/dependency_links.txt
writing requirements to python/motion_correction.egg-info/requires.txt
writing top-level names to python/motion_correction.egg-info/top_level.txt
reading manifest file 'python/motion_correction.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'test_example.py'
warning: no files found matching '*.dll' under directory 'python'
writing manifest file 'python/motion_correction.egg-info/SOURCES.txt'
Copying python/motion_correction.egg-info to build/bdist.macosx-26.0-arm64/wheel/./motion_correction-1.0.0-py3.13.egg-info
running install_scripts
creating build/bdist.macosx-26.0-arm64/wheel/motion_correction-1.0.0.dist-info/WHEEL
creating 'dist/motion_correction-1.0.0-cp313-cp313-macosx_26_0_arm64.whl' and adding 'build/bdist.macosx-26.0-arm64/wheel' to it
adding 'motion_correction/__init__.py'
adding 'motion_correction/_motion_correction.cpython-313-darwin.so'
adding 'motion_correction/motion_postprocess.py'
adding 'motion_correction-1.0.0.dist-info/METADATA'
adding 'motion_correction-1.0.0.dist-info/WHEEL'
adding 'motion_correction-1.0.0.dist-info/top_level.txt'
adding 'motion_correction-1.0.0.dist-info/RECORD'
removing build/bdist.macosx-26.0-arm64/wheel

2. Motion correction package install 

$ python -m pip install dist/motion_correction-1.0.0-cp313-cp313-macosx_26_0_arm64.whl

Which platforms are used for testing?

  • Mac Mini M1
  • Macbook Pro M3 Pro

@Aero-Ex Aero-Ex merged commit b9c286b into Aero-Ex:main Apr 27, 2026
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2 participants

@trK54Ylmz @Aero-Ex