Massive code relocation and a new (real) build system using CMake

CMakeLists.txt

@@ -0,0 +1,131 @@
+cmake_minimum_required(VERSION 2.8)
+project(HyPhy)
+
+set(DEFAULT_COMPILE_FLAGS "-w -c -fsigned-char -fast -O3")
+
+set(CMAKE_INSTALL_PREFIX /usr/local CACHE PATH "Installation prefix")
+
+add_subdirectory(contrib/gtest-1.6.0)
+set_property(
+    TARGET gtest gtest_main
+    PROPERTY EXCLUDE_FROM_ALL true
+)
+
+# file(GLOB_RECURSE HYPHY_STDLIB res/)
+# add_custom_command(OUTPUT ${HYPHY_STDLIB}
+
+install(DIRECTORY res/ DESTINATION lib/hyphy)
+
+# uninstall target
+configure_file(
+    "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
+    "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
+    IMMEDIATE @ONLY
+)
+add_custom_target(uninstall
+    COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake
+)
+
+file(GLOB SRC_CORE src/core/*.cpp)
+file(GLOB SRC_NEW src/new/*.cpp)
+file(GLOB SRC_GTESTS tests/gtests/*.cpp)
+
+set(SRC_LINK src/lib/Link/THyPhy.cpp)
+set(SRC_PREFS src/gui/preferences.cpp)
+set(SRC_SQLITE3 contrib/SQLite-3.6.17/sqlite3.c)
+set(SRC_UNIXMAIN src/mains/unix.cpp)
+set(SRC_UTILS src/utils/hyphyunixutils.cpp)
+
+set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_SQLITE3} ${SRC_UTILS})
+
+set_property(
+    SOURCE ${SRC_SQLITE3}
+    APPEND PROPERTY COMPILE_FLAGS "-Wno-int-to-pointer-cast -Wno-pointer-to-int-cast"
+)
+
+add_library(hyphy_mp SHARED
+    EXCLUDE_FROM_ALL
+    ${SRC_COMMON} ${SRC_LINK} ${SRC_PREFS}
+)
+target_link_libraries(hyphy_mp curl ssl crypto)
+install(TARGETS hyphy_mp
+    LIBRARY DESTINATION lib
+    OPTIONAL
+)
+add_custom_target(LIB DEPENDS hyphy_mp)
+
+add_executable(HYPHYMP
+    EXCLUDE_FROM_ALL
+    ${SRC_COMMON} ${SRC_UNIXMAIN}
+)
+target_link_libraries(HYPHYMP curl ssl crypto)
+install(TARGETS HYPHYMP
+    RUNTIME DESTINATION bin
+    OPTIONAL
+)
+add_custom_target(MP2 DEPENDS HYPHYMP)
+
+add_executable(HYPHYMPI
+    EXCLUDE_FROM_ALL
+    ${SRC_COMMON} ${SRC_UNIXMAIN}
+)
+target_link_libraries(HYPHYMPI curl ssl crypto)
+install(TARGETS HYPHYMPI
+    RUNTIME DESTINATION bin
+    OPTIONAL
+)
+add_custom_target(MPI DEPENDS HYPHYMPI)
+
+add_executable(HYPHYGTEST
+    EXCLUDE_FROM_ALL
+    ${SRC_COMMON} ${SRC_GTESTS} ${SRC_UNIXMAIN}
+)
+add_dependencies(HYPHYGTEST gtest)
+target_link_libraries(HYPHYGTEST curl ssl crypto gtest)
+add_custom_target(GTEST DEPENDS HYPHYGTEST)
+
+include_directories(src/core/include src/gui/include src/lib/Link src/new/include contrib contrib/gtest-1.6.0/include tests/gtests)
+add_definitions(-D_SLKP_LFENGINE_REWRITE_ -DINTPTR_TYPE=long)
+
+if(UNIX)
+    add_definitions(-D__UNIX__)
+endif(UNIX)
+
+if(CMAKE_SIZEOF_VOID_P EQUAL 8)
+    add_definitions(-D__HYPHY_64__)
+endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
+
+set_property(
+    TARGET hyphy_mp
+    APPEND PROPERTY COMPILE_DEFINITIONS __HEADLESS__
+)
+
+set_property(
+    TARGET hyphy_mp HYPHYMP
+    APPEND PROPERTY COMPILE_DEFINITIONS __MP__ __MP2__
+)
+
+set_property(
+    TARGET HYPHYMPI
+    PROPERTY COMPILE_DEFINITIONS __HYPHYMPI__
+)
+
+set_property(
+    TARGET HYPHYGTEST
+    APPEND PROPERTY COMPILE_DEFINITIONS __UNITTEST__
+)
+
+set_property(
+    TARGET HYPHYMP HYPHYMPI HYPHYGTEST
+    APPEND PROPERTY COMPILE_DEFINITIONS _HYPHY_BASEDIRECTORY_="${CMAKE_INSTALL_PREFIX}/lib/hyphy"
+)
+
+set_property(
+    TARGET hyphy_mp HYPHYMP HYPHYMPI
+    PROPERTY COMPILE_FLAGS ${DEFAULT_COMPILE_FLAGS}
+)
+
+set_property(
+    TARGET HYPHYGTEST
+    PROPERTY COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -g -fprofile-arcs -ftest-coverage"
+)

cmake/cmake_uninstall.cmake.in

@@ -0,0 +1,24 @@
+if (NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+    message(FATAL_ERROR "Cannot find install manifest: \"@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt\"")
+endif(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+
+# suppress nauseating output
+cmake_policy(SET CMP0007 OLD)
+file(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files)
+string(REGEX REPLACE "\n" ";" files "${files}")
+list(REVERSE files)
+foreach (file ${files})
+    message(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"")
+    if (EXISTS "$ENV{DESTDIR}${file}")
+        execute_process(
+            COMMAND @CMAKE_COMMAND@ -E remove "$ENV{DESTDIR}${file}"
+            OUTPUT_VARIABLE rm_out
+            RESULT_VARIABLE rm_retval
+        )
+        if(NOT ${rm_retval} EQUAL 0)
+            message(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"")
+        endif (NOT ${rm_retval} EQUAL 0)
+    else (EXISTS "$ENV{DESTDIR}${file}")
+        message(STATUS "File \"$ENV{DESTDIR}${file}\" does not exist.")
+    endif (EXISTS "$ENV{DESTDIR}${file}")
+endforeach(file)

trunk/UnitTests/gtest-1.6.0/xcode/Config/General.xcconfig → contrib/gtest-1.6.0/xcode/Config/General.xcconfig

@@ -8,7 +8,7 @@
 // 
 
 // Build for PPC and Intel, 32- and 64-bit
-ARCHS = i386
+ARCHS = i386 x86_64 ppc ppc64
 
 // Zerolink prevents link warnings so turn it off
 ZERO_LINK = NO
@@ -33,9 +33,9 @@ ALWAYS_SEARCH_USER_PATHS = NO
 GCC_DYNAMIC_NO_PIC = YES
 
 // Default SDK and minimum OS version is 10.4
-SDKROOT = $(DEVELOPER_SDK_DIR)/MacOSX10.6.sdk
-MACOSX_DEPLOYMENT_TARGET = 10.6
-GCC_VERSION = 4.2
+SDKROOT = $(DEVELOPER_SDK_DIR)/MacOSX10.4u.sdk
+MACOSX_DEPLOYMENT_TARGET = 10.4
+GCC_VERSION = 4.0
 
 // VERSIONING BUILD SETTINGS (used in Info.plist)
 GTEST_VERSIONINFO_ABOUT =  © 2008 Google Inc.

trunk/UnitTests/gtest-1.6.0/xcode/gtest.xcodeproj/project.pbxproj → contrib/gtest-1.6.0/xcode/gtest.xcodeproj/project.pbxproj

@@ -582,7 +582,6 @@
 			isa = PBXProject;
 			buildConfigurationList = 4FADC24608B4156D00ABE55E /* Build configuration list for PBXProject "gtest" */;
 			compatibilityVersion = "Xcode 2.4";
-			developmentRegion = English;
 			hasScannedForEncodings = 1;
 			knownRegions = (
 				English,