Changes in / [4c9101:a91710]


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  • LinearAlgebra/src/LinearAlgebra/Makefile.am

    r4c9101 ra91710  
    22# Also indentation by a single tab
    33
    4 INCLUDES = -I$(top_srcdir)/src
    5 
    64AM_LDFLAGS = -ldl
    7 AM_CPPFLAGS = $(BOOST_CPPFLAGS) ${CodePatterns_CFLAGS}
     5AM_CPPFLAGS = -I$(top_srcdir)/src $(BOOST_CPPFLAGS) ${CodePatterns_CFLAGS}
    86
    97LINALGSOURCE = \

  • LinearAlgebra/src/unittests/Makefile.am

    r4c9101 ra91710  
    22# Also indentation by a single tab
    33
    4 INCLUDES = -I$(top_srcdir)/src/LinearAlgebra
    5 
    64AM_LDFLAGS = ${CodePatterns_LIBS} $(CPPUNIT_LIBS) -ldl
    7 AM_CPPFLAGS = $(CPPUNIT_CFLAGS) $(BOOST_CPPFLAGS) ${CodePatterns_CFLAGS}
     5AM_CPPFLAGS = -I$(top_srcdir)/src/LinearAlgebra $(CPPUNIT_CFLAGS) $(BOOST_CPPFLAGS) ${CodePatterns_CFLAGS}
    86
    97if CONDCPPUNIT
    … …  
    9593        VectorUnitTest.cpp \
    9694        VectorUnitTest.hpp
    97 VectorUnitTest_LDADD = ${GSLLIBS}
     95VectorUnitTest_LDADD = ${GSLLIBS} \
     96        $(BOOST_SYSTEM_LDFLAGS) $(BOOST_SYSTEM_LIBS)
    9897
    9998VectorSetUnitTest_SOURCES = UnitTestMain.cpp \

  • configure.ac

    r4c9101 ra91710  
    1313# color-tests: us coloring to indicate success/failure when available
    1414# tar-pax: use newer tar implementation with longer filename (>99 chars)
    15 AM_INIT_AUTOMAKE([dist-bzip2 1.5 parallel-tests color-tests tar-pax])
     15AM_INIT_AUTOMAKE([dist-bzip2 1.5 parallel-tests color-tests tar-pax subdir-objects])
    1616
    1717# Checks for programs.

  • m4/boost.m4

    r4c9101 ra91710  
    11# boost.m4: Locate Boost headers and libraries for autoconf-based projects.
    2 # Copyright (C) 2007, 2008, 2009, 2010, 2011  Benoit Sigoure <tsuna@lrde.epita.fr>
     2# Copyright (C) 2007-2011, 2014  Benoit Sigoure <tsuna@lrde.epita.fr>
    33#
    44# This program is free software: you can redistribute it and/or modify
    … …  
    2323
    2424m4_define([_BOOST_SERIAL], [m4_translit([
    25 # serial 16
     25# serial 22
    2626], [#
    2727], [])])
    … …  
    6060# value of any macro.
    6161m4_define([_BOOST_SED_CPP],
    62 [AC_LANG_PREPROC_REQUIRE()dnl
     62[AC_LANG_PUSH([C++])dnl
     63AC_LANG_PREPROC_REQUIRE()dnl
    6364AC_REQUIRE([AC_PROG_SED])dnl
    6465AC_LANG_CONFTEST([AC_LANG_SOURCE([[$2]])])
    … …  
    7879  [$4])
    7980rm -rf conftest*
    80 ])# AC_EGREP_CPP
     81AC_LANG_POP([C++])dnl
     82])# _BOOST_SED_CPP
    8183
    8284
    … …  
    135137    # If the user provided a value to --with-boost, use it and only it.
    136138    case $with_boost in #(
    137       ''|yes) set x '' /usr/local/include /usr/include \
    138               /opt/local/include /opt/include \
    139               C:/Boost/include;; #(
     139      ''|yes) set x '' /opt/local/include /usr/local/include /opt/include \
     140                 /usr/include C:/Boost/include;; #(
    140141      *)      set x "$with_boost/include" "$with_boost";;
    141142    esac
    … …  
    223224])# BOOST_REQUIRE
    224225
     226
    225227# BOOST_STATIC()
    226228# --------------
    … …  
    229231AC_DEFUN([BOOST_STATIC],
    230232  [AC_ARG_ENABLE([static-boost],
    231      [AC_HELP_STRING([--enable-static-boost],
     233     [AS_HELP_STRING([--enable-static-boost],
    232234               [Prefer the static boost libraries over the shared ones [no]])],
    233235     [enable_static_boost=yes],
    234236     [enable_static_boost=no])])# BOOST_STATIC
     237
    235238
    236239# BOOST_FIND_HEADER([HEADER-NAME], [ACTION-IF-NOT-FOUND], [ACTION-IF-FOUND])
    … …  
    266269
    267270
    268 # BOOST_FIND_LIB([LIB-NAME], [PREFERRED-RT-OPT], [HEADER-NAME], [CXX-TEST],
    269 #                [CXX-PROLOGUE])
    270 # -------------------------------------------------------------------------
    271 # Look for the Boost library LIB-NAME (e.g., LIB-NAME = `thread', for
    272 # libboost_thread).  Check that HEADER-NAME works and check that
    273 # libboost_LIB-NAME can link with the code CXX-TEST.  The optional argument
    274 # CXX-PROLOGUE can be used to include some C++ code before the `main'
    275 # function.
     271# BOOST_FIND_LIBS([COMPONENT-NAME], [CANDIDATE-LIB-NAMES],
     272#                 [PREFERRED-RT-OPT], [HEADER-NAME], [CXX-TEST],
     273#                 [CXX-PROLOGUE])
     274# --------------------------------------------------------------
     275# Look for the Boost library COMPONENT-NAME (e.g., `thread', for
     276# libboost_thread) under the possible CANDIDATE-LIB-NAMES (e.g.,
     277# "thread_win32 thread").  Check that HEADER-NAME works and check that
     278# libboost_LIB-NAME can link with the code CXX-TEST.  The optional
     279# argument CXX-PROLOGUE can be used to include some C++ code before
     280# the `main' function.
    276281#
    277282# Invokes BOOST_FIND_HEADER([HEADER-NAME]) (see above).
    … …  
    287292# ...  If you want to make sure you have a specific version of Boost
    288293# (eg, >= 1.33) you *must* invoke BOOST_REQUIRE before this macro.
    289 AC_DEFUN([BOOST_FIND_LIB],
     294AC_DEFUN([BOOST_FIND_LIBS],
    290295[AC_REQUIRE([BOOST_REQUIRE])dnl
    291296AC_REQUIRE([_BOOST_FIND_COMPILER_TAG])dnl
    … …  
    301306AS_VAR_PUSHDEF([Boost_lib_LDPATH], [boost_cv_lib_$1_LDPATH])dnl
    302307AS_VAR_PUSHDEF([Boost_lib_LIBS], [boost_cv_lib_$1_LIBS])dnl
    303 BOOST_FIND_HEADER([$3])
     308BOOST_FIND_HEADER([$4])
    304309boost_save_CPPFLAGS=$CPPFLAGS
    305310CPPFLAGS="$CPPFLAGS $BOOST_CPPFLAGS"
    306 # Now let's try to find the library.  The algorithm is as follows: first look
    307 # for a given library name according to the user's PREFERRED-RT-OPT.  For each
    308 # library name, we prefer to use the ones that carry the tag (toolset name).
    309 # Each library is searched through the various standard paths were Boost is
    310 # usually installed.  If we can't find the standard variants, we try to
    311 # enforce -mt (for instance on MacOSX, libboost_threads.dylib doesn't exist
    312 # but there's -obviously- libboost_threads-mt.dylib).
    313311AC_CACHE_CHECK([for the Boost $1 library], [Boost_lib],
    314   [Boost_lib=no
    315   case "$2" in #(
    316     mt | mt-) boost_mt=-mt; boost_rtopt=;; #(
    317     mt* | mt-*) boost_mt=-mt; boost_rtopt=`expr "X$2" : 'Xmt-*\(.*\)'`;; #(
    318     *) boost_mt=; boost_rtopt=$2;;
     312               [_BOOST_FIND_LIBS($@)])
     313case $Boost_lib in #(
     314  (no) _AC_MSG_LOG_CONFTEST
     315    AC_MSG_ERROR([cannot find the flags to link with Boost $1])
     316    ;;
     317esac
     318AC_SUBST(AS_TR_CPP([BOOST_$1_LDFLAGS]), [$Boost_lib_LDFLAGS])dnl
     319AC_SUBST(AS_TR_CPP([BOOST_$1_LDPATH]), [$Boost_lib_LDPATH])dnl
     320AC_SUBST([BOOST_LDPATH], [$Boost_lib_LDPATH])dnl
     321AC_SUBST(AS_TR_CPP([BOOST_$1_LIBS]), [$Boost_lib_LIBS])dnl
     322CPPFLAGS=$boost_save_CPPFLAGS
     323AS_VAR_POPDEF([Boost_lib])dnl
     324AS_VAR_POPDEF([Boost_lib_LDFLAGS])dnl
     325AS_VAR_POPDEF([Boost_lib_LDPATH])dnl
     326AS_VAR_POPDEF([Boost_lib_LIBS])dnl
     327AC_LANG_POP([C++])dnl
     328fi
     329])
     330
     331
     332# BOOST_FIND_LIB([LIB-NAME],
     333#                [PREFERRED-RT-OPT], [HEADER-NAME], [CXX-TEST],
     334#                [CXX-PROLOGUE])
     335# --------------------------------------------------------------
     336# Backward compatibility wrapper for BOOST_FIND_LIBS.
     337AC_DEFUN([BOOST_FIND_LIB],
     338[BOOST_FIND_LIBS([$1], $@)])
     339
     340
     341# _BOOST_FIND_LIBS([LIB-NAME], [CANDIDATE-LIB-NAMES],
     342#                 [PREFERRED-RT-OPT], [HEADER-NAME], [CXX-TEST],
     343#                 [CXX-PROLOGUE])
     344# --------------------------------------------------------------
     345# Real implementation of BOOST_FIND_LIBS: rely on these local macros:
     346# Boost_lib, Boost_lib_LDFLAGS, Boost_lib_LDPATH, Boost_lib_LIBS
     347#
     348# The algorithm is as follows: first look for a given library name
     349# according to the user's PREFERRED-RT-OPT.  For each library name, we
     350# prefer to use the ones that carry the tag (toolset name).  Each
     351# library is searched through the various standard paths were Boost is
     352# usually installed.  If we can't find the standard variants, we try
     353# to enforce -mt (for instance on MacOSX, libboost_thread.dylib
     354# doesn't exist but there's -obviously- libboost_thread-mt.dylib).
     355AC_DEFUN([_BOOST_FIND_LIBS],
     356[Boost_lib=no
     357  case "$3" in #(
     358    (mt | mt-) boost_mt=-mt; boost_rtopt=;; #(
     359    (mt* | mt-*) boost_mt=-mt; boost_rtopt=`expr "X$3" : 'Xmt-*\(.*\)'`;; #(
     360    (*) boost_mt=; boost_rtopt=$3;;
    319361  esac
    320362  if test $enable_static_boost = yes; then
    … …  
    323365  # Find the proper debug variant depending on what we've been asked to find.
    324366  case $boost_rtopt in #(
    325     *d*) boost_rt_d=$boost_rtopt;; #(
    326     *[[sgpn]]*) # Insert the `d' at the right place (in between `sg' and `pn')
     367    (*d*) boost_rt_d=$boost_rtopt;; #(
     368    (*[[sgpn]]*) # Insert the `d' at the right place (in between `sg' and `pn')
    327369      boost_rt_d=`echo "$boost_rtopt" | sed 's/\(s*g*\)\(p*n*\)/\1\2/'`;; #(
    328     *) boost_rt_d='-d';;
     370    (*) boost_rt_d='-d';;
    329371  esac
    330372  # If the PREFERRED-RT-OPT are not empty, prepend a `-'.
    … …  
    337379  boost_save_ac_objext=$ac_objext
    338380  # Generate the test file.
    339   AC_LANG_CONFTEST([AC_LANG_PROGRAM([#include <$3>
    340 $5], [$4])])
     381  AC_LANG_CONFTEST([AC_LANG_PROGRAM([#include <$4>
     382$6], [$5])])
    341383dnl Optimization hacks: compiling C++ is slow, especially with Boost.  What
    342384dnl we're trying to do here is guess the right combination of link flags
    … …  
    360402  ac_objext=$boost_save_ac_objext
    361403  boost_failed_libs=
    362 # Don't bother to ident the 6 nested for loops, only the 2 innermost ones
    363 # matter.
     404# Don't bother to ident the following nested for loops, only the 2
     405# innermost ones matter.
     406for boost_lib_ in $2; do
    364407for boost_tag_ in -$boost_cv_lib_tag ''; do
    365408for boost_ver_ in -$boost_cv_lib_version ''; do
    366 for boost_mt_ in $boost_mt '' -mt; do
     409for boost_mt_ in $boost_mt -mt ''; do
    367410for boost_rtopt_ in $boost_rtopt '' -d; do
    368411  for boost_lib in \
    369     boost_$1$boost_tag_$boost_mt_$boost_rtopt_$boost_ver_ \
    370     boost_$1$boost_tag_$boost_rtopt_$boost_ver_ \
    371     boost_$1$boost_tag_$boost_mt_$boost_ver_ \
    372     boost_$1$boost_tag_$boost_ver_
     412    boost_$boost_lib_$boost_tag_$boost_mt_$boost_rtopt_$boost_ver_ \
     413    boost_$boost_lib_$boost_tag_$boost_rtopt_$boost_ver_ \
     414    boost_$boost_lib_$boost_tag_$boost_mt_$boost_ver_ \
     415    boost_$boost_lib_$boost_tag_$boost_ver_
    373416  do
    374417    # Avoid testing twice the same lib
    375418    case $boost_failed_libs in #(
    376       *@$boost_lib@*) continue;;
     419      (*@$boost_lib@*) continue;;
    377420    esac
    378421    # If with_boost is empty, we'll search in /lib first, which is not quite
    … …  
    381424    test x"$with_boost" = x && boost_tmp_lib=${boost_cv_inc_path%/include}
    382425    for boost_ldpath in "$boost_tmp_lib/lib" '' \
    383              /usr/local/lib* /usr/lib* \
    384              "$with_boost" C:/Boost/lib /lib* \
    385              /opt/local/lib* /opt/lib*
     426             /opt/local/lib* /usr/local/lib* /opt/lib* /usr/lib* \
     427             "$with_boost" C:/Boost/lib /lib*
    386428    do
    387       test -e "$boost_ldpath" || continue
     429      # Don't waste time with directories that don't exist.
     430      if test x"$boost_ldpath" != x && test ! -e "$boost_ldpath"; then
     431        continue
     432      fi
    388433      boost_save_LDFLAGS=$LDFLAGS
    389434      # Are we looking for a static library?
    390435      case $boost_ldpath:$boost_rtopt_ in #(
    391         *?*:*s*) # Yes (Non empty boost_ldpath + s in rt opt)
     436        (*?*:*s*) # Yes (Non empty boost_ldpath + s in rt opt)
    392437          Boost_lib_LIBS="$boost_ldpath/lib$boost_lib.$libext"
    393438          test -e "$Boost_lib_LIBS" || continue;; #(
    394         *) # No: use -lboost_foo to find the shared library.
     439        (*) # No: use -lboost_foo to find the shared library.
    395440          Boost_lib_LIBS="-l$boost_lib";;
    396441      esac
    … …  
    406451      LIBS=$boost_save_LIBS
    407452      if test x"$Boost_lib" = xyes; then
    408         Boost_lib_LDFLAGS="-L$boost_ldpath -Wl,-R$boost_ldpath"
     453        # Check or used cached result of whether or not using -R or
     454        # -rpath makes sense.  Some implementations of ld, such as for
     455        # Mac OSX, require -rpath but -R is the flag known to work on
     456        # other systems.  https://github.com/tsuna/boost.m4/issues/19
     457        AC_CACHE_VAL([boost_cv_rpath_link_ldflag],
     458          [case $boost_ldpath in
     459           '') # Nothing to do.
     460             boost_cv_rpath_link_ldflag=
     461             boost_rpath_link_ldflag_found=yes;;
     462           *)
     463            for boost_cv_rpath_link_ldflag in -Wl,-R, -Wl,-rpath,; do
     464              LDFLAGS="$boost_save_LDFLAGS -L$boost_ldpath $boost_cv_rpath_link_ldflag$boost_ldpath"
     465              LIBS="$boost_save_LIBS $Boost_lib_LIBS"
     466              _BOOST_AC_LINK_IFELSE([],
     467                [boost_rpath_link_ldflag_found=yes
     468                break],
     469                [boost_rpath_link_ldflag_found=no])
     470            done
     471            ;;
     472          esac
     473          AS_IF([test "x$boost_rpath_link_ldflag_found" != "xyes"],
     474            [AC_MSG_ERROR([Unable to determine whether to use -R or -rpath])])
     475          LDFLAGS=$boost_save_LDFLAGS
     476          LIBS=$boost_save_LIBS
     477          ])
     478        test x"$boost_ldpath" != x &&
     479          Boost_lib_LDFLAGS="-L$boost_ldpath $boost_cv_rpath_link_ldflag$boost_ldpath"
    409480        Boost_lib_LDPATH="$boost_ldpath"
    410         break 6
     481        break 7
    411482      else
    412483        boost_failed_libs="$boost_failed_libs@$boost_lib@"
    … …  
    418489done
    419490done
     491done # boost_lib_
    420492rm -f conftest.$ac_objext
    421493])
    422 case $Boost_lib in #(
    423   no) _AC_MSG_LOG_CONFTEST
    424     AC_MSG_ERROR([cannot find the flags to link with Boost $1])
    425     ;;
    426 esac
    427 AC_SUBST(AS_TR_CPP([BOOST_$1_LDFLAGS]), [$Boost_lib_LDFLAGS])dnl
    428 AC_SUBST(AS_TR_CPP([BOOST_$1_LDPATH]), [$Boost_lib_LDPATH])dnl
    429 AC_SUBST([BOOST_LDPATH], [$Boost_lib_LDPATH])dnl
    430 AC_SUBST(AS_TR_CPP([BOOST_$1_LIBS]), [$Boost_lib_LIBS])dnl
    431 CPPFLAGS=$boost_save_CPPFLAGS
    432 AS_VAR_POPDEF([Boost_lib])dnl
    433 AS_VAR_POPDEF([Boost_lib_LDFLAGS])dnl
    434 AS_VAR_POPDEF([Boost_lib_LDPATH])dnl
    435 AS_VAR_POPDEF([Boost_lib_LIBS])dnl
    436 AC_LANG_POP([C++])dnl
    437 fi
    438 ])# BOOST_FIND_LIB
     494
    439495
    440496
    … …  
    483539BOOST_FIND_HEADER([boost/asio.hpp])])
    484540
     541
    485542# BOOST_BIMAP()
    486543# ------------
    … …  
    489546[BOOST_FIND_HEADER([boost/bimap.hpp])])
    490547
     548
    491549# BOOST_BIND()
    492550# ------------
    493 # Look for Boost.Bind
     551# Look for Boost.Bind.
    494552BOOST_DEFUN([Bind],
    495553[BOOST_FIND_HEADER([boost/bind.hpp])])
     554
    496555
    497556# BOOST_CAST()
    … …  
    500559BOOST_DEFUN([Cast],
    501560[BOOST_FIND_HEADER([boost/cast.hpp])])
     561
     562
     563# BOOST_CHRONO()
     564# --------------
     565# Look for Boost.Chrono.
     566BOOST_DEFUN([Chrono],
     567[# Do we have to check for Boost.System?  This link-time dependency was
     568# added as of 1.35.0.  If we have a version <1.35, we must not attempt to
     569# find Boost.System as it didn't exist by then.
     570if test $boost_major_version -ge 135; then
     571  BOOST_SYSTEM([$1])
     572fi # end of the Boost.System check.
     573boost_filesystem_save_LIBS=$LIBS
     574boost_filesystem_save_LDFLAGS=$LDFLAGS
     575m4_pattern_allow([^BOOST_SYSTEM_(LIBS|LDFLAGS)$])dnl
     576LIBS="$LIBS $BOOST_SYSTEM_LIBS"
     577LDFLAGS="$LDFLAGS $BOOST_SYSTEM_LDFLAGS"
     578BOOST_FIND_LIB([chrono], [$1],
     579                [boost/chrono.hpp],
     580                [boost::chrono::thread_clock d;])
     581if test $enable_static_boost = yes && test $boost_major_version -ge 135; then
     582  BOOST_FILESYSTEM_LIBS="$BOOST_FILESYSTEM_LIBS $BOOST_SYSTEM_LIBS"
     583fi
     584LIBS=$boost_filesystem_save_LIBS
     585LDFLAGS=$boost_filesystem_save_LDFLAGS
     586])# BOOST_CHRONO
     587
    502588
    503589# BOOST_CONVERSION()
    … …  
    508594BOOST_FIND_HEADER([boost/lexical_cast.hpp])
    509595])# BOOST_CONVERSION
     596
     597
     598# BOOST_CRC()
     599# -----------
     600# Look for Boost.CRC
     601BOOST_DEFUN([CRC],
     602[BOOST_FIND_HEADER([boost/crc.hpp])
     603])# BOOST_CRC
    510604
    511605
    … …  
    539633# find Boost.System as it didn't exist by then.
    540634if test $boost_major_version -ge 135; then
    541 BOOST_SYSTEM([$1])
     635  BOOST_SYSTEM([$1])
    542636fi # end of the Boost.System check.
    543637boost_filesystem_save_LIBS=$LIBS
    … …  
    549643                [boost/filesystem/path.hpp], [boost::filesystem::path p;])
    550644if test $enable_static_boost = yes && test $boost_major_version -ge 135; then
    551     AC_SUBST([BOOST_FILESYSTEM_LIBS], ["$BOOST_FILESYSTEM_LIBS $BOOST_SYSTEM_LIBS"])
     645  BOOST_FILESYSTEM_LIBS="$BOOST_FILESYSTEM_LIBS $BOOST_SYSTEM_LIBS"
    552646fi
    553647LIBS=$boost_filesystem_save_LIBS
    … …  
    556650
    557651
     652# BOOST_FUSION()
     653# -----------------
     654# Look for Boost.Fusion
     655BOOST_DEFUN([Fusion],
     656[BOOST_FIND_HEADER([boost/fusion/sequence.hpp])])
     657
     658
     659# BOOST_FLYWEIGHT()
     660# -----------------
     661# Look for Boost.Flyweight.
     662BOOST_DEFUN([Flyweight],
     663[dnl There's a hidden dependency on pthreads.
     664AC_REQUIRE([_BOOST_PTHREAD_FLAG])dnl
     665BOOST_FIND_HEADER([boost/flyweight.hpp])
     666AC_SUBST([BOOST_FLYWEIGHT_LIBS], [$boost_cv_pthread_flag])
     667])
     668
     669
    558670# BOOST_FOREACH()
    559671# ---------------
    560 # Look for Boost.Foreach
     672# Look for Boost.Foreach.
    561673BOOST_DEFUN([Foreach],
    562674[BOOST_FIND_HEADER([boost/foreach.hpp])])
    … …  
    565677# BOOST_FORMAT()
    566678# --------------
    567 # Look for Boost.Format
     679# Look for Boost.Format.
    568680# Note: we can't check for boost/format/format_fwd.hpp because the header isn't
    569681# standalone.  It can't be compiled because it triggers the following error:
    … …  
    581693
    582694
    583 # BOOST_FUSION()
     695# BOOST_GEOMETRY()
    584696# ----------------
    585 # Look for Boost.Fusion
    586 BOOST_DEFUN([Fusion],
    587 [BOOST_FIND_HEADER([boost/fusion/sequence.hpp])])
     697# Look for Boost.Geometry (new since 1.47.0).
     698BOOST_DEFUN([Geometry],
     699[BOOST_FIND_HEADER([boost/geometry.hpp])
     700])# BOOST_GEOMETRY
    588701
    589702
    … …  
    632745# BOOST_LOG([PREFERRED-RT-OPT])
    633746# -----------------------------
    634 # Look for Boost.Log For the documentation of PREFERRED-RT-OPT, see the
     747# Look for Boost.Log. For the documentation of PREFERRED-RT-OPT, see the
    635748# documentation of BOOST_FIND_LIB above.
    636749BOOST_DEFUN([Log],
    … …  
    643756# BOOST_LOG_SETUP([PREFERRED-RT-OPT])
    644757# -----------------------------------
    645 # Look for Boost.Log For the documentation of PREFERRED-RT-OPT, see the
     758# Look for Boost.Log. For the documentation of PREFERRED-RT-OPT, see the
    646759# documentation of BOOST_FIND_LIB above.
    647760BOOST_DEFUN([Log_Setup],
    648761[AC_REQUIRE([BOOST_LOG])dnl
    649762BOOST_FIND_LIB([log_setup], [$1],
    650     [boost/log/utility/init/from_settings.hpp],
     763    [boost/log/utility/setup/from_settings.hpp],
    651764    [boost::log::basic_settings<char> bs; bs.empty();])
    652765])# BOOST_LOG_SETUP
    … …  
    665778
    666779
     780# BOOST_MPI([PREFERRED-RT-OPT])
     781# -------------------------------
     782# Look for Boost MPI.  For the documentation of PREFERRED-RT-OPT, see the
     783# documentation of BOOST_FIND_LIB above.  Uses MPICXX variable if it is
     784# set, otherwise tries CXX
     785#
     786BOOST_DEFUN([MPI],
     787[boost_save_CXX=${CXX}
     788boost_save_CXXCPP=${CXXCPP}
     789if test x"${MPICXX}" != x; then
     790  CXX=${MPICXX}
     791  CXXCPP="${MPICXX} -E"
     792fi
     793BOOST_FIND_LIB([mpi], [$1],
     794               [boost/mpi.hpp],
     795               [int argc = 0;
     796                char **argv = 0;
     797                boost::mpi::environment env(argc,argv);])
     798CXX=${boost_save_CXX}
     799CXXCPP=${boost_save_CXXCPP}
     800])# BOOST_MPI
     801
     802
     803# BOOST_MPL()
     804# ------------------
     805# Look for Boost.MPL
     806BOOST_DEFUN([MPL],
     807[BOOST_FIND_HEADER([boost/mpl/for_each.hpp])])
     808
     809
    667810# BOOST_MULTIARRAY()
    668811# ------------------
    669812# Look for Boost.MultiArray
    670813BOOST_DEFUN([MultiArray],
    671 [BOOST_FIND_HEADER([boost/mpl/list.hpp])])
    672 
    673 
    674 # BOOST_MMPL()
    675 # ------------------
    676 # Look for Boost.MPL
    677 BOOST_DEFUN([MPL],
    678 [BOOST_FIND_HEADER([boost/mpl/for_each.hpp])])
     814[BOOST_FIND_HEADER([boost/multi_array.hpp])])
     815
     816
     817# BOOST_NUMERIC_UBLAS()
     818# --------------------------
     819# Look for Boost.NumericUblas (Basic Linear Algebra)
     820BOOST_DEFUN([Numeric_Ublas],
     821[BOOST_FIND_HEADER([boost/numeric/ublas/vector.hpp])
     822])# BOOST_NUMERIC_UBLAS
     823
    679824
    680825# BOOST_NUMERIC_CONVERSION()
    … …  
    764909_BOOST_PYTHON_CONFIG([LIBS],      [libs])
    765910m4_pattern_allow([^BOOST_PYTHON_MODULE$])dnl
    766 BOOST_FIND_LIB([python], [$1],
    767                [boost/python.hpp],
    768                [], [BOOST_PYTHON_MODULE(empty) {}])
     911BOOST_FIND_LIBS([python], [python python3], [$1],
     912                [boost/python.hpp],
     913                [], [BOOST_PYTHON_MODULE(empty) {}])
    769914CPPFLAGS=$boost_python_save_CPPFLAGS
    770915LDFLAGS=$boost_python_save_LDFLAGS
    … …  
    812957                [boost::signal<void ()> s;])
    813958])# BOOST_SIGNALS
     959
     960
     961# BOOST_SIGNALS2()
     962# ----------------
     963# Look for Boost.Signals2 (new since 1.39.0).
     964BOOST_DEFUN([Signals2],
     965[BOOST_FIND_HEADER([boost/signals2.hpp])
     966])# BOOST_SIGNALS2
    814967
    815968
    … …  
    8641017
    8651018
    866 # BOOST_THREADS([PREFERRED-RT-OPT])
     1019# BOOST_THREAD([PREFERRED-RT-OPT])
    8671020# ---------------------------------
    8681021# Look for Boost.Thread.  For the documentation of PREFERRED-RT-OPT, see the
    8691022# documentation of BOOST_FIND_LIB above.
    870 # FIXME: Provide an alias "BOOST_THREAD".
    871 BOOST_DEFUN([Threads],
     1023BOOST_DEFUN([Thread],
    8721024[dnl Having the pthread flag is required at least on GCC3 where
    8731025dnl boost/thread.hpp would complain if we try to compile without
    8741026dnl -pthread on GNU/Linux.
    8751027AC_REQUIRE([_BOOST_PTHREAD_FLAG])dnl
    876 boost_threads_save_LIBS=$LIBS
    877 boost_threads_save_CPPFLAGS=$CPPFLAGS
    878 LIBS="$LIBS $boost_cv_pthread_flag"
    879 # Yes, we *need* to put the -pthread thing in CPPFLAGS because with GCC3,
    880 # boost/thread.hpp will trigger a #error if -pthread isn't used:
    881 #   boost/config/requires_threads.hpp:47:5: #error "Compiler threading support
    882 #   is not turned on. Please set the correct command line options for
    883 #   threading: -pthread (Linux), -pthreads (Solaris) or -mthreads (Mingw32)"
     1028boost_thread_save_LIBS=$LIBS
     1029boost_thread_save_LDFLAGS=$LDFLAGS
     1030boost_thread_save_CPPFLAGS=$CPPFLAGS
     1031# Link-time dependency from thread to system was added as of 1.49.0.
     1032if test $boost_major_version -ge 149; then
     1033BOOST_SYSTEM([$1])
     1034fi # end of the Boost.System check.
     1035m4_pattern_allow([^BOOST_SYSTEM_(LIBS|LDFLAGS)$])dnl
     1036LIBS="$LIBS $BOOST_SYSTEM_LIBS $boost_cv_pthread_flag"
     1037LDFLAGS="$LDFLAGS $BOOST_SYSTEM_LDFLAGS"
    8841038CPPFLAGS="$CPPFLAGS $boost_cv_pthread_flag"
    885 BOOST_FIND_LIB([thread], [$1],
    886                [boost/thread.hpp], [boost::thread t; boost::mutex m;])
    887 BOOST_THREAD_LIBS="$BOOST_THREAD_LIBS $boost_cv_pthread_flag"
     1039
     1040# When compiling for the Windows platform, the threads library is named
     1041# differently.
     1042case $host_os in
     1043  (*mingw*) boost_thread_lib_ext=_win32;;
     1044esac
     1045BOOST_FIND_LIBS([thread], [thread$boost_thread_lib_ext],
     1046                [$1],
     1047                [boost/thread.hpp], [boost::thread t; boost::mutex m;])
     1048
     1049BOOST_THREAD_LIBS="$BOOST_THREAD_LIBS $BOOST_SYSTEM_LIBS $boost_cv_pthread_flag"
     1050BOOST_THREAD_LDFLAGS="$BOOST_SYSTEM_LDFLAGS"
    8881051BOOST_CPPFLAGS="$BOOST_CPPFLAGS $boost_cv_pthread_flag"
    889 LIBS=$boost_threads_save_LIBS
    890 CPPFLAGS=$boost_threads_save_CPPFLAGS
    891 ])# BOOST_THREADS
     1052LIBS=$boost_thread_save_LIBS
     1053LDFLAGS=$boost_thread_save_LDFLAGS
     1054CPPFLAGS=$boost_thread_save_CPPFLAGS
     1055])# BOOST_THREAD
     1056
     1057AU_ALIAS([BOOST_THREADS], [BOOST_THREAD])
    8921058
    8931059
    … …  
    9381104
    9391105
     1106# BOOST_POINTER_CONTAINER()
     1107# ------------------------
     1108# Look for Boost.PointerContainer
     1109BOOST_DEFUN([Pointer_Container],
     1110[BOOST_FIND_HEADER([boost/ptr_container/ptr_deque.hpp])
     1111BOOST_FIND_HEADER([boost/ptr_container/ptr_list.hpp])
     1112BOOST_FIND_HEADER([boost/ptr_container/ptr_vector.hpp])
     1113BOOST_FIND_HEADER([boost/ptr_container/ptr_array.hpp])
     1114BOOST_FIND_HEADER([boost/ptr_container/ptr_set.hpp])
     1115BOOST_FIND_HEADER([boost/ptr_container/ptr_map.hpp])
     1116])# BOOST_POINTER_CONTAINER
     1117
     1118
    9401119# BOOST_WAVE([PREFERRED-RT-OPT])
    9411120# ------------------------------
    9421121# NOTE: If you intend to use Wave/Spirit with thread support, make sure you
    943 # call BOOST_THREADS first.
     1122# call BOOST_THREAD first.
    9441123# Look for Boost.Wave.  For the documentation of PREFERRED-RT-OPT, see the
    9451124# documentation of BOOST_FIND_LIB above.
    … …  
    9501129boost_wave_save_LDFLAGS=$LDFLAGS
    9511130m4_pattern_allow([^BOOST_((FILE)?SYSTEM|DATE_TIME|THREAD)_(LIBS|LDFLAGS)$])dnl
    952 LIBS="$LIBS $BOOST_SYSTEM_LIBS $BOOST_FILESYSTEM_LIBS $BOOST_DATE_TIME_LIBS\
     1131LIBS="$LIBS $BOOST_SYSTEM_LIBS $BOOST_FILESYSTEM_LIBS $BOOST_DATE_TIME_LIBS \
    9531132$BOOST_THREAD_LIBS"
    954 LDFLAGS="$LDFLAGS $BOOST_SYSTEM_LDFLAGS $BOOST_FILESYSTEM_LDFLAGS\
     1133LDFLAGS="$LDFLAGS $BOOST_SYSTEM_LDFLAGS $BOOST_FILESYSTEM_LDFLAGS \
    9551134$BOOST_DATE_TIME_LDFLAGS $BOOST_THREAD_LDFLAGS"
    9561135BOOST_FIND_LIB([wave], [$1],
    … …  
    9761155# _BOOST_PTHREAD_FLAG()
    9771156# ---------------------
    978 # Internal helper for BOOST_THREADS.  Based on ACX_PTHREAD:
    979 # http://autoconf-archive.cryp.to/acx_pthread.html
     1157# Internal helper for BOOST_THREAD.  Computes boost_cv_pthread_flag
     1158# which must be used in CPPFLAGS and LIBS.
     1159#
     1160# Yes, we *need* to put the -pthread thing in CPPFLAGS because with GCC3,
     1161# boost/thread.hpp will trigger a #error if -pthread isn't used:
     1162#   boost/config/requires_threads.hpp:47:5: #error "Compiler threading support
     1163#   is not turned on. Please set the correct command line options for
     1164#   threading: -pthread (Linux), -pthreads (Solaris) or -mthreads (Mingw32)"
     1165#
     1166# Based on ACX_PTHREAD: http://autoconf-archive.cryp.to/acx_pthread.html
    9801167AC_DEFUN([_BOOST_PTHREAD_FLAG],
    9811168[AC_REQUIRE([AC_PROG_CXX])dnl
    … …  
    10451232["defined __GNUC__ && __GNUC__ == $1 && __GNUC_MINOR__ == $2 && !defined __ICC @ gcc$1$2"])dnl
    10461233
     1234# _BOOST_mingw_test(MAJOR, MINOR)
     1235# -----------------------------
     1236# Internal helper for _BOOST_FIND_COMPILER_TAG.
     1237m4_define([_BOOST_mingw_test],
     1238["defined __GNUC__ && __GNUC__ == $1 && __GNUC_MINOR__ == $2 && !defined __ICC && \
     1239  (defined WIN32 || defined WINNT || defined _WIN32 || defined __WIN32 \
     1240         || defined __WIN32__ || defined __WINNT || defined __WINNT__) @ mgw$1$2"])dnl
     1241
    10471242
    10481243# _BOOST_FIND_COMPILER_TAG()
    … …  
    10721267  # the same defines as GCC's).
    10731268  for i in \
     1269    _BOOST_mingw_test(4,8) \
     1270    _BOOST_gcc_test(4, 8) \
     1271    _BOOST_mingw_test(4,7) \
     1272    _BOOST_gcc_test(4, 7) \
     1273    _BOOST_mingw_test(4,6) \
    10741274    _BOOST_gcc_test(4, 6) \
     1275    _BOOST_mingw_test(4,5) \
    10751276    _BOOST_gcc_test(4, 5) \
     1277    _BOOST_mingw_test(4,4) \
    10761278    _BOOST_gcc_test(4, 4) \
     1279    _BOOST_mingw_test(4,3) \
    10771280    _BOOST_gcc_test(4, 3) \
     1281    _BOOST_mingw_test(4,2) \
    10781282    _BOOST_gcc_test(4, 2) \
     1283    _BOOST_mingw_test(4,1) \
    10791284    _BOOST_gcc_test(4, 1) \
     1285    _BOOST_mingw_test(4,0) \
    10801286    _BOOST_gcc_test(4, 0) \
    10811287    "defined __GNUC__ && __GNUC__ == 3 && !defined __ICC \
    … …  
    11431349AC_DEFUN([_BOOST_GUESS_WHETHER_TO_USE_MT],
    11441350[# Check whether we do better use `mt' even though we weren't ask to.
     1351AC_LANG_PUSH([C++])dnl
    11451352AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
    11461353#if defined _REENTRANT || defined _MT || defined __MT__
    … …  
    11501357#endif
    11511358]])], [boost_guess_use_mt=:], [boost_guess_use_mt=false])
     1359AC_LANG_POP([C++])dnl
    11521360])
    11531361
    … …  
    11731381  _AS_ECHO_LOG([re-using the existing conftest.$ac_objext])
    11741382AS_IF([_AC_DO_STDERR($ac_link) && {
    1175         test -z "$ac_[]_AC_LANG_ABBREV[]_werror_flag" ||
    1176         test ! -s conftest.err
     1383        test -z "$ac_[]_AC_LANG_ABBREV[]_werror_flag" ||
     1384        test ! -s conftest.err
    11771385       } && test -s conftest$ac_exeext && {
    1178         test "$cross_compiling" = yes ||
    1179         $as_executable_p conftest$ac_exeext
     1386        test "$cross_compiling" = yes ||
     1387        $as_executable_p conftest$ac_exeext
    11801388dnl FIXME: use AS_TEST_X instead when 2.61 is widespread enough.
    11811389       }],

  • m4/qwt.m4

    r4c9101 ra91710  
    8080  AC_TRY_LINK(
    8181    [#include <qwt_plot.h>],
    82     [QwtPlot * plot = new QwtPlot(QString("Two Curves"));],
     82    [QwtPlot * plot = new QwtPlot();],
    8383    [mol_ac_have_qwt=true])
    8484  AC_LANG_RESTORE

  • src/Actions/ActionQueue.cpp

    r4c9101 ra91710  
    145145      run_thread.sleep(boost::get_system_time() + boost::posix_time::milliseconds(100));
    146146#else
    147       run_thread.sleep_for(100);
     147      boost::this_thread::sleep_for(boost::chrono::milliseconds(100));
    148148#endif
    149149    } catch(boost::thread_interrupted &e) {

  • src/Actions/Action_impl_python.hpp

    r4c9101 ra91710  
    2121#include <boost/preprocessor/punctuation/comma_if.hpp>
    2222#include <boost/preprocessor/punctuation/paren.hpp>
     23#include <boost/preprocessor/seq/elem.hpp>
     24#include <boost/preprocessor/seq/size.hpp>
     25#include <boost/preprocessor/seq/transform.hpp>
    2326
    2427// some derived names: if CATEGORY is not given, we don't prefix with it
    … …  
    4851BOOST_PP_ASSERT_MSG(BOOST_PP_EQUAL(MAXPARAMTYPES, BOOST_PP_SEQ_SIZE(paramdescriptions)),\
    4952  ERROR: There are not the same number of "paramtokens" and "paramdescriptions" in: __FILE__ \
     53)
     54#endif
     55#ifdef paramreferences
     56BOOST_PP_ASSERT_MSG(BOOST_PP_EQUAL(MAXPARAMTYPES, BOOST_PP_SEQ_SIZE(paramreferences)),\
     57  ERROR: There are not the same number of "paramtokens" and "paramreferences" in: __FILE__ \
     58)
     59#endif
     60
     61#ifdef paramtypes
     62BOOST_PP_ASSERT_MSG(BOOST_PP_EQUAL(MAXPARAMTYPES, BOOST_PP_SEQ_SIZE(paramtypes)),\
     63  ERROR: There are not the same number of "paramtokens" and "paramtypes" in: __FILE__ \
    5064)
    5165#endif
    … …  
    8397// print a list of type ref followed, i.e. "int i, double position"
    8498#define type_list(z,n,TYPELIST, VARLIST) \
    85   BOOST_PP_COMMA_IF(n)\
     99  BOOST_PP_COMMA_IF(n) \
    86100  BOOST_PP_SEQ_ELEM(n, TYPELIST) \
    87101  BOOST_PP_SEQ_ELEM(n, VARLIST)
    … …  
    90104#define value_print(z, n, container, prefix) \
    91105  prefix \
    92   BOOST_PP_SEQ_ELEM(n, container)\
    93   .set(\
    94   BOOST_PP_SEQ_ELEM(n, container)\
     106  BOOST_PP_SEQ_ELEM(n, container) \
     107  .set( \
     108  BOOST_PP_SEQ_ELEM(n, container) \
    95109  );
    96110
    … …  
    110124BOOST_PP_CAT( COMMAND, _stringargs)(
    111125#if defined paramtypes
    112 #define BOOST_PP_LOCAL_MACRO(n) type_list(~, n, BOOST_PP_SEQ_TRANSFORM( type2string, , paramtypes), paramreferences)
     126#define BOOST_PP_LOCAL_MACRO(n) type_list(~, n, BOOST_PP_SEQ_TRANSFORM( type2string, ~, paramtypes), paramreferences)
    113127#define BOOST_PP_LOCAL_LIMITS  (0, MAXPARAMTYPES-1)
    114128#include BOOST_PP_LOCAL_ITERATE()

  • src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

    r4c9101 ra91710  
    175175        params.executable.get().string()
    176176        );
     177    if (NoJobs != NumberJobs) {
     178      ELOG(1, "Not all jobs were added succesfully.");
     179      return Action::failure;
     180    }
    177181    LOG(1, "INFO: Added " << NoJobs << " from FragmentJobsQueue.");
    178182

  • src/Actions/unittests/Makefile.am

    r4c9101 ra91710  
    2525
    2626ACTIONLIBS = \
     27        libUnitTest.la \
     28        ../libMolecuilder.la \
    2729        ../libMolecuilderUI.la
    2830if CONDJOBMARKET
    … …  
    3335# note that DummyUI inherits Dialog which depends on boost/file_system ...
    3436
    35 ActionRegistryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     37ActionRegistryUnitTest_SOURCES = \
    3638        ../Actions/unittests/ActionRegistryUnitTest.cpp \
    3739        ../Actions/unittests/ActionRegistryUnitTest.hpp \
    … …  
    4042        ../Parameters/unittests/stubs/BoxVectorValidatorStub.cpp \
    4143        ../Parameters/unittests/stubs/TimeStepPresentValidatorStub.cpp
    42 ActionRegistryUnitTest_LDADD = ${ACTIONLIBS}
     44ActionRegistryUnitTest_LDADD = ${ACTIONLIBS} \
     45        $(BOOST_SYSTEM_LDFLAGS) $(BOOST_SYSTEM_LIBS)
    4346
    44 ActionSequenceUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     47ActionSequenceUnitTest_SOURCES = \
    4548        ../Actions/unittests/ActionSequenceUnitTest.cpp \
    4649        ../Actions/unittests/ActionSequenceUnitTest.hpp \
    … …  
    5558        $(BOOST_SYSTEM_LDFLAGS) $(BOOST_SYSTEM_LIBS)
    5659
    57 AtomsCalculationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     60AtomsCalculationUnitTest_SOURCES = \
    5861        ../Actions/unittests/AtomsCalculationUnitTest.cpp \
    5962        ../Actions/unittests/AtomsCalculationUnitTest.hpp
    6063AtomsCalculationUnitTest_LDADD = ${ACTIONLIBS}
    6164
    62 ManipulateAtomsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     65ManipulateAtomsUnitTest_SOURCES = \
    6366        ../Actions/unittests/ManipulateAtomsUnitTest.cpp \
    6467        ../Actions/unittests/ManipulateAtomsUnitTest.hpp \

  • src/Analysis/unittests/Makefile.am

    r4c9101 ra91710  
    2828
    2929ANALYSISLIBS = \
     30        libUnitTest.la \
    3031        ../libMolecuilderAnalysis.la \
    3132        ../libMolecuilderUI.la \
    … …  
    4041        $(BOOST_LIB)
    4142
    42 AnalysisBondsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     43AnalysisBondsUnitTest_SOURCES = \
    4344        ../Analysis/unittests/AnalysisBondsUnitTest.cpp \
    4445        ../Analysis/unittests/AnalysisBondsUnitTest.hpp
    4546AnalysisBondsUnitTest_LDADD = ${ANALYSISLIBS}
    4647
    47 AnalysisCorrelationToPointUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     48AnalysisCorrelationToPointUnitTest_SOURCES = \
    4849        ../Analysis/unittests/AnalysisCorrelationToPointUnitTest.cpp \
    4950        ../Analysis/unittests/AnalysisCorrelationToPointUnitTest.hpp
    5051AnalysisCorrelationToPointUnitTest_LDADD = ${ANALYSISLIBS}
    5152
    52 AnalysisCorrelationToSurfaceUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     53AnalysisCorrelationToSurfaceUnitTest_SOURCES = \
    5354        ../Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp \
    5455        ../Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp
    5556AnalysisCorrelationToSurfaceUnitTest_LDADD = ${ANALYSISLIBS}
    5657
    57 AnalysisPairCorrelationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     58AnalysisPairCorrelationUnitTest_SOURCES = \
    5859        ../Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp \
    5960        ../Analysis/unittests/AnalysisPairCorrelationUnitTest.hpp
    6061AnalysisPairCorrelationUnitTest_LDADD = ${ANALYSISLIBS}
    6162
    62 CountBondsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     63CountBondsUnitTest_SOURCES = \
    6364        ../Analysis/unittests/CountBondsUnitTest.cpp \
    6465        ../Analysis/unittests/CountBondsUnitTest.hpp

  • src/Atom/unittests/Makefile.am

    r4c9101 ra91710  
    2121
    2222ATOMTESTLIBS = \
     23        libUnitTest.la \
     24        ../libMolecuilder.la \
    2325        ../libMolecuilderUI.la
    2426ATOMTESTLIBS += \
    … …  
    2729        $(BOOST_LIB)
    2830
    29 AtomObserverUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     31AtomObserverUnitTest_SOURCES = \
    3032        ../Atom/unittests/AtomObserverUnitTest.cpp \
    3133        ../Atom/unittests/AtomObserverUnitTest.hpp \
    … …  
    3436AtomObserverUnitTest_LDADD = ${ATOMTESTLIBS}
    3537
    36 CopyAtomsInterfaceUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     38CopyAtomsInterfaceUnitTest_SOURCES = \
    3739        ../Atom/unittests/CopyAtomsInterfaceUnitTest.cpp \
    3840        ../Atom/unittests/CopyAtomsInterfaceUnitTest.hpp

  • src/Descriptors/unittests/Makefile.am

    r4c9101 ra91710  
    1919
    2020DESCRIPTORLIBS = \
     21        libUnitTest.la \
     22        ../libMolecuilder.la \
    2123        ../libMolecuilderUI.la
    2224if CONDJOBMARKET
    … …  
    3032
    3133
    32 AtomDescriptorUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     34AtomDescriptorUnitTest_SOURCES = \
    3335        ../Descriptors/unittests/AtomDescriptorUnitTest.cpp \
    3436        ../Descriptors/unittests/AtomDescriptorUnitTest.hpp
    3537AtomDescriptorUnitTest_LDADD = ${DESCRIPTORLIBS}
    3638
    37 MoleculeDescriptorTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     39MoleculeDescriptorTest_SOURCES = \
    3840        ../Descriptors/unittests/MoleculeDescriptorUnitTest.cpp \
    3941        ../Descriptors/unittests/MoleculeDescriptorUnitTest.hpp

  • src/Element/unittests/Makefile.am

    r4c9101 ra91710  
    2222
    2323ELEMENTLIBS = \
     24        libUnitTest.la \
     25        ../libMolecuilder.la \
    2426        ../libMolecuilderElement.la \
    2527        ../libMolecuilderHelpers.la \
     28        $(BOOST_SYSTEM_LDFLAGS) $(BOOST_SYSTEM_LIBS) \
    2629        $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
    2730        ${CodePatterns_LIBS}
    2831
    29 ElementUnitTest_SOURCES =   $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     32ElementUnitTest_SOURCES = \
    3033  ../Element/unittests/ElementUnitTest.cpp \
    3134  ../Element/unittests/ElementUnitTest.hpp
    3235ElementUnitTest_LDADD = $(ELEMENTLIBS)
    3336
    34 IonUnitTest_SOURCES =   $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     37IonUnitTest_SOURCES = \
    3538  ../Element/unittests/IonUnitTest.cpp \
    3639  ../Element/unittests/IonUnitTest.hpp
    3740IonUnitTest_LDADD = $(ELEMENTLIBS)
    3841
    39 PeriodentafelUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     42PeriodentafelUnitTest_SOURCES = \
    4043        ../Element/unittests/PeriodentafelUnitTest.cpp \
    4144        ../Element/unittests/PeriodentafelUnitTest.hpp

  • src/Filling/unittests/Makefile.am

    r4c9101 ra91710  
    3434
    3535FILLINGLIBS = \
     36        libUnitTest.la \
     37        ../libMolecuilder.la \
    3638        ../libMolecuilderFilling.la \
    37         ../libMolecuilderUI.la \
    38         ../libMolecuilder.la
     39        ../libMolecuilderShapes.la \
     40        ../libMolecuilderUI.la
    3941if CONDJOBMARKET
    4042FILLINGLIBS += \
    … …  
    4648        $(BOOST_LIB)
    4749
    48 ClusterUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     50ClusterUnitTest_SOURCES = \
    4951        ../Filling/unittests/ClusterUnitTest.cpp \
    5052        ../Filling/unittests/ClusterUnitTest.hpp
    5153ClusterUnitTest_LDADD = $(FILLINGLIBS)
    5254
    53 FillerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     55FillerUnitTest_SOURCES = \
    5456        ../Filling/unittests/FillerUnitTest.cpp \
    5557        ../Filling/unittests/FillerUnitTest.hpp
    5658FillerUnitTest_LDADD = $(FILLINGLIBS)
    5759
    58 IsInsideDomain_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     60IsInsideDomain_FillPredicateUnitTest_SOURCES = \
    5961        ../Filling/unittests/IsInsideDomain_FillPredicateUnitTest.cpp \
    6062        ../Filling/unittests/IsInsideDomain_FillPredicateUnitTest.hpp
    6163IsInsideDomain_FillPredicateUnitTest_LDADD = $(FILLINGLIBS)
    6264
    63 IsInsideSurface_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     65IsInsideSurface_FillPredicateUnitTest_SOURCES = \
    6466        ../Filling/unittests/IsInsideSurface_FillPredicateUnitTest.cpp \
    6567        ../Filling/unittests/IsInsideSurface_FillPredicateUnitTest.hpp
    6668IsInsideSurface_FillPredicateUnitTest_LDADD = $(FILLINGLIBS)
    6769
    68 IsValidInDomain_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     70IsValidInDomain_FillPredicateUnitTest_SOURCES = \
    6971        ../Filling/unittests/IsValidInDomain_FillPredicateUnitTest.cpp \
    7072        ../Filling/unittests/IsValidInDomain_FillPredicateUnitTest.hpp
    7173IsValidInDomain_FillPredicateUnitTest_LDADD = $(FILLINGLIBS)
    7274
    73 IsVoidNode_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     75IsVoidNode_FillPredicateUnitTest_SOURCES = \
    7476        ../Filling/unittests/IsVoidNode_FillPredicateUnitTest.cpp \
    7577        ../Filling/unittests/IsVoidNode_FillPredicateUnitTest.hpp
    7678IsVoidNode_FillPredicateUnitTest_LDADD = $(FILLINGLIBS)
    7779
    78 Ops_FillPredicateUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     80Ops_FillPredicateUnitTest_SOURCES = \
    7981        ../Filling/unittests/Ops_FillPredicateUnitTest.cpp \
    8082        ../Filling/unittests/Ops_FillPredicateUnitTest.hpp

  • src/Fragmentation/Automation/MPQCCommandFragmentController.cpp

    r4c9101 ra91710  
    7474//    job->DoValenceOnly = _DoValenceOnly;
    7575#ifndef HAVE_JOBMARKET
    76     job->setId(getAvailableId());
     76    JobId_t id = getAvailableId();
     77    if (id == (JobId_t)JobId::IllegalJob) {
     78      queue.clear();
     79      break;
     80    }
     81    job->setId(id);
    7782    if (!_executable.empty())
    7883      job->setCommand(_executable);

  • src/Fragmentation/Automation/MPQCFragmentController.cpp

    r4c9101 ra91710  
    6767    job->DoValenceOnly = _DoValenceOnly;
    6868    JobId_t id = getAvailableId();
    69     if (id == FragmentJob::IllegalJob) {
     69    if (id == (JobId_t)JobId::IllegalJob) {
    7070      status = false;
    7171      break;
    … …  
    7474  }
    7575  // add the jobs
    76   addJobs(newjobs);
     76  if (status)
     77    addJobs(newjobs);
    7778  status &= (newjobs.size() != 0);
    7879

  • src/Fragmentation/Automation/Makefile.am

    r4c9101 ra91710  
    4040noinst_LTLIBRARIES += libMolecuilderFragmentationAutomation.la
    4141libMolecuilderFragmentationAutomation_la_includedir = $(includedir)/MoleCuilder/
    42 libMolecuilderFragmentationAutomation_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS)
     42libMolecuilderFragmentationAutomation_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS)
    4343libMolecuilderFragmentationAutomation_la_LDFLAGS = -ldl ${BOOST_LDFLAGS}
    4444libMolecuilderFragmentationAutomation_la_LIBADD = \

  • src/Fragmentation/Automation/SpecificFragmentController_ReceiveResultContainer_impl.hpp

    r4c9101 ra91710  
    3232  // convert
    3333  std::vector<T> fragmentData;
    34   ConvertFragmentResultTo(fragmentresults, fragmentData);
     34  SpecificFragmentController::ReceiveResultContainer<T>::ConvertFragmentResultTo(
     35    fragmentresults,
     36    fragmentData);
    3537
    3638  // insert into map
    37   insertResults(fragmentresults, fragmentData);
     39  SpecificFragmentController::ReceiveResultContainer<T>::insertResults(
     40    fragmentresults,
     41    fragmentData);
    3842
    3943  return fragmentData.size();

  • src/Fragmentation/Exporters/unittests/Makefile.am

    r4c9101 ra91710  
    2222
    2323FRAGMENTATIONEXPORTERSLIBS = \
     24        libUnitTest.la \
     25        ../libMolecuilder.la \
    2426        ../libMolecuilderFragmentation.la \
    2527        ${CodePatterns_LIBS} \
    2628        $(BOOST_LIB)
    2729
    28 HydrogenPoolUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     30HydrogenPoolUnitTest_SOURCES = \
    2931        ../Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.cpp \
    3032        ../Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.hpp
    … …  
    3335        ${FRAGMENTATIONEXPORTERSLIBS}
    3436       
    35 SaturatedFragmentUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     37SaturatedFragmentUnitTest_SOURCES = \
    3638        ../Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp \
    3739        ../Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.hpp
    … …  
    4143        ${FRAGMENTATIONEXPORTERSLIBS}
    4244
    43 SaturationDistanceMaximizerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     45SaturationDistanceMaximizerUnitTest_SOURCES = \
    4446        ../Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.cpp \
    4547        ../Fragmentation/Exporters/unittests/SaturationDistanceMaximizerUnitTest.hpp \

  • src/Fragmentation/Homology/unittests/Makefile.am

    r4c9101 ra91710  
    2525
    2626FRAGMENTATIONHOMOLOGYLIBS = \
     27        libUnitTest.la \
     28        ../libMolecuilder.la \
    2729        ../libMolecuilderFragmentationSetValues.la \
    2830        ../libMolecuilderFragmentation.la \
    … …  
    3335        $(BOOST_LIB)
    3436
    35 FragmentEdgeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     37FragmentEdgeUnitTest_SOURCES = \
    3638        ../Fragmentation/Homology/unittests/FragmentEdgeUnitTest.cpp \
    3739        ../Fragmentation/Homology/unittests/FragmentEdgeUnitTest.hpp
    3840FragmentEdgeUnitTest_LDADD = ${FRAGMENTATIONHOMOLOGYLIBS}
    3941
    40 FragmentNodeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     42FragmentNodeUnitTest_SOURCES = \
    4143        ../Fragmentation/Homology/unittests/FragmentNodeUnitTest.cpp \
    4244        ../Fragmentation/Homology/unittests/FragmentNodeUnitTest.hpp
    4345FragmentNodeUnitTest_LDADD = ${FRAGMENTATIONHOMOLOGYLIBS}
    4446       
    45 HomologyContainerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     47HomologyContainerUnitTest_SOURCES = \
    4648        ../Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp \
    4749        ../Fragmentation/Homology/unittests/HomologyContainerUnitTest.hpp \
    … …  
    5456        $(BOOST_LIB)
    5557
    56 HomologyGraphUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     58HomologyGraphUnitTest_SOURCES = \
    5759        ../Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp \
    5860        ../Fragmentation/Homology/unittests/HomologyGraphUnitTest.hpp

  • src/Fragmentation/Interfragmenter.cpp

    r4c9101 ra91710  
    136136    // create a lookup specific to this fragment
    137137    atomkeyset_t fragmentmap;
    138     for (candidates_t::const_iterator iter = candidates.begin();
    139         iter != candidates.end(); ++iter) {
    140       const atom * _atom = *iter;
     138    for (candidates_t::const_iterator candidateiter = candidates.begin();
     139        candidateiter != candidates.end(); ++candidateiter) {
     140      const atom * _atom = *candidateiter;
    141141      atomkeyset_t::const_iterator iter = atomkeyset.find(_atom);
    142142      ASSERT( iter != atomkeyset.end(),
    … …  
    153153      const atom *_atom = *candidateiter;
    154154      LOG(3, "DEBUG: Current candidate is " << *_atom << ".");
    155       atomkeyset_t::iterator iter = fragmentmap.find(_atom);
    156       ASSERT( iter != fragmentmap.end(),
     155      atomkeyset_t::iterator finditer = fragmentmap.find(_atom);
     156      ASSERT( finditer != fragmentmap.end(),
    157157          "Interfragmenter::operator() - could not find atom "
    158158          +toString(_atom->getId())+" in fragment specific lookup.");
    159       keysets_t &othersets = iter->second;
     159      keysets_t &othersets = finditer->second;
    160160      keysets_t::iterator otheriter = othersets.begin();
    161161      while (otheriter != othersets.end()) {

  • src/Fragmentation/Summation/Containers/Makefile.am

    r4c9101 ra91710  
    4141noinst_LTLIBRARIES += libMolecuilderFragmentationContainers.la
    4242libMolecuilderFragmentationContainers_la_includedir = $(includedir)/MoleCuilder/
    43 libMolecuilderFragmentationContainers_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS)
     43libMolecuilderFragmentationContainers_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS)
    4444libMolecuilderFragmentationContainers_la_LDFLAGS = -ldl ${BOOST_LDFLAGS}
    4545libMolecuilderFragmentationContainers_la_LIBADD = \

  • src/Fragmentation/Summation/Containers/unittests/Makefile.am

    r4c9101 ra91710  
    1717
    1818FRAGMENTATIONCONTAINERLIBS = \
     19  libUnitTest.la \
     20  ../libMolecuilder.la \
    1921  ../libMolecuilderFragmentationSummation.la \
    2022  $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS) \
    … …  
    2426
    2527MPQCDataUnitTest_LDFLAGS = ${CodePatterns_LIBS} $(CPPUNIT_LIBS) -ldl
    26 MPQCDataUnitTest_CPPFLAGS = ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS}
    27 MPQCDataUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     28MPQCDataUnitTest_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS}
     29MPQCDataUnitTest_SOURCES = \
    2830  ../Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp \
    2931  ../Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.hpp

  • src/Fragmentation/Summation/Converter/Makefile.am

    r4c9101 ra91710  
    1010noinst_LTLIBRARIES += libMolecuilderFragmentationConverter.la
    1111libMolecuilderFragmentationConverter_la_includedir = $(includedir)/MoleCuilder/
    12 libMolecuilderFragmentationConverter_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     12libMolecuilderFragmentationConverter_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    1313libMolecuilderFragmentationConverter_la_LDFLAGS = -ldl ${BOOST_LDFLAGS}
    1414libMolecuilderFragmentationConverter_la_LIBADD = \

  • src/Fragmentation/Summation/Makefile.am

    r4c9101 ra91710  
    3434lib_LTLIBRARIES += libMolecuilderFragmentationSummation.la
    3535libMolecuilderFragmentationSummation_la_includedir = $(includedir)/MoleCuilder/
    36 libMolecuilderFragmentationSummation_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     36libMolecuilderFragmentationSummation_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    3737libMolecuilderFragmentationSummation_la_LDFLAGS = -ldl \
    3838        $(BOOST_SERIALIZATION_LDFLAGS) \

  • src/Fragmentation/Summation/SetValues/Makefile.am

    r4c9101 ra91710  
    2222noinst_LTLIBRARIES += libMolecuilderFragmentationSetValues.la
    2323libMolecuilderFragmentationSetValues_la_includedir = $(includedir)/MoleCuilder/
    24 libMolecuilderFragmentationSetValues_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     24libMolecuilderFragmentationSetValues_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    2525libMolecuilderFragmentationSetValues_la_LDFLAGS = -ldl ${BOOST_LDFLAGS}
    2626libMolecuilderFragmentationSetValues_la_LIBADD = \

  • src/Fragmentation/Summation/SetValues/unittests/Makefile.am

    r4c9101 ra91710  
    3131
    3232FRAGMENTATIONSETVALUESLIBS = \
     33        libUnitTest.la \
     34        ../libMolecuilder.la \
    3335        ../libMolecuilderFragmentationSetValues.la \
    3436        ${CodePatterns_LIBS} \
    3537        $(BOOST_LIB)
    3638
    37 EigenvaluesUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     39EigenvaluesUnitTest_SOURCES = \
    3840        ../Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.cpp \
    3941        ../Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.hpp
    … …  
    4244        $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS)
    4345
    44 FragmentUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     46FragmentUnitTest_SOURCES = \
    4547        ../Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp \
    4648        ../Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.hpp
    … …  
    4951        $(BOOST_SERIALIZATION_LDFLAGS) $(BOOST_SERIALIZATION_LIBS)
    5052
    51 HistogramUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     53HistogramUnitTest_SOURCES = \
    5254        ../Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp \
    5355        ../Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.hpp
    5456HistogramUnitTest_LDADD = ${FRAGMENTATIONSETVALUESLIBS}
    5557
    56 IndexedVectorsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     58IndexedVectorsUnitTest_SOURCES = \
    5759        ../Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp \
    5860        ../Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.hpp
    5961IndexedVectorsUnitTest_LDADD = ${FRAGMENTATIONSETVALUESLIBS}
    6062
    61 SamplingGridPropertiesUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     63SamplingGridPropertiesUnitTest_SOURCES = \
    6264        ../Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp \
    6365        ../Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp
    6466SamplingGridPropertiesUnitTest_LDADD = ${FRAGMENTATIONSETVALUESLIBS}
    6567
    66 SamplingGridUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     68SamplingGridUnitTest_SOURCES = \
    6769        ../Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp \
    6870        ../Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp

  • src/Fragmentation/Summation/unittests/Makefile.am

    r4c9101 ra91710  
    3434
    3535FRAGMENTATIONSUMMATIONLIBS = \
     36        libUnitTest.la \
     37        ../libMolecuilder.la \
    3638        ../libMolecuilderFragmentationSummation.la \
    3739        ${CodePatterns_LIBS} \
    … …  
    3941
    4042
    41 IndexSetUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     43IndexSetUnitTest_SOURCES = \
    4244        ../Fragmentation/Summation/unittests/IndexSetUnitTest.cpp \
    4345        ../Fragmentation/Summation/unittests/IndexSetUnitTest.hpp
    4446IndexSetUnitTest_LDADD = ${FRAGMENTATIONSUMMATIONLIBS}
    4547
    46 IndexSetContainerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     48IndexSetContainerUnitTest_SOURCES = \
    4749        ../Fragmentation/Summation/unittests/IndexSetContainerUnitTest.cpp \
    4850        ../Fragmentation/Summation/unittests/IndexSetContainerUnitTest.hpp
    … …  
    5355        ${FRAGMENTATIONSUMMATIONLIBS}
    5456
    55 OrthogonalSummationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     57OrthogonalSummationUnitTest_SOURCES = \
    5658        ../Fragmentation/Summation/unittests/OrthogonalSummationUnitTest.cpp \
    5759        ../Fragmentation/Summation/unittests/OrthogonalSummationUnitTest.hpp \
    … …  
    6062OrthogonalSummationUnitTest_LDADD = ${FRAGMENTATIONSUMMATIONLIBS}
    6163
    62 SetValueUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     64SetValueUnitTest_SOURCES = \
    6365        ../Fragmentation/Summation/unittests/SetValueUnitTest.cpp \
    6466        ../Fragmentation/Summation/unittests/SetValueUnitTest.hpp \
    … …  
    6769SetValueUnitTest_LDADD = ${FRAGMENTATIONSUMMATIONLIBS}
    6870
    69 SetValueMapUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     71SetValueMapUnitTest_SOURCES = \
    7072        ../Fragmentation/Summation/unittests/SetValueMapUnitTest.cpp \
    7173        ../Fragmentation/Summation/unittests/SetValueMapUnitTest.hpp
    7274SetValueMapUnitTest_LDADD = ${FRAGMENTATIONSUMMATIONLIBS}
    7375
    74 SubsetMapUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     76SubsetMapUnitTest_SOURCES = \
    7577        ../Fragmentation/Summation/unittests/SubsetMapUnitTest.cpp \
    7678        ../Fragmentation/Summation/unittests/SubsetMapUnitTest.hpp
    7779SubsetMapUnitTest_LDADD = ${FRAGMENTATIONSUMMATIONLIBS}
    7880
    79 SummationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     81SummationUnitTest_SOURCES = \
    8082        ../Fragmentation/Summation/unittests/SummationUnitTest.cpp \
    8183        ../Fragmentation/Summation/unittests/SummationUnitTest.hpp \

  • src/Fragmentation/unittests/Makefile.am

    r4c9101 ra91710  
    1919
    2020FRAGMENTATIONLIBS = \
     21        libUnitTest.la \
     22        ../libMolecuilder.la \
    2123        ../libMolecuilderFragmentation.la \
    2224        ../libMolecuilderFragmentation_KeysetsContainer.la \
    … …  
    2628
    2729
    28 KeySetsContainerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     30KeySetsContainerUnitTest_SOURCES = \
    2931        ../Fragmentation/unittests/KeySetsContainerUnitTest.cpp \
    3032        ../Fragmentation/unittests/KeySetsContainerUnitTest.hpp
    3133KeySetsContainerUnitTest_LDADD = ${FRAGMENTATIONLIBS}
    3234
    33 MatrixContainerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     35MatrixContainerUnitTest_SOURCES = \
    3436        ../Fragmentation/unittests/MatrixContainerUnitTest.cpp \
    3537        ../Fragmentation/unittests/MatrixContainerUnitTest.hpp

  • src/FunctionApproximation/unittests/Makefile.am

    r4c9101 ra91710  
    1919
    2020FUNCTIONAPPROXIMATIONLIBS = \
     21        libUnitTest.la \
     22        ../libMolecuilder.la \
    2123        ../libMolecuilderFunctionApproximation.la \
    2224        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    … …  
    2527        $(BOOST_LIB)
    2628
    27 ExtractorsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     29ExtractorsUnitTest_SOURCES = \
    2830        ../FunctionApproximation/unittests/ExtractorsUnitTest.cpp \
    2931        ../FunctionApproximation/unittests/ExtractorsUnitTest.hpp
    … …  
    3234        ${FUNCTIONAPPROXIMATIONLIBS}
    3335
    34 FunctionArgumentUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     36FunctionArgumentUnitTest_SOURCES = \
    3537        ../FunctionApproximation/unittests/FunctionArgumentUnitTest.cpp \
    3638        ../FunctionApproximation/unittests/FunctionArgumentUnitTest.hpp

  • src/Graph/unittests/Makefile.am

    r4c9101 ra91710  
    2020
    2121GRAPHLIBS = \
     22        libUnitTest.la \
     23        ../libMolecuilder.la \
    2224        ../libMolecuilderUI.la \
    2325        ../libMolecuilderGraph.la
    … …  
    3234
    3335
    34 AdjacencyListUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     36AdjacencyListUnitTest_SOURCES = \
    3537        ../Graph/unittests/AdjacencyListUnitTest.cpp \
    3638        ../Graph/unittests/AdjacencyListUnitTest.hpp
    3739AdjacencyListUnitTest_LDADD = ${ALLLIBS}
    3840
    39 BondGraphUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     41BondGraphUnitTest_SOURCES = \
    4042        ../Graph/unittests/BondGraphUnitTest.cpp \
    4143        ../Graph/unittests/BondGraphUnitTest.hpp

  • src/Jobs/Makefile.am

    r4c9101 ra91710  
    5656libMolecuilderJobs_la_includedir = $(includedir)/MoleCuilder/
    5757nobase_libMolecuilderJobs_la_include_HEADERS = $(JOBSHEADER)
    58 libMolecuilderJobs_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS} -Dvmg_float=double -Dvmg_int=int $(VMG_CFLAGS)
     58libMolecuilderJobs_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS} -Dvmg_float=double -Dvmg_int=int $(VMG_CFLAGS)
    5959libMolecuilderJobs_la_LDFLAGS = $(AM_LDFLAGS) \
    6060  $(BOOST_IOSTREAMS_LDFLAGS) \

  • src/Jobs/unittests/Makefile.am

    r4c9101 ra91710  
    1717
    1818JOBSLIBS = \
     19        libUnitTest.la \
     20        ../libMolecuilder.la \
    1921        ../libMolecuilderJobs.la \
    2022        ../libMolecuilderFragmentationContainers.la \
    … …  
    2729
    2830MPQCCommandJobUnitTest_LDFLAGS = ${CodePatterns_LIBS} $(CPPUNIT_LIBS) -ldl
    29 MPQCCommandJobUnitTest_CPPFLAGS = ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS}
    30 MPQCCommandJobUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     31MPQCCommandJobUnitTest_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS} ${JobMarket_CFLAGS}
     32MPQCCommandJobUnitTest_SOURCES = \
    3133  ../Jobs/unittests/MPQCCommandJobUnitTest.cpp \
    3234  ../Jobs/unittests/MPQCCommandJobUnitTest.hpp

  • src/LinkedCell/unittests/Makefile.am

    r4c9101 ra91710  
    2929
    3030LINKEDCELLLIBS = \
     31        libUnitTest.la \
     32        ../libMolecuilder.la \
    3133        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    3234        ${CodePatterns_LIBS} \
    3335        $(BOOST_LIB)
    3436
    35 linkedcellUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     37linkedcellUnitTest_SOURCES = \
    3638        ../LinkedCell/unittests/linkedcellUnitTest.cpp \
    3739        ../LinkedCell/unittests/linkedcellUnitTest.hpp
    … …  
    4648        $(LINKEDCELLLIBS)
    4749
    48 LinkedCellUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     50LinkedCellUnitTest_SOURCES = \
    4951        ../LinkedCell/unittests/LinkedCellUnitTest.cpp \
    5052        ../LinkedCell/unittests/LinkedCellUnitTest.hpp \
    … …  
    5456        $(LINKEDCELLLIBS)
    5557
    56 LinkedCell_ControllerUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     58LinkedCell_ControllerUnitTest_SOURCES = \
    5759        ../LinkedCell/unittests/LinkedCell_ControllerUnitTest.cpp \
    5860        ../LinkedCell/unittests/LinkedCell_ControllerUnitTest.hpp \
    … …  
    6466        ../LinkedCell/unittests/stubs/WorldTimeStub.cpp \
    6567        stubs/WorldStub.cpp \
    66         ../LinkedCell/PointCloudAdaptor.hpp \
    67         ../Box_BoundaryConditions.cpp \
    68         ../Box_BoundaryConditions.hpp
     68        ../LinkedCell/PointCloudAdaptor.hpp
    6969LinkedCell_ControllerUnitTest_LDADD = \
    70         ../libMolecuilderLinkedCell.la \
     70        ../libMolecuilderUI.la \
     71        ../libMolecuilder.la
     72if CONDJOBMARKET
     73LinkedCell_ControllerUnitTest_LDADD += \
     74        ../libMolecuilderJobs.la
     75endif
     76LinkedCell_ControllerUnitTest_LDADD += \
    7177        $(LINKEDCELLLIBS)
    7278
    73 LinkedCell_ModelUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     79LinkedCell_ModelUnitTest_SOURCES = \
    7480        ../LinkedCell/unittests/LinkedCell_ModelUnitTest.cpp \
    7581        ../LinkedCell/unittests/LinkedCell_ModelUnitTest.hpp \
    … …  
    8591        $(LINKEDCELLLIBS)
    8692
    87 LinkedCell_ViewUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     93LinkedCell_ViewUnitTest_SOURCES = \
    8894        ../LinkedCell/unittests/LinkedCell_ViewUnitTest.cpp \
    8995        ../LinkedCell/unittests/LinkedCell_ViewUnitTest.hpp \

  • src/Makefile.am

    r4c9101 ra91710  
    1010EXTRA_DIST =
    1111
    12 include Actions/Makefile.am
    13 include Analysis/Makefile.am
    14 include Atom/Makefile.am
    15 include Element/Makefile.am
    16 include Filling/Makefile.am
    17 include Fragmentation/Makefile.am
    18 include Fragmentation/Automation/Makefile.am
    19 include Fragmentation/Summation/Containers/Makefile.am
    20 include Fragmentation/Summation/Converter/Makefile.am
    21 include Fragmentation/Summation/Makefile.am
    22 include Fragmentation/Summation/SetValues/Makefile.am
    23 include FunctionApproximation/Makefile.am
    24 include Graph/Makefile.am
     12# libMolecuilder.la requires the libraries listed below
     13
    2514include Helpers/Makefile.am
    26 include Jobs/Makefile.am
    27 
    28 if CONDPYTHON
    29 include Python/Makefile.am
    30 endif
    31 
    32 include LinkedCell/Makefile.am
    33 include Parameters/Makefile.am
    34 include Parser/Makefile.am
    35 include Potentials/Makefile.am
    36 include RandomNumbers/Makefile.am
    3715include Shapes/Makefile.am
    3816include Tesselation/Makefile.am
    39 include UIElements/Makefile.am
     17
     18# then comes the library itself
    4019
    4120AM_LDFLAGS = -ldl ${BOOST_LDFLAGS} ${CodePatterns_LDFLAGS}
    42 AM_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     21AM_CPPFLAGS = \
     22        -I$(top_srcdir)/src/unittests \
     23        -I$(top_srcdir)/src/Actions \
     24        -I$(top_srcdir)/src/UIElements \
     25        -I$(top_srcdir)/LinearAlgebra/src \
     26        ${BOOST_CPPFLAGS} \
     27        ${CodePatterns_CFLAGS}
     28
    4329
    4430BONDSOURCE = \
    … …  
    195181  WorldTime.hpp
    196182
    197 noinst_LTLIBRARIES += libMolecuilder.la
     183lib_LTLIBRARIES += libMolecuilder.la
    198184libMolecuilder_la_includedir = $(includedir)/MoleCuilder/
    199185libMolecuilder_la_LDFLAGS = \
    … …  
    205191        libMolecuilderTesselation.la \
    206192        libMolecuilderShapes.la \
     193        libMolecuilderHelpers.la \
    207194        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    208195        ${CodePatterns_LIBS} \
    … …  
    228215## library file (.so).  The library ABI version is defined in configure.ac, so
    229216## that all version information is kept in one place.
    230 #libMolecuilder_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)
     217libMolecuilder_la_LDFLAGS += -version-info $(MOLECUILDER_SO_VERSION)
    231218
    232219## The generated configuration header is installed in its own subdirectory of
    … …  
    251238pkgconfig_DATA = $(top_builddir)/MoleCuilder.pc
    252239
    253 
    254 INCLUDES = \
    255         -I$(top_srcdir)/src/unittests \
    256         -I$(top_srcdir)/src/Actions \
    257         -I$(top_srcdir)/src/UIElements \
    258         -I$(top_srcdir)/LinearAlgebra/src
     240# then we compile the remainder of all other libraries, especially
     241# libMolecuilderUI.la, which requires libMolecuilder.la on install
     242
     243include Actions/Makefile.am
     244include Analysis/Makefile.am
     245include Atom/Makefile.am
     246include Element/Makefile.am
     247include Filling/Makefile.am
     248include Fragmentation/Makefile.am
     249include Fragmentation/Automation/Makefile.am
     250include Fragmentation/Summation/Containers/Makefile.am
     251include Fragmentation/Summation/Converter/Makefile.am
     252include Fragmentation/Summation/Makefile.am
     253include Fragmentation/Summation/SetValues/Makefile.am
     254include FunctionApproximation/Makefile.am
     255include Graph/Makefile.am
     256include Jobs/Makefile.am
     257
     258if CONDPYTHON
     259include Python/Makefile.am
     260endif
     261
     262include LinkedCell/Makefile.am
     263include Parameters/Makefile.am
     264include Parser/Makefile.am
     265include Potentials/Makefile.am
     266include RandomNumbers/Makefile.am
     267include UIElements/Makefile.am
    259268
    260269bin_PROGRAMS += molecuilder
    … …  
    283292        Actions/GlobalListOfActions.hpp \
    284293        Actions/ActionHistory.hpp
    285 pyMoleCuilder_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS) -I$(PYTHON_INCLUDE_DIR)
     294pyMoleCuilder_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} $(JobMarket_CFLAGS) -I$(PYTHON_INCLUDE_DIR)
    286295pyMoleCuilder_la_LDFLAGS = -module -avoid-version -shared $(BOOST_PYTHON_LDFLAGS)
    287296pyMoleCuilder_la_LIBADD = \
    … …  
    299308molecuilder_LDFLAGS = \
    300309        $(AM_LDFLAGS) \
     310        $(CodePatterns_LDFLAGS) \
    301311        $(BOOST_FILESYSTEM_LDFLAGS) \
    302312        $(BOOST_PROGRAM_OPTIONS_LDFLAGS) \
    … …  
    307317        builder.cpp \
    308318        builder_init.cpp \
    309         builder_init.hpp
     319        builder_init.hpp \
     320        Python/PythonScripting.hpp
    310321molecuilder_LDADD = \
     322        libMolecuilder.la \
    311323        libMolecuilderUI.la
    312324molecuilder_LDADD += \
    313         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    314325        ${CodePatterns_LIBS} \
    315326        $(BOOST_THREAD_LIBS) \
    … …  
    347358        $(BOOST_THREAD_LDFLAGS)
    348359molecuildergui_LDADD = \
     360        libMolecuilder.la \
    349361        libMolecuilderQtUI.la \
    350362        libMolecuilderUI.la
    351363molecuildergui_LDADD += \
    352         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    353364        ${CodePatterns_LIBS} \
    354365        $(BOOST_THREAD_LIBS) \

  • src/Parameters/Makefile.am

    r4c9101 ra91710  
    3333        Parameters/Parameter_impl.hpp \
    3434        Parameters/ParameterInterface.hpp \
     35        Parameters/StreamOperators.hpp \
    3536        Parameters/Validators/DiscreteValidator.hpp \
    3637        Parameters/Validators/DiscreteValidator_impl.hpp \

  • src/Parameters/unittests/Makefile.am

    r4c9101 ra91710  
    2929
    3030PARAMETERSLIBS = \
     31        libUnitTest.la \
     32        ../libMolecuilder.la \
    3133        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    3234        ${CodePatterns_LIBS} \
    … …  
    3436
    3537
    36 ContinuousValueTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     38ContinuousValueTest_SOURCES = \
    3739        ../Parameters/unittests/ContinuousValueTest.cpp \
    3840        ../Parameters/unittests/ContinuousValueTest.hpp \
    … …  
    4749        $(PARAMETERSLIBS)
    4850 
    49 ContinuousParameterTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     51ContinuousParameterTest_SOURCES = \
    5052        ../Parameters/unittests/ContinuousParameterTest.cpp \
    5153        ../Parameters/unittests/ContinuousParameterTest.hpp \
    … …  
    6062        $(PARAMETERSLIBS)
    6163 
    62 DiscreteValueTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     64DiscreteValueTest_SOURCES = \
    6365        ../Parameters/unittests/DiscreteValueTest.cpp \
    6466        ../Parameters/unittests/DiscreteValueTest.hpp \
    … …  
    7476        $(PARAMETERSLIBS)
    7577
    76 DiscreteParameterTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     78DiscreteParameterTest_SOURCES = \
    7779        ../Parameters/unittests/DiscreteParameterTest.cpp \
    7880        ../Parameters/unittests/DiscreteParameterTest.hpp \
    … …  
    9092        $(PARAMETERSLIBS)
    9193
    92 Ops_ValidatorTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     94Ops_ValidatorTest_SOURCES = \
    9395        ../Parameters/unittests/Ops_ValidatorTest.cpp \
    9496        ../Parameters/unittests/Ops_ValidatorTest.hpp \

  • src/Parser/Parameters/unittests/Makefile.am

    r4c9101 ra91710  
    2020
    2121PARSERPARAMETERSLIBS = \
     22        libUnitTest.la \
     23        ../libMolecuilder.la \
    2224        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    2325        ${CodePatterns_LIBS} \
    … …  
    2527
    2628
    27 ParameterStorageUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     29ParameterStorageUnitTest_SOURCES = \
    2830        ../Parser/Parameters/unittests/ParameterStorageUnitTest.cpp \
    29         ../Parser/Parameters/unittests/ParameterStorageUnitTest.hpp \
    30         ../Parser/Parameters/ParameterStorage.cpp \
    31         ../Parser/Parameters/ParameterStorage.hpp \
    32         ../Parameters/Parameter.hpp \
    33         ../Parameters/Validators/DummyValidator.hpp \
    34         ../Parameters/Validators/RangeValidator.hpp \
    35         ../Parameters/Validators/RangeValidator_impl.hpp \
    36         ../Parameters/Validators/Validator.hpp \
    37         ../Parameters/Value.hpp \
    38         ../Parameters/Value_impl.hpp \
    39         ../Parameters/ValueInterface.hpp
     31        ../Parser/Parameters/unittests/ParameterStorageUnitTest.hpp
    4032ParameterStorageUnitTest_LDADD = \
    41         $(PARSERPARAMETERSLIBS)
     33        ../libMolecuilderParser.la \
     34        $(PARSERPARAMETERSLIBS)
    4235
    43 StringParameterUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     36StringParameterUnitTest_SOURCES = \
    4437        ../Parser/Parameters/unittests/StringParameterUnitTest.cpp \
    45         ../Parser/Parameters/unittests/StringParameterUnitTest.hpp \
    46         ../Parameters/StreamOperators.hpp \
    47         ../Parameters/Validators/DiscreteValidator.hpp \
    48         ../Parameters/Validators/DiscreteValidator_impl.hpp \
    49         ../Parameters/Validators/DummyValidator.hpp \
    50         ../Parameters/Validators/RangeValidator.hpp \
    51         ../Parameters/Validators/RangeValidator_impl.hpp \
    52         ../Parameters/Validators/Validator.hpp \
    53         ../Parameters/Value.hpp \
    54         ../Parameters/Value_impl.hpp \
    55         ../Parameters/Value_string.hpp \
    56         ../Parameters/ValueInterface.hpp
     38        ../Parser/Parameters/unittests/StringParameterUnitTest.hpp
    5739StringParameterUnitTest_LDADD = \
    5840        ../libMolecuilderParameters.la \

  • src/Parser/unittests/Makefile.am

    r4c9101 ra91710  
    3939
    4040PARSERLIBS = \
     41        libUnitTest.la \
     42        ../libMolecuilder.la \
    4143        ../libMolecuilderUI.la
    4244if CONDJOBMARKET
    … …  
    5052
    5153
    52 ParserMpqcUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     54ParserMpqcUnitTest_SOURCES = \
    5355        ../Parser/unittests/ParserMpqcUnitTest.cpp \
    5456        ../Parser/unittests/ParserMpqcUnitTest.hpp
    5557ParserMpqcUnitTest_LDADD = ${PARSERLIBS}
    5658
    57 ParserPcpUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     59ParserPcpUnitTest_SOURCES = \
    5860        ../Parser/unittests/ParserPcpUnitTest.cpp \
    5961        ../Parser/unittests/ParserPcpUnitTest.hpp
    6062ParserPcpUnitTest_LDADD = ${PARSERLIBS}
    6163
    62 ParserPdbUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     64ParserPdbUnitTest_SOURCES = \
    6365        ../Parser/unittests/ParserPdbUnitTest.cpp \
    6466        ../Parser/unittests/ParserPdbUnitTest.hpp
    6567ParserPdbUnitTest_LDADD = ${PARSERLIBS}
    6668
    67 ParserPsi3UnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     69ParserPsi3UnitTest_SOURCES = \
    6870        ../Parser/unittests/ParserPsi3UnitTest.cpp \
    6971        ../Parser/unittests/ParserPsi3UnitTest.hpp
    7072ParserPsi3UnitTest_LDADD = ${PARSERLIBS}
    7173
    72 ParserTremoloUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     74ParserTremoloUnitTest_SOURCES = \
    7375        ../Parser/unittests/ParserTremoloUnitTest.cpp \
    7476        ../Parser/unittests/ParserTremoloUnitTest.hpp
    7577ParserTremoloUnitTest_LDADD = ${PARSERLIBS}
    7678
    77 ParserTremolo_ElementKeysUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     79ParserTremolo_ElementKeysUnitTest_SOURCES = \
    7880        ../Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp \
    7981        ../Parser/unittests/ParserTremolo_ElementKeysUnitTest.hpp
    8082ParserTremolo_ElementKeysUnitTest_LDADD = ${PARSERLIBS}
    8183
    82 ParserXmlUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     84ParserXmlUnitTest_SOURCES = \
    8385        ../Parser/unittests/ParserXmlUnitTest.cpp \
    8486        ../Parser/unittests/ParserXmlUnitTest.hpp
    8587ParserXmlUnitTest_LDADD = ${PARSERLIBS}
    8688
    87 ParserXyzUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     89ParserXyzUnitTest_SOURCES = \
    8890        ../Parser/unittests/ParserXyzUnitTest.cpp \
    8991        ../Parser/unittests/ParserXyzUnitTest.hpp

  • src/Potentials/Specifics/unittests/Makefile.am

    r4c9101 ra91710  
    3737
    3838POTENTIALSSPECIFICSLIBS = \
     39        libUnitTest.la \
     40        ../libMolecuilder.la \
    3941        ../libMolecuilderPotentials.la \
    4042        ../libMolecuilderFragmentation.la \
    … …  
    4850        $(BOOST_LIB)
    4951
    50 ConstantPotentialUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     52ConstantPotentialUnitTest_SOURCES = \
    5153        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp \
    5254        ../Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp
    5355ConstantPotentialUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    5456
    55 FourBodyPotential_ImproperUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     57FourBodyPotential_ImproperUnitTest_SOURCES = \
    5658        ../Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp \
    5759        ../Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.hpp
    5860FourBodyPotential_ImproperUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    5961
    60 FourBodyPotential_TorsionUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     62FourBodyPotential_TorsionUnitTest_SOURCES = \
    6163        ../Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp \
    6264        ../Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.hpp
    6365FourBodyPotential_TorsionUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    6466
    65 ManyBodyPotential_TersoffUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     67ManyBodyPotential_TersoffUnitTest_SOURCES = \
    6668        ../Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp \
    6769        ../Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp
    6870ManyBodyPotential_TersoffUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    6971
    70 PairPotential_HarmonicUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     72PairPotential_HarmonicUnitTest_SOURCES = \
    7173        ../Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp \
    7274        ../Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.hpp
    7375PairPotential_HarmonicUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    7476
    75 PairPotential_LennardJonesUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     77PairPotential_LennardJonesUnitTest_SOURCES = \
    7678        ../Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp \
    7779        ../Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.hpp
    7880PairPotential_LennardJonesUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    7981
    80 PairPotential_MorseUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     82PairPotential_MorseUnitTest_SOURCES = \
    8183        ../Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp \
    8284        ../Potentials/Specifics/unittests/PairPotential_MorseUnitTest.hpp
    8385PairPotential_MorseUnitTest_LDADD = ${POTENTIALSSPECIFICSLIBS}
    8486
    85 ThreeBodyPotential_AngleUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     87ThreeBodyPotential_AngleUnitTest_SOURCES = \
    8688        ../Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp \
    8789        ../Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.hpp

  • src/Potentials/unittests/Makefile.am

    r4c9101 ra91710  
    2222
    2323POTENTIALSLIBS = \
     24        libUnitTest.la \
     25        ../libMolecuilder.la \
    2426        ../libMolecuilderPotentials.la \
    2527        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    … …  
    2830        $(BOOST_LIB)
    2931
    30 CompoundPotentialUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     32CompoundPotentialUnitTest_SOURCES = \
    3133        ../Potentials/unittests/CompoundPotentialUnitTest.cpp \
    3234        ../Potentials/unittests/CompoundPotentialUnitTest.hpp
    3335CompoundPotentialUnitTest_LDADD = \
     36        libUnitTest.la \
    3437        ../libMolecuilderPotentials.la \
    3538        ../libMolecuilderFragmentation.la \
    … …  
    4346        $(BOOST_LIB)
    4447
    45 PartialNucleiChargeFitterUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     48PartialNucleiChargeFitterUnitTest_SOURCES = \
    4649        ../Potentials/unittests/PartialNucleiChargeFitterUnitTest.cpp \
    4750        ../Potentials/unittests/PartialNucleiChargeFitterUnitTest.hpp
    … …  
    5053        ${POTENTIALSLIBS}
    5154
    52 SerializablePotentialUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     55SerializablePotentialUnitTest_SOURCES = \
    5356        ../Potentials/unittests/SerializablePotentialUnitTest.cpp \
    5457        ../Potentials/unittests/SerializablePotentialUnitTest.hpp \

  • src/RandomNumbers/Makefile.am

    r4c9101 ra91710  
    11# PLEASE adhere to the alphabetical ordering in this Makefile!
    22# Also indentation by a single tab
    3 
    4 #INCLUDES = -I$(top_srcdir)/src
    53
    64# Position-Independent Code necessary for shared library
    … …  
    4240
    4341lib_LTLIBRARIES += libMolecuilderRandomNumbers.la
    44 libMolecuilderRandomNumbers_includedir = $(includedir)/MoleCuilder/
    45 nobase_libMolecuilderRandomNumbers_include_HEADERS = ${RANDOMHEADER} ${RANDOMDEFS}
     42libMolecuilderRandomNumbers_la_includedir = $(includedir)/MoleCuilder/
     43libMolecuilderRandomNumbers_la_LIBADD = \
     44        ${CodePatterns_LIBS}
     45nobase_libMolecuilderRandomNumbers_la_include_HEADERS = ${RANDOMHEADER} ${RANDOMDEFS}
    4646
    4747## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"

  • src/RandomNumbers/unittests/Makefile.am

    r4c9101 ra91710  
    11# PLEASE adhere to the alphabetical ordering in this Makefile!
    22# Also indentation by a single tab
    3 
    4 #INCLUDES = -I$(top_srcdir)/src
    53
    64#AM_LDFLAGS = ${CodePatterns_LIBS} $(CPPUNIT_LIBS) -ldl ${BOOST_LDFLAGS}
    … …  
    3028
    3129RANDOMNUMBERLIBS = \
     30        libUnitTest.la \
     31        ../libMolecuilder.la \
    3232        ../libMolecuilderRandomNumbers.la \
    3333        ${CodePatterns_LIBS} \
    3434        $(BOOST_LIB)
    3535
    36 RandomNumberDistributionFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     36RandomNumberDistributionFactoryUnitTest_SOURCES = \
    3737        ../RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.cpp \
    3838        ../RandomNumbers/unittests/RandomNumberDistributionFactoryUnitTest.hpp
    3939RandomNumberDistributionFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS}
    4040
    41 RandomNumberEngineFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     41RandomNumberEngineFactoryUnitTest_SOURCES = \
    4242        ../RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp \
    4343        ../RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.hpp
    4444RandomNumberEngineFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS}
    4545
    46 RandomNumberGeneratorFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     46RandomNumberGeneratorFactoryUnitTest_SOURCES = \
    4747        ../RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp \
    4848        ../RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.hpp
    4949RandomNumberGeneratorFactoryUnitTest_LDADD = ${RANDOMNUMBERLIBS}
    5050
    51 RandomNumberGeneratorUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     51RandomNumberGeneratorUnitTest_SOURCES = \
    5252        ../RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp \
    5353        ../RandomNumbers/unittests/RandomNumberGeneratorUnitTest.hpp

  • src/Shapes/Makefile.am

    r4c9101 ra91710  
    2121lib_LTLIBRARIES += libMolecuilderShapes.la
    2222libMolecuilderShapes_la_includedir = $(includedir)/MoleCuilder/
     23libMolecuilderShapes_la_LIBADD = \
     24        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
     25        ${CodePatterns_LIBS}
    2326nobase_libMolecuilderShapes_la_include_HEADERS = ${SHAPEHEADER}
    2427

  • src/Shapes/unittests/Makefile.am

    r4c9101 ra91710  
    2929
    3030SHAPELIBS = \
    31         ../libMolecuilderShapes.la \
     31        libUnitTest.la \
     32        ../libMolecuilder.la \
     33        ../libMolecuilderUI.la \
    3234        $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    3335        ${CodePatterns_LIBS}
    3436#       $(BOOST_LIB)
    3537
    36 BaseShapesUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     38BaseShapesUnitTest_SOURCES = \
    3739        ../Shapes/unittests/BaseShapesUnitTest.cpp \
    3840        ../Shapes/unittests/BaseShapesUnitTest.hpp \
    3941        ../Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp \
    4042        ../Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp
    41 nodist_BaseShapesUnitTest_SOURCES = \
    42         ../Helpers/defs.hpp \
    43         ../Helpers/defs.cpp
    44 BaseShapesUnitTest_LDADD = $(SHAPELIBS)
     43BaseShapesUnitTest_LDADD = \
     44        ../libMolecuilderShapes.la \
     45        $(SHAPELIBS)
    4546
    46 ShapeFactoryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     47ShapeFactoryUnitTest_SOURCES = \
    4748        ../Shapes/unittests/ShapeFactoryUnitTest.cpp \
    4849        ../Shapes/unittests/ShapeFactoryUnitTest.hpp \
    … …  
    5152        ../Shapes/unittests/stubs/moleculeStub.cpp \
    5253        ../Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp
    53 nodist_ShapeFactoryUnitTest_SOURCES = \
    54         ../Helpers/defs.hpp \
    55         ../Helpers/defs.cpp \
    56         ../Shapes/ShapeFactory.cpp \
    57         ../Shapes/ShapeFactory.hpp
    5854ShapeFactoryUnitTest_LDADD = \
    59         ../libMolecuilderElement.la \
     55        ../libMolecuilderShapes.la \
    6056        $(SHAPELIBS)
    6157
    62 ShapeOpsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     58ShapeOpsUnitTest_SOURCES = \
    6359        ../Shapes/unittests/ShapeOpsUnitTest.cpp \
    6460        ../Shapes/unittests/ShapeOpsUnitTest.hpp \
    6561        ../Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp \
    6662        ../Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp
    67 nodist_ShapeOpsUnitTest_SOURCES = \
    68         ../Helpers/defs.hpp \
    69         ../Helpers/defs.cpp
    70 ShapeOpsUnitTest_LDADD = $(SHAPELIBS)
     63ShapeOpsUnitTest_LDADD = \
     64        ../libMolecuilderShapes.la \
     65        $(SHAPELIBS)
    7166
    72 ShapeRegistryUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     67ShapeRegistryUnitTest_SOURCES = \
    7368        ../Shapes/unittests/ShapeRegistryUnitTest.cpp \
    7469        ../Shapes/unittests/ShapeRegistryUnitTest.hpp \
    7570        ../Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp \
    7671        ../Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp
    77 nodist_ShapeRegistryUnitTest_SOURCES = \
    78         ../Helpers/defs.hpp \
    79         ../Helpers/defs.cpp
    80 ShapeRegistryUnitTest_LDADD = $(SHAPELIBS)
     72ShapeRegistryUnitTest_LDADD = \
     73        ../libMolecuilderShapes.la \
     74        $(SHAPELIBS)
    8175
    82 Shape_HomogeneousPointsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     76Shape_HomogeneousPointsUnitTest_SOURCES = \
    8377        ../Shapes/unittests/Shape_HomogeneousPointsUnitTest.cpp \
    8478        ../Shapes/unittests/Shape_HomogeneousPointsUnitTest.hpp \
    8579        ../Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp \
    8680        ../Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp
    87 nodist_Shape_HomogeneousPointsUnitTest_SOURCES = \
    88         ../Helpers/defs.hpp \
    89         ../Helpers/defs.cpp
    90 Shape_HomogeneousPointsUnitTest_LDADD = $(SHAPELIBS)
     81Shape_HomogeneousPointsUnitTest_LDADD = \
     82        ../libMolecuilderShapes.la \
     83        $(SHAPELIBS)
    9184
    9285

  • src/Tesselation/unittests/Makefile.am

    r4c9101 ra91710  
    2222
    2323TESSELATIONLIBS = \
     24        libUnitTest.la \
     25        ../libMolecuilder.la \
    2426        ../libMolecuilderUI.la \
    2527        ../libMolecuilder.la
    … …  
    3436
    3537
    36 TesselationUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     38TesselationUnitTest_SOURCES = \
    3739        ../Tesselation/unittests/TesselationUnitTest.cpp \
    3840        ../Tesselation/unittests/TesselationUnitTest.hpp
    3941TesselationUnitTest_LDADD = ${TESSELATIONLIBS}
    4042
    41 Tesselation_BoundaryTriangleUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     43Tesselation_BoundaryTriangleUnitTest_SOURCES = \
    4244        ../Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.cpp \
    4345        ../Tesselation/unittests/Tesselation_BoundaryTriangleUnitTest.hpp
    4446Tesselation_BoundaryTriangleUnitTest_LDADD = ${TESSELATIONLIBS}
    4547
    46 Tesselation_InOutsideUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     48Tesselation_InOutsideUnitTest_SOURCES = \
    4749        ../Tesselation/unittests/Tesselation_InsideOutsideUnitTest.cpp \
    4850        ../Tesselation/unittests/Tesselation_InsideOutsideUnitTest.hpp

  • src/UIElements/CommandLineUI/unittests/Makefile.am

    r4c9101 ra91710  
    1515noinst_PROGRAMS += $(UIELEMENTSCOMMANDLINEPARSERTESTS)
    1616
    17 CommandLineParser_ActionRegistry_ConsistencyUnitTest_SOURCES =  $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     17CommandLineParser_ActionRegistry_ConsistencyUnitTest_SOURCES = \
    1818  ../UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.cpp \
    1919  ../UIElements/CommandLineUI/unittests/CommandLineParser_ActionRegistry_ConsistencyUnitTest.hpp
    2020CommandLineParser_ActionRegistry_ConsistencyUnitTest_LDADD = \
     21  libUnitTest.la \
     22  ../libMolecuilder.la \
    2123  ../libMolecuilderUI.la
    2224if CONDJOBMARKET

  • src/UIElements/Makefile.am

    r4c9101 ra91710  
    226226lib_LTLIBRARIES += libMolecuilderUI.la
    227227libMolecuilderUI_la_includedir = $(includedir)/MoleCuilder/
    228 libMolecuilderUI_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
     228libMolecuilderUI_la_CPPFLAGS = $(AM_CPPFLAGS) ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}
    229229if CONDJOBMARKET
    230230libMolecuilderUI_la_CPPFLAGS += ${JobMarket_CFLAGS}
    … …  
    344344
    345345libMolecuilderQtUI_la_includedir = $(includedir)/MoleCuilder/
    346 libMolecuilderQtUI_la_CPPFLAGS = ${QT_CFLAGS} ${GLU_CXXFLAGS} ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}  ${JobMarket_CFLAGS} $(mol_ac_qwt_cxxflags)
     346libMolecuilderQtUI_la_CPPFLAGS = $(AM_CPPFLAGS) ${QT_CFLAGS} ${GLU_CXXFLAGS} ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}  ${JobMarket_CFLAGS} $(mol_ac_qwt_cxxflags)
    347347libMolecuilderQtUI_la_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_RANDOM_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS) $(mol_ac_qwt_ldflags)
    348348

  • src/UIElements/Menu/unittests/Makefile.am

    r4c9101 ra91710  
    1919
    2020MENULIBS = \
     21  libUnitTest.la \
     22  ../libMolecuilder.la \
    2123  ../libMolecuilderUI.la
    2224if CONDJOBMARKET
    … …  
    2931  $(BOOST_LIB)
    3032
    31 MenuDescriptionUnitTest_SOURCES =  $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     33MenuDescriptionUnitTest_SOURCES = \
    3234  ../UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp \
    33   ../UIElements/Menu/unittests/MenuDescriptionUnitTest.hpp \
    34   ../UIElements/Menu/MenuDescription.cpp \
    35   ../UIElements/Menu/MenuDescription.hpp
     35  ../UIElements/Menu/unittests/MenuDescriptionUnitTest.hpp
    3636MenuDescriptionUnitTest_CXXFLAGS = -I$(top_srcdir)/src/UIElements
    3737MenuDescriptionUnitTest_LDADD = $(MENULIBS)
    3838
    39 MenuDescription_ActionRegistry_ConsistencyUnitTest_SOURCES =  $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     39MenuDescription_ActionRegistry_ConsistencyUnitTest_SOURCES = \
    4040  ../UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.cpp \
    4141  ../UIElements/Menu/unittests/MenuDescription_ActionRegistry_ConsistencyUnitTest.hpp

  • src/UIElements/Views/Qt4/Plotting/Makefile.am

    r4c9101 ra91710  
    3737
    3838libMolecuilderQwtUI_la_includedir = $(includedir)/MoleCuilder/
    39 libMolecuilderQwtUI_la_CPPFLAGS = ${QT_CFLAGS} ${GLU_CXXFLAGS} ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}  ${JobMarket_CFLAGS} $(mol_ac_qwt_cxxflags)
     39libMolecuilderQwtUI_la_CPPFLAGS = $(AM_CPPFLAGS) ${QT_CFLAGS} ${GLU_CXXFLAGS} ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS}  ${JobMarket_CFLAGS} $(mol_ac_qwt_cxxflags)
    4040libMolecuilderQwtUI_la_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_RANDOM_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS) $(mol_ac_qwt_ldflags)
    4141

  • src/builder_init.cpp

    r4c9101 ra91710  
    5454#include "CodePatterns/Log.hpp"
    5555
    56 #include "Graph/BondGraph.hpp"
    57 
    58 #include "Parser/ChangeTracker.hpp"
    59 #include "Parser/FormatParserStorage.hpp"
     56//#include "Graph/BondGraph.hpp"
    6057
    6158#include "UIElements/UIFactory.hpp"
    … …  
    6966
    7067#include "version.h"
    71 
    72 #include "World.hpp"
    7368
    7469#include <boost/filesystem.hpp>
    … …  
    116111void initUI(int argc, char **argv)
    117112{
    118   std::string BondGraphFileName("\n");
     113  //std::string BondGraphFileName("\n");
    119114  // Parse command line options and if present create respective UI
    120115  // construct bond graph
    121   if (boost::filesystem::exists(BondGraphFileName)) {
    122     std::ifstream input(BondGraphFileName.c_str());
    123     if ((input.good()) && (World::getInstance().getBondGraph()->LoadBondLengthTable(input))) {
    124       LOG(0, "Bond length table loaded successfully.");
    125     } else {
    126       ELOG(1, "Bond length table loading failed.");
    127     }
    128     input.close();
    129   }
     116  //if (boost::filesystem::exists(BondGraphFileName)) {
     117  //  std::ifstream input(BondGraphFileName.c_str());
     118  //  if ((input.good()) && (World::getInstance().getBondGraph()->LoadBondLengthTable(input))) {
     119  //    LOG(0, "Bond length table loaded successfully.");
     120  //  } else {
     121  //    ELOG(1, "Bond length table loading failed.");
     122  //  }
     123  //  input.close();
     124  //}
    130125
    131126  // if we have python, autoexecute a molecuilder script in current folder

  • src/documentation/install.dox

    r4c9101 ra91710  
    6464 *  -# autotools: autoconf automake autoheader autoconf libtool
    6565 *
     66 *      Under Ubuntu 14.04 the required packages remain the same but the following
     67 *  notes apply:
     68 *  -# boost must be at least 1.50 as there is some bug with recognizing
     69 *     pthreads with the new gcc version.
     70 *  -# no need to compile VTK on your own, just use the VTK-5.8 that comes with
     71 *     this Ubuntu version.
     72 *  -# note that prior to 1.4.7 Ubuntu 14.04 is not supported and requires some
     73 *     changes in the automake/autoconf parts.
     74 *
    6675 * \subsection install-prerequisites-other Other packages
    6776 *
    … …  
    333342 *  from a distributed archive. This is checked for each release version.
    334343 *
    335  * \date 2014-03-10
     344 * \date 2014-08-21
    336345 */

  • src/unittests/Makefile.am

    r4c9101 ra91710  
    77XFAIL_TESTS =
    88MOSTLYCLEANFILES =
     9noinst_LTLIBRARIES =
     10
     11#AUTOMAKE_OPTIONS = no-dependencies
    912
    1013if CONDCPPUNIT
    … …  
    4043include ../../src/UIElements/Menu/unittests/Makefile.am
    4144
    42 INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/LinearAlgebra/src
    43 
    4445AM_LDFLAGS = \
    4546        ${CodePatterns_LIBS} \
    4647        $(CPPUNIT_LIBS) \
    4748        -ldl
    48 AM_CPPFLAGS = ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS}
     49AM_CPPFLAGS = -I$(top_srcdir)/src -I$(top_srcdir)/LinearAlgebra/src ${BOOST_CPPFLAGS} $(CPPUNIT_CFLAGS) ${CodePatterns_CFLAGS}
    4950
    5051GENERALTESTS = \
    … …  
    6869endif
    6970
     71noinst_LTLIBRARIES += libUnitTest.la
     72libUnitTest_la_LDFLAGS = \
     73        $(AM_LDFLAGS)
     74libUnitTest_la_LIBADD =
     75
     76#nobase_libUnitTest_la_include_HEADERS =
     77
     78## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
     79## target.  Note that @MOLECUILDER_API_VERSION@ is not interpreted by Automake and
     80## will therefore be treated as if it were literally part of the target name,
     81## and the variable name derived from that.
     82## The file extension .cc is recognized by Automake, and makes it produce
     83## rules which invoke the C++ compiler to produce a libtool object file (.lo)
     84## from each source file.  Note that it is not necessary to list header files
     85## which are already listed elsewhere in a _HEADERS variable assignment.
     86libUnitTest_la_SOURCES = UnitTestMain.cpp
     87
     88## Instruct libtool to include ABI version information in the generated shared
     89## library file (.so).  The library ABI version is defined in configure.ac, so
     90## that all version information is kept in one place.
     91#libUnitTest_la_LDFLAGS = -version-info $(MOLECUILDER_SO_VERSION)
     92
     93## The generated configuration header is installed in its own subdirectory of
     94## $(libdir).  The reason for this is that the configuration information put
     95## into this header file describes the target platform the installed library
     96## has been built for.  Thus the file must not be installed into a location
     97## intended for architecture-independent files, as defined by the Filesystem
     98## Hierarchy Standard (FHS).
     99## The nodist_ prefix instructs Automake to not generate rules for including
     100## the listed files in the distribution on 'make dist'.  Files that are listed
     101## in _HEADERS variables are normally included in the distribution, but the
     102## configuration header file is generated at configure time and should not be
     103## shipped with the source tarball.
     104#libUnitTest_la_libincludedir = $(libdir)/MoleCuilder/include
     105#nodist_libUnitTest_la_libinclude_HEADERS = $(top_builddir)/libmolecuilder_config.h
     106
     107## Install the generated pkg-config file (.pc) into the expected location for
     108## architecture-dependent package configuration information.  Occasionally,
     109## pkg-config files are also used for architecture-independent data packages,
     110## in which case the correct install location would be $(datadir)/pkgconfig.
     111#pkgconfigdir = $(libdir)/pkgconfig
     112#pkgconfig_DATA = $(top_builddir)/MoleCuilder.pc
     113
    70114
    71115BOOST_LIB = \
    … …  
    83127
    84128ALLLIBS = \
     129        libUnitTest.la \
     130        ../libMolecuilder.la \
    85131        ../libMolecuilderUI.la
    86132if CONDJOBMARKET
    … …  
    146192 
    147193
    148 BoxUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     194BoxUnitTest_SOURCES = \
    149195        BoxUnitTest.cpp \
    150196        BoxUnitTest.hpp \
    … …  
    154200        ../Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp
    155201BoxUnitTest_LDADD = \
    156         ../libMolecuilder.la \
    157         ../libMolecuilderShapes.la \
    158         ../libMolecuilderHelpers.la \
    159         $(top_builddir)/LinearAlgebra/src/LinearAlgebra/libLinearAlgebra.la \
    160         ${CodePatterns_LIBS} \
    161         $(BOOST_LIB)
    162 
    163 AtomIdSetUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     202        $(ALLLIBS) \
     203        ../libMolecuilderShapes.la \
     204        ../libMolecuilderHelpers.la
     205
     206AtomIdSetUnitTest_SOURCES = \
    164207        AtomIdSetUnitTest.cpp \
    165208        AtomIdSetUnitTest.hpp
    166209AtomIdSetUnitTest_LDADD =  $(ALLLIBS)
    167210
    168 Box_BoundaryConditionsTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     211Box_BoundaryConditionsTest_SOURCES = \
    169212        Box_BoundaryConditionsUnitTest.cpp \
    170         Box_BoundaryConditionsUnitTest.hpp \
    171         ../Box_BoundaryConditions.cpp \
    172         ../Box_BoundaryConditions.hpp
     213        Box_BoundaryConditionsUnitTest.hpp
    173214Box_BoundaryConditionsTest_LDADD = \
    174         ${CodePatterns_LIBS} \
    175         $(BOOST_LIB)
    176 
    177 FormulaUnittest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     215        $(ALLLIBS) \
     216        ../libMolecuilderShapes.la \
     217        ../libMolecuilderHelpers.la
     218
     219FormulaUnittest_SOURCES = \
    178220        FormulaUnitTest.cpp \
    179221        FormulaUnitTest.hpp
    180222FormulaUnittest_LDADD = $(ALLLIBS)
    181223
    182 ListOfBondsUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     224ListOfBondsUnitTest_SOURCES = \
    183225        ListOfBondsUnitTest.cpp \
    184226        ListOfBondsUnitTest.hpp
    185227ListOfBondsUnitTest_LDADD = $(ALLLIBS)
    186228
    187 MoleculeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     229MoleculeUnitTest_SOURCES = \
    188230        MoleculeUnitTest.cpp \
    189231        MoleculeUnitTest.hpp
    … …  
    193235        ../libMolecuilderHelpers.la
    194236
    195 WorldTimeUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     237WorldTimeUnitTest_SOURCES = \
    196238        WorldTimeUnitTest.cpp \
    197         WorldTimeUnitTest.hpp \
    198         ../WorldTime.cpp \
    199         ../WorldTime.hpp
    200 WorldTimeUnitTest_LDADD = ${BOOST_LIB}
     239        WorldTimeUnitTest.hpp
     240WorldTimeUnitTest_LDADD = \
     241        $(ALLLIBS) \
     242        ../libMolecuilderShapes.la \
     243        ../libMolecuilderHelpers.la
    201244
    202245

  • tests/JobMarket/Makefile.am

    r4c9101 ra91710  
    22
    33if CONDJOBMARKET
    4 mpqc_SOURCES = $(srcdir)/mpqc.cpp
    5 mpqc_CPPFLAGS = ${CodePatterns_CFLAGS} $(BOOST_CPPFLAGS)
     4mpqc_SOURCES = mpqc.cpp
     5mpqc_CPPFLAGS = $(AM_CPPFLAGS) ${CodePatterns_CFLAGS} $(BOOST_CPPFLAGS)
    66mpqc_LDADD = \
    77        ${CodePatterns_LIBS}
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