added checks for apple sillicon and cmake4.0+ version

Author: Harieasswar Lakshmidevi

CMakeLists.txt

@@ -38,7 +38,6 @@ include(FeatureSummary)
 
 find_package(PkgConfig REQUIRED)
 find_package(pybind11 CONFIG)
-find_package(OpenMP)
 # Find CUDA if GPU option is enabled
 if (USE_GPU)
     find_package(CUDA REQUIRED)  # Adjust this if you're using modern CMake with FindCUDAToolkit.
@@ -59,6 +58,23 @@ feature_summary(
 pkg_check_modules(SDSLLITE sdsl-lite)
 pkg_check_modules(LIBDIVSUFSORT libdivsufsort)
 
+# --- Start: Logic for using JEMALLOC on Apple Silicon ---
+set(JEMALLOC_LINK_LIBRARIES "jemalloc")
+
+if (APPLE AND (CMAKE_SYSTEM_PROCESSOR MATCHES "arm64" OR CMAKE_SYSTEM_PROCESSOR MATCHES "aarch64"))
+  pkg_check_modules(HOMEBREW_JEMALLOC QUIET jemalloc)
+  if (HOMEBREW_JEMALLOC_FOUND)
+    set(JEMALLOC_LINK_LIBRARIES ${HOMEBREW_JEMALLOC_LINK_LIBRARIES})
+    message(STATUS "Apple Silicon: Found Homebrew Jemalloc. Will use it.")
+    message(STATUS "  Homebrew jemalloc Includes: ${HOMEBREW_JEMALLOC_INCLUDE_DIRS}")
+    message(STATUS "  Homebrew jemalloc Link Libraries: ${HOMEBREW_JEMALLOC_LINK_LIBRARIES}")
+  else()
+    message(WARNING "Apple Silicon: Homebrew jemalloc not found via pkg-config. Will try using default jemalloc.")
+  endif ()
+  message(STATUS "jemalloc Link Library: ${JEMALLOC_LINK_LIBRARIES}")
+endif ()
+# --- End: Logic for using Homebrew HTSlib, GSL, and LibDeflate on Apple Silicon ---
+
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE Release CACHE STRING
           "Choose the type of build, options are: Release Debug Generic." FORCE)
@@ -140,14 +156,18 @@ if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin") # untested
   set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
   set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS} -lomp")
-elseif (${CMAKE_SYSTEM_NAME} MATCHES "Linux")
-  find_package(OpenMP REQUIRED)
+  set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -lomp")  # explicitly link OpenMP for building shared libs
   # add the flags it detects to the compile flags
   set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS} -fopenmp")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS} -fopenmp")
   set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
 endif()
 
+if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "4.0")
+  # Compatibility with CMake < 3.5 has been removed from CMake starting 4.0
+  set(CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_POLICY_VERSION_MINIMUM=3.5")
+endif()
+
 # Set the output folder where your program will be created
 set(CMAKE_BINARY_DIR ${CMAKE_SOURCE_DIR}/bin) # TODO Do we want to comment out this line so the binary lands in the actual build directory?
 set(EXECUTABLE_OUTPUT_PATH ${CMAKE_BINARY_DIR})
@@ -323,6 +343,7 @@ endif (NOT INLINE_HANDLEGRAPH_SOURCES)
 # taywee's C++ args library, header only
 ExternalProject_Add(tayweeargs
   SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/args"
+  CMAKE_ARGS "${CMAKE_ARGS}"
   UPDATE_COMMAND ""
   INSTALL_COMMAND "")
 ExternalProject_Get_property(tayweeargs SOURCE_DIR)
@@ -709,7 +730,7 @@ if (USE_GPU)
 endif (USE_GPU)
 
 set(odgi_LIBS
-  jemalloc
+  ${JEMALLOC_LINK_LIBRARIES}
   ${SDSLLITE_LINK_LIBRARIES}
   ${LIBDIVSUFSORT_LINK_LIBRARIES}
   "-L${CMAKE_SOURCE_DIR}/lib"