Merge pull request #12 from yhuang43/dev

prepare for integration into FS

CMakeLists.txt

@@ -45,13 +45,22 @@ message(STATUS "ITK_DIR=${ITK_DIR} pybind11_DIR=${pybind11_DIR}")
 # --------------------------------------------------
 #             build settings
 # --------------------------------------------------
+# set -DAPPLE_ARM64=ON on cmake command line for arm64 build
+# when building with freesurfer, CMAKE_C_COMPILER and CMAKE_CXX_COMPILER will be specified on the cmake command line
+if(APPLE_ARM64)
+  set(CMAKE_OSX_ARCHITECTURES "arm64")
+  add_definitions(-DARM64 -DDarwin -DPNG_ARM_NEON_OPT=0)
+endif()
+message(STATUS "CMAKE_C_COMPILER=${CMAKE_C_COMPILER}, CMAKE_C_COMPILER_ID=${CMAKE_C_COMPILER_ID}, CMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}, CMAKE_CXX_COMPILER_ID=${CMAKE_CXX_COMPILER_ID}")
 
 # warnings
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Werror -Wno-absolute-value -Wno-sign-compare -Wno-write-strings -Wno-unused-result -Wno-unused-parameter")
+if(NOT APPLE_ARM64)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Werror -Wno-absolute-value -Wno-sign-compare -Wno-write-strings -Wno-unused-result -Wno-unused-parameter")
+endif()
 
 # clang complains about -Wno-unused-but-set-variable and says to use -Wno-unused-const-variable
 if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-const-variable -Wno-inconsistent-missing-override")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-non-c-typedef-for-linkage -Wno-unused-const-variable -Wno-inconsistent-missing-override -Wno-self-assign-field -Wno-tautological-overlap-compare -Wno-tautological-compare -Wno-unused-value -Wno-range-loop-analysis -Wno-return-stack-address -Wno-dangling-gsl")
 else()
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-but-set-variable")
 endif()
@@ -75,6 +84,10 @@ if(PROFILING)
   set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -pg")
 endif()
 
+message(STATUS "C/C++ standard set to ${CMAKE_CXX_STANDARD}, CMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}")
+message(STATUS "For HOST_OS=${HOST_OS} CMAKE_CXX_COMPILER_ID=${CMAKE_CXX_COMPILER_ID}")
+message(STATUS "For HOST_OS=${HOST_OS} CMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}")
+
 # --------------------------------------------------
 #                 build samseg
 # --------------------------------------------------

gems/CMakeLists.txt

@@ -30,10 +30,14 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${GEMS_RUNTIME_PATH})
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${GEMS_RUNTIME_PATH})
 
 set(CMAKE_CXX_STANDARD 11)
-set(CMAKE_CXX_FLAGS "-fPIC -fpermissive -msse2 -mfpmath=sse")
+if(NOT APPLE_ARM64)
+  set(CMAKE_CXX_FLAGS "-fPIC -fpermissive -msse2 -mfpmath=sse")
+endif()
 
-# SC 2023/04/04: Commented out as it causes problem with Windows build
-# add_compile_options(-Wno-inconsistent-missing-override -Wno-self-assign-field)
+if(NOT WIN32)
+  # SC 2023/04/04: Commented out as it causes problem with Windows build
+  add_compile_options(-Wno-inconsistent-missing-override -Wno-self-assign-field)
+endif()
 
 # to set additional debug cxxflags:
 #   export GEMS_DEBUG_CXXFLAG="-DGEMS_DEBUG_RASTERIZE_VOXEL_COUNT"
@@ -158,6 +162,8 @@ set(SOURCES_DYN
   kvlAtlasMeshJacobianDeterminantDrawer.cxx
 )
 
+message(WARNING "ZLIB_LIBRARIES=${ZLIB_LIBRARIES} ITK_LIBRARIES=${ITK_LIBRARIES}")
+
 # gems libary
 add_library(kvlGEMSCommon ${SOURCES})
 target_link_libraries(kvlGEMSCommon ${ZLIB_LIBRARIES} ${ITK_LIBRARIES})

setup.py

@@ -24,7 +24,7 @@ def run(self):
                 '-H.'
             ]
             # Pass environment variables to CMake
-            for k in ['ITK_DIR', 'ZLIB_INCLUDE_DIR', 'ZLIB_LIBRARY']:
+            for k in ['ITK_DIR', 'ZLIB_INCLUDE_DIR', 'ZLIB_LIBRARY', 'pybind11_DIR', 'CMAKE_C_COMPILER', 'CMAKE_CXX_COMPILER', 'APPLE_ARM64', 'CMAKE_VERBOSE_MAKEFILE', 'CMAKE_RULE_MESSAGES']:
                 try:
                     path = os.path.abspath(os.environ[k].replace('"', ''))
                 except KeyError: