CMakeLists.txt

# Instructions:
# $ mkdir build
# $ cd build
# $ cmake ..
# $ make

### Policies need to be set *BEFORE* calling 'project()' !!!
# Needed for hardening-flags in Fedora.  This policy will pass
# all compiler-flags to stuff like 'FIND_PACKAGE()'.  Introduced
# with CMake 3.2.0.  See documentation:
# http://www.cmake.org/cmake/help/v3.3/policy/CMP0056.html
IF(POLICY CMP0056)
	CMAKE_POLICY(SET CMP0056 NEW)
	SET(CMAKE_POLICY_DEFAULT_CMP0056 NEW)
ENDIF(POLICY CMP0056)

project(shogun)
cmake_minimum_required(VERSION 2.8.8)
SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake")
include(ShogunUtils)

############# minimum library versions ###################
SET(EIGEN_VERSION_MINIMUM 3.1.2)
SET(VIENNACL_VERSION_MINIMUM 1.5.0)

# Store system's or distribution's C[XX]FLAGS.
SET(SYSTEM_C_FLAGS "${CMAKE_C_FLAGS}")
SET(SYSTEM_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE_UC)
IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
	SET(CMAKE_C_FLAGS "")
	SET(CMAKE_CXX_FLAGS "")
ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))

# CCACHE
OPTION(ENABLE_CCACHE "Enable ccache for compilation" ON)
FIND_PACKAGE(CCache)
if(CCACHE_FOUND AND ENABLE_CCACHE)
	SET(CCACHE "ccache" CACHE STRING "ccache")
	SET(CMAKE_C_COMPILER_ARG1 ${CMAKE_C_COMPILER})
	SET(CMAKE_C_COMPILER ${CCACHE})
	SET(CMAKE_CXX_COMPILER_ARG1 ${CMAKE_CXX_COMPILER})
	SET(CMAKE_CXX_COMPILER ${CCACHE})
	SET(CMAKE_C_FLAGS "${CCACHE_FLAGS} ${CMAKE_C_FLAGS}")
	SET(CMAKE_CXX_FLAGS "${CCACHE_FLAGS} ${CMAKE_CXX_FLAGS}")
endif()

################# VARIABLES #####################
SET(INCLUDES "")

SET(EXT_SRC_HEADER "h")
SET(EXT_SRC_C "c")
SET(EXT_SRC_CPP "cpp")
SET(EXT_SRC_SWIG "_wrap.cxx")
SET(EXT_SRC_TEST "_unittest.cc")
SET(EXT_INP_SWIG "i")
SET(EXT_IF_SWIG "py")
SET(EXT_CPP_TMP "${EXT_SRC_CPP}.templ")
SET(EXT_CPP_SH "${EXT_SRC_CPP}.sh")
SET(EXT_CPP_PY "${EXT_SRC_CPP}.py")
SET(EXT_SRC_TEST_TMP "${EXT_SRC_TEST}.jinja2")

SET(THIRD_PARTY_DIR ${CMAKE_SOURCE_DIR}/third_party)
SET(LIBSHOGUN_SRC_DIR ${CMAKE_SOURCE_DIR}/src/shogun)
SET(COMMON_MODULAR_SRC_DIR ${CMAKE_SOURCE_DIR}/src/interfaces/modular/)

INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/src
	${CMAKE_SOURCE_DIR}/src/shogun
	${CMAKE_BINARY_DIR}/src
	${CMAKE_BINARY_DIR}/src/shogun)

# check whether any of the modular interfaces are turned ON
IF (
	PythonModular OR LuaModular OR RModular OR
	OctaveModular OR JavaModular OR PerlModular OR
	RubyModular OR CSharpModular
   )

	SET(SWIG_VERSION_MINIMUM 2.0.4)
	IF(CSharpModular)
		# We require SWIG 3.0.7 to support functions with a few SGVector or
		# SGMatrix arguments. The required SWIG feature is called
		# "Support for special variable expansion in typemap attributes."
		# and was introduced just in 3.0.7.
		SET(SWIG_VERSION_MINIMUM 3.0.7)

		# SWIG >= 3.0.0 has some new handling with C# (Mono) and breaks
		# typemapping created for earlier versions of SWIG.
		# see: http://www.swig.org/Doc3.0/CSharp.html#CSharp_introduction_swig2_compatibility
		LIST(APPEND CMAKE_SWIG_FLAGS "-DSWIG2_CSHARP")
	ELSEIF(RModular)
		SET(SWIG_VERSION_MINIMUM 2.0.5)
	ENDIF()
	FIND_PACKAGE(SWIG ${SWIG_VERSION_MINIMUM} REQUIRED)

	# use our own UseSWIG.cmake in order to be able to enable ccache-swig
	SET(SWIG_USE_FILE ${CMAKE_SOURCE_DIR}/cmake/UseSWIG.cmake)
	IF(ENABLE_CCACHE AND CCACHE_SWIG)
		SET(CCACHE_SWIG_EXECUTABLE ${CCACHE_SWIG})
	ENDIF()
	SET(COMPILE_MODULAR_INTERFACE 1)
ENDIF()

# Detect OS
IF(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
	SET(DARWIN 1)
ELSEIF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
	SET(LINUX 1)
ELSEIF(${CMAKE_SYSTEM_NAME} MATCHES "FreeBSD")
	SET(FREEBSD 1)
ENDIF()

# Get processor type, sets MACHINE macro
SET(MACHINE ${CMAKE_SYSTEM_PROCESSOR})

SET(EXT_LIB_SWIG_RUBY_MODULAR ".so")
if(DARWIN)
	SET(EXT_LIB_SWIG_RUBY_MODULAR ".bundle")
ENDIF()

################ COMPILER #######################
# g++ version needs to be => 4.3
IF(CMAKE_COMPILER_IS_GNUCXX)
	# in order to support cmake 2.8.7 and older
	IF(NOT CMAKE_CXX_COMPILER_VERSION)
		include(CheckCompiler)
	ENDIF()
	IF("${CMAKE_CXX_COMPILER_VERSION}" VERSION_LESS "4.3.0")
		MESSAGE(FATAL_ERROR "g++ version is too old")
	ENDIF()
ENDIF()

#Build type
if( NOT CMAKE_BUILD_TYPE )
  set( CMAKE_BUILD_TYPE Release CACHE STRING
       "Choose the type of build, options are: Debug Release Distribution."
       FORCE )
endif()

# set the flags for the build types
IF(MSVC)
	SET(COMPILER_WARNINGS "/Wall")
ELSE()
	SET(COMPILER_WARNINGS "-Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated")
ENDIF()

IF(CMAKE_COMPILER_IS_GNUCXX)
	SET(RELEASE_COMPILER_FLAGS "-fexpensive-optimizations -frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2 -fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops -mfpmath=sse")
ELSEIF("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
	SET(RELEASE_COMPILER_FLAGS "-funroll-loops")
ENDIF()
SET(SWIG_CXX_COMPILER_FLAGS "-O0 -g")
SET(CMAKE_C_FLAGS "${COMPILER_WARNINGS} ${CMAKE_C_FLAGS}")
SET(CMAKE_CXX_FLAGS "${COMPILER_WARNINGS} ${CMAKE_CXX_FLAGS}")
SET(CMAKE_C_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
SET(CMAKE_CXX_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
SET(CMAKE_C_FLAGS_DISTRIBUTION "-O2")
SET(CMAKE_CXX_FLAGS_DISTRIBUTION "-O2")
SET(CMAKE_C_FLAGS_DEBUG "-g")
SET(CMAKE_CXX_FLAGS_DEBUG "-g")

OPTION(ENABLE_COVERAGE "Enable code coverage" OFF)
IF(ENABLE_COVERAGE)
	IF(NOT CMAKE_COMPILER_IS_GNUCXX)
		MESSAGE(FATAL_ERROR "Compiler is not GNU gcc! Aborting...")
	ENDIF()
	IF (NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
		MESSAGE(WARNING "Code coverage results with an optimised (non-Debug) build may be misleading")
	ENDIF()
	SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} --coverage")
	SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
	SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} --coverage")
	SET(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} --coverage")
ENDIF()

IF(ENABLE_TSAN)
	IF (NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
		MESSAGE(WARNING "Thread-sanitizer results with an optimised (non-Debug) build may be misleading")
	ENDIF()
	SET(SANITIZER_FLAGS "-fsanitize=thread -fPIE")
	SET(SANITIZER_LIBRARY -pie)
	IF(CMAKE_COMPILER_IS_GNUCXX)
		LIST(APPEND SANITIZER_LIBRARY -ltsan)
	ELSEIF("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
		LIST(APPEND SANITIZER_LIBRARY -fsanitize=thread)
	ENDIF()
ENDIF()

IF(ENABLE_ASAN)
	IF (NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
		MESSAGE(WARNING "Address-sanitizer results with an optimised (non-Debug) build may be misleading")
	ENDIF()
	SET(SANITIZER_FLAGS "-fsanitize=address -fno-omit-frame-pointer")
	SET(SANITIZER_LIBRARY -fsanitize=address)
	IF(CMAKE_COMPILER_IS_GNUCXX)
		LIST(APPEND SANITIZER_LIBRARY -lasan)
	ENDIF()
ENDIF()

IF(ENABLE_MSAN)
	IF (NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
		MESSAGE(WARNING "Memory-sanitizer results with an optimised (non-Debug) build may be misleading")
	ENDIF()
	SET(SANITIZER_FLAGS "-fsanitize=memory -fsanitize-memory-track-origins -fno-omit-frame-pointer")
	SET(SANITIZER_LIBRARY)
	IF(CMAKE_COMPILER_IS_GNUCXX)
		LIST(APPEND SANITIZER_LIBRARY -lmsan)
	ELSEIF("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
		LIST(APPEND SANITIZER_LIBRARY -fsanitize=memory)
	ENDIF()
ENDIF()

IF(ENABLE_UBSAN)
	IF (NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
		MESSAGE(WARNING "Memory-sanitizer results with an optimised (non-Debug) build may be misleading")
	ENDIF()
	SET(SANITIZER_FLAGS "-fsanitize=undefined")
	SET(SANITIZER_LIBRARY)
	IF(CMAKE_COMPILER_IS_GNUCXX)
		LIST(APPEND SANITIZER_LIBRARY -lubsan)
	ELSEIF("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
		LIST(APPEND SANITIZER_LIBRARY -fsanitize=undefined)
	ENDIF()
ENDIF()

# check for supported c++11 features
#
# clang with -std=c++11 and -stdlib=libc++ does not work
# well with swig generated cxx hence disable c++11 for this case.

# this has been only fixed in swig 2.0.12 or later.
IF (NOT ((CYGWIN AND ENABLE_TESTING) OR (DARWIN AND COMPILE_MODULAR_INTERFACE
	AND SWIG_VERSION VERSION_LESS "2.0.12") OR MatlabStatic))
	INCLUDE(CheckCXX11Features)

	IF(_HAS_CXX11_FLAG)
		SET(HAVE_CXX11 1)
		SET(CMAKE_CXX_FLAGS "${CXX11_COMPILER_FLAGS} ${CMAKE_CXX_FLAGS}")
		SET(SWIG_CXX_COMPILER_FLAGS "${CXX11_COMPILER_FLAGS} ${SWIG_CXX_COMPILER_FLAGS}")
	ENDIF()

	IF(_HAS_CXX0X_FLAG)
		SET(HAVE_CXX0X 1)
		SET(CMAKE_CXX_FLAGS "${CXX11_COMPILER_FLAGS} ${CMAKE_CXX_FLAGS}")
		SET(SWIG_CXX_COMPILER_FLAGS "${CXX11_COMPILER_FLAGS} ${SWIG_CXX_COMPILER_FLAGS}")
	ENDIF()

ELSEIF(DARWIN AND ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang") AND NOT (CMAKE_CXX_COMPILER_VERSION VERSION_LESS "5.0.0"))
	# osx clang 5.0.0 or later uses libc++ by default
	# this is causing problems with source generated by swig version earlier than 3.0.0
	# force to use libstdc++ for compilation of sources
	SET(CMAKE_CXX_FLAGS "-stdlib=libstdc++ ${CMAKE_CXX_FLAGS}")
	SET(SWIG_CXX_COMPILER_FLAGS "-stdlib=libstdc++ ${SWIG_CXX_COMPILER_FLAGS}")
ENDIF()

# Fix build on Mac OSX 10.10 Yosemite when using mp-gcc-4X.
# See: https://github.com/shogun-toolbox/shogun/issues/2635
IF(DARWIN AND (NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang"))
	SET(CMAKE_CXX_FLAGS "-mno-avx -flax-vector-conversions -D'__has_extension(x)=0' -DvImage_Utilities_h -DvImage_CVUtilities_h ${CMAKE_CXX_FLAGS}")
	SET(SWIG_CXX_COMPILER_FLAGS "-mno-avx -flax-vector-conversions -D'__has_extension(x)=0' -DvImage_Utilities_h -DvImage_CVUtilities_h ${SWIG_CXX_COMPILER_FLAGS}")
ENDIF(DARWIN AND (NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang"))

include(CheckIncludeFileCXX)
CHECK_INCLUDE_FILE_CXX("unordered_map" HAVE_STD_UNORDERED_MAP)

###### MALLOC LIBRARY ###########
SET(EXTERNAL_MALLOC_CFLAGS "-fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free")
if (MALLOC_REPLACEMENT MATCHES "Jemalloc")
	include(external/Jemalloc)

	SET(USE_JEMALLOC 1)
	LIST(INSERT INCLUDES 0 ${Jemalloc_INCLUDE_DIR})
	SET(CMAKE_CXX_FLAGS "${EXTERNAL_MALLOC_CFLAGS} ${CMAKE_CXX_FLAGS}")
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${Jemalloc_LIBRARIES})
elseif(MALLOC_REPLACEMENT MATCHES "TCMalloc")
	include(external/TCMalloc)

	SET(USE_TCMALLOC 1)
	LIST(INSERT INCLUDES 0 ${TCMalloc_INCLUDE_DIR})
	SET(CMAKE_CXX_FLAGS "${EXTERNAL_MALLOC_CFLAGS} ${CMAKE_CXX_FLAGS}")
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${TCMalloc_LIBRARIES})
elseif(MALLOC_REPLACEMENT MATCHES "Hoard")
	find_package(Hoard)
	if (Hoard_FOUND)
		SET(USE_HOARD 1)
		SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${Hoard_LIBRARIES})
	else ()
	message(FATAL_ERROR "Unable to use hoard malloc: library not found")
	endif ()
else()
	message(STATUS "Using system's malloc")
endif()

############### VERSION #####################
FILE(STRINGS "${CMAKE_SOURCE_DIR}/NEWS" NEWS LIMIT_COUNT 5)
STRING(REGEX REPLACE ".*SHOGUN Release version ([0-9.]*).*" "\\1" VERSION "${NEWS}")
STRING(REGEX REPLACE ".*SHOGUN Release version.*\\(libshogun ([0-9.]*).*" "\\1" LIBSHOGUNVER "${NEWS}")
STRING(REGEX REPLACE ".*SHOGUN Release version.*\\(libshogun ([0-9]*).*" "\\1" LIBSHOGUNSO "${NEWS}")
STRING(REGEX REPLACE ".*SHOGUN Release version.*data ([0-9.]*).*" "\\1" DATAVER "${NEWS}")
STRING(REGEX REPLACE "([0-9]*).[0-9]*.[0-9]*" "\\1" SHOGUN_VERSION_MAJOR "${VERSION}")
STRING(REGEX REPLACE "[0-9]*.([0-9]*).[0-9]*" "\\1" SHOGUN_VERSION_MINOR "${VERSION}")
STRING(REGEX REPLACE "[0-9]*.[0-9]*.([0-9]*)" "\\1" SHOGUN_VERSION_PATCH "${VERSION}")

SET(BUILD_STATIC "Build a statically linked binary" OFF)
################# EXAMPLES ##################
OPTION(BUILD_EXAMPLES "Build Examples" ON)
OPTION(BUILD_META_EXAMPLES "Generate API examples from meta-examples" ON)
# note the examples dir is added below after tests have been defined

################# DATATYPES #################
IF(COMPILE_MODULAR_INTERFACE)
	OPTION(USE_CHAR "Support for char datatype" ON)
	OPTION(USE_BOOL "Support for bool datatype" ON)
	OPTION(USE_UINT8 "Support for uint8_t datatype" ON)
	OPTION(USE_UINT16 "Support for uint16_t datatype" ON)
	OPTION(USE_UINT32 "Support for uint32_t datatype" OFF)
	OPTION(USE_UINT64 "Support for uint64_t datatype" ON)
	OPTION(USE_INT8 "Support for int8_t datatype" OFF)
	OPTION(USE_INT16 "Support for int16_t datatype" OFF)
	OPTION(USE_INT32 "Support for int32_t datatype" ON)
	OPTION(USE_INT64 "Support for int64_t datatype" ON)
	OPTION(USE_FLOAT32 "Support for float32_t datatype" ON)
	OPTION(USE_FLOAT64 "Support for float64_t datatype" ON)
	OPTION(USE_COMPLEX128 "Support for complex128_t datatype" ON)
	OPTION(USE_FLOATMAX "Support for floatmax_t datatype" OFF)
ENDIF(COMPILE_MODULAR_INTERFACE)

IF(MSVC)
	include(external/MSIntTypes)
	LIST(APPEND INCLUDES ${THIRD_PARTY_DIR}/MSIntTypes)

	include(external/MSDirent)
	LIST(APPEND INCLUDES ${MSDIRENT_INCLUDE_DIR})
ENDIF()

# detect word size
IF(CMAKE_SIZEOF_VOID_P EQUAL 8 AND NOT DARWIN)
	SET(SWIGWORDSIZE64 TRUE)
ENDIF()

#integration
OPTION(OpenCV "OpenCV Integration" OFF)

#interfaces
OPTION(PythonModular "Python Modular" OFF)
OPTION(LuaModular "Lua Modular" OFF)
OPTION(RModular "R Modular" OFF)
OPTION(OctaveModular "Octave Modular" OFF)
OPTION(JavaModular "Java Modular" OFF)
OPTION(PerlModular "Perl Modular" OFF)
OPTION(RubyModular "Ruby Modular" OFF)
OPTION(CSharpModular "CSharp Modular" OFF)

OPTION(PythonStatic "Python Static" OFF)
OPTION(RStatic "R Static" OFF)
OPTION(CmdLineStatic "CmdLine Static" OFF)
OPTION(MatlabStatic "Matlab Static" OFF)
OPTION(OctaveStatic "Octave Static" OFF)

# Debugging Python-interface with CTest
OPTION(ENABLE_PYTHON_DEBUG "Enable Python-interface-debugging with CTest" OFF)

# Allow to hide non-bsd compatible codes
OPTION(LICENSE_GPL_SHOGUN "Include GPL codes of Shogun (non-BSD compatible) in build" ON)
IF (LICENSE_GPL_SHOGUN)
	SET(USE_GPL_SHOGUN 1)
ELSE()
	SET(USE_GPL_SHOGUN 0)
ENDIF()

# SVMLight
OPTION(USE_SVMLIGHT "SVMLight" ON)
IF(USE_SVMLIGHT AND NOT USE_GPL_SHOGUN)
	MESSAGE(FATAL_ERROR "Can only use SVMLight when GPL codes are included")
ENDIF()
SET(SVMLightWarning "\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
SET(SVMLightWarning "${SVMLightWarning}\nWARNING: SHOGUN is built using SVMlight which was written")
SET(SVMLightWarning "${SVMLightWarning}\nby Thorsten Joachims and uses a different non GPL compatible license.")
SET(SVMLightWarning "${SVMLightWarning}\nTo build a fully GPL'd SHOGUN use")
SET(SVMLightWarning "${SVMLightWarning}\nThe SVMlight license can be found in LICENSE.SVMlight.  In case")
SET(SVMLightWarning "${SVMLightWarning}\nyou do not know or cannot agree to the licensing terms expressed in")
SET(SVMLightWarning "${SVMLightWarning}\nLICENSE.SVMlight press ctrl+c to abort configure now.")
SET(SVMLightWarning "${SVMLightWarning}\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")

#Trace memory allocs
OPTION(TRACE_MEMORY_ALLOCS "Memory allocation tracing" OFF)

# HMM
OPTION(USE_HMMDEBUG "HMM cache" OFF)

OPTION(USE_HMMCACHE "HMM cache" ON)

OPTION(USE_HMMPARALLEL "Parallel structures in hmm training" OFF)
IF(USE_HMMPARALLEL)
	SET(USE_HMMPARALLEL_STRUCTURES 1)
ENDIF()

# Viterbi path debug
OPTION(USE_PATHDEBUG "Viterbi path debugging" OFF)

# big states
OPTION(USE_BIGSTATES "Big (16bit) state" ON)

# Large file
OPTION(HAVE_LARGEFILE "Large file support" ON)

#kernelcache to use 4-byte-floating-point values instead of 8-byte-doubles
OPTION(USE_SHORTREAL_KERNELCACHE "Kernelcache to use 4-byte-floating-point values instead of 8-byte-doubles" ON)

# PRNG settings
SET(MEXP "19937" CACHE STRING "PRNG Mersenne exponent")
SET(SFMT_MEXP ${MEXP})
SET(DSFMT_MEXP ${MEXP})

# Reference counting
OPTION(USE_REFERENCE_COUNTING "Reference Counting" ON)

OPTION(USE_LOGCACHE "Use (1+exp(x)) log cache (is much faster but less accurate)" OFF)

OPTION(USE_LOGSUMARRAY "Use sum array, supposed to be a bit more accurate" OFF)

######################### LIBRARIES #########################

#check for symbols
include (CheckCXXSymbolExists)
CHECK_CXX_SYMBOL_EXISTS(isfinite "cmath" HAVE_DECL_ISFINITE)
CHECK_CXX_SYMBOL_EXISTS(isinf "cmath" HAVE_DECL_ISINF)
CHECK_CXX_SYMBOL_EXISTS(isnan "cmath" HAVE_DECL_ISNAN)
CHECK_CXX_SYMBOL_EXISTS(signgam "cmath" HAVE_DECL_SIGNGAM)
CHECK_CXX_SYMBOL_EXISTS(fdopen "stdio.h" HAVE_FDOPEN)

# check for math functions
include(CheckFunctionExists)
IF(UNIX)
	SET(CMAKE_REQUIRED_LIBRARIES m)
ENDIF()
CHECK_FUNCTION_EXISTS(log2 HAVE_LOG2)
CHECK_FUNCTION_EXISTS(powl HAVE_POWL)
CHECK_FUNCTION_EXISTS(lgammal HAVE_LGAMMAL)
CHECK_FUNCTION_EXISTS(sqrtl HAVE_SQRTL)

CHECK_FUNCTION_EXISTS(finite HAVE_FPCLASS)
CHECK_FUNCTION_EXISTS(fpclass HAVE_FPCLASS)
CHECK_FUNCTION_EXISTS(isfinite HAVE_ISFINITE)
CHECK_FUNCTION_EXISTS(isinf HAVE_ISINF)
CHECK_FUNCTION_EXISTS(isnan HAVE_ISNAN)

include(CheckCXXSourceCompiles)
CHECK_CXX_SOURCE_COMPILES(
  "#include <cmath>\nint main() { return std::isinf( 0 ); }\n"
  HAVE_STD_ISINF )
CHECK_CXX_SOURCE_COMPILES(
  "#include <cmath>\nint main() { return std::isfinite( 0 ); }\n"
  HAVE_STD_ISFINITE )
CHECK_CXX_SOURCE_COMPILES(
  "#include <cmath>\nint main() { return std::isnan( 0 ); }\n"
  HAVE_STD_ISNAN )

# check SSE and SSE2 intrinsics header
OPTION(DISABLE_SSE "Disable SSE and SSE2 features." OFF)
IF((NOT CYGWIN) AND (NOT DISABLE_SSE))
include(CheckIncludeFile)
CHECK_INCLUDE_FILE(xmmintrin.h HAVE_BUILTIN_VECTOR)
CHECK_INCLUDE_FILE(emmintrin.h HAVE_SSE2)
ENDIF((NOT CYGWIN) AND (NOT DISABLE_SSE))

###### checks for random
CHECK_FUNCTION_EXISTS(arc4random HAVE_ARC4RANDOM)
IF(NOT HAVE_ARC4RANDOM)
    # assume that /dev/random is non-blocking if /dev/urandom does not exist
    if(EXISTS /dev/urandom)
      set(DEV_RANDOM "/dev/urandom" CACHE INTERNAL "" FORCE)
    elseif( EXISTS /dev/random )
      set(DEV_RANDOM "/dev/random" CACHE INTERNAL "" FORCE)
    endif()
ENDIF()

FIND_PACKAGE(GDB)
IF (GDB_FOUND)
	SET(GDB_DEFAULT_SCRIPT ${CMAKE_CURRENT_SOURCE_DIR}/src/.gdb)
ENDIF()

FIND_PACKAGE(Mosek)
IF (MOSEK_FOUND)
	SET(USE_MOSEK 1)
	LIST(APPEND INCLUDES ${MOSEK_INCLUDE_DIR})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${MOSEK_LIBRARY})
ENDIF()

FIND_PACKAGE(Threads)
IF (CMAKE_USE_PTHREADS_INIT)
	SET(HAVE_PTHREAD 1)
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${CMAKE_THREAD_LIBS_INIT})
ENDIF()

FIND_PACKAGE(OpenMP)
if (OPENMP_FOUND)
	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}")
endif()

FIND_PACKAGE(PkgConfig)

# prefer original LAPACK, if needed
OPTION(USE_ORIGINAL_LAPACK "Original LAPACK" OFF)

FIND_PACKAGE(LAPACK)
IF (LAPACK_FOUND)
	# find out whether it is Accelerate.framework we found for LaPack/BLAS
	IF("${LAPACK_LIBRARIES}" MATCHES ".*/Accelerate.framework$")
		SET(HAVE_MVEC 1)

		#Accelerate framework provides HAVE_CATLAS
		SET(HAVE_CATLAS 1)

		SET(HAVE_LAPACK 1)
		SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${LAPACK_LIBRARIES})
	ELSEIF("${LAPACK_LIBRARIES}" MATCHES ".*/mkl_.*")
		SET(HAVE_LAPACK 1)
		SET(HAVE_MKL 1)
	ELSE()
		FIND_PACKAGE(Atlas)
		IF(ATLAS_FOUND)
			SET(HAVE_ATLAS 1)
			SET(HAVE_LAPACK 1)
			LIST(APPEND INCLUDES ${ATLAS_INCLUDES})
			IF(USE_ORIGINAL_LAPACK)
				SET(ATLAS_CLAPACK_LIBRARY)
				FOREACH(ITR ${ATLAS_LIBRARIES})
					IF(ITR MATCHES ".*atlas.*lapack.*" OR ITR MATCHES ".*lapack.*atlas.*")
					STRING(REGEX REPLACE "lapack" "clapack" ITR ${ITR})
					LIST(APPEND ATLAS_CLAPACK_LIBRARY ${ITR})
					ENDIF(ITR MATCHES ".*atlas.*lapack.*" OR ITR MATCHES ".*lapack.*atlas.*")
				ENDFOREACH(ITR ${ATLAS_LIBRARIES})
				MESSAGE(STATUS "using ATLAS-CLAPACK from: ${ATLAS_CLAPACK_LIBRARY}")
				SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${LAPACK_LIBRARIES} ${ATLAS_CLAPACK_LIBRARY} ${ATLAS_LIBRARIES})
			ELSE(USE_ORIGINAL_LAPACK)
				SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${ATLAS_LIBRARIES})
			ENDIF(USE_ORIGINAL_LAPACK)
		ELSE()
			FIND_PACKAGE(CBLAS)
		    if(CBLAS_LIBRARY)
				SET(HAVE_LAPACK 1)
				SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${LAPACK_LIBRARIES} ${CBLAS_LIBRARY})
			else()
				SET(HAVE_LAPACK 1)
				SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${LAPACK_LIBRARIES})
		    endif()
		ENDIF()
	ENDIF()
ENDIF()

FIND_PACKAGE(GLPK)
IF (GLPK_FOUND)
	SET(USE_GLPK 1)
	LIST(APPEND INCLUDES ${GLPK_INCLUDE_DIRS})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${GLPK_LIBRARY})
ENDIF()

FIND_PACKAGE(CPLEX)
IF (CPLEX_FOUND)
	SET(USE_CPLEX 1)
	LIST(APPEND INCLUDES ${CPLEX_INCLUDE_DIR})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${CPLEX_LIBRARY})
ENDIF()

FIND_PACKAGE(ARPACK)
IF (ARPACK_FOUND)
	SET(HAVE_ARPACK 1)
	LIST(APPEND INCLUDES ${ARPACK_INCLUDE_DIR})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${ARPACK_LIB})
ENDIF()

FIND_PACKAGE(Eigen3 ${EIGEN_VERSION_MINIMUM})
IF(NOT EIGEN3_FOUND)
	include(external/Eigen3)
	LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR})
ELSE()
	LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR})
ENDIF()

# OpenCL/ViennaCL detection
OPTION(ENABLE_VIENNACL "Enable ViennaCL" ON)
FIND_PACKAGE(ViennaCL ${VIENNACL_VERSION_MINIMUM})
IF (VIENNACL_FOUND AND ENABLE_VIENNACL)
	SET(HAVE_VIENNACL 1)
	LIST(APPEND INCLUDES ${VIENNACL_INCLUDE_DIRS})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${VIENNACL_LIBRARIES})
	SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OPENCL_C_FLAGS}")
	SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OPENCL_CXX_FLAGS}")
	SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OPENCL_EXE_LINKER_FLAGS}")
ENDIF()

IF (OpenCV)
	# find OpenCV library if intended by the user.
	FIND_PACKAGE(OpenCV)
	IF (OpenCV_FOUND)
		SET(HAVE_OPENCV 1)
		LIST(APPEND INCLUDES ${OpenCV_INCLUDE_DIRS})
		SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${OpenCV_LIBRARIES})
	ENDIF()
ENDIF()

# COLPACK
OPTION(BUNDLE_COLPACK "Bundle COLPACK" OFF)
IF(BUNDLE_COLPACK)
	include(external/ColPack)
	SET(HAVE_COLPACK 1)
	LIST(APPEND INCLUDES ${COLPACK_INCLUDE_DIRS})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${COLPACK_LDFLAGS})
ELSE()
	IF (PKG_CONFIG_FOUND)
		pkg_search_module(COLPACK libColPack>=1.0.9 ColPack>=1.0.9)
		IF (COLPACK_FOUND)
			SET(HAVE_COLPACK 1)
			LIST(APPEND INCLUDES ${COLPACK_INCLUDE_DIRS})
			SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${COLPACK_LDFLAGS})
		ENDIF()
	ENDIF()
ENDIF()

OPTION(BUNDLE_NLOPT "Bundle NLOPT" OFF)
IF(BUNDLE_NLOPT)
	include(external/NLopt)
	SET(HAVE_NLOPT 1)
	LIST(APPEND INCLUDES ${NLOPT_INCLUDE_DIR})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${NLOPT_LIBRARIES})
ELSE()
	FIND_PACKAGE(NLopt)
	IF (NLOPT_FOUND)
		SET(HAVE_NLOPT 1)
		LIST(APPEND INCLUDES ${NLOPT_INCLUDE_DIR})
		SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${NLOPT_LIBRARIES})
	ENDIF()
ENDIF()

FIND_PACKAGE(LpSolve)
IF (LPSOLVE_FOUND)
	SET(USE_LPSOLVE 1)
	#LIST(APPEND DEFINES USE_LPSOLVE YY_NEVER_INTERACTIVE PARSER_LP INVERSE_ACTIVE=INVERSE_LUSOL RoleIsExternalInvEngine)
	LIST(APPEND INCLUDES ${LPSOLVE_INCLUDE_DIR})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${LPSOLVE_LIBRARIES})
ENDIF()

FIND_PACKAGE(ColPack)
IF(COLPACK_FOUND)
	SET(HAVE_COLPACK 1)
	LIST(APPEND INCLUDES ${COLPACK_INCLUDE_DIR})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${COLPACK_LIBRARIES})
ENDIF()

OPTION(USE_ARPREC "Use ARPREC (bundle if not found)" OFF)
IF(USE_ARPREC AND NOT LICENSE_GPL_SHOGUN)
	MESSAGE(FATAL_ERROR "ARPREC can only be used if USE_GPL_SHOGUN is enabled ")
ENDIF()
IF(USE_ARPREC)
	FIND_PACKAGE(ARPREC)
	IF(ARPREC_FOUND)
		SET(HAVE_ARPREC 1)
		LIST(APPEND INCLUDES ${ARPREC_INCLUDE_DIR})
		SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${ARPREC_LIBRARIES})
	ELSE()
		include(external/ARPREC)
		SET(HAVE_ARPREC 1)
		LIST(APPEND INCLUDES ${ARPREC_INCLUDE_DIR})
		SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${ARPREC_LIBRARIES})
	ENDIF()
ENDIF()


FIND_PACKAGE(Doxygen 1.8.6)
IF(DOXYGEN_FOUND)
	SET(HAVE_DOXYGEN 1)
ENDIF()

# detect PYTHON
FIND_PACKAGE(PythonInterp REQUIRED)

# Meta examples and dependencies
IF(BUILD_META_EXAMPLES)
    FIND_PACKAGE(PLY REQUIRED)
    IF(NOT PLY_FOUND)
        message(FATAL_ERROR "Python module ply required for meta examples. Disable meta examples or install python-ply")
    ENDIF()

    FIND_PACKAGE(Ctags)
    IF(NOT CTAGS_FOUND)
        message(FATAL_ERROR "Ctags required for meta examples.")
    ENDIF()
ENDIF(BUILD_META_EXAMPLES)

# add meta example dir below after tests have been defined

# cookbook and dependencies
find_package(Sphinx)
IF(BUILD_META_EXAMPLES AND SPHINX_FOUND)
    SET(BUILD_COOKBOOK 1)
ENDIF()

# JSON
OPTION(BUNDLE_JSON "Bundle JSON" OFF)
IF(BUNDLE_JSON)
	include(external/JSON)
	SET(HAVE_JSON 1)
	LIST(APPEND INCLUDES ${JSON_INCLUDE_DIRS})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${JSON_LDFLAGS})
ELSE()
	IF (PKG_CONFIG_FOUND)
		pkg_search_module(JSON libjson>=0.11 json>=0.11 json-c>=0.11)
		IF (JSON_FOUND)
			SET(HAVE_JSON 1)
			LIST(APPEND INCLUDES ${JSON_INCLUDE_DIRS})
			SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${JSON_LDFLAGS})
		ENDIF()
	ENDIF()
ENDIF()

FIND_PACKAGE(LibXml2)
IF (LIBXML2_FOUND)
	SET(HAVE_XML 1)
	LIST(APPEND INCLUDES ${LIBXML2_INCLUDE_DIR})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${LIBXML2_LIBRARIES})
ENDIF()

OPTION(USE_HDF5 "Use HDF5" ON)
FIND_PACKAGE(HDF5)
IF (HDF5_FOUND AND USE_HDF5)
	SET(HAVE_HDF5 1)
	LIST(APPEND INCLUDES ${HDF5_INCLUDE_DIRS})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${HDF5_LIBRARIES})
ENDIF()

FIND_PACKAGE(CURL)
IF (CURL_FOUND)
	SET(HAVE_CURL 1)
	LIST(APPEND INCLUDES ${CURL_INCLUDE_DIRS})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${CURL_LIBRARIES})
ENDIF(CURL_FOUND)

FIND_PACKAGE(ZLIB)
IF (ZLIB_FOUND)
	SET(USE_GZIP 1)
	LIST(APPEND INCLUDES ${ZLIB_INCLUDE_DIRS})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${ZLIB_LIBRARIES})
ENDIF()

FIND_PACKAGE(BZip2)
IF (BZIP2_FOUND)
	SET(USE_BZIP2 1)
	LIST(APPEND INCLUDES ${BZIP_INCLUDE_DIRS})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${BZIP2_LIBRARIES})
ENDIF()

FIND_PACKAGE(LibLZMA)
IF (LIBLZMA_FOUND)
	SET(USE_LZMA 1)
	LIST(APPEND INCLUDES ${LIBLZMA_INCLUDE_DIRS})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${LIBLZMA_LIBRARIES})
ENDIF()

FIND_PACKAGE(SNAPPY)
IF (SNAPPY_FOUND)
	SET(USE_SNAPPY 1)
	LIST(APPEND INCLUDES ${SNAPPY_INCLUDE_DIR})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${SNAPPY_LIBRARIES})
ENDIF()

FIND_PACKAGE(LZO)
IF (LZO_FOUND)
	SET(USE_LZO 1)
	LIST(APPEND INCLUDES ${LZO_INCLUDE_DIR})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${LZO_LIBS})
ENDIF()

FIND_PACKAGE(Spinlock)
IF (SPINLOCK_FOUND)
	SET(USE_SPINLOCKS 1)
ENDIF()

FIND_PACKAGE(Protobuf)
IF (PROTOBUF_FOUND)
	SET(HAVE_PROTOBUF 1)
	LIST(APPEND INCUDES ${PROTOBUF_INCLUDE_DIRS})
	SET(POSTLINKFLAGS ${POSTLINKFLAGS} ${PROTOBUF_LIBRARIES})
ENDIF()

# Check if supported linear algebra backend is found
IF (HAVE_CXX0X OR HAVE_CXX11)
	SET(HAVE_LINALG_LIB 1)
ELSE ()
	MESSAGE ("-- LINALG uses c++11 features. Please use a supported compiler")
ENDIF ()

# Linear algebra default global backend setups
OPTION (LinAlgBackend "Set global linear algebra backend library for all modules")
IF (LinAlgBackend STREQUAL "EIGEN3")
	SET(USE_EIGEN3 1)
	MESSAGE("-- Eigen3 set as default global linear algebra backend library")
ELSEIF (LinAlgBackend STREQUAL "VIENNACL")
	FIND_PACKAGE(ViennaCL ${VIENNACL_VERSION_MINIMUM} REQUIRED)
	IF (VIENNACL_FOUND AND ENABLE_VIENNACL)
		SET(USE_VIENNACL 1)
		MESSAGE("-- ViennaCL set as default global linear algebra backend library")
	ELSE ()
		MESSAGE("-- Could NOT set ViennaCL as default global linear algebra backend")
	ENDIF ()
ENDIF ()

# Linear algebra default module specific backend setup

# Core module
OPTION (CoreLib "Set linear algebra backend library for core module")
IF (CoreLib STREQUAL "EIGEN3")
	SET(USE_EIGEN3_CORE 1)
	MESSAGE("-- Eigen3 set as default core module (linalg) backend library")
ELSEIF (CoreLib STREQUAL "VIENNACL")
	FIND_PACKAGE(ViennaCL ${VIENNACL_VERSION_MINIMUM} REQUIRED)
	IF (VIENNACL_FOUND AND ENABLE_VIENNACL)
		SET(USE_VIENNACL_CORE 1)
		MESSAGE("-- ViennaCL set as default core module (linalg) backend library")
	ELSE ()
		MESSAGE("-- Could NOT set ViennaCL as default core module (linalg) backend")
	ENDIF ()
ENDIF ()

# Reduction module
OPTION (ReduxLib "Set linear algebra backend library for reduction module")
IF (ReduxLib STREQUAL "EIGEN3")
	SET(USE_EIGEN3_REDUX 1)
	MESSAGE("-- Eigen3 set as default reduction module (linalg) backend library")
ELSEIF (ReduxLib STREQUAL "VIENNACL")
	FIND_PACKAGE(ViennaCL ${VIENNACL_VERSION_MINIMUM} REQUIRED)
	IF (VIENNACL_FOUND AND ENABLE_VIENNACL)
		SET(USE_VIENNACL_REDUX 1)
		MESSAGE("-- ViennaCL set as default reduction module (linalg) backend library")
	ELSE ()
		MESSAGE("-- Could NOT set ViennaCL as default reduction module (linalg) backend")
	ENDIF ()
ENDIF ()

# Linear solver module
OPTION (LinSolverLib "Set linear algebra backend library for linear solver module")
IF (LinSolverLib STREQUAL "EIGEN3")
	SET(USE_EIGEN3_LINSLV 1)
	MESSAGE("-- Eigen3 set as default linear solver module (linalg) backend library")
ELSEIF (LinSolverLib STREQUAL "VIENNACL")
	FIND_PACKAGE(ViennaCL ${VIENNACL_VERSION_MINIMUM} REQUIRED)
	IF (VIENNACL_FOUND AND ENABLE_VIENNACL)
		SET(USE_VIENNACL_LINSLV 1)
		MESSAGE("-- ViennaCL set as default linear solver module (linalg) backend library")
	ELSE ()
		MESSAGE("-- Could NOT set ViennaCL as default linear solver module (linalg) backend")
	ENDIF ()
ENDIF ()

# Eigen solver module
OPTION (EigenSolver "Set linear algebra backend library for eigen solver module")
IF (EigenSolver STREQUAL "EIGEN3")
	SET(USE_EIGEN3_EIGSLV 1)
	MESSAGE("-- Eigen3 set as default eigen solver module (linalg) backend library")
ELSEIF (EigenSolver STREQUAL "VIENNACL")
	FIND_PACKAGE(ViennaCL ${VIENNACL_VERSION_MINIMUM} REQUIRED)
	IF (VIENNACL_FOUND AND ENABLE_VIENNACL)
		SET(USE_VIENNACL_EIGSLV 1)
		MESSAGE("-- ViennaCL set as default eigen solver module (linalg) backend library")
	ELSE ()
		MESSAGE("-- Could NOT set ViennaCL as default eigen solver module (linalg) backend")
	ENDIF ()
ENDIF ()

#SWIG Interfaces
LIST(APPEND CMAKE_SWIG_FLAGS "-w473")
LIST(APPEND CMAKE_SWIG_FLAGS "-w454")
LIST(APPEND CMAKE_SWIG_FLAGS "-w312")
LIST(APPEND CMAKE_SWIG_FLAGS "-w325")
LIST(APPEND CMAKE_SWIG_FLAGS "-fvirtual")

OPTION(SWIG_SINGLE_THREADED "Build modular interfaces single-threaded to reduce memory usage" OFF)

OPTION(USE_SWIG_DIRECTORS "Enable SWIG director classes" OFF)

# Respect system's or distribution's C[XX]FLAGS.
OPTION(SWIG_WITH_SYSTEM_CFLAGS "Enable system's C[XX]FLAGS for compilation of swig-binaries" ON)

IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
	SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${SYSTEM_C_FLAGS}")
	SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SYSTEM_CXX_FLAGS}")
ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))

IF(SWIG_WITH_SYSTEM_CFLAGS)
	SET(SWIG_CXX_COMPILER_FLAGS "${SWIG_CXX_COMPILER_FLAGS} ${SYSTEM_CXX_FLAGS}")
ENDIF(SWIG_WITH_SYSTEM_CFLAGS)

OPTION(REDUCE_SWIG_DEBUG "Reduce debuginfo when compiling interfaces" OFF)
IF(REDUCE_SWIG_DEBUG)
	SET(SWIG_CXX_COMPILER_FLAGS "${SWIG_CXX_COMPILER_FLAGS} -g1")
ENDIF(REDUCE_SWIG_DEBUG)

# python modular
IF (PythonModular OR PythonStatic)
	# find python library for the found python interpreter
	# i.e. versions should match!
	FIND_PACKAGE(PythonLibs REQUIRED)
	FIND_PACKAGE(NumPy REQUIRED)

	SET(HAVE_PYTHON 1)

	IF(PythonModular)
		#custom swig flags for python modular interface
		IF(${PYTHON_VERSION_MAJOR} VERSION_EQUAL 3)
			SET(TARGET_SWIGFLAGS "-builtin\;-modern\;-modernargs\;-py3")
			SET(PYTHON3 1)
		ELSE()
			SET(TARGET_SWIGFLAGS "-builtin\;-modern\;-modernargs")
		ENDIF()

		# SWIG was broken for combining -builtin and -modernargs
		# from v3.0.0 and until 3.0.4.  This bug was fixed in
		# v3.0.5.  Make CMake emit an error and fail to configure.
		IF((NOT "${SWIG_VERSION}" VERSION_LESS "3.0.0") AND
			("${SWIG_VERSION}" VERSION_LESS "3.0.5"))
			MESSAGE(FATAL_ERROR
				"This version of SWIG is broken for building Python_modular interface.  Use SWIG < 3.0.0 or >= 3.0.5.")
		ENDIF((NOT "${SWIG_VERSION}" VERSION_LESS "3.0.0") AND
			("${SWIG_VERSION}" VERSION_LESS "3.0.5"))

		# SWIG-generated Python-wrappers fail to build
		# for Python >=3.5 with SWIG < 3.0.8.  Make CMake
		# emit an error and fail to configure.
		IF ((NOT "${PYTHON_VERSION_STRING}" VERSION_LESS "3.5") AND
			("${SWIG_VERSION}" VERSION_LESS "3.0.8"))
			MESSAGE(FATAL_ERROR
				"Building Python_modular interface for Python >= 3.5 requires SWIG >= 3.0.8.")
		ENDIF ((NOT "${PYTHON_VERSION_STRING}" VERSION_LESS "3.5") AND
			("${SWIG_VERSION}" VERSION_LESS "3.0.8"))

		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/python_modular)
			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/python_modular)
		ENDIF()
	ENDIF()

	IF(PythonStatic)
		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/python_static)
			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/python_static)
		ENDIF()
	ENDIF()
ENDIF()

# lua modular
IF (LuaModular)
	#FIND_PACKAGE(Lua51 REQUIRED)
	pkg_search_module(LUA REQUIRED lua lua5.1)
	IF (NOT LUA_FOUND)
	MESSAGE(FATAL_ERROR "Lua could not be found!\n"
		"Lua is required for compiling lua modular interface!")
    ENDIF ()
	SET(LUA_EXECUTABLE lua)
	UNSET(TARGET_SWIGFLAGS)
	IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/lua_modular)
		add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/lua_modular)
	ENDIF()
ENDIF()

# java modular
IF (JavaModular)
	FIND_PACKAGE(Java REQUIRED)
	FIND_PACKAGE(JNI REQUIRED)

	#find jblas
	INCLUDE(UseJava)
	FIND_JAR(JBLAS NAMES jblas jblas-1.2.0
			PATHS /usr/lib/java /opt/local/share/java
				  ENV JBLAS_PATH)
	IF(JBLAS)
		SET(HAVE_JBLAS 1)
	ELSE()
		MESSAGE(FATAL_ERROR "JBlas could not be found!\n"
			"It is required for java modular interface!!!")
	ENDIF()

	SET(TARGET_SWIGFLAGS "-package\;org.shogun")
	IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/java_modular)
		add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/java_modular)
	ENDIF()
ENDIF()

# ruby modular
IF (RubyModular)
	FIND_PACKAGE(Ruby REQUIRED)
	FIND_PACKAGE(RubyNArray REQUIRED)
	SET(NARRAY_LIB ${RUBY_NARRAY_LIBRARY})
	UNSET(TARGET_SWIGFLAGS)
	add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/ruby_modular)
ENDIF()

# octave modular
IF (OctaveModular OR OctaveStatic)
	FIND_PACKAGE(Octave 3.6 REQUIRED)
	SET(OCTAVE_APIVERSION ${OCTAVE_API_VERSION})

	IF(OctaveModular)
		UNSET(TARGET_SWIGFLAGS)
		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/octave_modular)
			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/octave_modular)
		ENDIF()
	ENDIF()

	IF(OctaveStatic)
		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/octave_static)
			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/octave_static)
		ENDIF()
	ENDIF()
ENDIF()

# csharp modular
IF (CSharpModular)
	FIND_PACKAGE(CSharp REQUIRED)
	UNSET(TARGET_SWIGFLAGS)
	IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/csharp_modular)
		add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/csharp_modular)
	ENDIF()
ENDIF()

# r modular
IF (RModular OR RStatic)
	FIND_PACKAGE(R REQUIRED)

	IF (RModular)
		UNSET(TARGET_SWIGFLAGS)
		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/r_modular)
			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/r_modular)
		ENDIF()
	ENDIF()

	IF (RStatic)
		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/r_static)
			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/r_static)
		ENDIF()
	ENDIF()
ENDIF()

# perl modular
IF (PerlModular)
	FIND_PACKAGE(FindPerlLibs REQUIRED)
	UNSET(TARGET_SWIGFLAGS)
	IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/perl_modular)
		#add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/perl_modular)
	ENDIF()
ENDIF()

IF (MatlabStatic)
	FIND_PACKAGE(Matlab REQUIRED)
	IF(MATLAB_FOUND)
		IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/matlab_static)
			add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/matlab_static)
		ENDIF()
	ELSE()
		MESSAGE(FATAL_ERROR "Could not find Matlab, which is required for compiling matlab_static interface. Try setting MATLAB_ROOT enviroment variable to the right path")
	ENDIF()
ENDIF()

IF (CmdLineStatic)
	IF(EXISTS ${CMAKE_SOURCE_DIR}/src/interfaces/cmdline_static)
		add_subdirectory(${CMAKE_SOURCE_DIR}/src/interfaces/cmdline_static)
	ENDIF()
ENDIF()

IF (SVMLight)
	MESSAGE(STATUS ${SVMLightWarning})
ENDIF()

################# TESTING ###################
#TODO: finish!!!
OPTION(BUILD_DASHBOARD_REPORTS "Set to ON to activate reporting of Shogun builds" OFF)
IF(BUILD_DASHBOARD_REPORTS)
	file(TO_CMAKE_PATH "${CMAKE_SOURCE_DIR}/configs/valgrind.supp" VALGRIND_SUPPRESSION_FILE)
	SET(MEMORYCHECK_SUPPRESSIONS_FILE ${VALGRIND_SUPPRESSION_FILE} CACHE FILEPATH "File that contains suppressions for the memory checker")
	SET(MEMORYCHECK_COMMAND_OPTIONS "-q --tool=memcheck --leak-check=full --track-origins=yes --num-callers=50 --error-exitcode=1")
	include(CTest)
ENDIF()

OPTION(ENABLE_TESTING "Enable testing" OFF)
OPTION(TRAVIS_DISABLE_UNIT_TESTS "Disable unit testing to speed up jobs on travis-ci" OFF)
OPTION(TRAVIS_DISABLE_LIBSHOGUN_TESTS "Disable libshogun tests to speed up jobs on travis-ci" OFF)
OPTION(INTEGRATION_TESTS_ENABLED "Enable integration testing (legacy)" OFF)
OPTION(TRAVIS_DISABLE_META_INTEGRATION_TESTS "Disable meta integration testing to speed up  jobs on travis-ci" OFF)

IF(ENABLE_TESTING)
	FIND_PACKAGE(Jinja2)
	IF(NOT BUILD_DASHBOARD_REPORTS)
		enable_testing()
	ENDIF()

	IF(EXISTS ${CMAKE_SOURCE_DIR}/tests)
		if (INTEGRATION_TESTS_ENABLED AND EXISTS ${CMAKE_SOURCE_DIR}/tests/integration)
			add_subdirectory(${CMAKE_SOURCE_DIR}/tests/integration)
		ENDIF()

		IF (NOT TRAVIS_DISABLE_UNIT_TESTS AND EXISTS ${CMAKE_SOURCE_DIR}/tests/unit)
			add_subdirectory(${CMAKE_SOURCE_DIR}/tests/unit)
		ENDIF()
		
		IF(BUILD_META_EXAMPLES)
		    IF(NOT TRAVIS_DISABLE_META_INTEGRATION_TESTS AND EXISTS ${CMAKE_SOURCE_DIR}/tests/meta)
                add_subdirectory(${CMAKE_SOURCE_DIR}/tests/meta)
            ENDIF()
        ENDIF()
	ENDIF()
ENDIF()

# save configuration options
MergeCFLAGS()
SET(CONFIGURE_OPTIONS "TODO")
SET(COMPFLAGS_CPP "${MERGED_CXX_FLAGS}")
SET(LINKFLAGS "${POSTLINKFLAGS}")

IF(EXISTS ${CMAKE_SOURCE_DIR}/src/shogun)
	add_subdirectory(${CMAKE_SOURCE_DIR}/src/shogun)
ENDIF()

IF(EXISTS ${CMAKE_SOURCE_DIR}/examples)
	IF(ENABLE_TESTING AND NOT BUILD_EXAMPLES)
	    message(STATUS "Tests require (disabled) examples, enabling.")
	ENDIF()
    IF(ENABLE_TESTING OR BUILD_EXAMPLES)
	    add_subdirectory(${CMAKE_SOURCE_DIR}/examples)
	ENDIF()
	IF(BUILD_META_EXAMPLES)
        # allow meta examples without adding examples dir itself
        add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/examples/meta)
    ENDIF()
ENDIF()

IF(EXISTS ${CMAKE_SOURCE_DIR}/doc)
	add_subdirectory(${CMAKE_SOURCE_DIR}/doc)
ENDIF()

include(ShogunPackaging)

message(STATUS "===================================================================================================================")
message(STATUS "Summary of Configuration Variables")
include(FeatureSummary)
feature_summary(WHAT ALL)

message(STATUS "===================================================================================================================")
message(STATUS "Enabled Integration")

PrintInterfaceStatus("OpenCV Integration" OpenCV)

message(STATUS
"===================================================================================================================")
message(STATUS "Enabled Interfaces")

message(STATUS "  libshogun is ON")

PrintInterfaceStatus("python modular" PythonModular)
PrintInterfaceStatus("octave modular" OctaveModular)
PrintInterfaceStatus("java modular" JavaModular)
PrintInterfaceStatus("perl modular" PerlModular)
PrintInterfaceStatus("ruby modular" RubyModular)
PrintInterfaceStatus("csharp modular" CSharpModular)
PrintInterfaceStatus("R modular" RModular)
PrintInterfaceStatus("lua modular" LuaModular)

message(STATUS "")
message(STATUS "")
message(STATUS "------------------------------------")
IF(LICENSE_GPL_SHOGUN)
	message(STATUS "Shogun will be built GPL3 compatible")
ELSE()
	message(STATUS "Shogun will be built BSD3 compatible")
ENDIF()
message(STATUS "------------------------------------")
message(STATUS "")

message(STATUS "")
message(STATUS "Enabled legacy interfaces")
PrintInterfaceStatus("cmdline static" CmdLineStatic)
PrintInterfaceStatus("python static" PythonStatic)
PrintInterfaceStatus("octave static" OctaveStatic)
PrintInterfaceStatus("matlab static" MatlabStatic)
PrintInterfaceStatus("R static" RStatic)

message(STATUS "===================================================================================================================")

message(STATUS "To compile shogun type")
message(STATUS "  make")
message(STATUS "")
message(STATUS "To install shogun to ${CMAKE_INSTALL_PREFIX} type")
message(STATUS "  make install")
message(STATUS "")
message(STATUS "or to install to a custom directory")
message(STATUS "  make install DESTDIR=/my/special/path")
message(STATUS "  (or rerun cmake with -DCMAKE_INSTALL_PREFIX=/my/special/path) to just change the prefix")
message(STATUS "===================================================================================================================")