<commit_before># Begin CVS Header 
#   $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/common.pri,v $ 
#   $Revision: 1.111 $ 
#   $Name:  $ 
#   $Author: shoops $ 
#   $Date: 2009/11/10 17:01:25 $ 
# End CVS Header 

# Copyright (C) 2008 by <NAME>, Virginia Tech Intellectual
# Properties, Inc., EML Research, gGmbH, University of Heidelberg,
# and The University of Manchester.
# All rights reserved.

# Copyright (C) 2001 - 2007 by <NAME>, Virginia Tech Intellectual
# Properties, Inc. and EML Research, gGmbH.
# All rights reserved.

######################################################################
# $Revision: 1.111 $ $Author: shoops $ $Date: 2009/11/10 17:01:25 $  
######################################################################

# In the case the BUILD_OS is not specified we make a guess.
isEmpty(BUILD_OS) {
  win32 {
    BUILD_OS = WIN32

    MY_QT4DIR = $$system(echo %QT4DIR%)
    contains(MY_QT4DIR, %QT4DIR%) {
      My_QTDIR = $$system(echo %QTDIR%)
      contains(MY_QTDIR, %QTDIR%) {
        QMAKE_QMAKE = qmake.exe
        !build_pass: message("Configuring for $${BUILD_OS} with QTDIR=???.")
      } else {
        QMAKE_QMAKE = $(QTDIR)\bin\qmake.exe
        !build_pass: message("Configuring for $${BUILD_OS} with QTDIR=$(QTDIR).")
      }
	} else {
      !build_pass: message("Configuring for $${BUILD_OS} with QTDIR=$(QT4DIR).")
	}

  } else {
    BUILD_OS = $$system(uname)
    message("Configuring for $${BUILD_OS} with QTDIR=$(QTDIR).")
  }
}
DEFINES += $$BUILD_OS

TARGETDEPS += Makefile

# Common configuration settings
CONFIG += exceptions
CONFIG += rtti
CONFIG += thread

#ifdef COPASI_LICENSE_COM
# COPASI License to use
DEFINES -= COPASI_LICENSE_US
DEFINES -= COPASI_LICENSE_DE
DEFINES -= COPASI_LICENSE_COM
DEFINES += COPASI_LICENSE_$$USE_LICENSE
#endif // COPASI_LICENSE_COM

INCLUDEPATH += ../..
QMAKE_CFLAGS   += $$(CFLAGS)
QMAKE_CXXFLAGS += $$(CXXFLAGS)
QMAKE_LFLAGS  += $$(LDFLAGS)

debug {
  DEFINES += COPASI_DEBUG
  DEFINES += COPASI_EXTUNIT

  isEmpty(COPASI_SRC_PACKAGE) {
    # DEFINES += COPASI_TSS
    #  stoichiometric stability analysis:
    # DEFINES += COPASI_SSA
  }
}

isEmpty(COPASI_SRC_PACKAGE) {
  DEFINES += HAVE_MML
}

win32: STATIC_LINKAGE = yes

contains(STATIC_LINKAGE, yes) {
  DEFINES += XML_STATIC
  DEFINES += LIBSBML_STATIC
  DEFINES += LIBLAX_STATIC
  DEFINES += RAPTOR_STATIC
  DEFINES += SBW_STATIC
}

!contains(BUILD_OS, WIN32) {
  #Release code optimization
  QMAKE_CFLAGS_RELEASE -= -O1
  QMAKE_CFLAGS_RELEASE -= -O2
  QMAKE_CFLAGS_RELEASE -= -O4
  QMAKE_CFLAGS_RELEASE += -O3

  QMAKE_CXXFLAGS_RELEASE -= -O1
  QMAKE_CXXFLAGS_RELEASE -= -O2
  QMAKE_CXXFLAGS_RELEASE -= -O4
  QMAKE_CXXFLAGS_RELEASE += -O3

  QMAKE_LEX = ../../admin/flex.sh
  QMAKE_YACC = ../../admin/yacc.sh
  
  # The character # (hex 23) can not be escaped we therefore create 
  # a variable containing it
  HASH = $$system(echo "\\043")
  contains(HASH, \\043){
    HASH = $$system(echo -e "\\043")
  }
}


contains(BUILD_OS, Darwin) {  
  release {
    contains(TEMPLATE, app) {
      QMAKE_POST_LINK = strip $(TARGET)
    }

    MY_UNIVERSAL = $$system(echo $UNIVERSAL)
    contains(MY_UNIVERSAL, yes) {
       message("Creating universal 32 bit binaries.")
       CONFIG += x86 ppc
       QMAKE_MAC_SDK = /Developer/SDKs/MacOSX10.4u.sdk
    }
  }
 
  INCLUDEPATH += /System/Library/Frameworks/Accelerate.framework/Headers
  INCLUDEPATH += /System/Library/Frameworks/Carbon.framework/Headers

  !isEmpty(SBML_PATH){
    LIBS +=  $${SBML_PATH}/lib/libsbml.a
    INCLUDEPATH += $${SBML_PATH}/include
  } else {
    LIBS += -lsbml
  }

  !isEmpty(EXPAT_PATH){
    LIBS+=  $${EXPAT_PATH}/lib/libexpat.a
    INCLUDEPATH += $${EXPAT_PATH}/include
  } else {
    LIBS += -lexpat
  }

  !isEmpty(RAPTOR_PATH){
    LIBS+=  $${RAPTOR_PATH}/lib/libraptor.a
    INCLUDEPATH += $${RAPTOR_PATH}/include
  } else {
    LIBS += -lraptor
  }

  contains(CONFIG, qt) {
    !isEmpty(SBW_PATH){
      LIBS+=  $${SBW_PATH}/lib/libSBW.a
      INCLUDEPATH += $${SBW_PATH}/include
      DEFINES += COPASI_SBW_INTEGRATION
      DEFINES += LINUX DARWIN 
    } 
  
    !isEmpty(QWT_PATH){
       LIBS+=  $${QWT_PATH}/lib/libqwt.a
       INCLUDEPATH += $${QWT_PATH}/include
    } else {
      LIBS += -lqwt
    }
    
    !isEmpty(QWT3D_PATH){
      LIBS +=  $${QWT3D_PATH}/lib/libqwtplot3d.a
      INCLUDEPATH += $${QWT3D_PATH}/include
    } else {
      LIBS += -lqwtplot3d
    }
  }

  LIBS += -framework Accelerate
  LIBS += -framework Carbon
  LIBS += -framework QuickTime
  LIBS += -lz
}

contains(BUILD_OS, WIN32) {
  CONFIG += debug_and_release

  win32-icc: {
     !build_pass: message("Using Intel Compiler.")
     DEFINES += COPASI_ICC
     DEFINES += _CRT_SECURE_NO_WARNINGS
  }
  
  QMAKE_LEX = C:\cygwin\bin\bash ../../admin/flex.sh
  QMAKE_YACC = C:\cygwin\bin\bash ../../admin/yacc.sh

  DEFINES -= UNICODE
   
  #Release code optimization
  QMAKE_CFLAGS_RELEASE   -= -O1
  QMAKE_CFLAGS_RELEASE   *= -O2

  QMAKE_CXXFLAGS_RELEASE -= -O1
  QMAKE_CXXFLAGS_RELEASE *= -O2
  
  contains(RUNTIME, MT) {
    release: RUNTIME = MT
    debug:   RUNTIME = MTd
    
    QMAKE_CFLAGS_RELEASE   -= -MD
    QMAKE_CFLAGS_RELEASE   *= -MT
    QMAKE_CFLAGS_DEBUG     -= -MDd
    QMAKE_CFLAGS_DEBUG     *= -MTd
	
    QMAKE_CXXFLAGS_RELEASE -= -MD
    QMAKE_CXXFLAGS_RELEASE *= -MT
    QMAKE_CXXFLAGS_DEBUG   -= -MDd
    QMAKE_CXXFLAGS_DEBUG   *= -MTd
	
    QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcrt.lib"
    QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcrtd.lib"
    QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcprt.lib"
    QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcprtd.lib"
    
    release: QMAKE_LFLAGS *= /NODEFAULTLIB:"libcmtd.lib"
    
    debug: QMAKE_LFLAGS *= /NODEFAULTLIB:"libcmt.lib"
  } else {
    release: RUNTIME = MD
    debug:   RUNTIME = MDd
    
    QMAKE_CFLAGS_RELEASE   -= -MT
    QMAKE_CFLAGS_RELEASE   *= -MD
    QMAKE_CFLAGS_DEBUG     -= -MTd
    QMAKE_CFLAGS_DEBUG     *= -MDd
       
    QMAKE_CXXFLAGS_RELEASE -= -MT
    QMAKE_CXXFLAGS_RELEASE *= -MD
    QMAKE_CXXFLAGS_DEBUG   -= -MTd
    QMAKE_CXXFLAGS_DEBUG   *= -MDd
	
    QMAKE_LFLAGS *= /NODEFAULTLIB:"libcmt.lib"
    QMAKE_LFLAGS *= /NODEFAULTLIB:"libcmtd.lib"
    
    release {
      QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcrtd.lib"
      QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcprtd.lib"
    }
    
    debug {
      QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcrt.lib"
      QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcprt.lib"
    }
  }    

  !isEmpty(MKL_PATH) {
    DEFINES += USE_MKL
    QMAKE_CXXFLAGS += -I\"$${MKL_PATH}\include\"
    QMAKE_LFLAGS += /LIBPATH:\"$${MKL_PATH}\ia32\lib\"
    QMAKE_LFLAGS += /LIBPATH:\"$${MKL_PATH}\..\lib\ia32\"
    LIBS += mkl_intel_c.lib mkl_intel_thread.lib mkl_core.lib
    LIBS += libiomp5mt.lib
  } else {
    !isEmpty(CLAPACK_PATH) {
      DEFINES += USE_CLAPACK
      QMAKE_CXXFLAGS   += -I\"$${CLAPACK_PATH}\include\"
      QMAKE_LFLAGS += /LIBPATH:\"$${CLAPACK_PATH}\lib\"
      LIBS += clapack.lib
    } else {
      error( "Either MKL_PATH or CLAPACK_PATH must be specified" )
    }
  }


#expat library
  contains(RUNTIME, MT) | contains (RUNTIME, MTd) {
    LIBS += libexpatMT.lib
  } else {
    DEFINES -= XML_STATIC
    LIBS += libexpat.lib
  }

  !isEmpty(EXPAT_PATH) {
    QMAKE_CXXFLAGS += -I\"$${EXPAT_PATH}\Source\lib\"
    QMAKE_CXXFLAGS += -I\"$${EXPAT_PATH}\include\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${EXPAT_PATH}\StaticLibs\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${EXPAT_PATH}\bin\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${EXPAT_PATH}\lib\"
  } else {
    error( "EXPAT_PATH must be specified" )
  }

  LIBS += libsbml$${RUNTIME}.lib
  
  !isEmpty(SBML_PATH) {
    QMAKE_CXXFLAGS += -I\"$${SBML_PATH}\include\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${SBML_PATH}\lib\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${SBML_PATH}\bin\"
  } else {
    error( "SBML_PATH must be specified" )
  }

# The raptor library
  LIBS += raptor$${RUNTIME}.lib
    
  !isEmpty(RAPTOR_PATH) {
    QMAKE_CXXFLAGS += -I\"$${RAPTOR_PATH}\include\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${RAPTOR_PATH}\lib\"
  } else {
    error( "RAPTOR_PATH must be specified" )
  }
  
  contains(CONFIG, qt) {
    LIBS    += SBW$${RUNTIME}.lib ws2_32.lib

    !isEmpty(SBW_PATH){
      QMAKE_CXXFLAGS += -I"$${SBW_PATH}\include"
      QMAKE_LFLAGS   += /LIBPATH:"$${SBW_PATH}\lib"
      
      DEFINES += COPASI_SBW_INTEGRATION
      DEFINES *= WIN32
    }
     
    !isEmpty(QWT_PATH){
       LIBS+=  -L$${QWT_PATH}/lib
       INCLUDEPATH += $${QWT_PATH}/include
    }
    LIBS += -lqwt
    
    !isEmpty(QWT3D_PATH){
      LIBS += -L$${QWT3D_PATH}/lib/
      INCLUDEPATH += $${QWT3D_PATH}/include
    } 

#    DEFINES        += QWT3D_NODLL

    release: LIBS += -lqwtplot3d
    debug: LIBS += -lqwtplot3dD
  }
} 

contains(BUILD_OS, SunOS) {
contains(STATIC_LINKAGE, yes) {
# :TODO: This should be set through configure.
  LIBS += -L/export/home/shoops/copasi/gcc/lib
}

  release { 
    contains(TEMPLATE, app) {
# Note: This must be the SunOS strip command.
      QMAKE_POST_LINK = /usr/ccs/bin/strip $(TARGET)
    }
  }
 
  !isEmpty(CLAPACK_PATH) {
    DEFINES += USE_CLAPACK
    INCLUDEPATH += $${CLAPACK_PATH}/include
#    LIBS += -llapack -lblas -lF77 -lfl
    LIBS += -llapack -lblas -lF77
    LIBS += -L$${CLAPACK_PATH}/lib
  } else {
    !isEmpty(LAPACK_PATH) {
      message("Using lapack.")
      DEFINES += USE_LAPACK
      INCLUDEPATH += $${LAPACK_PATH}/include
      LIBS += -llapack -lblas  -lg2c
      LIBS += -L$${LAPACK_PATH}/lib
    } else {
      message("Using sunperf.")
      DEFINES += USE_SUNPERF
      LIBS += -lsunperf
      QMAKE_CFLAGS   += -dalign
      QMAKE_CXXFLAGS   += -dalign
    }
  }
  !isEmpty(EXPAT_PATH){
      LIBS+=  -L$${EXPAT_PATH}/lib
      INCLUDEPATH += $${EXPAT_PATH}/include
  }
  !isEmpty(SBML_PATH){
      LIBS+=  -L$${SBML_PATH}/lib
      INCLUDEPATH += $${SBML_PATH}/include
  }

  LIBS += -lsbml -lexpat

# The raptor library
  LIBS += -lraptor
  !isEmpty(RAPTOR_PATH){
      LIBS+=  -L$${RAPTOR_PATH}/lib
      INCLUDEPATH += $${RAPTOR_PATH}/include
  }
  
  contains(CONFIG, qt) {
    !isEmpty(SBW_PATH){
      LIBS+=  $${SBW_PATH}/lib/libSBW.a
      INCLUDEPATH += $${SBW_PATH}/include
      DEFINES += COPASI_SBW_INTEGRATION
      DEFINES += LINUX SOLARIS
    } 

    !isEmpty(QWT_PATH){
       LIBS+=  -L$${QWT_PATH}/lib
       INCLUDEPATH += $${QWT_PATH}/include
    }
    LIBS += -lqwt
    
    !isEmpty(QWT3D_PATH){
      LIBS += -L$${QWT3D_PATH}/lib/
      INCLUDEPATH += $${QWT3D_PATH}/include
    } else {
      LIBS += -lqwtplot3d
    }
    
    LIBS += -lSM
  } else {
    QMAKE_LIBS_THREAD -= -lpthread
    QMAKE_LIBS_THREAD -= -lrt
  }
}
 
contains(BUILD_OS, Linux) {
  release {
    contains(TEMPLATE, app) {
      QMAKE_POST_LINK = strip $(TARGET)
    }
  }

  contains(PACKAGE, yes) {
    QMAKE_LFLAGS -= -static
  }
  else {
    contains(STATIC_LINKAGE, yes) {
      QMAKE_LFLAGS += -static
    }
    else {
      QMAKE_LFLAGS -= -static
    }
  }

  !isEmpty(SBML_PATH){
    INCLUDEPATH += $${SBML_PATH}/include
    INCLUDEPATH += $${SBML_PATH}/include/sbml

    contains(PACKAGE, yes) {
      LIBS += $${SBML_PATH}/lib/libsbml.a
    }
    else {
      LIBS += -L$${SBML_PATH}/lib
      LIBS += -lsbml
    }
  }
  else { 
    contains(PACKAGE, yes) {
      error("SBML_PATH must be given.")
    }
    else {
      LIBS += -lsbml
    }
  }

  !isEmpty(EXPAT_PATH){
    INCLUDEPATH += $${EXPAT_PATH}/include

    contains(PACKAGE, yes) {
      LIBS += $${EXPAT_PATH}/lib/libexpat.a
    }
    else {
      LIBS += -L$${EXPAT_PATH}/lib
      LIBS += -lexpat
    }
  }
  else { 
    contains(PACKAGE, yes) {
      error("EXPAT_PATH must be given.")
    }
    else {
      LIBS += -lexpat
    }
  }

# The raptor library
  !isEmpty(RAPTOR_PATH){
      LIBS +=  -L$${RAPTOR_PATH}/lib
      INCLUDEPATH += $${RAPTOR_PATH}/include

    contains(PACKAGE, yes) {
      LIBS += $${RAPTOR_PATH}/lib/libraptor.a
    }
    else {
      LIBS += -L$${RAPTOR_PATH}/lib
      LIBS += -lraptor
    }
  }
  else { 
    contains(PACKAGE, yes) {
      error("RAPTOR_PATH must be given.")
    }
    else {
      LIBS += -lraptor
    }
  }
  
  !isEmpty(MKL_PATH) {
    DEFINES += USE_MKL
    INCLUDEPATH += $${MKL_PATH}/include

    LIBS += $${MKL_PATH}/lib/32/libmkl_solver.a \
            -Wl,--start-group \
              $${MKL_PATH}/lib/32/libmkl_intel.a \
              $${MKL_PATH}/lib/32/libmkl_sequential.a \
              $${MKL_PATH}/lib/32/libmkl_core.a \
            -Wl,--end-group \
            -lpthread

  } else {
    !isEmpty(CLAPACK_PATH) {
      DEFINES += USE_CLAPACK
      INCLUDEPATH += $${CLAPACK_PATH}/include
#      LIBS += -llapack -lblas -lF77 -lfl
      LIBS += -llapack -lblas -lF77
      LIBS += -L$${CLAPACK_PATH}/lib 
    } else {
      !isEmpty(LAPACK_PATH) {
        message("Using lapack.")
        DEFINES += USE_LAPACK
        INCLUDEPATH += $${LAPACK_PATH}/include

        contains(PACKAGE, yes) {
          LIBS += $${LAPACK_PATH}/lib/liblapack.a 
          LIBS += $${LAPACK_PATH}/lib/libblas.a
          LIBS += $$system(locate libg2c.a)
        }
        else {
          LIBS += -L$${LAPACK_PATH}/lib
          LIBS += -llapack 
          LIBS += -lblas
          HAVE_G2C = $$system(locate libg2c)
          !isEmpty(HAVE_G2C) LIBS += -lg2c
        }
      } else {
        error( "Either MKL_PATH, CLAPACK_PATH, or LAPACK_PATH must be specified" )
      }
    }
  }

  contains(CONFIG, qt) {
    !isEmpty(SBW_PATH){
      LIBS+=  $${SBW_PATH}/lib/libSBW.a
      INCLUDEPATH += $${SBW_PATH}/include
      DEFINES += COPASI_SBW_INTEGRATION
      DEFINES += LINUX 
    }
     
    !isEmpty(QWT_PATH){
       LIBS +=  -L$${QWT_PATH}/lib
       INCLUDEPATH += $${QWT_PATH}/include
    }
    LIBS += -lqwt

    !isEmpty(QWT3D_PATH){
      LIBS += -L$${QWT3D_PATH}/lib/
      INCLUDEPATH += $${QWT3D_PATH}/include
    } else {
      LIBS += -lqwtplot3d
    }
  }
}

DEP1.target   = depend
DEP1.depends  = qmake

QMAKE_EXTRA_UNIX_TARGETS += DEP1

!equals(TEMPLATE, subdirs) {
  # Copy the sources for the tar ball
  src_distribution.depends = Makefile
  src_distribution.commands =   \
    $(CHK_DIR_EXISTS) ../../copasi_src || $(MKDIR) ../../copasi_src; \
    $(CHK_DIR_EXISTS) ../../copasi_src/copasi || \
      $(MKDIR) ../../copasi_src/copasi; \
    $(CHK_DIR_EXISTS) ../../copasi_src/copasi/$$SRC_TARGET || \
      $(MKDIR) ../../copasi_src/copasi/$$SRC_TARGET; \
    $(COPY_FILE) --parents $(SOURCES) $(HEADERS) $(FORMS) $(DIST) \
      ../../copasi_src/copasi/$$SRC_TARGET/

  QMAKE_EXTRA_UNIX_TARGETS += src_distribution
}

# addSubdirs(subdirs,deps): Adds directories to the project that depend on
# other directories
defineTest(addSubdirs) {
    for(subdirs, 1) {
        entries = $$files($$subdirs)
        for(entry, entries) {
            name = $$replace(entry, [/\\\\], _)
            SUBDIRS += $$name
            eval ($${name}.subdir = $$entry)
            for(dep, 2):eval ($${name}.depends += $$replace(dep, [/\\\\], _))
            export ($${name}.subdir)
            export ($${name}.depends)
        }
    }
    export (SUBDIRS)
}
<commit_msg>activate csp method for time scale separation analysis<commit_after># Begin CVS Header 
#   $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/common.pri,v $ 
#   $Revision: 1.112 $ 
#   $Name:  $ 
#   $Author: ssahle $ 
#   $Date: 2009/11/23 10:53:32 $ 
# End CVS Header 

# Copyright (C) 2008 by <NAME>, Virginia Tech Intellectual
# Properties, Inc., EML Research, gGmbH, University of Heidelberg,
# and The University of Manchester.
# All rights reserved.

# Copyright (C) 2001 - 2007 by <NAME>, Virginia Tech Intellectual
# Properties, Inc. and EML Research, gGmbH.
# All rights reserved.

######################################################################
# $Revision: 1.112 $ $Author: ssahle $ $Date: 2009/11/23 10:53:32 $  
######################################################################

# In the case the BUILD_OS is not specified we make a guess.
isEmpty(BUILD_OS) {
  win32 {
    BUILD_OS = WIN32

    MY_QT4DIR = $$system(echo %QT4DIR%)
    contains(MY_QT4DIR, %QT4DIR%) {
      My_QTDIR = $$system(echo %QTDIR%)
      contains(MY_QTDIR, %QTDIR%) {
        QMAKE_QMAKE = qmake.exe
        !build_pass: message("Configuring for $${BUILD_OS} with QTDIR=???.")
      } else {
        QMAKE_QMAKE = $(QTDIR)\bin\qmake.exe
        !build_pass: message("Configuring for $${BUILD_OS} with QTDIR=$(QTDIR).")
      }
	} else {
      !build_pass: message("Configuring for $${BUILD_OS} with QTDIR=$(QT4DIR).")
	}

  } else {
    BUILD_OS = $$system(uname)
    message("Configuring for $${BUILD_OS} with QTDIR=$(QTDIR).")
  }
}
DEFINES += $$BUILD_OS

TARGETDEPS += Makefile

# Common configuration settings
CONFIG += exceptions
CONFIG += rtti
CONFIG += thread

#ifdef COPASI_LICENSE_COM
# COPASI License to use
DEFINES -= COPASI_LICENSE_US
DEFINES -= COPASI_LICENSE_DE
DEFINES -= COPASI_LICENSE_COM
DEFINES += COPASI_LICENSE_$$USE_LICENSE
#endif // COPASI_LICENSE_COM

INCLUDEPATH += ../..
QMAKE_CFLAGS   += $$(CFLAGS)
QMAKE_CXXFLAGS += $$(CXXFLAGS)
QMAKE_LFLAGS  += $$(LDFLAGS)

DEFINES += WITH_CSPMETHOD

debug {
  DEFINES += COPASI_DEBUG
  DEFINES += COPASI_EXTUNIT
  #DEFINES += WITH_MERGEMODEL

  isEmpty(COPASI_SRC_PACKAGE) {
    # DEFINES += COPASI_TSS
    #  stoichiometric stability analysis:
    # DEFINES += COPASI_SSA
  }
}

isEmpty(COPASI_SRC_PACKAGE) {
  DEFINES += HAVE_MML
}

win32: STATIC_LINKAGE = yes

contains(STATIC_LINKAGE, yes) {
  DEFINES += XML_STATIC
  DEFINES += LIBSBML_STATIC
  DEFINES += LIBLAX_STATIC
  DEFINES += RAPTOR_STATIC
  DEFINES += SBW_STATIC
}

!contains(BUILD_OS, WIN32) {
  #Release code optimization
  QMAKE_CFLAGS_RELEASE -= -O1
  QMAKE_CFLAGS_RELEASE -= -O2
  QMAKE_CFLAGS_RELEASE -= -O4
  QMAKE_CFLAGS_RELEASE += -O3

  QMAKE_CXXFLAGS_RELEASE -= -O1
  QMAKE_CXXFLAGS_RELEASE -= -O2
  QMAKE_CXXFLAGS_RELEASE -= -O4
  QMAKE_CXXFLAGS_RELEASE += -O3

  QMAKE_LEX = ../../admin/flex.sh
  QMAKE_YACC = ../../admin/yacc.sh
  
  # The character # (hex 23) can not be escaped we therefore create 
  # a variable containing it
  HASH = $$system(echo "\\043")
  contains(HASH, \\043){
    HASH = $$system(echo -e "\\043")
  }
}


contains(BUILD_OS, Darwin) {  
  release {
    contains(TEMPLATE, app) {
      QMAKE_POST_LINK = strip $(TARGET)
    }

    MY_UNIVERSAL = $$system(echo $UNIVERSAL)
    contains(MY_UNIVERSAL, yes) {
       message("Creating universal 32 bit binaries.")
       CONFIG += x86 ppc
       QMAKE_MAC_SDK = /Developer/SDKs/MacOSX10.4u.sdk
    }
  }
 
  INCLUDEPATH += /System/Library/Frameworks/Accelerate.framework/Headers
  INCLUDEPATH += /System/Library/Frameworks/Carbon.framework/Headers

  !isEmpty(SBML_PATH){
    LIBS +=  $${SBML_PATH}/lib/libsbml.a
    INCLUDEPATH += $${SBML_PATH}/include
  } else {
    LIBS += -lsbml
  }

  !isEmpty(EXPAT_PATH){
    LIBS+=  $${EXPAT_PATH}/lib/libexpat.a
    INCLUDEPATH += $${EXPAT_PATH}/include
  } else {
    LIBS += -lexpat
  }

  !isEmpty(RAPTOR_PATH){
    LIBS+=  $${RAPTOR_PATH}/lib/libraptor.a
    INCLUDEPATH += $${RAPTOR_PATH}/include
  } else {
    LIBS += -lraptor
  }

  contains(CONFIG, qt) {
    !isEmpty(SBW_PATH){
      LIBS+=  $${SBW_PATH}/lib/libSBW.a
      INCLUDEPATH += $${SBW_PATH}/include
      DEFINES += COPASI_SBW_INTEGRATION
      DEFINES += LINUX DARWIN 
    } 
  
    !isEmpty(QWT_PATH){
       LIBS+=  $${QWT_PATH}/lib/libqwt.a
       INCLUDEPATH += $${QWT_PATH}/include
    } else {
      LIBS += -lqwt
    }
    
    !isEmpty(QWT3D_PATH){
      LIBS +=  $${QWT3D_PATH}/lib/libqwtplot3d.a
      INCLUDEPATH += $${QWT3D_PATH}/include
    } else {
      LIBS += -lqwtplot3d
    }
  }

  LIBS += -framework Accelerate
  LIBS += -framework Carbon
  LIBS += -framework QuickTime
  LIBS += -lz
}

contains(BUILD_OS, WIN32) {
  CONFIG += debug_and_release

  win32-icc: {
     !build_pass: message("Using Intel Compiler.")
     DEFINES += COPASI_ICC
     DEFINES += _CRT_SECURE_NO_WARNINGS
  }
  
  QMAKE_LEX = C:\cygwin\bin\bash ../../admin/flex.sh
  QMAKE_YACC = C:\cygwin\bin\bash ../../admin/yacc.sh

  DEFINES -= UNICODE
   
  #Release code optimization
  QMAKE_CFLAGS_RELEASE   -= -O1
  QMAKE_CFLAGS_RELEASE   *= -O2

  QMAKE_CXXFLAGS_RELEASE -= -O1
  QMAKE_CXXFLAGS_RELEASE *= -O2
  
  contains(RUNTIME, MT) {
    release: RUNTIME = MT
    debug:   RUNTIME = MTd
    
    QMAKE_CFLAGS_RELEASE   -= -MD
    QMAKE_CFLAGS_RELEASE   *= -MT
    QMAKE_CFLAGS_DEBUG     -= -MDd
    QMAKE_CFLAGS_DEBUG     *= -MTd
	
    QMAKE_CXXFLAGS_RELEASE -= -MD
    QMAKE_CXXFLAGS_RELEASE *= -MT
    QMAKE_CXXFLAGS_DEBUG   -= -MDd
    QMAKE_CXXFLAGS_DEBUG   *= -MTd
	
    QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcrt.lib"
    QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcrtd.lib"
    QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcprt.lib"
    QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcprtd.lib"
    
    release: QMAKE_LFLAGS *= /NODEFAULTLIB:"libcmtd.lib"
    
    debug: QMAKE_LFLAGS *= /NODEFAULTLIB:"libcmt.lib"
  } else {
    release: RUNTIME = MD
    debug:   RUNTIME = MDd
    
    QMAKE_CFLAGS_RELEASE   -= -MT
    QMAKE_CFLAGS_RELEASE   *= -MD
    QMAKE_CFLAGS_DEBUG     -= -MTd
    QMAKE_CFLAGS_DEBUG     *= -MDd
       
    QMAKE_CXXFLAGS_RELEASE -= -MT
    QMAKE_CXXFLAGS_RELEASE *= -MD
    QMAKE_CXXFLAGS_DEBUG   -= -MTd
    QMAKE_CXXFLAGS_DEBUG   *= -MDd
	
    QMAKE_LFLAGS *= /NODEFAULTLIB:"libcmt.lib"
    QMAKE_LFLAGS *= /NODEFAULTLIB:"libcmtd.lib"
    
    release {
      QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcrtd.lib"
      QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcprtd.lib"
    }
    
    debug {
      QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcrt.lib"
      QMAKE_LFLAGS *= /NODEFAULTLIB:"msvcprt.lib"
    }
  }    

  !isEmpty(MKL_PATH) {
    DEFINES += USE_MKL
    QMAKE_CXXFLAGS += -I\"$${MKL_PATH}\include\"
    QMAKE_LFLAGS += /LIBPATH:\"$${MKL_PATH}\ia32\lib\"
    QMAKE_LFLAGS += /LIBPATH:\"$${MKL_PATH}\..\lib\ia32\"
    LIBS += mkl_intel_c.lib mkl_intel_thread.lib mkl_core.lib
    LIBS += libiomp5mt.lib
  } else {
    !isEmpty(CLAPACK_PATH) {
      DEFINES += USE_CLAPACK
      QMAKE_CXXFLAGS   += -I\"$${CLAPACK_PATH}\include\"
      QMAKE_LFLAGS += /LIBPATH:\"$${CLAPACK_PATH}\lib\"
      LIBS += clapack.lib
    } else {
      error( "Either MKL_PATH or CLAPACK_PATH must be specified" )
    }
  }


#expat library
  contains(RUNTIME, MT) | contains (RUNTIME, MTd) {
    LIBS += libexpatMT.lib
  } else {
    DEFINES -= XML_STATIC
    LIBS += libexpat.lib
  }

  !isEmpty(EXPAT_PATH) {
    QMAKE_CXXFLAGS += -I\"$${EXPAT_PATH}\Source\lib\"
    QMAKE_CXXFLAGS += -I\"$${EXPAT_PATH}\include\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${EXPAT_PATH}\StaticLibs\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${EXPAT_PATH}\bin\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${EXPAT_PATH}\lib\"
  } else {
    error( "EXPAT_PATH must be specified" )
  }

  LIBS += libsbml$${RUNTIME}.lib
  
  !isEmpty(SBML_PATH) {
    QMAKE_CXXFLAGS += -I\"$${SBML_PATH}\include\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${SBML_PATH}\lib\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${SBML_PATH}\bin\"
  } else {
    error( "SBML_PATH must be specified" )
  }

# The raptor library
  LIBS += raptor$${RUNTIME}.lib
    
  !isEmpty(RAPTOR_PATH) {
    QMAKE_CXXFLAGS += -I\"$${RAPTOR_PATH}\include\"
    QMAKE_LFLAGS   += /LIBPATH:\"$${RAPTOR_PATH}\lib\"
  } else {
    error( "RAPTOR_PATH must be specified" )
  }
  
  contains(CONFIG, qt) {
    LIBS    += SBW$${RUNTIME}.lib ws2_32.lib

    !isEmpty(SBW_PATH){
      QMAKE_CXXFLAGS += -I"$${SBW_PATH}\include"
      QMAKE_LFLAGS   += /LIBPATH:"$${SBW_PATH}\lib"
      
      DEFINES += COPASI_SBW_INTEGRATION
      DEFINES *= WIN32
    }
     
    !isEmpty(QWT_PATH){
       LIBS+=  -L$${QWT_PATH}/lib
       INCLUDEPATH += $${QWT_PATH}/include
    }
    LIBS += -lqwt
    
    !isEmpty(QWT3D_PATH){
      LIBS += -L$${QWT3D_PATH}/lib/
      INCLUDEPATH += $${QWT3D_PATH}/include
    } 

#    DEFINES        += QWT3D_NODLL

    release: LIBS += -lqwtplot3d
    debug: LIBS += -lqwtplot3dD
  }
} 

contains(BUILD_OS, SunOS) {
contains(STATIC_LINKAGE, yes) {
# :TODO: This should be set through configure.
  LIBS += -L/export/home/shoops/copasi/gcc/lib
}

  release { 
    contains(TEMPLATE, app) {
# Note: This must be the SunOS strip command.
      QMAKE_POST_LINK = /usr/ccs/bin/strip $(TARGET)
    }
  }
 
  !isEmpty(CLAPACK_PATH) {
    DEFINES += USE_CLAPACK
    INCLUDEPATH += $${CLAPACK_PATH}/include
#    LIBS += -llapack -lblas -lF77 -lfl
    LIBS += -llapack -lblas -lF77
    LIBS += -L$${CLAPACK_PATH}/lib
  } else {
    !isEmpty(LAPACK_PATH) {
      message("Using lapack.")
      DEFINES += USE_LAPACK
      INCLUDEPATH += $${LAPACK_PATH}/include
      LIBS += -llapack -lblas  -lg2c
      LIBS += -L$${LAPACK_PATH}/lib
    } else {
      message("Using sunperf.")
      DEFINES += USE_SUNPERF
      LIBS += -lsunperf
      QMAKE_CFLAGS   += -dalign
      QMAKE_CXXFLAGS   += -dalign
    }
  }
  !isEmpty(EXPAT_PATH){
      LIBS+=  -L$${EXPAT_PATH}/lib
      INCLUDEPATH += $${EXPAT_PATH}/include
  }
  !isEmpty(SBML_PATH){
      LIBS+=  -L$${SBML_PATH}/lib
      INCLUDEPATH += $${SBML_PATH}/include
  }

  LIBS += -lsbml -lexpat

# The raptor library
  LIBS += -lraptor
  !isEmpty(RAPTOR_PATH){
      LIBS+=  -L$${RAPTOR_PATH}/lib
      INCLUDEPATH += $${RAPTOR_PATH}/include
  }
  
  contains(CONFIG, qt) {
    !isEmpty(SBW_PATH){
      LIBS+=  $${SBW_PATH}/lib/libSBW.a
      INCLUDEPATH += $${SBW_PATH}/include
      DEFINES += COPASI_SBW_INTEGRATION
      DEFINES += LINUX SOLARIS
    } 

    !isEmpty(QWT_PATH){
       LIBS+=  -L$${QWT_PATH}/lib
       INCLUDEPATH += $${QWT_PATH}/include
    }
    LIBS += -lqwt
    
    !isEmpty(QWT3D_PATH){
      LIBS += -L$${QWT3D_PATH}/lib/
      INCLUDEPATH += $${QWT3D_PATH}/include
    } else {
      LIBS += -lqwtplot3d
    }
    
    LIBS += -lSM
  } else {
    QMAKE_LIBS_THREAD -= -lpthread
    QMAKE_LIBS_THREAD -= -lrt
  }
}
 
contains(BUILD_OS, Linux) {
  release {
    contains(TEMPLATE, app) {
      QMAKE_POST_LINK = strip $(TARGET)
    }
  }

  contains(PACKAGE, yes) {
    QMAKE_LFLAGS -= -static
  }
  else {
    contains(STATIC_LINKAGE, yes) {
      QMAKE_LFLAGS += -static
    }
    else {
      QMAKE_LFLAGS -= -static
    }
  }

  !isEmpty(SBML_PATH){
    INCLUDEPATH += $${SBML_PATH}/include
    INCLUDEPATH += $${SBML_PATH}/include/sbml

    contains(PACKAGE, yes) {
      LIBS += $${SBML_PATH}/lib/libsbml.a
    }
    else {
      LIBS += -L$${SBML_PATH}/lib
      LIBS += -lsbml
    }
  }
  else { 
    contains(PACKAGE, yes) {
      error("SBML_PATH must be given.")
    }
    else {
      LIBS += -lsbml
    }
  }

  !isEmpty(EXPAT_PATH){
    INCLUDEPATH += $${EXPAT_PATH}/include

    contains(PACKAGE, yes) {
      LIBS += $${EXPAT_PATH}/lib/libexpat.a
    }
    else {
      LIBS += -L$${EXPAT_PATH}/lib
      LIBS += -lexpat
    }
  }
  else { 
    contains(PACKAGE, yes) {
      error("EXPAT_PATH must be given.")
    }
    else {
      LIBS += -lexpat
    }
  }

# The raptor library
  !isEmpty(RAPTOR_PATH){
      LIBS +=  -L$${RAPTOR_PATH}/lib
      INCLUDEPATH += $${RAPTOR_PATH}/include

    contains(PACKAGE, yes) {
      LIBS += $${RAPTOR_PATH}/lib/libraptor.a
    }
    else {
      LIBS += -L$${RAPTOR_PATH}/lib
      LIBS += -lraptor
    }
  }
  else { 
    contains(PACKAGE, yes) {
      error("RAPTOR_PATH must be given.")
    }
    else {
      LIBS += -lraptor
    }
  }
  
  !isEmpty(MKL_PATH) {
    DEFINES += USE_MKL
    INCLUDEPATH += $${MKL_PATH}/include

    LIBS += $${MKL_PATH}/lib/32/libmkl_solver.a \
            -Wl,--start-group \
              $${MKL_PATH}/lib/32/libmkl_intel.a \
              $${MKL_PATH}/lib/32/libmkl_sequential.a \
              $${MKL_PATH}/lib/32/libmkl_core.a \
            -Wl,--end-group \
            -lpthread

  } else {
    !isEmpty(CLAPACK_PATH) {
      DEFINES += USE_CLAPACK
      INCLUDEPATH += $${CLAPACK_PATH}/include
#      LIBS += -llapack -lblas -lF77 -lfl
      LIBS += -llapack -lblas -lF77
      LIBS += -L$${CLAPACK_PATH}/lib 
    } else {
      !isEmpty(LAPACK_PATH) {
        message("Using lapack.")
        DEFINES += USE_LAPACK
        INCLUDEPATH += $${LAPACK_PATH}/include

        contains(PACKAGE, yes) {
          LIBS += $${LAPACK_PATH}/lib/liblapack.a 
          LIBS += $${LAPACK_PATH}/lib/libblas.a
          LIBS += $$system(locate libg2c.a)
        }
        else {
          LIBS += -L$${LAPACK_PATH}/lib
          LIBS += -llapack 
          LIBS += -lblas
          HAVE_G2C = $$system(locate libg2c)
          !isEmpty(HAVE_G2C) LIBS += -lg2c
        }
      } else {
        error( "Either MKL_PATH, CLAPACK_PATH, or LAPACK_PATH must be specified" )
      }
    }
  }

  contains(CONFIG, qt) {
    !isEmpty(SBW_PATH){
      LIBS+=  $${SBW_PATH}/lib/libSBW.a
      INCLUDEPATH += $${SBW_PATH}/include
      DEFINES += COPASI_SBW_INTEGRATION
      DEFINES += LINUX 
    }
     
    !isEmpty(QWT_PATH){
       LIBS +=  -L$${QWT_PATH}/lib
       INCLUDEPATH += $${QWT_PATH}/include
    }
    LIBS += -lqwt

    !isEmpty(QWT3D_PATH){
      LIBS += -L$${QWT3D_PATH}/lib/
      INCLUDEPATH += $${QWT3D_PATH}/include
    } else {
      LIBS += -lqwtplot3d
    }
  }
}

DEP1.target   = depend
DEP1.depends  = qmake

QMAKE_EXTRA_UNIX_TARGETS += DEP1

!equals(TEMPLATE, subdirs) {
  # Copy the sources for the tar ball
  src_distribution.depends = Makefile
  src_distribution.commands =   \
    $(CHK_DIR_EXISTS) ../../copasi_src || $(MKDIR) ../../copasi_src; \
    $(CHK_DIR_EXISTS) ../../copasi_src/copasi || \
      $(MKDIR) ../../copasi_src/copasi; \
    $(CHK_DIR_EXISTS) ../../copasi_src/copasi/$$SRC_TARGET || \
      $(MKDIR) ../../copasi_src/copasi/$$SRC_TARGET; \
    $(COPY_FILE) --parents $(SOURCES) $(HEADERS) $(FORMS) $(DIST) \
      ../../copasi_src/copasi/$$SRC_TARGET/

  QMAKE_EXTRA_UNIX_TARGETS += src_distribution
}

# addSubdirs(subdirs,deps): Adds directories to the project that depend on
# other directories
defineTest(addSubdirs) {
    for(subdirs, 1) {
        entries = $$files($$subdirs)
        for(entry, entries) {
            name = $$replace(entry, [/\\\\], _)
            SUBDIRS += $$name
            eval ($${name}.subdir = $$entry)
            for(dep, 2):eval ($${name}.depends += $$replace(dep, [/\\\\], _))
            export ($${name}.subdir)
            export ($${name}.depends)
        }
    }
    export (SUBDIRS)
}

{'fraction_non_alphanumeric': 0.156092548395651, 'fraction_numerical': 0.010010607265977195, 'mean_word_length': 2.5306026916325335, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5854531', 'n_tokens_mistral': 12672, 'n_tokens_neox': 11583, 'n_words': 1921}