#                                               -*- Autoconf -*-
# Process this file with autoconf to produce a configure script.

AC_PREREQ(2.59)
AC_INIT(MoleCuilder, 1.6.1, [bug@molecuilder.de], [molecuilder], [http://www.molecuilder.de/])
AC_CONFIG_AUX_DIR([build-aux])
AC_CONFIG_SRCDIR([src/builder.cpp])
AC_CONFIG_HEADER([config.h libmolecuilder_config.h])
AC_CONFIG_MACRO_DIR([m4])
AC_CONFIG_SUBDIRS([ThirdParty/LinearAlgebra])
AC_CONFIG_SUBDIRS([ThirdParty/mpqc_open])

# parallel-tests: use parallel test druver
# color-tests: us coloring to indicate success/failure when available
# tar-pax: use newer tar implementation with longer filename (>99 chars)
AM_INIT_AUTOMAKE([dist-bzip2 1.5 parallel-tests color-tests tar-pax subdir-objects])

# Checks for programs.
AC_PROG_CXX
AC_PROG_INSTALL

# check for cppunit (taken from svn.apache.org/../xmlbeanscxx)
AM_PATH_CPPUNIT(1.9.6)
AM_CONDITIONAL(CONDCPPUNIT, test "$CPPUNIT_LIBS")

dnl Check if we have enable python
# python module-
AC_MSG_CHECKING(whether to enable python module)
AC_ARG_ENABLE(
	[python],
	AS_HELP_STRING([--enable-python],[turn on python module [default=yes]]),
	enable_python=$enableval,
	enable_python="yes")
AC_MSG_RESULT($enable_python)
AS_IF([test x"$enable_python" != x"no"],[
  # Python (for boost::python)
  AM_PATH_PYTHON([2.2])
  AX_PYTHON
  AC_DEFINE(HAVE_PYTHON,1, ["Build python module and scripts."])
])
AM_CONDITIONAL([CONDPYTHON], [test x"$enable_python" != x"no"])
AC_SUBST(HAVE_PYTHON)

dnl Check whether no extra thread for ActionQueue shall be used
AC_MSG_CHECKING(whether to enable ActionQueue's run thread)
AC_ARG_ENABLE(
	[action_thread],
	AS_HELP_STRING([--enable-action-thread],[turn on extra run thread for ActionQueue [default=yes]]),
	enable_action_thread=$enableval,
	enable_action_thread="no"
)
AC_MSG_RESULT($enable_action_thread)
AS_IF([test x"$enable_action_thread" != x"no"],[
  AC_DEFINE(HAVE_ACTION_THREAD,1, ["Have extra run thread for ActionQueue."])
])
AM_CONDITIONAL([CONDACTIONTHREAD], [test x"$enable_action_thread" != x"no"])
AC_SUBST(HAVE_ACTION_THREAD)

dnl Check if we have enable qtgui
# Qt programs
AC_MSG_CHECKING(whether to enable Qt-based GUI)
AC_ARG_ENABLE(
	[qtgui], 
	AS_HELP_STRING([--enable-qtgui],[turn on Qt GUI compilation [default=yes]]),
	enable_qtgui=$enableval,
	enable_qtgui="yes")
AC_MSG_RESULT($enable_qtgui)
AS_IF([test x"$enable_qtgui" != x"no"],[
	AC_ARG_WITH(
		[Qt-bin],
		[AS_HELP_STRING([--with-Qt-bin], [give path to Qt binaries])],
		[have_qtgui_path=$withval],
		have_qtgui_path="")
	AS_IF([test x"$have_qtgui_path" != x""],[
		AC_PATH_PROGS([QT_MOC],
			[moc-qt4 moc], 
			[AC_MSG_ERROR(["Qts moc not found, please use --with-Qt-bin."])],
			[$have_qtgui_path]
		)
		AC_PATH_PROGS([QT_RCC],
			[rcc-qt4 rcc], 
			[AC_MSG_ERROR(["Qts rcc not found, please use --with-Qt-bin."])],
			[$have_qtgui_path]
		)
		AC_PATH_PROGS([QT_UIC], 
			[uic-qt4 uic], 
			[AC_MSG_ERROR(["Qts uic not found, please use --with-Qt-bin."])],
			[$have_qtgui_path]
		)
	],[
		AC_PATH_PROGS([QT_MOC],
			[moc-qt4 moc], 
			[AC_MSG_ERROR(["Qts moc not found, please use --with-Qt-bin."])]
		)
		AC_PATH_PROGS([QT_RCC],
			[rcc-qt4 rcc], 
			[AC_MSG_ERROR(["Qts rcc not found, please use --with-Qt-bin."])]
		)
		AC_PATH_PROGS([QT_UIC], 
			[uic-qt4 uic], 
			[AC_MSG_ERROR(["Qts uic not found, please use --with-Qt-bin."])]
		)
	])
	PKG_CHECK_MODULES([QT], [QtCore QtGui Qt3D], [
	:
	])
	AC_SUBST([QT_CFLAGS])
	AC_SUBST([QT_LIBS])
	AC_DEFINE(HAVE_QTGUI,1, ["Build Qt-based GUI"])
])
AM_CONDITIONAL([CONDQTGUI], [test x"$enable_qtgui" != x"no"])
AC_SUBST(HAVE_QTGUI)

dnl Check whether qtgui captures log or not
AC_MSG_CHECKING(whether to capture stdout in qtgui)
AC_ARG_ENABLE(
	[qtgui_capture_log],
	AS_HELP_STRING([--enable-qtgui-capture-log],[turn on capturing of log inside qtgui [default=yes]]),
	enable_qtgui_capture_log=$enableval,
	enable_qtgui_capture_log="yes"
)
AC_MSG_RESULT($enable_qtgui_capture_log)
AS_IF([test x"$enable_qtgui_capture_log" != x"no"],[
  AC_DEFINE(QT_CAPTURES_LOG,1, ["Have QtGui capture the stdout."])
])
AC_SUBST(QT_CAPTURES_LOG)


# check additionally for QWT to enable plotting of potentials
AC_MSG_CHECKING(whether to enable Qwt-based plotting)
#enable_qwt=yes
AC_ARG_ENABLE(
	[qwt], 
	AS_HELP_STRING([--enable-qwt],[turn on Qwt compilation [default=yes]]),
	enable_qwt=$enableval,
	enable_qwt="yes")
AC_MSG_RESULT($enable_qwt)
AS_IF([test x"$enable_qwt" != x"no"],[
	MOL_AC_HAVE_QWT_IFELSE(
		[
			enable_qwt=yes
			AC_DEFINE(HAVE_QWT,1, ["Build Qwt-based plotting"])
		],
		[
			enable_qwt=no
			AC_MSG_WARN([Qwt not found, disabling plotting in QtUI.])
		]
	)
])
AM_CONDITIONAL([CONDQWT], [test x"$enable_qwt" != x"no"])
AC_SUBST(HAVE_QWT)

# use doxygen
DX_HTML_FEATURE(ON)
DX_PS_FEATURE(OFF)
DX_PDF_FEATURE(OFF)
DX_INIT_DOXYGEN(MoleCuilder, Doxyfile, ${docdir})

# use docbook
AX_CHECK_DOCBOOK

# use libtool
LT_INIT([static])
AC_SUBST([LIBTOOL_DEPS])

# Define these substitions here to keep all version information in one place.
# For information on how to properly maintain the library version information,
# refer to the libtool manual, section "Updating library version information":
# http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html
AC_SUBST([MOLECUILDER_SO_VERSION], [18:0:1])
AC_SUBST([MOLECUILDER_API_VERSION], [1.6.1])

dnl this macro is used to get the arguments supplied
dnl to the configure script (./configure --enable-debug)
dnl Check if we have enable debug support.
AC_MSG_CHECKING(whether to enable debugging)
have_debug="no"
AC_ARG_ENABLE(
	[debug],
	AS_HELP_STRING([--enable-debug],[turn on debugging [default=no]]),
	enable_debug=$enableval,
	enable_debug="no")
AC_MSG_RESULT($enable_debug)
AS_IF([test x"$enable_debug" = x"yes"],[
  AC_DEFINE(MEMDEBUG,1, ["Use memory debugger."])
  AC_DEFINE(HAVE_DEBUG,1, ["Use debug setting to compile code."])
  have_debug="yes"
],[
	AS_IF([test x"$enable_debug" = x"full"],[
	  AC_DEFINE(MEMDEBUG,1, ["Use memory debugger."])
	  AC_DEFINE(LOG_OBSERVER,1, ["Use observer log."])
	  AC_DEFINE(HAVE_DEBUG,2, ["Use debug setting to compile code."])
	  dnl AC_DEFINE(QT_DEBUG,, ["Enable Qt debug messages."])
	  have_debug="full"
	],[
	  AC_DEFINE(NDEBUG,1, ["Don't compile in debugging code."])
	  AC_DEFINE(HAVE_DEBUG,0, ["Use debug setting to compile code."])
	  AC_DEFINE(QT_NO_DEBUG_OUTPUT,, ["Disable Qt debug messages."])
	  have_debug="no"
	])
])
AC_SUBST(HAVE_DEBUG)

dnl this macro is used to get the arguments supplied
dnl to the configure script (./configure --enable-debug)
dnl Check if we have enable debug support.
AC_MSG_CHECKING(whether to enable internal caching/lazy evaluation)
AC_ARG_ENABLE(
	[cache],
	AS_HELP_STRING([--enable-cache],[turn on internal lazy evaluation [default=yes]]),
	enable_cache=$enableval,
	enable_cache="yes")
AC_MSG_RESULT($enable_cache)
AS_IF([test x"$enable_cache" != x"no"],[
  AC_DEFINE(HAVE_CACHE,1, ["cache variables to speed up the code."])
],[
  AC_DEFINE(NO_CACHING,1, ["Don't use caching code."])
  AC_DEFINE(HAVE_CACHE,0, ["cache variables to speed up the code."])
])
AC_SUBST(HAVE_CACHE)

# Checks for libraries.
AC_CHECK_LIB(m, sqrt, , AC_MSG_ERROR([compatible libc math library not found]))

# Pthreads
ACX_PTHREAD()

# Boost
BOOST_REQUIRE([1.40])

# Boost headers only
BOOST_ANY
BOOST_ARRAY
BOOST_BIMAP
BOOST_BIND
BOOST_CAST
BOOST_CONVERSION
BOOST_EXCEPTION
BOOST_FOREACH
BOOST_FUNCTION
BOOST_FUSION
BOOST_GRAPH
BOOST_ITERATOR
BOOST_MULTIARRAY
BOOST_MULTIINDEXCONTAINER
BOOST_MPL
BOOST_PREPROCESSOR
BOOST_RANDOM
BOOST_SMART_PTR
BOOST_STRING_ALGO
BOOST_TOKENIZER

# Boost headers with libraries
BOOST_FILESYSTEM
BOOST_IOSTREAMS
BOOST_PROGRAM_OPTIONS
AS_IF([test x"$enable_python" != x"no"], [BOOST_PYTHON])
BOOST_SERIALIZATION
BOOST_THREADS


# CodePatterns library (requiring UnobservedIterator)
compile_codepatterns="no"
AM_PATH_CODEPATTERNS([1.3.2], $have_debug,,[
	# compile from ThirdParty
	AC_CONFIG_SUBDIRS([ThirdParty/CodePatterns])
	compile_codepatterns="yes"
	[CodePatterns_LDFLAGS='-L$(top_builddir)/ThirdParty/CodePatterns/src']
	[CodePatterns_CFLAGS='-I$(top_srcdir)/ThirdParty/CodePatterns/src']
	AS_IF([test x"$enable_debug" != x"no"], [
		[CodePatterns_LIBS='-lcodepatterns-debug']
	],[
		[CodePatterns_LIBS='-lcodepatterns']
	])
	AC_SUBST(CodePatterns_LDFLAGS)
	AC_SUBST(CodePatterns_CFLAGS)
	AC_SUBST(CodePatterns_LIBS)
	#AC_MSG_ERROR([Missing CodePatterns library, please specify PKG_CONFIG_PATH or use --with-codepatterns...])
])
AC_MSG_CHECKING(whether to compile codepatterns)
AC_MSG_RESULT($compile_codepatterns)
AM_CONDITIONAL([COND_COMPILE_CODEPATTERNS], [test x"$compile_codepatterns" = x"yes"])

# JobMarket library (needs boost/archive/iserializer.hpp before MemDebug.hpp)
AC_MSG_CHECKING(whether to enable jobmarket)
AC_ARG_ENABLE(
  [jobmarket],
  AS_HELP_STRING([--enable-jobmarket],[turn on JobMarket feature [default=yes]]),
  enable_jobmarket=$enableval,
  enable_jobmarket="yes")
AC_MSG_RESULT($enable_jobmarket)
compile_jobmarket="no"
AC_MSG_CHECKING(whether to compile jobmarket)
AS_IF([test x"$enable_jobmarket" != x"no"],[
  # the following is only required if we use JobMarket
  BOOST_ASIO
  AC_DEFINE(HAVE_JOBMARKET,1, ["use JobMarket to calculate fragment jobs."])
  # JobMarket library (needs SystemCommandJob with suffix)
  AM_PATH_JOBMARKET([1.1.6], $have_debug,
    ,[
	AC_CONFIG_SUBDIRS([ThirdParty/JobMarket])
	compile_jobmarket="yes"
	[JobMarket_CFLAGS='-I$(top_srcdir)/ThirdParty/JobMarket/src']
	[JobMarket_LDFLAGS='-L$(top_builddir)/ThirdParty/JobMarket/src/JobMarket']
	[JobMarket_LIBS='-lJobMarket']
	[JobMarket_Controller_LIBS='-lJobMarketController']
	[JobMarket_Server_LIBS='-lJobMarketServer']
	[JobMarket_PoolWorker_LIBS='-lJobMarketPoolWorker']
	AC_SUBST(JobMarket_CFLAGS)
	AC_SUBST(JobMarket_LDFLAGS)
	AC_SUBST(JobMarket_LIBS)
	AC_SUBST(JobMarket_Controller_LIBS)
	AC_SUBST(JobMarket_Server_LIBS)
	AC_SUBST(JobMarket_PoolWorker_LIBS)
    ])
]
AC_MSG_RESULT($compile_jobmarket)
#[
#  AC_DEFINE(HAVE_JOBMARKET,0, ["use JobMarket to calculate fragment jobs."])
#]
)
AC_SUBST(HAVE_JOBMARKET)
AM_CONDITIONAL([COND_COMPILE_JOBMARKET], [test x"$compile_jobmarket" = x"yes"])
AM_CONDITIONAL([CONDJOBMARKET], [test x"$enable_jobmarket" = x"yes"])

# VMG library
AC_MSG_CHECKING(whether to compile in long-range support via vmg)
AC_ARG_ENABLE(
  [vmg],
  [AS_HELP_STRING([--enable-vmg], [turn on long-range potential calculation via VMG [default=no]])],
  [enable_vmg=$enableval],
  enable_vmg="no")
AC_MSG_RESULT($enable_vmg)
compile_vmg="no"
AC_MSG_CHECKING(whether to compile vmg library)
AS_IF([test x"$enable_vmg" != x"no"],[
  PKG_CHECK_MODULES(VMG, VMG >= 0.1, [enable_vmg="yes"], [enable_vmg="no"])
  AS_IF([test x"$enable_vmg" = x"no"],[
	AC_CONFIG_SUBDIRS([ThirdParty/vmg])
	compile_vmg="yes"
	enable_vmg="yes"
	[VMG_CFLAGS='-I$(top_srcdir)/ThirdParty/vmg/src']
	[VMG_LDFLAGS='-L$(top_builddir)/ThirdParty/vmg/src']
	[VMG_LIBS='-lvmg']
  ])
  AC_SUBST(VMG_CFLAGS)
  AC_SUBST(VMG_LDFLAGS)
  AC_SUBST(VMG_LIBS)
  AC_DEFINE(HAVE_VMG,1, ["use VMG to calculate long-range contributions."])

  # check whether to use mpi
  AC_ARG_WITH(
      [vmg-mpi], 
      [AS_HELP_STRING([--with-vmg-mpi], [whether to use MPI for communication in VMGJobs])],
      [with_vmg_mpi=yes],
      [with_vmg_mpi=no])
  AS_IF(
    [test "x$with_vmg_mpi" != xno],
    [
      AC_LANG_SAVE
      AC_LANG_CPLUSPLUS
      LX_FIND_MPI
      AC_LANG_RESTORE
      AS_IF([test "x$have_CXX_mpi" = xyes],[
            AC_DEFINE([MPICH_SKIP_MPICXX], [1], [Skip C++ bindings])
            AC_DEFINE([OMPI_SKIP_MPICXX], [1], [Skip C++ bindings])
            AC_DEFINE([MPI_NO_CPPBIND], [1], [Skip C++ bindings])
            AC_DEFINE([_MPICC_H], [1], [Skip C++ bindings])
            AC_DEFINE([MPIBULL_SKIP_MPICXX], [1], [Skip C++ bindings])
	    #ac_configure_args="$ac_configure_args --with-mpi-thread=single --with-default-parallel=mpi --with-include=\"$MPI_CXXFLAGS\" --with-libs=\"$MPI_CXXLDFLAGS\""
	    ac_configure_args="$ac_configure_args --with-default-parallel=none"
           ])
    ],
    [])
])
AC_MSG_RESULT($compile_vmg)
AM_CONDITIONAL([CONDVMG], [test x"$enable_vmg" = x"yes"])
AM_CONDITIONAL([CONDVMGMPI], [test x"$have_CXX_mpi" = x"yes"])
AM_CONDITIONAL([COND_COMPILE_VMG], [test x"$compile_vmg" = x"yes"])


# Check for Levenberg-Marquardt implementation
AC_MSG_CHECKING(whether to enable function fitting via levmar)
AC_ARG_ENABLE(
  [levmar],
  AS_HELP_STRING([--enable-levmar],[turn on LevMar feature [default=no]]),
  enable_levmar=$enableval,
  enable_levmar="no")
AC_MSG_RESULT($enable_levmar)
# don't use AS_IF here as it expands (and tests) AC_F77_FUN even if levmar
# is disabled.
compile_levmar="no"
AS_IF([test x"$enable_levmar" = xyes],[
	AC_MSG_CHECKING(for levmar presence via given path )
	AC_ARG_WITH(
		[levmar],
		[AS_HELP_STRING([--with-levmar], [give path to LevMar package])],
		[have_levmar_path=$withval
		enable_levmar=yes],
	[
		enable_levmar=no
	])
	AC_MSG_RESULT($enable_levmar)
	AS_IF([test -n "$have_levmar_path"],[
		LEVMAR_CPPFLAGS="-I${have_levmar_path}/include"
		LEVMAR_LDFLAGS="-L${have_levmar_path}/lib"
		LEVMAR_LIBS="-llevmar"],
		[PKG_CHECK_MODULES([LEVMAR],[levmar],[enable_levmar=yes],[enable_levmar=no])
	])
	],[enable_levmar=no]
)
if test x"$enable_levmar" = xyes; then
	AX_LAPACK([enable_levmar=yes],
		[enable_levmar=no
		AC_MSG_WARN(["Missing LAPACK, disabling off levmar"])
		]
	)
else
			AC_CONFIG_SUBDIRS([ThirdParty/levmar])
			compile_levmar="yes"
			enable_levmar="yes"
			LEVMAR_CPPFLAGS='-I$(top_srcdir)/ThirdParty/levmar/src'
			LEVMAR_LDFLAGS='-L$(top_builddir)/ThirdParty/levmar/src'
			LEVMAR_LIBS='-llevmar'
fi
AC_MSG_CHECKING(for levmar usability)
AS_IF([test x"$enable_levmar" = xyes],[
	AC_SUBST(LEVMAR_CPPFLAGS)
	AC_SUBST(LEVMAR_LDFLAGS)
	AC_SUBST(LEVMAR_LIBS)
        AC_DEFINE(HAVE_LEVMAR,1, ["use levmar for non-linear minimisation/potential fitting."])])
AC_MSG_RESULT($enable_levmar)
AM_CONDITIONAL([CONDLEVMAR], [test x"$enable_levmar" = x"yes"])
AM_CONDITIONAL([COND_COMPILE_LEVMAR], [test x"$compile_levmar" = x"yes"])

# Checks for header files.
AC_HEADER_STDC
AC_CHECK_HEADERS([sys/time.h])
AC_HEADER_STDBOOL

AC_FUNC_MALLOC
AC_FUNC_REALLOC
AC_CHECK_FUNCS([floor pow sqrt strchr])

# Checks for typedefs, structures, and compiler characteristics.
AC_C_CONST
AC_C_INLINE
AC_C_RESTRICT
AC_TYPE_SIZE_T

# Checks for library functions.
# check for GNU Scientific Library
AC_CHECK_HEADERS([gsl/gsl_blas.h])
AC_SEARCH_LIBS(dnrm2, gslblas gslcblas goto blas cblas)
AC_SEARCH_LIBS(cblas_dnrm2, gslblas gslcblas blas cblas)
AC_SEARCH_LIBS(gsl_blas_dnrm2,, gsl)
#AC_CHECK_LIB(gsl, gsl_blas_dnrm2, , [AC_MSG_ERROR(["No working BLAS found for GSL, stopping."])])
AC_CHECK_LIB(gsl, main)

# use CppUnit TestRunner or not
AC_MSG_CHECKING(whether to enable ECut TestRunnerClient)
AC_ARG_ENABLE(
	[ecut],
	AS_HELP_STRING([--enable-ecut],[Use ECut TestRunnerClient [default=no]]),
	enable_ecut=$disableval,
	enable_ecut="no")
AC_MSG_RESULT($enable_ecut)
AS_IF([test x"$enable_ecut" = x"yes"],[
  AC_DEFINE(HAVE_ECUT,1, ["Use ECut TestRunnerClient instead of our own."])
  AC_SUBST(HAVE_ECUT)
])
AM_CONDITIONAL([CONDECUT], [test x"$enable_ecut" = x"yes"])

# with valgrinding testsuite or not
AC_MSG_CHECKING(whether to enable valgrind memory checking in testsuite)
AC_ARG_ENABLE(
	[valgrind],
	AS_HELP_STRING([--enable-valgrind],[Use Valgrind on the testsuite [default=no]]),
        enable_valgrind=$enableval,
	enable_valgrind="no")
AC_MSG_RESULT($enable_valgrind)
AS_IF([test x"$enable_valgrind" = x"yes"], [
  AC_CHECK_HEADER([valgrind/valgrind.h],
    [
      # check header
      AC_DEFINE(HAVE_VALGRIND_TESTSUITE,1, ["Use Valgrind to check the testsuite."])
      # check path
      AC_PATH_PROG(VALGRIND, [valgrind], [/bin/false])
      # set variables 
      AC_SUBST(HAVE_VALGRIND_TESTSUITE)
      AC_SUBST(VALGRIND)
    ],
    [
      AC_MSG_ERROR(["Valgrind support requested but headers not available."])
    ]
  )
])

# Check for "extern inline", using a modified version
# of the test for AC_C_INLINE from acspecific.mt
AC_CACHE_CHECK([for extern inline], ac_cv_c_extern_inline,
[ac_cv_c_extern_inline=no
AC_TRY_COMPILE([extern $ac_cv_c_inline double foo(double x);
extern $ac_cv_c_inline double foo(double x) { return x+1.0; };
double foo (double x) { return x + 1.0; };], 
[  foo(1.0)  ],
[ac_cv_c_extern_inline="yes"])
])

if test "$ac_cv_c_inline" != no ; then
  AC_DEFINE(HAVE_INLINE,1, ["May use inline routines"])
  AC_SUBST(HAVE_INLINE)
fi

#AC_MSG_NOTICE(["CFLAGS: $CFLAGS, CXXFLAGS: $CXXFLAGS, LDFLAGS: $LDFLAGS, CC: $CC, CXX:, $CXX, MPICC: $MPICC, MPILIBS: $MPILIBS, LIBS: $LIBS"])

# test suite

AC_CONFIG_FILES([
	tests/Makefile])

AC_CONFIG_TESTDIR(tests/Calculations)
AC_CONFIG_FILES([
	tests/Calculations/atlocal 
	tests/Calculations/Makefile])
AC_CONFIG_FILES([tests/Calculations/molecuilder], [chmod +x tests/Calculations/molecuilder])
AC_CONFIG_FILES([tests/Calculations/molecuilder_poolworker], [chmod +x tests/Calculations/molecuilder_poolworker])

AC_CONFIG_TESTDIR(tests/CodeChecks)
AC_CONFIG_FILES([
	tests/CodeChecks/atlocal 
	tests/CodeChecks/Makefile])

AC_CONFIG_TESTDIR(tests/Fragmentations)
AC_CONFIG_FILES([
	tests/Fragmentations/atlocal 
	tests/Fragmentations/Makefile])
AC_CONFIG_FILES([tests/Fragmentations/molecuilder], [chmod +x tests/Fragmentations/molecuilder])

AC_CONFIG_TESTDIR(tests/GuiChecks)
AC_CONFIG_FILES([
	tests/GuiChecks/atlocal 
	tests/GuiChecks/Makefile])
AC_CONFIG_FILES([tests/GuiChecks/molecuilder], [chmod +x tests/GuiChecks/molecuilder])
AC_CONFIG_FILES([tests/GuiChecks/molecuilderguitest], [chmod +x tests/GuiChecks/molecuilderguitest])
AC_CONFIG_FILES([tests/GuiChecks/adjacencymatcher], [chmod +x tests/GuiChecks/adjacencymatcher])
AC_CONFIG_FILES([tests/GuiChecks/difffragmentresultcontainer], [chmod +x tests/GuiChecks/difffragmentresultcontainer])
AC_CONFIG_FILES([tests/GuiChecks/trianglematcher], [chmod +x tests/GuiChecks/trianglematcher])

AC_CONFIG_TESTDIR(tests/JobMarket)
AC_CONFIG_FILES([
  tests/JobMarket/atlocal 
  tests/JobMarket/Makefile])
AC_CONFIG_FILES([tests/JobMarket/molecuilder], [chmod +x tests/JobMarket/molecuilder])

AC_CONFIG_TESTDIR(tests/integration)
AC_CONFIG_FILES([
  tests/integration/atlocal 
  tests/integration/Makefile])
AC_CONFIG_FILES([tests/integration/molecuilder], [chmod +x tests/integration/molecuilder])
AC_CONFIG_FILES([tests/integration/molecuilder_poolworker], [chmod +x tests/integration/molecuilder_poolworker])

AC_CONFIG_TESTDIR(tests/regression)
AC_CONFIG_FILES([
	tests/regression/atlocal 
	tests/regression/Makefile])
AC_CONFIG_FILES([tests/regression/molecuilder], [chmod +x tests/regression/molecuilder])
AC_CONFIG_FILES([tests/regression/adjacencymatcher], [chmod +x tests/regression/adjacencymatcher])
AC_CONFIG_FILES([tests/regression/difffragmentresultcontainer], [chmod +x tests/regression/difffragmentresultcontainer])
AC_CONFIG_FILES([tests/regression/trianglematcher], [chmod +x tests/regression/trianglematcher])
AC_CONFIG_FILES([tests/regression/runpython], [chmod +x tests/regression/runpython])

AC_CONFIG_TESTDIR(tests/Tesselations)
AC_CONFIG_FILES([
	tests/Tesselations/atlocal 
	tests/Tesselations/Makefile])
AC_CONFIG_FILES([tests/Tesselations/molecuilder], [chmod +x tests/Tesselations/molecuilder])
AC_CONFIG_FILES([tests/Tesselations/trianglematcher], [chmod +x tests/Tesselations/trianglematcher])

AC_CONFIG_TESTDIR(tests/Examples)
AC_CONFIG_FILES([
	tests/Examples/atlocal 
	tests/Examples/Makefile])
AC_CONFIG_FILES([tests/Examples/molecuilder], [chmod +x tests/Examples/molecuilder])
AC_CONFIG_FILES([tests/Examples/molecuilder_poolworker], [chmod +x tests/Examples/molecuilder_poolworker])

AC_CONFIG_FILES([
	doc/molecuilder.xml])
AC_CONFIG_FILES([
	doc/userguide/catalog.xml:doc/userguide/catalog.xml.in])
AC_CONFIG_FILES([
	MoleCuilder.pc:MoleCuilder.pc.in])
AC_CONFIG_FILES([
	doc/Makefile
	doc/userguide/Makefile
])
AC_CONFIG_FILES([
	Makefile 
	python/Makefile
	src/Makefile
	src/Bond/AdjacencyMatcher/Makefile
	src/Tesselation/TriangleMatcher/Makefile
	ThirdParty/Makefile
	data/icons/Makefile
	utils/Makefile
])
AC_CONFIG_FILES([
	src/unittests/Makefile
])

# produce python scripts and tests only when python's present
AC_CONFIG_TESTDIR([tests/Python])
AC_CONFIG_FILES([tests/Python/atlocal])
AM_COND_IF([CONDPYTHON],[
	AC_CONFIG_FILES([utils/Python/boxmaker.py:utils/Python/boxmaker.py.in], [chmod +x utils/Python/boxmaker.py])
	AC_CONFIG_FILES([utils/Python/python_wrapper:utils/Python/python_wrapper.in], [chmod +x utils/Python/python_wrapper])
	AC_CONFIG_FILES([tests/Python/run], [chmod +x tests/Python/run])
])
AC_CONFIG_FILES([tests/Python/Makefile])

AC_OUTPUT