update cmakke

.gitmodules

@@ -1,9 +0,0 @@
-[submodule "lib/pybind11"]
-	path = lib/pybind11
-	url = https://github.com/pybind/pybind11.git
-[submodule "lib/hedgehog"]
-	path = lib/hedgehog
-	url = https://github.com/usnistgov/hedgehog.git
-[submodule "lib/fastloader"]
-	path = lib/fastloader
-	url = https://github.com/usnistgov/FastLoader.git

CMakeLists.txt

@@ -187,14 +187,26 @@ endif()
 
 find_file(Z5 "z5/z5.hxx" REQUIRED)
 
-find_package(FastLoader)
-if(FastLoader_FOUND)
-	list(APPEND Nyxus_LIBRARIES ${FastLoader_LIBRARIES})
-	SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${FastLoader_CXX_FLAGS}")
-	include_directories(${FastLoader_INCLUDE_DIR})
-else()
-	message(FATAL_ERROR "Unable to find FastLoader which is required for Nyxus.")
-endif()
+# find_package(FastLoader)
+# if(FastLoader_FOUND)
+# 	list(APPEND Nyxus_LIBRARIES ${FastLoader_LIBRARIES})
+# 	SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${FastLoader_CXX_FLAGS}")
+# 	include_directories(${FastLoader_INCLUDE_DIR})
+# else()
+# 	message(FATAL_ERROR "Unable to find FastLoader which is required for Nyxus.")
+# endif()
+
+find_package(Threads QUIET)
+if (Threads_FOUND)
+    if (CMAKE_USE_PTHREADS_INIT)
+		SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
+    endif (CMAKE_USE_PTHREADS_INIT)
+    list(APPEND Nyxus_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+else ()
+	message(STATUS "Unable to find threads. Nyxus must have a threading library i.e. pthreads.")
+endif ()
+message(STATUS "FL FLAGS ${CMAKE_CXX_FLAGS}")
+message(STATUS "FL LIBS ${Nyxus_LIBRARIES}")
 
 if(USEGPU)
 	set(GPU_SOURCE_FILES

tests/CMakeLists.txt

@@ -110,6 +110,19 @@ set(TEST_SRC
 
 add_executable(runAllTests ${TEST_SRC})
 
+find_package(Threads QUIET)
+if (Threads_FOUND)
+    if (CMAKE_USE_PTHREADS_INIT)
+		SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
+    endif (CMAKE_USE_PTHREADS_INIT)
+    list(APPEND runAllTests_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+else ()
+	message(STATUS "Unable to find threads. Nyxus must have a threading library i.e. pthreads.")
+endif ()
+message(STATUS "FL FLAGS ${CMAKE_CXX_FLAGS}")
+message(STATUS "FL LIBS ${runAllTests_LIBRARIES}")
+
+
 if(USEGPU)
 
 	set(GPU_SOURCE_FILES