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CMakeLists.txt
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CMakeLists.txt
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# Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the
# University of Virginia, University of Heidelberg, and University
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2017 - 2018 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., University of Heidelberg, and University of
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2012 - 2016 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., University of Heidelberg, and The University
# of Manchester.
# All rights reserved.
##############################################################################
#
# Description : CMake build script for COPASI
# Original author(s): Ralph Gauges <ralph.gauges@bioquant.uni-heidelberg.de>
# Frank Bergmann <fbergman@caltech.edu>
#
# This file is part of COPASI. Please visit http://COPASI.org for more
# information about COPASI, and the latest version of COPASI.
#
#
#
#
###############################################################################
# we need at least cmake 2.8 for the FindLAPACK functions
cmake_minimum_required (VERSION 2.8.12...3.19.1)
if(POLICY CMP0048)
cmake_policy(SET CMP0048 NEW)
endif(POLICY CMP0048)
# add an option to override the version
set(COPASI_OVERRIDE_VERSION "" CACHE STRING "Version String to override the version parsed from the header" )
mark_as_advanced(COPASI_OVERRIDE_VERSION)
# if the header file is not present, then set the override version to this one
if (NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/copasi/CopasiVersion.h" AND NOT COPASI_OVERRIDE_VERSION)
set(COPASI_OVERRIDE_VERSION "4.12.65")
endif()
set(COPASI_VERSION_MAJOR)
set(COPASI_VERSION_MINOR)
set(COPASI_VERSION_BUILD)
set(COPASI_VERSION_COMMENT)
# if override version is set, parse it and configure the header file with it
if (COPASI_OVERRIDE_VERSION)
# parse the override string
string(STRIP "${COPASI_OVERRIDE_VERSION}" VersionString)
string(REPLACE "." ";" VersionString "${VersionString}" )
string(REPLACE "-" ";" VersionString "${VersionString}" )
list(LENGTH VersionString versionLength)
list(GET VersionString 0 COPASI_VERSION_MAJOR )
list(GET VersionString 1 COPASI_VERSION_MINOR )
list(GET VersionString 2 COPASI_VERSION_BUILD )
if(${versionLength} GREATER 3)
list(GET VersionString 3 COPASI_VERSION_COMMENT )
endif()
# configure file
configure_file (
"${CMAKE_CURRENT_SOURCE_DIR}/copasi/CopasiVersion.h.in"
"${CMAKE_CURRENT_SOURCE_DIR}/copasi/CopasiVersion.h"
)
endif()
set(COPASI_VERSION)
# the CopasiVersion file only exists when the git tools have been configured
# and used. if that is not the case, we default to the canned version.
if (EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/copasi/CopasiVersion.h")
file(READ "${CMAKE_CURRENT_SOURCE_DIR}/copasi/CopasiVersion.h" COPASI_VERSION)
endif()
if (COPASI_VERSION)
string(REGEX REPLACE ".*COPASI_VERSION_MAJOR ([0-9]+).*" "\\1" COPASI_VERSION_MAJOR "${COPASI_VERSION}")
string(REGEX REPLACE ".*COPASI_VERSION_MINOR ([0-9]+).*" "\\1" COPASI_VERSION_MINOR "${COPASI_VERSION}")
string(REGEX REPLACE ".*COPASI_VERSION_BUILD ([0-9]+).*" "\\1" COPASI_VERSION_BUILD "${COPASI_VERSION}")
endif()
project (COPASI VERSION "${COPASI_VERSION_MAJOR}.${COPASI_VERSION_MINOR}.${COPASI_VERSION_BUILD}")
set (CONAN_INFO)
if (EXISTS ${CMAKE_CURRENT_BINARY_DIR}/conanbuildinfo.cmake)
set (CONAN_INFO ${CMAKE_CURRENT_BINARY_DIR}/conanbuildinfo.cmake)
elseif (EXISTS ${CMAKE_BINARY_DIR}/../conanbuildinfo.cmake)
set (CONAN_INFO ${CMAKE_BINARY_DIR}/../conanbuildinfo.cmake)
endif()
if (CONAN_INFO)
include(${CONAN_INFO})
conan_basic_setup(SKIP_STD)
endif()
include (CMakeTestCCompiler)
include (CheckCSourceCompiles)
include (CheckCXXSourceCompiles)
include (CheckStructHasMember)
include (CheckLibraryExists)
include (CheckFunctionExists)
include (CheckCCompilerFlag)
include (CheckCSourceRuns)
include (CheckSymbolExists)
include (CheckTypeSize)
if (${CMAKE_VERSION} VERSION_GREATER 2.8.4)
include(GNUInstallDirs)
else ()
set (CMAKE_INSTALL_LIBDIR "lib")
set (CMAKE_INSTALL_INCLUDEDIR "include")
set (CMAKE_INSTALL_BINDIR "bin")
set (CMAKE_INSTALL_DATADIR "share")
set (CMAKE_INSTALL_FULL_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib")
set (CMAKE_INSTALL_FULL_INCLUDEDIR "${CMAKE_INSTALL_PREFIX}/include")
endif ()
# preferably link against the static versions
# as compared to the dynamic ones
option(PREFER_STATIC "Preferably link against the static library versions" ON)
if (NOT WIN32 AND PREFER_STATIC)
SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
endif()
if (CMAKE_MAJOR_VERSION LESS 3 OR CMAKE_MINOR_VERSION LESS 1)
set(CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} "-std=c++11")
else()
set(CMAKE_CXX_STANDARD 11)
endif()
CHECK_FUNCTION_EXISTS(strptime HAVE_STRPTIME)
CHECK_TYPE_SIZE("void*" CMAKE_SIZEOF_VOID_P)
CHECK_TYPE_SIZE("unsigned int" CMAKE_SIZEOF_UINT)
CHECK_TYPE_SIZE("size_t" CMAKE_SIZEOF_SIZE_T)
if (NOT CMAKE_SIZEOF_SIZE_T EQUAL CMAKE_SIZEOF_UINT)
# will be written in config file
set (DATAVALUE_NEEDS_SIZE_T_MEMBERS 1)
endif()
set(COPASI_BUILD_TYPE "native")
if (CMAKE_SIZEOF_VOID_P EQUAL 4)
set(COPASI_BUILD_TYPE "32bit")
else()
set(COPASI_BUILD_TYPE "64bit")
endif()
# On OSX it is common to build universal binaries to support multiple
# processor architectures. The default behavior is not to build
# multiple architectures, as most users might not need that.
option(ENABLE_UNIVERSAL "Create universal binaries on Mac OS X." OFF)
if (APPLE AND ENABLE_UNIVERSAL)
set(COPASI_BUILD_TYPE "universal")
endif()
set(COPASI_DEPENDENCY_DIR "" CACHE PATH "Dependency Directory containing, when set dependencies will be overwritten" )
mark_as_advanced(COPASI_DEPENDENCY_DIR)
if (COPASI_DEPENDENCY_DIR AND EXISTS ${COPASI_DEPENDENCY_DIR})
include(cmake-set-dependencies.cmake)
endif(COPASI_DEPENDENCY_DIR AND EXISTS ${COPASI_DEPENDENCY_DIR})
if (EXISTS ${CMAKE_BINARY_DIR}/conan_paths.cmake)
include(${CMAKE_BINARY_DIR}/conan_paths.cmake)
endif()
set(CMAKE_MODULE_PATH "${COPASI_SOURCE_DIR}/CMakeModules;${CMAKE_MODULE_PATH}")
IF(DEFINED CMAKE_BUILD_TYPE)
SET(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING
"Choose the type of build, options are: Debug or Release."
FORCE)
ELSE()
SET(CMAKE_BUILD_TYPE Release CACHE STRING
"Choose the type of build, options are: Debug or Release."
FORCE)
ENDIF()
# set test timeout to 3000 as the normal time limit is not sufficient
# for the comp tests
SET(DART_TESTING_TIMEOUT "3000" CACHE STRING "" FORCE)
enable_testing()
if (UNIX)
# setup valgrind
set(CMAKE_MEMORYCHECK_COMMAND valgrind)
set(CMAKE_MEMORYCHECK_COMMAND_OPTIONS
"--error-exitcode=1 --trace-children=yes --leak-check=full --show-reachable=yes --leak-resolution=high --track-origins=yes --error-limit=no ")
set(MEMCHECK_COMMAND
"${CMAKE_MEMORYCHECK_COMMAND} ${CMAKE_MEMORYCHECK_COMMAND_OPTIONS}")
separate_arguments(MEMCHECK_COMMAND)
endif()
include(CTest)
set (DEFAULT_EXTUNIT ON)
# set (DEFAULT_NONLIN OFF)
set (DEFAULT_DEBUG_TRACING OFF)
set (DEFAULT_HYBRIDODE45 OFF)
if(CMAKE_BUILD_TYPE STREQUAL "Debug")
# for the debug version we need to enable
# COPASI_DEBUG
add_definitions(-D_DEBUG)
add_definitions(-DCOPASI_DEBUG)
set (DEFAULT_HYBRIDODE45 ON)
set (DEFAULT_EXTUNIT ON)
set (DEFAULT_NONLIN ON)
set (DEFAULT_DEBUG_TRACING ON)
endif(CMAKE_BUILD_TYPE STREQUAL "Debug")
# there should be an option to disable the debug flag, as it litters the
# file system with trace files all over the place (or rather everywhere the
# program is started)
if (NOT WIN32)
option(ENABLE_COPASI_DEBUG_TRACE "Enable COPASI Debug Tracing" ${DEFAULT_DEBUG_TRACING})
mark_as_advanced(ENABLE_COPASI_DEBUG_TRACE)
endif()
# another option to create the COPASI SE library directly from the files, instead of first building an
# object library (necessary sometimes as the object library messes up debugging on VS2013-2019)
option(DISABLE_CORE_OBJECT_LIBRARY "Disable creation of libCOPASISE-core object library and just create libCOPASISE-static" OFF)
mark_as_advanced(DISABLE_CORE_OBJECT_LIBRARY)
# Sven developed an option of scaling the residuals in the parameter estimation
# by the current simulation value (instead of 0) this removes the bias when
# using value scaled experimental data.
option(ENABLE_COPASI_PARAMETERFITTING_RESIDUAL_SCALING "Scale parameter estimation residuals with the simulation value" OFF)
option(ENABLE_COPASI_BANDED_GRAPH "Enable the banded graph widget" ON)
option(ENABLE_COPASI_NONLIN_DYN_OSCILLATION "Oscillation Widget" OFF)
option(ENABLE_COPASI_EXTUNIT "Extended Unit Support" ${DEFAULT_EXTUNIT})
option(ENABLE_ANALYTICS "Enable Analytics Task" OFF)
option(COPASI_INSTALL_C_API "Enable this option to also install the COPASI C API" OFF)
option (BUILD_GUI "Disable this if you do not want to build the COPASI GUI (CopasiUI)." ON)
option(ENABLE_FLEX_BISON "Enable the use of flex and bison to create parsers." OFF)
option(ENABLE_GPROF "Enable compiling and linking for gprof analysis." OFF)
if (ENABLE_GPROF)
set(CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} "-pg")
set(CMAKE_EXE_LINKER_FLAGS "-pg")
endif (ENABLE_GPROF)
option(CLAPACK_NO_BLASWRAP "If defined the NO_BLASWRAP compile option will be added" OFF)
set (ENABLE_JIT_DEFAULT OFF)
if (APPLE)
if (CMAKE_OSX_ARCHITECTURES STREQUAL arm64)
set (ENABLE_JIT_DEFAULT OFF)
else()
set (ENABLE_JIT_DEFAULT ON)
endif()
else()
set (ENABLE_JIT_DEFAULT ON)
endif()
option(ENABLE_JIT "Enable Just In Time compilation for math expressions" ${ENABLE_JIT_DEFAULT})
option(ENABLE_OMP "Enable the OpenMP support" OFF)
set(EXTRA_DEFS "" CACHE STRING
"additional definitions to be used." )
set(EXTRA_LIBS "" CACHE STRING
"List of additional libraries to link against. Separate multiple names using semicolons." )
set(EXTRA_INCLUDE_DIRS "" CACHE STRING
"List of additional include directories to use during compilation. Separate multiple directories using semicolons." )
if(EXTRA_DEFS)
add_definitions(${EXTRA_DEFS})
endif(EXTRA_DEFS)
if(EXTRA_INCLUDE_DIRS)
foreach(dir ${EXTRA_INCLUDE_DIRS})
include_directories(BEFORE ${dir})
endforeach()
endif()
SET(COPASI_INCLUDE_DIRS ${CMAKE_SOURCE_DIR} ${CMAKE_BINARY_DIR})
include_directories(
${COPASI_INCLUDE_DIRS}
${LAPACK_INCLUDE_DIR}
)
#platform specific defines
if(UNIX)
if(APPLE)
add_definitions(-DDarwin)
if(CMAKE_GENERATOR AND XCODE_VERSION)
option (COPASI_OVERWRITE_XCODE_GENERATOR "If true, will default to llvmgcc42 rather than clang." OFF)
if(COPASI_OVERWRITE_XCODE_GENERATOR AND CMAKE_GENERATOR MATCHES "Xcode" AND (${XCODE_VERSION} VERSION_EQUAL 4 OR ${XCODE_VERSION} VERSION_GREATER 4))
# Xcode 4 defaults to the Apple LLVM Compiler.
set(CMAKE_XCODE_ATTRIBUTE_GCC_VERSION "com.apple.compilers.llvmgcc42")
endif()
endif()
# Since we are encountering errors with the use of libc++ on OSX
# this option allows to override which stdlib to use (needed for R
# bindings on mavericks / yosemite ...)
if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
option(CLANG_USE_STDLIB "Use libstdc++ rather than libc++" OFF)
if (CLANG_USE_STDLIB)
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++" )
endif()
endif()
if (NOT CMAKE_OSX_ARCHITECTURES )
set(CMAKE_OSX_ARCHITECTURES "${CMAKE_OSX_ARCHITECTURES}" CACHE STRING
"A semicolon-separated list of build architectures to be used.")
endif()
if(ENABLE_UNIVERSAL)
# if universal binaries are requested and none defined so far
# overwrite them with all three common architectures. If the user
# specified their own list of architectures do not touch!
if(CMAKE_OSX_ARCHITECTURES STREQUAL "")
STRING(REGEX REPLACE "^.*MacOSX([0-9]*\\.[0-9]*)\\.sdk$" "\\1"
OSX_SDK_VERSION "${CMAKE_OSX_SYSROOT}")
if(OSX_SDK_VERSION VERSION_EQUAL "10.7" OR OSX_SDK_VERSION VERSION_EQUAL "10.8")
# OSX Lion no longer supports ppc architecture
set(CMAKE_OSX_ARCHITECTURES "i386;x86_64" CACHE STRING
"A semicolon-separated list of build architectures to be used." FORCE)
else()
set(CMAKE_OSX_ARCHITECTURES "i386;ppc;x86_64" CACHE STRING
"A semicolon-separated list of build architectures to be used." FORCE)
endif()
endif()
endif(ENABLE_UNIVERSAL)
else()
option(ENABLE_LIBCOPASISE_SHARED "Enable building of libCOPASISE as shared object." OFF)
add_definitions(-DLinux)
if(NOT CYGWIN)
# on cygwin all code is position independent so -fPIC is not needed
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-strict-aliasing -fPIC")
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fno-strict-aliasing -fPIC")
endif()
endif()
else()
if (CYGWIN)
add_definitions(-DCygwin)
else()
add_definitions(-DWIN32)
endif()
endif()
IF(${CMAKE_SYSTEM_NAME} MATCHES "FreeBSD")
add_definitions(-DFreeBSD)
include_directories(/usr/local/include)
link_directories(/usr/local/lib)
endif()
# find packages now after all flag definitions have been made
find_package(EXPAT REQUIRED)
find_package(LIBSBML REQUIRED)
find_package(LIBSEDML REQUIRED)
find_package(LIBCOMBINE REQUIRED)
if (ENABLE_FLEX_BISON)
find_package(FLEX REQUIRED)
find_package(BISON REQUIRED)
set(FLEX_BINARY ${FLEX_EXECUTABLE})
set(FLEX_EXECUTABLE "${COPASI_SOURCE_DIR}/admin/flex.sh")
set(BISON_BINARY ${BISON_EXECUTABLE})
set(BISON_EXECUTABLE "${COPASI_SOURCE_DIR}/admin/yacc.sh")
endif (ENABLE_FLEX_BISON)
if ( NOT CLAPACK_FOUND )
find_package(CLAPACK REQUIRED)
endif ()
include_directories(BEFORE ${CLAPACK_INCLUDE_DIR})
# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${LAPACK_CFLAGS}")
find_package(CROSSGUID REQUIRED)
include_directories(BEFORE ${CROSSGUID_INCLUDE_DIR})
if (ENABLE_JIT)
find_package(NATIVEJIT REQUIRED)
include_directories(BEFORE ${NATIVEJIT_INCLUDE_DIR})
set(USE_JIT 1)
find_package(CPUFEATURES REQUIRED)
include_directories(BEFORE ${CPUFEATURE_INCLUDE_DIR})
endif (ENABLE_JIT)
if (ENABLE_OMP)
set(USE_OMP 1)
if (APPLE)
find_package (OpenMP)
if(NOT OpenMP_FOUND)
# libomp 15.0+ from brew is keg-only, so have to search in other locations.
# See https://github.com/Homebrew/homebrew-core/issues/112107#issuecomment-1278042927.
execute_process(COMMAND brew --prefix libomp
OUTPUT_VARIABLE HOMEBREW_LIBOMP_PREFIX
OUTPUT_STRIP_TRAILING_WHITESPACE)
set(OpenMP_C_FLAGS "-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include")
set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include")
set(OpenMP_C_LIB_NAMES omp)
set(OpenMP_CXX_LIB_NAMES omp)
set(OpenMP_omp_LIBRARY ${HOMEBREW_LIBOMP_PREFIX}/lib/libomp.dylib)
endif()
endif()
find_package (OpenMP REQUIRED)
if (OpenMP_CXX_SPEC_DATE GREATER_EQUAL "201811")
# OpenMP 5.0 will always have monotonic scheduling
set(OMP_HAVE_MONOTONIC 1 CACHE INTERNAL "" FORCE)
else()
# otherwise we need to check
include_directories(BEFORE ${OpenMP_INCLUDE_PATH} ${OpenMP_CXX_INCLUDE_DIRS})
include(CheckCXXSourceCompiles)
function(detect_code_compiled code macro msg)
message(STATUS "Detecting ${msg}")
check_cxx_source_compiles("${code}" "${macro}" FAIL_REGEX "warning")
if(${macro})
message(STATUS "Detecting ${msg} - supported")
else(${macro})
message(STATUS "Detecting ${msg} - not supported")
endif(${macro})
endfunction(detect_code_compiled)
# Detect std::optional
detect_code_compiled("
#include <omp.h>
int main()
{
omp_sched_t schedule = omp_sched_monotonic;
}"
OMP_HAVE_MONOTONIC
"omp_sched_monotonic")
endif()
endif(ENABLE_OMP)
# TODO raptor should be restricted to a version which is at least
# 1.4.18, but lower then 2.0
find_package(RAPTOR REQUIRED)
# actually iconv is only needed on BSD like systems
find_package(ICONV)
if(BUILD_GUI)
set(OpenGL_GL_PREFERENCE LEGACY)
if (UNIX AND NOT APPLE)
FIND_LIBRARY(OPENGL_gl_LIBRARY NAMES GL PATHS /usr/lib/x86_64-linux-gnu/mesa)
endif (UNIX AND NOT APPLE)
find_package(OpenGL REQUIRED)
include(${CMAKE_CURRENT_SOURCE_DIR}/ChooseQtVersion.cmake)
# first try to find whether Qt5 is present
option(QT_USE_TEXTBROWSER "Use QTextBrowser instead of Webkit / WebEngine for display of notes" ON)
if (QT_USE_TEXTBROSWSER)
set(QT_USE_TEXTBROWSER ON)
endif()
if (${SELECT_QT} MATCHES "Qt5" OR
${SELECT_QT} MATCHES "Qt6" OR
${SELECT_QT} MATCHES "Any")
# then narrow down the precise modules we need
option(QT5_USE_WEBENGINE "Use QWebEngine instead of the deprecated QtWebKit for notes" OFF)
option(QT5_USE_DATAVISUALIZATION "Use Qt5DataVisualization instead of the deprecated QwtPlot3D" ON)
if (QT5_USE_DATAVISUALIZATION)
option(WITH_DATAVISUALIZATION_NAMESPACES "The DataVisualization modeule uses c++ namespaces" ON)
endif()
option(COPASI_USE_QTCHARTS "Use QtCharts instead of the Qwt" OFF)
option(COPASI_USE_QCUSTOMPLOT "Use QCustomPlot instead of the Qwt" OFF)
if (COPASI_USE_QCUSTOMPLOT)
find_package(QCP REQUIRED)
endif()
option(WITH_LEGACY_OPENGL "Use Legacy OpenGL visualization" OFF)
set (ADDITIONAL_QT5_MODULES)
if (QT5_USE_DATAVISUALIZATION)
set (ADDITIONAL_QT5_MODULES ${ADDITIONAL_QT5_MODULES} DataVisualization)
endif()
if (COPASI_USE_QTCHARTS)
set (ADDITIONAL_QT5_MODULES ${ADDITIONAL_QT5_MODULES} Charts)
endif()
if(${SELECT_QT} MATCHES "Qt6")
# for xml sax parser and qregex
set (ADDITIONAL_QT5_MODULES ${ADDITIONAL_QT5_MODULES} Core5Compat)
endif()
if (QT_USE_TEXTBROWSER)
QT_FIND_MODULES( Concurrent
Core
Gui
Widgets
Network
OpenGL
PrintSupport
Svg
Xml
${ADDITIONAL_QT5_MODULES}
)
elseif (QT5_USE_WEBENGINE)
QT_FIND_MODULES( Concurrent
Core
Gui
Widgets
Network
OpenGL
PrintSupport
Svg
WebEngine
WebEngineWidgets
Xml
${ADDITIONAL_QT5_MODULES}
)
else()
QT_FIND_MODULES( Concurrent
Core
Gui
Widgets
Network
OpenGL
PrintSupport
Svg
WebKit
WebKitWidgets
Xml
${ADDITIONAL_QT5_MODULES}
)
endif()
set(QTVERSION 5)
else()
# using qt 4.8
if (QT_USE_TEXTBROWSER)
QT_FIND_MODULES(Core Gui Network OpenGL Svg Xml)
else(QT_USE_TEXTBROWSER)
QT_FIND_MODULES(Core Gui Network OpenGL Svg WebKit Xml)
endif(QT_USE_TEXTBROWSER)
endif()
# find Qt4
#find_package(Qt4 4.7.0 REQUIRED QtCore QtOpenGL QtGui QtXml QtWebKit QtNetwork)
# check for qwt, TODO check if the version is OK
find_package(QWT REQUIRED)
if (QWT_FOUND)
set(COPASI_USE_QWT ON)
endif()
# check for qwtplot3d
if (NOT QT5_USE_DATAVISUALIZATION)
find_package(QWTPLOT3D REQUIRED)
endif()
# if the MML widget is available, we need to enable "HAVE_MML"
option(ENABLE_MML "Enable the MML widget" ON)
if(ENABLE_MML)
find_package(MML REQUIRED)
endif(ENABLE_MML)
# check for sbw
option(ENABLE_SBW_INTEGRATION "Enable SBW Integration" ON)
if (ENABLE_SBW_INTEGRATION)
find_package(SBW REQUIRED)
# set up definitions for SBW
if(UNIX)
if(APPLE)
add_definitions(-DDARWIN)
endif()
add_definitions(-DLINUX)
endif()
endif(ENABLE_SBW_INTEGRATION)
if (APPLE)
# TODO Carbon is only needed for the GUI
include_directories(BEFORE /System/Library/Frameworks/Carbon.framework/Headers)
find_library(CARBON_LIBRARY Carbon)
find_library(QUICKTIME_LIBRARY QuickTime)
find_package(ZLIB)
endif (APPLE)
endif(BUILD_GUI)
# define what shall be build
option (BUILD_CXX_EXAMPLES "Build the C++ examples." OFF)
include(CMakeDependentOption)
# for the language bindings we need swig
option (ENABLE_CSHARP "Enable language bindings for the C# language." OFF)
option (ENABLE_JAVA "Enable language bindings for the Java language." OFF)
option (ENABLE_PYTHON "Enable language bindings for the Python language." OFF)
option (ENABLE_PERL "Enable language bindings for the Perl language." OFF)
option (ENABLE_OCTAVE "Enable language bindings for the Octave language." OFF)
option (ENABLE_R "Enable language bindings for the R language." OFF)
# we need swig for the language bindings. Only if SWIG was found, the options to
# build the different language bindings are enabled
# TODO test the SWIG version
if (ENABLE_CSHARP OR ENABLE_JAVA OR ENABLE_PYTHON OR ENABLE_PERL OR ENABLE_OCTAVE OR ENABLE_R)
if (EXISTS "$ENV{SWIG_DIR}")
SET (SWIG_DIR "$ENV{SWIG_DIR}")
SET (SWIG_EXECUTABLE "$ENV{SWIG_DIR}/bin/swig")
endif ()
find_package(SWIG REQUIRED)
endif ()
option (ENABLE_TIME_SENS "Enables Time Sensitivities task in UI." ON)
mark_as_advanced(ENABLE_TIME_SENS)
#Option for the COPASI support for Provenance Framework currently being developed by Peyman
option (ENABLE_PROVENANCE "Enables Provenance support." OFF)
mark_as_advanced(ENABLE_PROVENANCE)
#Option for the COPASI support for Versioning Framework currently being developed by Peyman
option (ENABLE_VERSIONING "Enables Versioning support." OFF)
mark_as_advanced(ENABLE_VERSIONING)
if(ENABLE_PROVENANCE AND NOT ENABLE_VERSIONING)
set(ENABLE_VERSIONING ON CACHE BOOL "Enable Versioning Support" FORCE)
endif(ENABLE_PROVENANCE AND NOT ENABLE_VERSIONING)
option (BUILD_SEMANTIC_TESTSUITE "Build the program to run the SBML semantic testsuite." OFF)
option (BUILD_STEADY_STATE_RUNNER "Build the program to run the comparisons on steady state results." OFF)
option (BUILD_MCA_RUNNER "Build the program to run the comparisons on MCA results." OFF)
option (BUILD_SBML_TESTSUITE "Build the program to run the new SBML testsuite." OFF)
option (BUILD_STOCHASTIC_TESTSUITE "Build the program to run the SBML stochastic testsuite." OFF)
option (BUILD_FRANKS_TESTSUITE "Build the program to run the Frank Bergmann's SBML tests." OFF)
option (BUILD_TESTS "Compiles CPPUNIT/Catch2 Testrunners." OFF)
mark_as_advanced(BUILD_TESTS)
if (BUILD_TESTS)
find_path(CPPUNIT_INCLUDE_DIR cppunit/Test.h )
find_library(CPPUNIT_LIBRARY NAMES cppunit)
endif(BUILD_TESTS)
mark_as_advanced(BUILD_SEMANTIC_TESTSUITE)
mark_as_advanced(BUILD_STEADY_STATE_RUNNER)
mark_as_advanced(BUILD_MCA_RUNNER)
mark_as_advanced(BUILD_SBML_TESTSUITE)
mark_as_advanced(BUILD_STOCHASTIC_TESTSUITE)
mark_as_advanced(BUILD_FRANKS_TESTSUITE)
option (BUILD_HYB_ODE_TESTS "Hybrid ODE Test." ON)
mark_as_advanced(BUILD_HYB_ODE_TESTS)
option (BUILD_HYB_TESTS "Hybrid Test." ON)
mark_as_advanced(BUILD_HYB_TESTS)
set(FILE_SEP)
set(PATH_SEP)
if(UNIX OR CYGWIN)
set(PATH_SEP "/")
set(FILE_SEP ":")
else()
set(PATH_SEP "\\")
set(FILE_SEP ";")
endif()
# we need to be able to set the paths to some files
# java headers, java compiler
# python headers and library
# perl binary
# mkoctfile
# R binary
#if we link statically, which is the default under windows, we need the following defines
# XML_STATIC
# LIBSBML_STATIC
# LIBLAX_STATIC
# RAPTOR_STATIC
# SBW_STATIC
# we need to define the following paths
# for the backend
# to expat
# to raptor
# to libsbml
# to clapack, lapack or mkl
# for clapack we need to define whether we use BLASWRAP or not
# for the frontend
# to sbw
# to qwt
# to qwtplot3d
# windows needs the following define
#DEFINES -= UNICODE
#DEFINES += _CRT_SECURE_NO_WARNINGS
# are we using the intel compiler
set(USING_INTEL)
if ((WIN32 OR (UNIX AND NOT APPLE))
AND CMAKE_C_COMPILER
AND ${CMAKE_C_COMPILER} MATCHES ".*ic[cl].*$")
message(STATUS "Detected Intel Compiler")
set(USING_INTEL TRUE)
endif ()
# if using msvc or intel windows compiler allow for the use of the static runtime
if(MSVC OR USING_INTEL)
add_definitions(-D_CRT_SECURE_NO_WARNINGS -D_CRT_NONSTDC_NO_DEPRECATE -DWIN32_LEAN_AND_MEAN)
set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -D_CRT_SECURE_NO_WARNINGS")
option(WITH_STATIC_RUNTIME "Compile using the static MSVC Runtime." OFF)
if(WITH_STATIC_RUNTIME)
foreach(flag_var
CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
if(${flag_var} MATCHES "/MD")
string(REGEX REPLACE "/MD" "/MT" ${flag_var} "${${flag_var}}")
endif(${flag_var} MATCHES "/MD")
endforeach(flag_var)
add_definitions( -D_MT)
set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
endif(WITH_STATIC_RUNTIME)
# on VS enable multiprocessor build
if (MSVC)
SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /MP")
endif()
option(COPASI_USE_VLD "When running debug builds with MSVC use Visual Leak Detector." OFF)
mark_as_advanced(COPASI_USE_VLD)
if (COPASI_USE_VLD)
add_definitions( -DCOPASI_USE_VLD)
endif (COPASI_USE_VLD)
# CMake no longer creates PDB files for static libraries after 2.8.11
# so we store debug information in the object files instead
if (${CMAKE_VERSION} VERSION_GREATER "2.8.11")
foreach(flag_var
CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
if(${flag_var} MATCHES "/Zi")
STRING(REPLACE "/Zi" "/Z7" "${flag_var}" "${${flag_var}}")
endif(${flag_var} MATCHES "/Zi")
endforeach(flag_var)
if (MSVC AND WIN32 AND NOT MSVC_VERSION VERSION_LESS 142 AND CMAKE_VERSION VERSION_GREATER 3.13)
# enable edit & continue for debug builds of msvc
add_link_options($<$<CONFIG:Debug>:/INCREMENTAL>)
add_compile_options($<$<CONFIG:Debug>:/ZI>)
add_compile_options("$<$<CXX_COMPILER_ID:MSVC>:/EHsc>")
endif()
endif()
endif(MSVC OR USING_INTEL)
if (EMSCRIPTEN)
add_compile_options(-fexceptions)
add_link_options(-fexceptions -sINITIAL_MEMORY=65536000 -sALLOW_MEMORY_GROWTH=1)
endif(EMSCRIPTEN)
set(APPS "" CACHE INTERNAL "")
set(DIRS "${COPASI_DEPENDENCY_DIR}/bin;${COPASI_DEPENDENCY_DIR}/lib" CACHE INTERNAL "")
if (QT_BINARY_DIR)
set(DIRS ${DIRS} ${QT_BINARY_DIR} CACHE INTERNAL "")
endif()
if (QT_LIBRARY_DIR)
set(DIRS ${DIRS} ${QT_LIBRARY_DIR} CACHE INTERNAL "")
endif()
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "COPASI is a software application for simulation and analysis of biochemical networks and their dynamics..")
set(CPACK_PACKAGE_NAME "COPASI")
set(CPACK_PACKAGE_VENDOR "copasi.org")
set(CPACK_PACKAGE_CONTACT "COPASI Support <support@copasi.org>")
set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/copasi/ArtisticLicense.txt")
set(CPACK_PACKAGE_VERSION_MAJOR "${COPASI_VERSION_MAJOR}")
set(CPACK_PACKAGE_VERSION_MINOR "${COPASI_VERSION_MINOR}")
set(CPACK_PACKAGE_VERSION_PATCH "${COPASI_VERSION_BUILD}")
set(CPACK_RPM_PACKAGE_LICENSE "Artistic License")
set(CPACK_RPM_PACKAGE_GROUP "Applications/Engineering")
set(CPACK_DEBIAN_PACKAGE_SECTION "Applications")
set(CPACK_SOURCE_GENERATOR "TGZ")
if (${CMAKE_SYSTEM_NAME} MATCHES "Linux")
if (${COPASI_BUILD_TYPE} MATCHES "64bit")
set(CPACK_SYSTEM_NAME "Linux-64bit")
else ()
set(CPACK_SYSTEM_NAME "Linux-32bit")
endif ()
elseif (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
if (${COPASI_BUILD_TYPE} MATCHES "64bit")
set(CPACK_SYSTEM_NAME "Windows-64bit")
else ()
set(CPACK_SYSTEM_NAME "Windows-32bit")
endif ()
endif ()
set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR};/.git/;/.svn/;/.libs/;/.deps/;/.bzr/;/.o$/;/.lo$/;/.la$/;/.vs/;/.vscode/;/dist/;/build/;${CPACK_SOURCE_IGNORE_FILES};/.DS_Store;/.svnignore;blib;libsbml-dist;/gps/;CopasiWS;userdocs;docs")
list (APPEND CPACK_SOURCE_IGNORE_FILES "/.*\\\\.tmp")
list (APPEND CPACK_SOURCE_IGNORE_FILES "/.*\\\\.bak")
list (APPEND CPACK_SOURCE_IGNORE_FILES "/.*\\\\.egg-info")
list (APPEND CPACK_SOURCE_IGNORE_FILES "/build_.*")
list (APPEND CPACK_SOURCE_IGNORE_FILES "/install_.*")
if(UNIX)
set(CPACK_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
set(CPACK_SET_DESTDIR "ON")
endif()
if(CMAKE_SIZEOF_VOID_P EQUAL 4)
set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "i386")
set(CPACK_RPM_PACKAGE_ARCHITECTURE "i386")
else()
set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "amd64")
set(CPACK_RPM_PACKAGE_ARCHITECTURE "x86_64")
endif()
include(CPack)
add_subdirectory(copasi)
if(BUILD_TESTS)
add_subdirectory(tests)
endif (BUILD_TESTS)
if(BUILD_SEMANTIC_TESTSUITE)
add_subdirectory(semantic-test-suite)
endif (BUILD_SEMANTIC_TESTSUITE)
if(BUILD_SBML_TESTSUITE)
add_subdirectory(sbml-testsuite)
endif (BUILD_SBML_TESTSUITE)
if(BUILD_STOCHASTIC_TESTSUITE)
add_subdirectory(stochastic-testsuite)
endif (BUILD_STOCHASTIC_TESTSUITE)
if(BUILD_FRANKS_TESTSUITE)
add_subdirectory(franks_testsuite)
endif (BUILD_FRANKS_TESTSUITE)
if(BUILD_STEADY_STATE_RUNNER)
add_subdirectory(steady_state_test_wrapper)
endif (BUILD_STEADY_STATE_RUNNER)
if(BUILD_MCA_RUNNER)
add_subdirectory(mca_test_wrapper)
endif (BUILD_MCA_RUNNER)
if(BUILD_HYB_ODE_TESTS)
if (EXISTS ${CMAKE_SOURCE_DIR}/hyb-ode-test-suite)
add_subdirectory(hyb-ode-test-suite)
endif()
endif (BUILD_HYB_ODE_TESTS)
if(BUILD_HYB_TESTS)
if (EXISTS ${CMAKE_SOURCE_DIR}/hyb-test-suite)
add_subdirectory(hyb-test-suite)
endif()
endif (BUILD_HYB_TESTS)
# also install additional files and examples
file(GLOB_RECURSE WIZARD_HELP_FILES "${PROJECT_SOURCE_DIR}/copasi/wizard/help_html" copasi/wizard/help_html/*.html)
file(GLOB_RECURSE WIZARD_IMAGE_FILES "${PROJECT_SOURCE_DIR}/copasi/wizard/help_html/figures" copasi/wizard/help_html/figures/*.png)
file(GLOB_RECURSE EXAMPLE_FILES "${PROJECT_SOURCE_DIR}/TestSuite/distribution" TestSuite/distribution/*.*)
install(FILES ${WIZARD_HELP_FILES} DESTINATION share/copasi/doc/html)
install(FILES ${WIZARD_IMAGE_FILES} DESTINATION share/copasi/doc/html/figures)
install(FILES ${EXAMPLE_FILES} DESTINATION share/copasi/examples)
install(FILES
"${PROJECT_SOURCE_DIR}/copasi/UI/icons/Copasi.ico"
"${PROJECT_SOURCE_DIR}/copasi/UI/icons/CopasiDoc.ico"
DESTINATION share/copasi/icons)
install(FILES
"${PROJECT_SOURCE_DIR}/copasi/MIRIAM/MIRIAMResources.xml"
DESTINATION share/copasi/config)
# set up variables for cpack
set(CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON)
include(InstallRequiredSystemLibraries)
get_directory_property(DirDefs COMPILE_DEFINITIONS)
message(STATUS "-----------------------------------------------------------
Building COPASI ${COPASI_VERSION_MAJOR}.${COPASI_VERSION_MINOR}.${COPASI_VERSION_BUILD} (${CMAKE_BUILD_TYPE})
Source Dir = ${CMAKE_SOURCE_DIR}
Binary Dir = ${CMAKE_BINARY_DIR}
Install Prefix = ${CMAKE_INSTALL_PREFIX}
Dependencies:
Vendor = ${BLA_VENDOR}
LAPACK Libs = ${CLAPACK_LIBRARIES}
LAPACK LDFLAGS = ${CLAPACK_LINKER_FLAGS}
crossguid Libs = ${CROSSGUID_LIBRARY}
cross include = ${CROSSGUID_INCLUDE_DIR}
Expat version = ${EXPAT_VERSION}
Expat Libs = ${EXPAT_LIBRARY}
Expat include = ${EXPAT_INCLUDE_DIR}
Raptor version = ${RAPTOR_VERSION}
Raptor Libs = ${RAPTOR_LIBRARY}
Raptor include = ${RAPTOR_INCLUDE_DIR}
libSBML version = ${LIBSBML_VERSION}
libSBML lib = ${LIBSBML_LIBRARY}
libSBML include = ${LIBSBML_INCLUDE_DIR}
Qt version = ${QT_VERSION}
Qt lib = ${QT_LIBRARIES}
Qt include = ${QT_INCLUDE_DIRS}
QWT version = ${QWT_VERSION_STRING} (0x${QWT_VERSION_NUMERIC})
QWT lib = ${QWT_LIBRARY}
QWT include = ${QWT_INCLUDE_DIR}
qwtplot3d lib = ${QWTPLOT3D_LIBRARY}
qwtplot3d include = ${QWTPLOT3D_INCLUDE_DIR}
qtmml lib = ${MML_LIBRARY}
qtmml include = ${MML_INCLUDE_DIR}
SBW version = ${SBW_VERSION}
SBW lib = ${SBW_LIBRARY}
SBW include = ${SBW_INCLUDE_DIR}
libSEDML version = ${LIBSEDML_VERSION}
libSEDML lib = ${LIBSEDML_LIBRARY}
libSEDML include = ${LIBSEDML_INCLUDE_DIR}
Combine version = ${LIBCOMBINE_VERSION}
Combine lib = ${LIBCOMBINE_LIBRARY}
Combine include = ${LIBCOMBINE_INCLUDE_DIR}
NativeJIT lib = ${NATIVEJIT_LIBRARY}
NativeJIT include = ${NATIVEJIT_INCLUDE_DIR}
NativeJIT CXX Flags = ${NATIVEJIT_COMPILE_OPTIONS}
cpu_features lib = ${CPUFEATURES_LIBRARY}
cpu_features include = ${CPUFEATURES_INCLUDE_DIR}
OpenMP Libs = ${OpenMP_C_LIB_NAMES}
OpenMP CXX Flags = ${OpenMP_CXX_FLAGS}
Options:
COPASI_EXTUNIT = ${ENABLE_COPASI_EXTUNIT}
SBW integration = ${ENABLE_SBW_INTEGRATION}
Model Merging = ON
SEDML support = ON
Combine Archive support = ON
SDE support = ON
GPROF support = ${ENABLE_GPROF}
UNDO framework = ON
Versioning framework = ${ENABLE_VERSIONING}