Thread: [Ecell-cvs] SF.net SVN: ecell:[3160] ecell3/branches/ecell-3.1

Status: Beta

Brought to you by: kozo2, moriyoshi, shafi

ecell-cvs

[Ecell-cvs] SF.net SVN: ecell:[3160] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-09 02:38:04

Revision: 3160
          http://ecell.svn.sourceforge.net/ecell/?rev=3160&view=rev
Author:   moriyoshi
Date:     2008-10-09 02:37:57 +0000 (Thu, 09 Oct 2008)

Log Message:
-----------
* touch

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
    ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp
    ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Defs.hpp.in
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/em.py

Modified: ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DMObject.hpp	2008-10-09 02:29:14 UTC (rev 3159)
+++ ecell3/branches/ecell-3.1/dmtool/DMObject.hpp	2008-10-09 02:37:57 UTC (rev 3160)
@@ -76,3 +76,4 @@
   $Date$
   $Locker$
 */
+

Modified: ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp	2008-10-09 02:29:14 UTC (rev 3159)
+++ ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp	2008-10-09 02:37:57 UTC (rev 3160)
@@ -266,3 +266,4 @@
   $Date$
   $Locker$
 */
+

Modified: ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp	2008-10-09 02:29:14 UTC (rev 3159)
+++ ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp	2008-10-09 02:37:57 UTC (rev 3160)
@@ -424,3 +424,4 @@
   $Date$
   $Locker$
 */
+

Modified: ecell3/branches/ecell-3.1/ecell/libecs/Defs.hpp.in
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/Defs.hpp.in	2008-10-09 02:29:14 UTC (rev 3159)
+++ ecell3/branches/ecell-3.1/ecell/libecs/Defs.hpp.in	2008-10-09 02:37:57 UTC (rev 3160)
@@ -536,3 +536,4 @@
 
 
 
+

Modified: ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp	2008-10-09 02:29:14 UTC (rev 3159)
+++ ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp	2008-10-09 02:37:57 UTC (rev 3160)
@@ -465,3 +465,4 @@
   $Date$
   $Locker$
 */
+

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/em.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/em.py	2008-10-09 02:29:14 UTC (rev 3159)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/em.py	2008-10-09 02:37:57 UTC (rev 3160)
@@ -3286,3 +3286,4 @@
     invoke(sys.argv[1:])
 
 if __name__ == '__main__': main()
+


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3161] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-09 02:39:52

Revision: 3161
          http://ecell.svn.sourceforge.net/ecell/?rev=3161&view=rev
Author:   moriyoshi
Date:     2008-10-09 02:39:42 +0000 (Thu, 09 Oct 2008)

Log Message:
-----------
* Touch.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
    ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp
    ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Defs.hpp.in
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/em.py

Modified: ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DMObject.hpp	2008-10-09 02:37:57 UTC (rev 3160)
+++ ecell3/branches/ecell-3.1/dmtool/DMObject.hpp	2008-10-09 02:39:42 UTC (rev 3161)
@@ -76,4 +76,3 @@
   $Date$
   $Locker$
 */
-

Modified: ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp	2008-10-09 02:37:57 UTC (rev 3160)
+++ ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp	2008-10-09 02:39:42 UTC (rev 3161)
@@ -266,4 +266,3 @@
   $Date$
   $Locker$
 */
-

Modified: ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp	2008-10-09 02:37:57 UTC (rev 3160)
+++ ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp	2008-10-09 02:39:42 UTC (rev 3161)
@@ -424,4 +424,3 @@
   $Date$
   $Locker$
 */
-

Modified: ecell3/branches/ecell-3.1/ecell/libecs/Defs.hpp.in
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/Defs.hpp.in	2008-10-09 02:37:57 UTC (rev 3160)
+++ ecell3/branches/ecell-3.1/ecell/libecs/Defs.hpp.in	2008-10-09 02:39:42 UTC (rev 3161)
@@ -536,4 +536,3 @@
 
 
 
-

Modified: ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp	2008-10-09 02:37:57 UTC (rev 3160)
+++ ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp	2008-10-09 02:39:42 UTC (rev 3161)
@@ -465,4 +465,3 @@
   $Date$
   $Locker$
 */
-

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/em.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/em.py	2008-10-09 02:37:57 UTC (rev 3160)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/em.py	2008-10-09 02:39:42 UTC (rev 3161)
@@ -3286,4 +3286,3 @@
     invoke(sys.argv[1:])
 
 if __name__ == '__main__': main()
-


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3192] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-11 07:35:26

Revision: 3192
          http://ecell.svn.sourceforge.net/ecell/?rev=3192&view=rev
Author:   moriyoshi
Date:     2008-10-11 07:35:21 +0000 (Sat, 11 Oct 2008)

Log Message:
-----------
* Specify ``make dist'' options because of such exsessive length of pathnames in the archive that cannot be held in the ancient TAR format.
* The reason the templates of configure.ac are required is that synthesized version numbers are not allowed in newer autoconf / automake convention.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/autogen.sh
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/config.py.in
    ecell3/branches/ecell-3.1/ecell_version.sh

Added Paths:
-----------
    ecell3/branches/ecell-3.1/configure.ac.in
    ecell3/branches/ecell-3.1/ecell/configure.ac.in

Removed Paths:
-------------
    ecell3/branches/ecell-3.1/configure.in
    ecell3/branches/ecell-3.1/ecell/configure.in

Property Changed:
----------------
    ecell3/branches/ecell-3.1/
    ecell3/branches/ecell-3.1/ecell/


Property changes on: ecell3/branches/ecell-3.1
___________________________________________________________________
Modified: svn:ignore
   - *.tar.bz2
*.tar.gz
*~
Makefile
Makefile.in
aclocal.m4
autom4te.cache
config.cache
config.guess
config.h.in
config.log
config.status
config.sub
configure
depcomp
ecell3.doxy
ecell3_config.h
ecell3_config.h.in
install
install-sh
libtool
libtool.cfg
ltmain.sh
missing
py-compile
stamp-h1

   + *.tar.bz2
*.tar.gz
*~
Makefile
Makefile.in
aclocal.m4
autom4te.cache
config.cache
config.guess
config.h.in
config.log
config.status
config.sub
configure
configure.ac
depcomp
ecell3.doxy
ecell3_config.h
ecell3_config.h.in
install
install-sh
libtool
libtool.cfg
ltmain.sh
missing
py-compile
stamp-h1


Modified: ecell3/branches/ecell-3.1/autogen.sh
===================================================================
--- ecell3/branches/ecell-3.1/autogen.sh	2008-10-11 07:27:47 UTC (rev 3191)
+++ ecell3/branches/ecell-3.1/autogen.sh	2008-10-11 07:35:21 UTC (rev 3192)
@@ -39,10 +39,13 @@
 
 [ ! -e doc/users-manual/users-manual ] && mkdir -p doc/users-manual/users-manual
 
+. ./ecell_version.sh
+
 for dir in . libltdl dmtool ecell
   do 
   echo -n "Running autotools for $dir ... "
   (cd $dir; \
+  { if [ -r configure.ac.in ]; then echo -n 'configure.ac ' && sed -e "s/@ECELL_VERSION_NUMBER@/$ECELL_VERSION_NUMBER/g" configure.ac.in > configure.ac; fi } && \
   { echo -n 'libtoolize '; $LIBTOOLIZE -c --force --automake; } && \
   { echo -n 'aclocal '; aclocal; } && \
   { echo -n 'autoheader '; autoheader -f ; } && \

Copied: ecell3/branches/ecell-3.1/configure.ac.in (from rev 3168, ecell3/branches/ecell-3.1/configure.in)
===================================================================
--- ecell3/branches/ecell-3.1/configure.ac.in	                        (rev 0)
+++ ecell3/branches/ecell-3.1/configure.ac.in	2008-10-11 07:35:21 UTC (rev 3192)
@@ -0,0 +1,68 @@
+AC_REVISION([$Id$])
+AC_INIT([ecell], [@ECELL_VERSION_NUMBER@])
+AC_CONFIG_SRCDIR([autogen.sh])
+
+AC_CANONICAL_TARGET([])
+AM_INIT_AUTOMAKE([filename-length-max=255 tar-ustar dist-bzip2])
+AC_PROG_MAKE_SET
+
+AC_LIBLTDL_CONVENIENCE
+AC_SUBST(INCLTDL)
+AC_SUBST(LIBLTDL)
+AC_LIBTOOL_DLOPEN
+AC_PROG_LIBTOOL
+
+AC_CONFIG_SUBDIRS([libltdl dmtool ecell])
+
+AC_ARG_ENABLE([gui],
+  AC_HELP_STRING([--disable-gui],
+                 [build ecell without gui frontends.]), [],
+  [enable_gui=yes]
+)
+AC_ARG_WITH([numpy-includes],
+  AC_HELP_STRING([--with-numpy-includes=DIR],
+                 [specify the numpy header location]),,)
+
+AC_ARG_ENABLE([compiler-extensions],
+  AC_HELP_STRING([--disable-compiler-extensions],
+                 [Don't exploit the compiler's special language syntax and optimizations that are not part of the standard (such as ISO C++).]))
+
+AM_CONFIG_HEADER(ecell3_config.h)
+
+AC_CHECK_TOOL([DB2HTML], [db2html])
+AC_CHECK_TOOL([DB2PDF], [db2pdf])
+AC_CHECK_TOOL([DB2PS], [db2ps])
+AC_CHECK_TOOL([DB2DVI], [db2dvi])
+AC_CHECK_TOOL([DOXYGEN], [doxygen])
+AC_CHECK_TOOL([DOT], [dot])
+
+HAVE_DOT="no"
+if test ! -z "$DOT"; then
+    HAVE_DOT="yes"
+fi
+AC_SUBST([HAVE_DOT])
+
+AM_CONDITIONAL([BUILD_USERS_MANUAL_html], [test ! -z "$DB2HTML"])
+AM_CONDITIONAL([BUILD_USERS_MANUAL_pdf], [test ! -z "$DB2PDF"])
+AM_CONDITIONAL([BUILD_USERS_MANUAL_ps], [test ! -z "$DB2PS"])
+AM_CONDITIONAL([BUILD_USERS_MANUAL_dvi], [test ! -z "$DB2DVI"])
+AM_CONDITIONAL([BUILD_API_REF_html], [test ! -z "$DOXYGEN"])
+
+dnl
+dnl Create the top-level Makefile.
+dnl
+AC_CONFIG_FILES([
+Makefile
+doc/Makefile
+doc/samples/Makefile
+doc/users-manual/Makefile
+osdep/Makefile
+osdep/win32/Makefile
+build/Makefile
+build/msvc/Makefile
+build/msvc/dm/Makefile
+doc/ecell3.doxy
+doc/users-manual/info.ent
+])
+dnl
+AC_OUTPUT


Property changes on: ecell3/branches/ecell-3.1/configure.ac.in
___________________________________________________________________
Added: svn:mime-type
   + text/plain
Added: svn:keywords
   + Author Date Id Revision
Added: svn:eol-style
   + native

Deleted: ecell3/branches/ecell-3.1/configure.in
===================================================================
--- ecell3/branches/ecell-3.1/configure.in	2008-10-11 07:27:47 UTC (rev 3191)
+++ ecell3/branches/ecell-3.1/configure.in	2008-10-11 07:35:21 UTC (rev 3192)
@@ -1,75 +0,0 @@
-AC_REVISION([$Id$])
-AC_INIT
-AC_CONFIG_SRCDIR([autogen.sh])
-
-dnl
-sinclude([./ecell_version.sh])
-
-dnl AC_CONFIG_AUX_DIR()
-
-AC_CANONICAL_TARGET([])
-AM_INIT_AUTOMAKE([ecell],${ECELL_VERSION_NUMBER})
-AC_PROG_MAKE_SET
-
-dnl AC_LIBLTDL_INSTALLABLE
-
-AC_LIBLTDL_CONVENIENCE
-AC_SUBST(INCLTDL)
-AC_SUBST(LIBLTDL)
-AC_LIBTOOL_DLOPEN
-AC_PROG_LIBTOOL
-
-AC_CONFIG_SUBDIRS([libltdl dmtool ecell])
-
-AC_ARG_ENABLE([gui],
-  AC_HELP_STRING([--disable-gui],
-                 [build ecell without gui frontends.]), [],
-  [enable_gui=yes]
-)
-AC_ARG_WITH([numpy-includes],
-  AC_HELP_STRING([--with-numpy-includes=DIR],
-                 [specify the numpy header location]),,)
-
-AC_ARG_ENABLE([compiler-extensions],
-  AC_HELP_STRING([--disable-compiler-extensions],
-                 [Don't exploit the compiler's special language syntax and optimizations that are not part of the standard (such as ISO C++).]))
-
-AM_CONFIG_HEADER(ecell3_config.h)
-
-AC_CHECK_TOOL([DB2HTML], [db2html])
-AC_CHECK_TOOL([DB2PDF], [db2pdf])
-AC_CHECK_TOOL([DB2PS], [db2ps])
-AC_CHECK_TOOL([DB2DVI], [db2dvi])
-AC_CHECK_TOOL([DOXYGEN], [doxygen])
-AC_CHECK_TOOL([DOT], [dot])
-
-HAVE_DOT="no"
-if test ! -z "$DOT"; then
-    HAVE_DOT="yes"
-fi
-AC_SUBST([HAVE_DOT])
-
-AM_CONDITIONAL([BUILD_USERS_MANUAL_html], [test ! -z "$DB2HTML"])
-AM_CONDITIONAL([BUILD_USERS_MANUAL_pdf], [test ! -z "$DB2PDF"])
-AM_CONDITIONAL([BUILD_USERS_MANUAL_ps], [test ! -z "$DB2PS"])
-AM_CONDITIONAL([BUILD_USERS_MANUAL_dvi], [test ! -z "$DB2DVI"])
-AM_CONDITIONAL([BUILD_API_REF_html], [test ! -z "$DOXYGEN"])
-
-dnl
-dnl Create the top-level Makefile.
-dnl
-AC_CONFIG_FILES([
-Makefile
-doc/Makefile
-doc/samples/Makefile
-doc/users-manual/Makefile
-osdep/Makefile
-osdep/win32/Makefile
-build/Makefile
-build/msvc/Makefile
-build/msvc/dm/Makefile
-doc/ecell3.doxy
-doc/users-manual/info.ent
-])
-dnl
-AC_OUTPUT


Property changes on: ecell3/branches/ecell-3.1/ecell
___________________________________________________________________
Modified: svn:ignore
   - Makefile
Makefile.in
aclocal.m4
autom4te.cache
config.cache
config.guess
config.h
config.h.in
config.log
config.status
config.sub
configure
depcomp
ecell_config.h
ecell_config.h.in
install-sh
libtool
ltmain.sh
missing
py-compile
stamp-h
stamp-h.in
stamp-h1
tmp

   + Makefile
Makefile.in
aclocal.m4
autom4te.cache
config.cache
config.guess
config.h
config.h.in
config.log
config.status
config.sub
configure
configure.ac
depcomp
ecell_config.h
ecell_config.h.in
install-sh
libtool
ltmain.sh
missing
py-compile
stamp-h
stamp-h.in
stamp-h1
tmp


Copied: ecell3/branches/ecell-3.1/ecell/configure.ac.in (from rev 3186, ecell3/branches/ecell-3.1/ecell/configure.in)
===================================================================
--- ecell3/branches/ecell-3.1/ecell/configure.ac.in	                        (rev 0)
+++ ecell3/branches/ecell-3.1/ecell/configure.ac.in	2008-10-11 07:35:21 UTC (rev 3192)
@@ -0,0 +1,316 @@
+AC_REVISION([$Id$])dnl
+
+dnl Process this file with autoconf to produce a configure script.
+
+AC_INIT([ecell], [@ECELL_VERSION_NUMBER@])
+AC_CONFIG_SRCDIR([libecs/Entity.hpp])
+
+sinclude([../ecell_version.sh])
+
+
+AM_CONFIG_HEADER(ecell_config.h)
+
+AM_INIT_AUTOMAKE
+
+ECELL_DIRNAME=${PACKAGE}-${ECELL_MAJOR_VERSION}.${ECELL_MINOR_VERSION}
+
+ECELL_VERSION_STRING=\"${ECELL_VERSION_NUMBER}\"
+
+AC_DEFINE_UNQUOTED(ECELL_MAJOR_VERSION, ${ECELL_MAJOR_VERSION}, [Major version of the software.])
+AC_DEFINE_UNQUOTED(ECELL_MINOR_VERSION, ${ECELL_MINOR_VERSION}, [Minor version of the software.])
+AC_DEFINE_UNQUOTED(ECELL_MICRO_VERSION, ${ECELL_MICRO_VERSION}, [Micro version of the software.])
+AC_DEFINE_UNQUOTED(ECELL_VERSION_STRING, ${ECELL_VERSION_STRING}, [Full version string of the software.])
+AC_SUBST([ECELL_DIRNAME])
+AC_SUBST([ECELL_MAJOR_VERSION])
+AC_SUBST([ECELL_MINOR_VERSION])
+AC_SUBST([ECELL_MICRO_VERSION])
+AC_SUBST([ECELL_VERSION_STRING])
+
+
+AM_SANITY_CHECK
+
+AC_CANONICAL_HOST
+
+if test "$prefix" = "NONE" ; then
+  PREFIX="$ac_default_prefix"
+else
+  PREFIX="$prefix"
+fi
+
+AC_SUBST([PREFIX])
+
+AC_ARG_ENABLE([gui], [
+  AC_HELP_STRING([--disable-gui],
+                 [build ecell without gui frontends.])
+  ], [],
+  [enable_gui=yes]
+)
+
+AC_MSG_CHECKING([whether to build GUI frontends])
+if test "$enable_gui" = "yes"; then
+  AC_MSG_RESULT([yes])
+else
+  AC_MSG_RESULT([no])
+fi
+
+AM_CONDITIONAL([ENABLE_GUI], [test "$enable_gui" = "yes"])
+dnl
+
+dnl Checks for programs.
+
+AC_PROG_CC
+AC_PROG_CXX
+AC_PROG_CPP
+AC_PROG_CXXCPP
+AC_PROG_INSTALL
+AC_PROG_LN_S
+AC_PROG_MAKE_SET
+AC_PROG_RANLIB
+
+AM_DISABLE_STATIC
+AC_LIBLTDL_CONVENIENCE(../libltdl)
+AC_SUBST(INCLTDL)
+AC_SUBST(LIBLTDL)
+AC_LIBTOOL_DLOPEN
+AC_PROG_LIBTOOL
+
+dnl to circumvent libltdl weirdness (already fixed in the newer versions)
+case $host_os in
+  *cygwin* | *mingw* | *win32*)
+    CPPFLAGS="$CPPFLAGS -DLT_SCOPE=extern"
+    ;;
+esac
+
+rm -f conftest
+./libtool --config > conftest
+. ./conftest
+rm -f conftest
+
+dnl compatibility for libtool 1.5.6
+
+LTDL_SHLIB_EXT=""
+if test -n "$shrext_cmds"; then
+    module=yes eval LTDL_SHLIB_EXT=\"$shrext_cmds\"
+    AC_SUBST(LTDL_SHLIB_EXT)
+dnl compatibility for libtool 1.5.0
+elif test -n "$shrext"; then
+    LTDL_SHLIB_EXT=$shrext
+    AC_SUBST(LTDL_SHLIB_EXT)
+dnl compatibility for libtool 1.4.x
+else
+  AC_CACHE_CHECK([which extension is used for shared libraries],
+    libltdl_cv_shlibext, [dnl
+  (
+    last=
+    for spec in $library_names_spec; do
+      last="$spec"
+    done
+  changequote(, )
+    echo "$last" | sed 's/\[.*\]//;s/^[^.]*//;s/\$.*$//;s/\.$//' > conftest
+  changequote([, ])
+  )
+  libltdl_cv_shlibext=`cat conftest`
+  rm -f conftest
+  ])
+  if test -n "$libltdl_cv_shlibext"; then
+    LTDL_SHLIB_EXT=$libltdl_cv_shlibext
+    AC_SUBST(LTDL_SHLIB_EXT)
+  fi
+fi
+
+
+
+AM_PATH_PYTHON(2.2)
+AC_SUBST(PYTHON)
+
+AC_LANG([C++])
+
+dnl Checks for libraries.
+
+dnl assuming libc and libm always present...
+
+AC_CHECK_LIB(m, sin, LIBM="-lm")
+AC_SUBST(LIBM)
+dnl
+AC_CHECK_LIB(c, open, LIBC="-lc")
+AC_SUBST(LIBC)
+dnl
+
+ECELL_CHECK_GSL
+
+AM_CHECK_PYMOD(numpy,,,[AC_MSG_ERROR([could not find Python numpy module])])
+AM_CHECK_PYMOD(xml,,,[AC_MSG_ERROR([could not find Python xml module])])
+
+if test "$enable_gui" = 'yes'; then
+   AM_CHECK_PYMOD(pygtk,,,[AC_MSG_ERROR([could not find Python pygtk module])])
+   AM_CHECK_PYMOD(gtk,,,[AC_MSG_ERROR([could not find Python gtk module])])
+   AM_CHECK_PYMOD(gtk.gdk,,,
+                [AC_MSG_ERROR([could not find Python gtk.gdk module])])
+   AM_CHECK_PYMOD(gtk.glade,,,
+                [AC_MSG_ERROR([could not find Python gtk.glade module])])
+   AM_CHECK_PYMOD(gnome.ui,,[AC_SUBST([GNOME_INSTALLED],yes)],[AC_SUBST([GNOME_INSTALLED],no)])
+   AM_CHECK_PYMOD(gnomecanvas,,,[AC_MSG_WARN(could not find gnomecanvas module. model-editor will not work. )])
+   AM_CHECK_PYMOD(xml.dom.minidom,,,[AC_MSG_WARN(could not find xml.dom.minidom module. model-editor will not work.)])
+fi
+
+
+dnl Checks for header files.
+
+AC_HEADER_DIRENT
+AC_HEADER_STDC
+
+AC_CHECK_HEADERS([fcntl.h unistd.h memory.h sys/stat.h sys/types.h sys/mman.h sys/param.h sys/statvfs.h sys/statfs.h sys/mount.h sys/vfs.h])
+AC_CHECK_HEADERS([unordered_map tr1/unordered_map])
+AC_CHECK_HEADERS([windows.h])
+
+AC_CHECK_HEADERS([stdint.h], [
+  INT64_T_DECLARATION="#include <stdint.h>"
+], [
+  AC_CHECK_TYPE([long long], [
+    INT64_T_DECLARATION="typedef long long int64_t; typedef unsigned long long uint64_t;"
+  ], [
+    AC_CHECK_TYPE([__int64], [
+      INT64_T_DECLARATION="typedef __int64 int64_t; typedef unsigned __int64 uint64_t;"
+    ], [
+      INT64_T_DECLARATION=
+    ])
+  ])
+])
+AC_SUBST([INT64_T_DECLARATION])
+
+ECELL_CHECK_MATH_HEADER
+ECELL_CHECK_INFINITY
+ECELL_CHECK_HUGE_VAL
+ECELL_CHECK_NUMERIC_LIMITS_DOUBLE_INFINITY
+
+if test "$HAVE_NUMERIC_LIMITS_DOUBLE_INFINITY" = 1; then
+  INFINITY_VAL="std::numeric_limits<double>::infinity()"
+elif test "$HAVE_INFINITY" = 1; then
+  INFINITY_VAL="INFINITY"
+elif test "$HAVE_HUGE_VAL" = 1; then
+  INFINITY_VAL="HUGE_VAL"
+fi
+AC_SUBST([INFINITY_VAL])
+
+ECELL_CHECK_PRETTY_FUNCTION
+
+EXT_GUESS="../../../.. ../../.. ../.. ../ ./ $prefix /usr /usr/local /opt"
+
+dnl dmtool package
+
+if test "$DMTOOL_DIR" = "" ; then
+  AC_MSG_CHECKING( for dmtool dir)
+  ac_cv_dmtool_dir="no"
+  for ac_dir in $EXT_GUESS ; do
+    if test -d $ac_dir/dmtool ; then
+      ac_cv_dmtool_dir=`(cd $ac_dir ; pwd)`
+      DMTOOL_DIR=$ac_cv_dmtool_dir
+    fi
+  done
+
+  if test "$DMTOOL_DIR" = "" ; then        
+    AC_MSG_ERROR("dmtool not found.")
+  fi
+
+  AC_MSG_RESULT($ac_cv_dmtool_dir)
+  DMTOOL_DIR=$ac_cv_dmtool_dir
+  DMTOOL_INCLUDE_DIR=$ac_cv_dmtool_dir
+fi
+AC_SUBST(DMTOOL_DIR)
+AC_SUBST(DMTOOL_INCLUDE_DIR)
+
+AM_CHECK_PYTHON_HEADERS(,[AC_MSG_ERROR([Failed to find Python headers.])])
+ECELL_CHECK_PYTHON_LIBS
+AM_CONDITIONAL([HAVE_PYTHON_LIB], [test ! -z "$PYTHON_LIBS"])
+AC_SUBST([PYTHON_LIBS])
+
+ECELL_CHECK_NUMPY
+
+AC_MSG_CHECKING( if use of compiler specific features are allowed )
+
+AC_ARG_ENABLE( compiler-extensions,,
+               USE_COMPILER_EXTENSIONS=$enable_compiler_features,
+               USE_COMPILER_EXTENSIONS=yes
+               )
+AC_MSG_RESULT( $USE_COMPILER_EXTENSIONS )
+
+if test "$USE_COMPILER_EXTENSIONS" != no ; then
+  AC_MSG_CHECKING( for special compiler options )
+  AC_SUBST(USE_COMPILER_EXTENSIONS)
+  AC_DEFINE([USE_COMPILER_EXTENSIONS],1,[make use of compiler specific language features])
+  CXXFLAGS="$CXXFLAGS -Wno-pmf-conversions"
+  AC_SUBST(CXXFLAGS)
+  AC_MSG_RESULT( $CXXFLAGS )
+fi
+   
+AC_LANG_PUSH([C])
+
+AC_SYS_LARGEFILE
+
+AC_C_CONST
+AC_C_INLINE
+if test "$ac_cv_c_inline" != no ; then
+  AC_DEFINE([HAVE_INLINE],1,[define if inline is supported])
+  AC_SUBST(HAVE_INLINE)
+fi
+
+AC_CHECK_TYPES([ssize_t],,,[
+#include <sys/types.h>
+])
+AC_TYPE_OFF_T
+AC_TYPE_SIZE_T
+AC_TYPE_SIGNAL
+AC_C_LONG_DOUBLE
+if test "$HAVE_LONG_DOUBLE" = 1; then
+  HIGHREAL_TYPE="long double"
+  HIGHREAL_IS_REAL=0
+else
+  HIGHREAL_TYPE="double"
+  HIGHREAL_IS_REAL=1
+fi
+AC_SUBST([HIGHREAL_TYPE])
+AC_SUBST([HIGHREAL_IS_REAL])
+
+AC_LANG_POP([])
+
+AC_CHECK_SIZEOF(int)
+AC_CHECK_SIZEOF(long)
+AC_CHECK_SIZEOF(long long)
+AC_CHECK_SIZEOF(double)
+AC_CHECK_SIZEOF(long double)
+
+
+dnl Checks for library functions.
+AC_TYPE_SIGNAL
+AC_CHECK_FUNCS(mkdir select strdup strerror strtod uname modf modfl)
+AC_CHECK_FUNCS(strdup strstr)
+
+AC_CONFIG_FILES([
+    Makefile
+    bin/Makefile
+    dm/Makefile
+    libecs/Defs.hpp  
+    libecs/Makefile
+    libecs/tests/Makefile
+    libemc/Makefile
+    pyecell/Makefile
+    pyecell/setup.py
+    pyecell/ecell/config.py
+    frontend/Makefile
+    frontend/session-monitor/Makefile
+    frontend/session-monitor/glade/Makefile
+    frontend/session-monitor/plugins/Makefile
+    frontend/model-editor/Makefile
+    frontend/model-editor/doc/Makefile
+    frontend/model-editor/glade/Makefile
+    frontend/model-editor/plugins/Makefile
+])
+AC_CONFIG_FILES([bin/ecell3-dmc], [chmod +x bin/ecell3-dmc])
+AC_CONFIG_FILES([pyecell/ecell3-python], [chmod +x pyecell/ecell3-python])
+AC_CONFIG_FILES([pyecell/ecell3-em2eml], [chmod +x pyecell/ecell3-em2eml])
+AC_CONFIG_FILES([pyecell/ecell3-eml2em], [chmod +x pyecell/ecell3-eml2em])
+AC_CONFIG_FILES([pyecell/ecell3-eml2sbml], [chmod +x pyecell/ecell3-eml2sbml])
+AC_CONFIG_FILES([pyecell/ecell3-sbml2eml], [chmod +x pyecell/ecell3-sbml2eml])
+AC_CONFIG_FILES([pyecell/ecell3-session], [chmod +x pyecell/ecell3-session])
+AC_CONFIG_FILES([pyecell/ecell3-session-manager], [chmod +x pyecell/ecell3-session-manager])
+AC_OUTPUT


Property changes on: ecell3/branches/ecell-3.1/ecell/configure.ac.in
___________________________________________________________________
Added: svn:mime-type
   + text/plain
Added: svn:keywords
   + Author Date Id Revision
Added: svn:eol-style
   + native

Deleted: ecell3/branches/ecell-3.1/ecell/configure.in
===================================================================
--- ecell3/branches/ecell-3.1/ecell/configure.in	2008-10-11 07:27:47 UTC (rev 3191)
+++ ecell3/branches/ecell-3.1/ecell/configure.in	2008-10-11 07:35:21 UTC (rev 3192)
@@ -1,316 +0,0 @@
-AC_REVISION([$Id$])dnl
-
-dnl Process this file with autoconf to produce a configure script.
-
-AC_INIT
-AC_CONFIG_SRCDIR([libecs/Entity.hpp])
-
-sinclude([../ecell_version.sh])
-
-
-AM_CONFIG_HEADER(ecell_config.h)
-
-AM_INIT_AUTOMAKE([ecell],${ECELL_VERSION_NUMBER})
-
-ECELL_DIRNAME=${PACKAGE}-${ECELL_MAJOR_VERSION}.${ECELL_MINOR_VERSION}
-
-ECELL_VERSION_STRING=\"${ECELL_VERSION_NUMBER}\"
-
-AC_DEFINE_UNQUOTED(ECELL_MAJOR_VERSION, ${ECELL_MAJOR_VERSION}, [Major version of the software.])
-AC_DEFINE_UNQUOTED(ECELL_MINOR_VERSION, ${ECELL_MINOR_VERSION}, [Minor version of the software.])
-AC_DEFINE_UNQUOTED(ECELL_MICRO_VERSION, ${ECELL_MICRO_VERSION}, [Micro version of the software.])
-AC_DEFINE_UNQUOTED(ECELL_VERSION_STRING, ${ECELL_VERSION_STRING}, [Full version string of the software.])
-AC_SUBST([ECELL_DIRNAME])
-AC_SUBST([ECELL_MAJOR_VERSION])
-AC_SUBST([ECELL_MINOR_VERSION])
-AC_SUBST([ECELL_MICRO_VERSION])
-AC_SUBST([ECELL_VERSION_STRING])
-
-
-AM_SANITY_CHECK
-
-AC_CANONICAL_HOST
-
-if test "$prefix" = "NONE" ; then
-  PREFIX="$ac_default_prefix"
-else
-  PREFIX="$prefix"
-fi
-
-AC_SUBST([PREFIX])
-
-AC_ARG_ENABLE([gui], [
-  AC_HELP_STRING([--disable-gui],
-                 [build ecell without gui frontends.])
-  ], [],
-  [enable_gui=yes]
-)
-
-AC_MSG_CHECKING([whether to build GUI frontends])
-if test "$enable_gui" = "yes"; then
-  AC_MSG_RESULT([yes])
-else
-  AC_MSG_RESULT([no])
-fi
-
-AM_CONDITIONAL([ENABLE_GUI], [test "$enable_gui" = "yes"])
-dnl
-
-dnl Checks for programs.
-
-AC_PROG_CC
-AC_PROG_CXX
-AC_PROG_CPP
-AC_PROG_CXXCPP
-AC_PROG_INSTALL
-AC_PROG_LN_S
-AC_PROG_MAKE_SET
-AC_PROG_RANLIB
-
-AM_DISABLE_STATIC
-AC_LIBLTDL_CONVENIENCE(../libltdl)
-AC_SUBST(INCLTDL)
-AC_SUBST(LIBLTDL)
-AC_LIBTOOL_DLOPEN
-AC_PROG_LIBTOOL
-
-dnl to circumvent libltdl weirdness (already fixed in the newer versions)
-case $host_os in
-  *cygwin* | *mingw* | *win32*)
-    CPPFLAGS="$CPPFLAGS -DLT_SCOPE=extern"
-    ;;
-esac
-
-rm -f conftest
-./libtool --config > conftest
-. ./conftest
-rm -f conftest
-
-dnl compatibility for libtool 1.5.6
-
-LTDL_SHLIB_EXT=""
-if test -n "$shrext_cmds"; then
-    module=yes eval LTDL_SHLIB_EXT=\"$shrext_cmds\"
-    AC_SUBST(LTDL_SHLIB_EXT)
-dnl compatibility for libtool 1.5.0
-elif test -n "$shrext"; then
-    LTDL_SHLIB_EXT=$shrext
-    AC_SUBST(LTDL_SHLIB_EXT)
-dnl compatibility for libtool 1.4.x
-else
-  AC_CACHE_CHECK([which extension is used for shared libraries],
-    libltdl_cv_shlibext, [dnl
-  (
-    last=
-    for spec in $library_names_spec; do
-      last="$spec"
-    done
-  changequote(, )
-    echo "$last" | sed 's/\[.*\]//;s/^[^.]*//;s/\$.*$//;s/\.$//' > conftest
-  changequote([, ])
-  )
-  libltdl_cv_shlibext=`cat conftest`
-  rm -f conftest
-  ])
-  if test -n "$libltdl_cv_shlibext"; then
-    LTDL_SHLIB_EXT=$libltdl_cv_shlibext
-    AC_SUBST(LTDL_SHLIB_EXT)
-  fi
-fi
-
-
-
-AM_PATH_PYTHON(2.2)
-AC_SUBST(PYTHON)
-
-AC_LANG([C++])
-
-dnl Checks for libraries.
-
-dnl assuming libc and libm always present...
-
-AC_CHECK_LIB(m, sin, LIBM="-lm")
-AC_SUBST(LIBM)
-dnl
-AC_CHECK_LIB(c, open, LIBC="-lc")
-AC_SUBST(LIBC)
-dnl
-
-ECELL_CHECK_GSL
-
-AM_CHECK_PYMOD(numpy,,,[AC_MSG_ERROR([could not find Python numpy module])])
-AM_CHECK_PYMOD(xml,,,[AC_MSG_ERROR([could not find Python xml module])])
-
-if test "$enable_gui" = 'yes'; then
-   AM_CHECK_PYMOD(pygtk,,,[AC_MSG_ERROR([could not find Python pygtk module])])
-   AM_CHECK_PYMOD(gtk,,,[AC_MSG_ERROR([could not find Python gtk module])])
-   AM_CHECK_PYMOD(gtk.gdk,,,
-                [AC_MSG_ERROR([could not find Python gtk.gdk module])])
-   AM_CHECK_PYMOD(gtk.glade,,,
-                [AC_MSG_ERROR([could not find Python gtk.glade module])])
-   AM_CHECK_PYMOD(gnome.ui,,[AC_SUBST([GNOME_INSTALLED],yes)],[AC_SUBST([GNOME_INSTALLED],no)])
-   AM_CHECK_PYMOD(gnomecanvas,,,[AC_MSG_WARN(could not find gnomecanvas module. model-editor will not work. )])
-   AM_CHECK_PYMOD(xml.dom.minidom,,,[AC_MSG_WARN(could not find xml.dom.minidom module. model-editor will not work.)])
-fi
-
-
-dnl Checks for header files.
-
-AC_HEADER_DIRENT
-AC_HEADER_STDC
-
-AC_CHECK_HEADERS([fcntl.h unistd.h memory.h sys/stat.h sys/types.h sys/mman.h sys/param.h sys/statvfs.h sys/statfs.h sys/mount.h sys/vfs.h])
-AC_CHECK_HEADERS([unordered_map tr1/unordered_map])
-AC_CHECK_HEADERS([windows.h])
-
-AC_CHECK_HEADERS([stdint.h], [
-  INT64_T_DECLARATION="#include <stdint.h>"
-], [
-  AC_CHECK_TYPE([long long], [
-    INT64_T_DECLARATION="typedef long long int64_t; typedef unsigned long long uint64_t;"
-  ], [
-    AC_CHECK_TYPE([__int64], [
-      INT64_T_DECLARATION="typedef __int64 int64_t; typedef unsigned __int64 uint64_t;"
-    ], [
-      INT64_T_DECLARATION=
-    ])
-  ])
-])
-AC_SUBST([INT64_T_DECLARATION])
-
-ECELL_CHECK_MATH_HEADER
-ECELL_CHECK_INFINITY
-ECELL_CHECK_HUGE_VAL
-ECELL_CHECK_NUMERIC_LIMITS_DOUBLE_INFINITY
-
-if test "$HAVE_NUMERIC_LIMITS_DOUBLE_INFINITY" = 1; then
-  INFINITY_VAL="std::numeric_limits<double>::infinity()"
-elif test "$HAVE_INFINITY" = 1; then
-  INFINITY_VAL="INFINITY"
-elif test "$HAVE_HUGE_VAL" = 1; then
-  INFINITY_VAL="HUGE_VAL"
-fi
-AC_SUBST([INFINITY_VAL])
-
-ECELL_CHECK_PRETTY_FUNCTION
-
-EXT_GUESS="../../../.. ../../.. ../.. ../ ./ $prefix /usr /usr/local /opt"
-
-dnl dmtool package
-
-if test "$DMTOOL_DIR" = "" ; then
-  AC_MSG_CHECKING( for dmtool dir)
-  ac_cv_dmtool_dir="no"
-  for ac_dir in $EXT_GUESS ; do
-    if test -d $ac_dir/dmtool ; then
-      ac_cv_dmtool_dir=`(cd $ac_dir ; pwd)`
-      DMTOOL_DIR=$ac_cv_dmtool_dir
-    fi
-  done
-
-  if test "$DMTOOL_DIR" = "" ; then        
-    AC_MSG_ERROR("dmtool not found.")
-  fi
-
-  AC_MSG_RESULT($ac_cv_dmtool_dir)
-  DMTOOL_DIR=$ac_cv_dmtool_dir
-  DMTOOL_INCLUDE_DIR=$ac_cv_dmtool_dir
-fi
-AC_SUBST(DMTOOL_DIR)
-AC_SUBST(DMTOOL_INCLUDE_DIR)
-
-AM_CHECK_PYTHON_HEADERS(,[AC_MSG_ERROR([Failed to find Python headers.])])
-ECELL_CHECK_PYTHON_LIBS
-AM_CONDITIONAL([HAVE_PYTHON_LIB], [test ! -z "$PYTHON_LIBS"])
-AC_SUBST([PYTHON_LIBS])
-
-ECELL_CHECK_NUMPY
-
-AC_MSG_CHECKING( if use of compiler specific features are allowed )
-
-AC_ARG_ENABLE( compiler-extensions,,
-               USE_COMPILER_EXTENSIONS=$enable_compiler_features,
-               USE_COMPILER_EXTENSIONS=yes
-               )
-AC_MSG_RESULT( $USE_COMPILER_EXTENSIONS )
-
-if test "$USE_COMPILER_EXTENSIONS" != no ; then
-  AC_MSG_CHECKING( for special compiler options )
-  AC_SUBST(USE_COMPILER_EXTENSIONS)
-  AC_DEFINE([USE_COMPILER_EXTENSIONS],1,[make use of compiler specific language features])
-  CXXFLAGS="$CXXFLAGS -Wno-pmf-conversions"
-  AC_SUBST(CXXFLAGS)
-  AC_MSG_RESULT( $CXXFLAGS )
-fi
-   
-AC_LANG_PUSH([C])
-
-AC_SYS_LARGEFILE
-
-AC_C_CONST
-AC_C_INLINE
-if test "$ac_cv_c_inline" != no ; then
-  AC_DEFINE([HAVE_INLINE],1,[define if inline is supported])
-  AC_SUBST(HAVE_INLINE)
-fi
-
-AC_CHECK_TYPES([ssize_t],,,[
-#include <sys/types.h>
-])
-AC_TYPE_OFF_T
-AC_TYPE_SIZE_T
-AC_TYPE_SIGNAL
-AC_C_LONG_DOUBLE
-if test "$HAVE_LONG_DOUBLE" = 1; then
-  HIGHREAL_TYPE="long double"
-  HIGHREAL_IS_REAL=0
-else
-  HIGHREAL_TYPE="double"
-  HIGHREAL_IS_REAL=1
-fi
-AC_SUBST([HIGHREAL_TYPE])
-AC_SUBST([HIGHREAL_IS_REAL])
-
-AC_LANG_POP([])
-
-AC_CHECK_SIZEOF(int)
-AC_CHECK_SIZEOF(long)
-AC_CHECK_SIZEOF(long long)
-AC_CHECK_SIZEOF(double)
-AC_CHECK_SIZEOF(long double)
-
-
-dnl Checks for library functions.
-AC_TYPE_SIGNAL
-AC_CHECK_FUNCS(mkdir select strdup strerror strtod uname modf modfl)
-AC_CHECK_FUNCS(strdup strstr)
-
-AC_CONFIG_FILES([
-    Makefile
-    bin/Makefile
-    dm/Makefile
-    libecs/Defs.hpp  
-    libecs/Makefile
-    libecs/tests/Makefile
-    libemc/Makefile
-    pyecell/Makefile
-    pyecell/setup.py
-    pyecell/ecell/config.py
-    frontend/Makefile
-    frontend/session-monitor/Makefile
-    frontend/session-monitor/glade/Makefile
-    frontend/session-monitor/plugins/Makefile
-    frontend/model-editor/Makefile
-    frontend/model-editor/doc/Makefile
-    frontend/model-editor/glade/Makefile
-    frontend/model-editor/plugins/Makefile
-])
-AC_CONFIG_FILES([bin/ecell3-dmc], [chmod +x bin/ecell3-dmc])
-AC_CONFIG_FILES([pyecell/ecell3-python], [chmod +x pyecell/ecell3-python])
-AC_CONFIG_FILES([pyecell/ecell3-em2eml], [chmod +x pyecell/ecell3-em2eml])
-AC_CONFIG_FILES([pyecell/ecell3-eml2em], [chmod +x pyecell/ecell3-eml2em])
-AC_CONFIG_FILES([pyecell/ecell3-eml2sbml], [chmod +x pyecell/ecell3-eml2sbml])
-AC_CONFIG_FILES([pyecell/ecell3-sbml2eml], [chmod +x pyecell/ecell3-sbml2eml])
-AC_CONFIG_FILES([pyecell/ecell3-session], [chmod +x pyecell/ecell3-session])
-AC_CONFIG_FILES([pyecell/ecell3-session-manager], [chmod +x pyecell/ecell3-session-manager])
-AC_OUTPUT

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/config.py.in
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/config.py.in	2008-10-11 07:27:47 UTC (rev 3191)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/config.py.in	2008-10-11 07:35:21 UTC (rev 3192)
@@ -29,6 +29,7 @@
 
 __all__ = (
     'PACKAGE',
+    'PACkAGE_TARNAME',
     'per_app_dir_name',
     'version',
     'version_info',
@@ -55,6 +56,7 @@
         return os.path.abspath( sys.argv[0] )
 
 PACKAGE = "@PACKAGE@"
+PACKAGE_TARNAME = "@PACKAGE_TARNAME@"
 per_app_dir_name = "@ECELL_DIRNAME@"
 version = "@VERSION@"
 version_info = {

Modified: ecell3/branches/ecell-3.1/ecell_version.sh
===================================================================
--- ecell3/branches/ecell-3.1/ecell_version.sh	2008-10-11 07:27:47 UTC (rev 3191)
+++ ecell3/branches/ecell-3.1/ecell_version.sh	2008-10-11 07:35:21 UTC (rev 3192)
@@ -1,6 +1,6 @@
 ECELL_MAJOR_VERSION=3
 ECELL_MINOR_VERSION=1
-ECELL_MICRO_VERSION=106
-ECELL_PACKAGE_REVISION=
+ECELL_MICRO_VERSION=107
+ECELL_PACKAGE_REVISION=dev
 ECELL_VERSION_NUMBER=${ECELL_MAJOR_VERSION}.${ECELL_MINOR_VERSION}.${ECELL_MICRO_VERSION}${ECELL_PACKAGE_REVISION}
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3198] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-14 03:00:58

Revision: 3198
          http://ecell.svn.sourceforge.net/ecell/?rev=3198&view=rev
Author:   moriyoshi
Date:     2008-10-14 03:00:48 +0000 (Tue, 14 Oct 2008)

Log Message:
-----------
* Include configure.ac.in in the distribution.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/Makefile.am
    ecell3/branches/ecell-3.1/ecell/Makefile.am

Modified: ecell3/branches/ecell-3.1/Makefile.am
===================================================================
--- ecell3/branches/ecell-3.1/Makefile.am	2008-10-14 02:58:50 UTC (rev 3197)
+++ ecell3/branches/ecell-3.1/Makefile.am	2008-10-14 03:00:48 UTC (rev 3198)
@@ -16,7 +16,8 @@
 	$(BASIC_DOCS) \
 	depcomp \
 	autogen.sh \
-	ecell_version.sh
+	ecell_version.sh \
+	configure.ac.in
 
 doc_DATA = $(BASIC_DOCS)
 

Modified: ecell3/branches/ecell-3.1/ecell/Makefile.am
===================================================================
--- ecell3/branches/ecell-3.1/ecell/Makefile.am	2008-10-14 02:58:50 UTC (rev 3197)
+++ ecell3/branches/ecell-3.1/ecell/Makefile.am	2008-10-14 03:00:48 UTC (rev 3198)
@@ -2,10 +2,12 @@
 
 SUBDIRS = libecs libemc pyecell bin dm frontend
 
-ECELL_DIRNAME=@ECELL_DIRNAME@
+ECELL_DIRNAME = @ECELL_DIRNAME@
 
-ecellheaderdir=${includedir}/${ECELL_DIRNAME}
-ecellheader_HEADERS= ecell_config.h
+ecellheaderdir = ${includedir}/${ECELL_DIRNAME}
+ecellheader_HEADERS = ecell_config.h
 
+EXTRA_DIST = configure.ac.in
+
 clean-local:
 	$(RM) -rf tmp


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3214] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-19 05:07:07

Revision: 3214
          http://ecell.svn.sourceforge.net/ecell/?rev=3214&view=rev
Author:   moriyoshi
Date:     2008-10-19 05:06:49 +0000 (Sun, 19 Oct 2008)

Log Message:
-----------
* API renewal for e-cell 3.2.
  * Thoroughly overhauled buggy DM / PropertiedClass ABI:

    BACKWARDS BINARY COMPATIBILITY IS LOST.
    (source-level compatibility is maintained almost completely)

    * Add DynamicModuleDescriptor class that is defined per one dynamic module,
      and retains the information and a few set of function pointers that
      are required in the instantiation of the dynamic module's class.
    * Add DynamicModuleInfo interface by which the meta-information
      regarding the dyamic module can be retrieved.
    * DMObject::getClassInfo() now returns the pointer to the PropertyInterface
      instead of synthesized Polymorph map.
    * Make PropertyInterface a subclass of DynamicModuleInfo.
    * PropertyInterface singleton objects are now initialized from within the
      associated ModuleMaker's constructor, rather than by the static
      initializers.
    * Add PropertyAttributes class that provides the information about a
      property in a type-safe way (used in place of Polymorph).
    * Remove PropertyInterface::getPropertyList().
    * Add PropertyInterface::getPropertyAttributes().
    * DM search paths are now model specific. Remove libecs::setDMSearchPath()
      and libecs::getDMSearchPath() and intruduce
      libecs::Model::setDMSearchPath() and libecs::Model::getDMSearchPath()
      respectively.

  * Polymorph refactoring:

    * "De-virtualate" Polymorph class and make it refcounted for the sake of
      efficiency.  Remove ConcretePolymorphValue and PolymorphNoneValue
      accordingly.
    * Make PolymorphValue hold the extrusive containers for
      strings and tuples instead of std::string and std::vector.
    * Move enum Polymorph::Type to PolymorphValue.
    * Deprecate Polymorph::asTYPE() in favor of Polymorph::as<TYPE>().

  * Obsolete features

    * Remove CompartmentSystem

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
    ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp
    ecell3/branches/ecell-3.1/dmtool/Makefile.am
    ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
    ecell3/branches/ecell-3.1/ecell/dm/ExpressionProcessBase.hpp
    ecell3/branches/ecell-3.1/ecell/dm/FluxDistributionStepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/GMAProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/PythonProcessBase.hpp
    ecell3/branches/ecell-3.1/ecell/dm/SSystemProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.cpp
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Constants.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/DMInfo.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ModelStore.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/PropertyEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell3-model-editor
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/opengui.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell3-session-monitor
    ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteEventStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteEventStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteTimeStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteTimeStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DynamicPriorityQueue.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Entity.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/EntityType.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/EventScheduler.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Exceptions.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/FullID.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Interpolant.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Logger.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Logger.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/LoggerAdapter.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/LoggerBroker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Makefile.am
    ecell3/branches/ecell-3.1/ecell/libecs/MethodProxy.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Model.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Model.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PassiveStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PhysicalLogger.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Polymorph.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Process.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Process.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/ProcessEvent.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedObjectMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertyInterface.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertyInterface.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlot.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxy.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxyLoggerAdapter.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Stepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/StepperEvent.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/System.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/SystemStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Util.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Variable.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Variable.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/VariableReference.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/convertTo.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/libecs.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/libecs.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/tests/Makefile.am
    ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.hpp
    ecell3/branches/ecell-3.1/ecell/libemc/Simulator.hpp
    ecell3/branches/ecell-3.1/ecell/libemc/SimulatorImplementation.hpp
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/Session.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/_ecs.cpp
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/ecs_constants.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-em2eml.in
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-eml2em.in
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-eml2sbml.in
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-sbml2eml.in
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-session-manager.in
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-session.in

Added Paths:
-----------
    ecell3/branches/ecell-3.1/dmtool/DMException.hpp
    ecell3/branches/ecell-3.1/dmtool/DynamicModuleDescriptor.hpp
    ecell3/branches/ecell-3.1/dmtool/DynamicModuleInfo.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertyAttributes.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/tests/Polymorph_test.cpp

Removed Paths:
-------------
    ecell3/branches/ecell-3.1/ecell/libecs/Polymorph.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/ProcessMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/ProcessMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedObjectMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/StepperMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/StepperMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/SystemMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/SystemMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/VariableMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/VariableMaker.hpp

Added: ecell3/branches/ecell-3.1/dmtool/DMException.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DMException.hpp	                        (rev 0)
+++ ecell3/branches/ecell-3.1/dmtool/DMException.hpp	2008-10-19 05:06:49 UTC (rev 3214)
@@ -0,0 +1,67 @@
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//       This file is part of the E-Cell System
+//
+//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 2005-2008 The Molecular Sciences Institute
+//
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//
+// E-Cell System is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public
+// License as published by the Free Software Foundation; either
+// version 2 of the License, or (at your option) any later version.
+// 
+// E-Cell System is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+// See the GNU General Public License for more details.
+// 
+// You should have received a copy of the GNU General Public
+// License along with E-Cell System -- see the file COPYING.
+// If not, write to the Free Software Foundation, Inc.,
+// 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+// 
+//END_HEADER
+
+#ifndef __DM_EXCEPTION_HPP
+#define __DM_EXCEPTION_HPP
+
+#include <exception>
+#include <string>
+
+/**
+   Exception class for dmtool.
+*/
+class DMException : public std::exception
+{
+public: 
+
+  DMException( const std::string& message ) 
+    : 
+    theMessage( message )
+  {
+    ; // do nothing
+  }
+
+  ~DMException() throw()
+  {
+    ; // do nothing
+  }
+
+  /**
+     Get dynamically created exception message.
+   */
+  virtual const char* what() const throw()
+  { 
+    return theMessage.c_str();
+  }
+
+private:
+  
+  const std::string theMessage;
+
+};
+
+#endif /* __DM_EXCEPTION_HPP */


Property changes on: ecell3/branches/ecell-3.1/dmtool/DMException.hpp
___________________________________________________________________
Added: svn:mime-type
   + text/plain
Added: svn:eol-style
   + native

Modified: ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DMObject.hpp	2008-10-14 10:12:22 UTC (rev 3213)
+++ ecell3/branches/ecell-3.1/dmtool/DMObject.hpp	2008-10-19 05:06:49 UTC (rev 3214)
@@ -28,37 +28,36 @@
 #ifndef __DMOBJECT_HPP
 #define __DMOBJECT_HPP
 
-
 #ifdef WIN32
 #define DM_IF __declspec(dllexport)
 #else
 #define DM_IF
 #endif /* WIN32 */
 
-/// an allocator function template
+#include "dmtool/DynamicModuleDescriptor.hpp"
 
-template< class Base, class Derived >
-Base* ObjectAllocator()
-{
-  return new Derived;
-}
+#define DM_DESCRIPTOR_ENTRY( CLASSNAME ) \
+    { \
+        #CLASSNAME, \
+        &CLASSNAME::createInstance, \
+        &CLASSNAME::getClassInfoPtr, \
+        &CLASSNAME::initializeModule, \
+    }
 
-
-
-#define DM_INIT( CLASSNAME, TYPE )\
+#define DM_INIT( CLASSNAME )\
   extern "C"\
   {\
-    DM_IF TYPE::AllocatorFuncPtr CreateObject =\
-    &ObjectAllocator<TYPE,CLASSNAME>;\
-    DM_IF const char* __DM_CLASSNAME = #CLASSNAME;\
-    DM_IF const char* __DM_TYPE = #TYPE;\
-    DM_IF const void *(*GetClassInfo)() = &CLASSNAME::getClassInfoPtr;\
+    DM_IF DynamicModuleDescriptor __dm_descriptor = DM_DESCRIPTOR_ENTRY( CLASSNAME ); \
   } // 
 
+#define DM_NEW_STATIC( MAKER, BASE, CLASSNAME )\
+  { \
+    static DynamicModuleDescriptor desc = DM_DESCRIPTOR_ENTRY( CLASSNAME ); \
+    ( MAKER )->addClass( new StaticDynamicModule< BASE >( desc ) ); \
+  } //
 
-#define DM_OBJECT( CLASSNAME, TYPE )\
- static TYPE* createInstance() { return new CLASSNAME ; }\
- static const char *getTypeName() { return #TYPE; }
+#define DM_OBJECT( CLASSNAME )\
+ static void* createInstance() { return new CLASSNAME ; }\
 
 
 #define DM_BASECLASS( CLASSNAME )\

Modified: ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp	2008-10-14 10:12:22 UTC (rev 3213)
+++ ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp	2008-10-19 05:06:49 UTC (rev 3214)
@@ -28,235 +28,175 @@
 #ifndef __DYNAMICMODULE_HPP
 #define __DYNAMICMODULE_HPP
 
-#include <exception>
-#include <string>
-#include "ltdl.h"
+#include "dmtool/DMException.hpp"
+#include "dmtool/DynamicModuleDescriptor.hpp"
+#include <ltdl.h>
 
-#if defined(WIN32) || defined(_WIN32)
-#undef GetClassInfo
-#endif /* _WIN32 */
-
 /// doc needed
 
-#define SimpleAllocator( BASE ) BASE* (*)()
-typedef const void*(*InfoLoaderType)();
-
-/**
-   Exception class for dmtool.
-*/
-
-class DMException : public std::exception
+template< typename T >
+struct SimpleAllocatorDef
 {
-public: 
+    typedef T* (*type)();
+};
 
-  DMException( const std::string& message ) 
-    : 
-    theMessage( message )
-  {
-    ; // do nothing
-  }
-
-  ~DMException() throw()
-  {
-    ; // do nothing
-  }
-
-  /**
-     Get dynamically created exception message.
-   */
-
-  const char* what() const throw()
-  { 
-    return theMessage.c_str();
-  }
-
-private:
-  
-  const std::string theMessage;
-
+enum DynamicModuleType
+{
+    DM_TYPE_STATIC,
+    DM_TYPE_SHARED
 };
 
+class DynamicModuleInfo;
+
 /**
   Common base class of DynamicModule and SharedDynamicModule
 */
   
-template <class Base,class _TAllocator = SimpleAllocator( Base )>
-class DynamicModuleBase
+template < class T, class _TAllocator = typename SimpleAllocatorDef< T >::type >
+class DynamicModule
 {
 public:
 
-  typedef _TAllocator DMAllocator;
+    typedef _TAllocator DMAllocator;
+    typedef const char* (DynamicModule::*FileNameGetterType)() const;
+    typedef void (DynamicModule::*FinalizerType)();
 
-public:		
+public:        
 
-  DynamicModuleBase( const std::string& moduleName,
-                     DMAllocator allocator,
-                     InfoLoaderType infoLoader,
-                     const std::string& typeName = "" );
-  virtual ~DynamicModuleBase(){}
-  
-  const std::string& getModuleName() const
-  {
-    return this->theModuleName;
-  }
+    DynamicModule( DynamicModuleDescriptor const& desc,
+                   enum DynamicModuleType aType,
+                   FileNameGetterType aFileNameGetter = 0,
+                   FinalizerType aFinalizer = 0 )
+        : theDescriptor( desc ), theFileNameGetter( aFileNameGetter ),
+          theFinalizer( aFinalizer )
+    {
+        desc.moduleInitializer();
+    }
 
-  virtual const std::string getFileName() const
-  {
-    return "";
-  }
+    ~DynamicModule()
+    {
+        if ( theFinalizer )
+            (this->*theFinalizer)();
+    }
 
-  const DMAllocator& getAllocator() const
-  {
-    return this->theAllocator;
-  }
+    const DynamicModuleDescriptor& getDescriptor()
+    {
+        return theDescriptor;
+    }
+ 
+    const char* getModuleName() const
+    {
+        return theDescriptor.moduleName;
+    }
 
-  const InfoLoaderType& getInfoLoader() const
-  {
-	return this->theInfoLoader;
-  }
+    const char* getFileName() const
+    {
+        return theFileNameGetter ? (this->*theFileNameGetter)(): 0;
+    }
 
-  const std::string getTypeName() const
-  {
-    return this->theTypeName;
-  }
+    DMAllocator getAllocator() const
+    {
+        return reinterpret_cast< DMAllocator >( theDescriptor.allocator );
+    }
 
+    const DynamicModuleInfo* getInfo() const
+    {
+        return theDescriptor.infoLoader ? (*theDescriptor.infoLoader)(): 0;
+    }
+
+    enum DynamicModuleType getType() const
+    {
+        return theType;
+    }
+
 protected:
 
-  const std::string theModuleName;
-  DMAllocator theAllocator;
-  InfoLoaderType theInfoLoader;
-  const std::string theTypeName;
+    DynamicModuleDescriptor const& theDescriptor;
+
+    FileNameGetterType theFileNameGetter;
+
+    FinalizerType theFinalizer;
+
+    enum DynamicModuleType theType;
 };
 
 
 /**
-   DynamicModule instantiates objects of a single class.
-*/
-
-template <class Base,class Derived,class DMAllocator = SimpleAllocator( Base )>
-class DynamicModule
-  :
-  public DynamicModuleBase< Base, DMAllocator >
+   StaticDynamicModule is a class statically linked to the binary
+   that utilizes ModuleMaker
+ */
+template < class T, class DMAllocator = typename SimpleAllocatorDef< T >::type >
+class StaticDynamicModule : public DynamicModule< T, DMAllocator >
 {
+public:
 
+    typedef DynamicModule< T, DMAllocator > Base;    
+
 public:
 
-  DynamicModule( const std::string& moduleName,
-		 const std::string& typeName = "" );
-  virtual ~DynamicModule(){}
+    StaticDynamicModule( DynamicModuleDescriptor const& desc )
+        : DynamicModule< T, DMAllocator >( desc, DM_TYPE_STATIC )
+    {
+        ; // do nothing
+    }
 };
 
-
-
 /**
    SharedDynamicModule loads a class from a shared object file
    and instantiate objects of the loaded class.
    It opens and loads a shared object(.so) file into memory
    when constructed. It closes the file when deleted.
 
-   The shared object must have followings:
-     - T* CreateObject()       - which returns a new object.
-   and
-     - void* GetClassInfo()    - which must be reinterpreted to PolymorphMap in libecs, sorry, 
-	 maybe later a pure string version should be implemented
-     - a full set of symbols needed to instantiate and use the class.
-*/
+   The shared object must have the following (in "C" signature):
+     - __dm_info                      - a DynamicModuleDescriptor
+                                        which holds the module information.
+ */
 
-template <class Base,class DMAllocator = SimpleAllocator( Base )>
-class SharedDynamicModule : public DynamicModuleBase< Base >
+template < class T, class DMAllocator = typename SimpleAllocatorDef< T >::type >
+class SharedDynamicModule : public DynamicModule< T, DMAllocator >
 {
+public:
 
+    typedef DynamicModule< T, DMAllocator > Base;    
+
 public:
 
-  SharedDynamicModule( const std::string& classname, DMAllocator allocator,
-                       InfoLoaderType infoLoader, const std::string& typeName,
-                       const std::string& fileName, lt_dlhandle handle );
-  virtual ~SharedDynamicModule();
-  const std::string getFileName() const;
+    SharedDynamicModule( DynamicModuleDescriptor const& desc,
+                         const std::string& fileName,
+                         lt_dlhandle handle )
+        : DynamicModule< T, DMAllocator >(
+            desc, DM_TYPE_SHARED,
+            reinterpret_cast< typename Base::FileNameGetterType >(
+                &SharedDynamicModule::getFileName ),
+            reinterpret_cast< typename Base::FinalizerType >(
+                &SharedDynamicModule::finalize ) )
+    {
+        ; // do nothing
+    }
 
 private:
 
-  lt_dlhandle theHandle;
-  std::string theFileName;
-  std::string theTypeName;
-};
+    void finalize()
+    {
+        if( this->theHandle )
+        {
+            lt_dlclose( this->theHandle );
+            this->theHandle = 0;
+        }
+    }
 
-/**
-   comments needed
-*/
 
-#define NewDynamicModule( BASE, DERIVED )\
-addClass( new DynamicModule< BASE, DERIVED >( #DERIVED, DERIVED::getTypeName() ) )
-
-/**
-   comments needed
-*/
-
-#define NewDynamicModuleWithAllocator( BASE, DERIVED, ALLOC )\
-addClass( new DynamicModule< BASE, DERIVED, ALLOC >( #DERIVED ) )
-
-
-//////////////////////////// begin implementation
-
-template < class Base, class DMAllocator >
-DynamicModuleBase< Base, DMAllocator >::
-DynamicModuleBase( const std::string& moduleName,
-		   DMAllocator allocator, InfoLoaderType infoLoader,
-		   const std::string& typeName )
-  : 
-  theModuleName( moduleName ),
-  theAllocator( allocator ),
-  theInfoLoader( infoLoader ),
-  theTypeName( typeName )
-{
-  ; // do nothing
-}
-
-template < class Base, class Derived, class DMAllocator >
-DynamicModule< Base, Derived, DMAllocator >::
-DynamicModule( const std::string& moduleName, const std::string& typeName )
-  : 
-  DynamicModuleBase<Base,DMAllocator>( moduleName,
-				       reinterpret_cast< DMAllocator >(
-                         &Derived::createInstance ),
-				       &Derived::getClassInfoPtr,
-				       typeName )
-{
-  ; // do nothing
-}
-
-template < class Base, class DMAllocator >
-SharedDynamicModule< Base, DMAllocator >::
-SharedDynamicModule( const std::string& classname, DMAllocator allocator,
-                     InfoLoaderType infoLoader, const std::string& typeName,
-                     const std::string& fileName, lt_dlhandle handle )
-  :
-  DynamicModuleBase<Base,DMAllocator>( classname, allocator, infoLoader,
-                                       typeName ), 
-  theFileName( fileName ),
-  theHandle( handle )
-{
-}
-
-template < class Base, class DMAllocator >
-SharedDynamicModule<Base,DMAllocator>::~SharedDynamicModule()
-{
-
-  if( this->theHandle )
+    const char* getFileName() const
     {
-      lt_dlclose( this->theHandle );
-      this->theHandle = 0;
+        return theFileName.c_str();
     }
-}
 
+private:
 
+    lt_dlhandle theHandle;
+    std::string theFileName;
+};
 
-template < class Base, class DMAllocator >
-const std::string SharedDynamicModule<Base,DMAllocator>::getFileName() const
-{
-  return this->theFileName;
-}
-
 #endif /* __DYNAMICMODULE_HPP */
 
 /*

Added: ecell3/branches/ecell-3.1/dmtool/DynamicModuleDescriptor.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DynamicModuleDescriptor.hpp	                        (rev 0)
+++ ecell3/branches/ecell-3.1/dmtool/DynamicModuleDescriptor.hpp	2008-10-19 05:06:49 UTC (rev 3214)
@@ -0,0 +1,49 @@
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//       This file is part of the E-Cell System
+//
+//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 2005-2008 The Molecular Sciences Institute
+//
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//
+// E-Cell System is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public
+// License as published by the Free Software Foundation; either
+// version 2 of the License, or (at your option) any later version.
+// 
+// E-Cell System is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+// See the GNU General Public License for more details.
+// 
+// You should have received a copy of the GNU General Public
+// License along with E-Cell System -- see the file COPYING.
+// If not, write to the Free Software Foundation, Inc.,
+// 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+// 
+//END_HEADER
+
+#ifndef __DYNAMIC_MODULE_DESCRIPTOR_HPP
+#define __DYNAMIC_MODULE_DESCRIPTOR_HPP
+
+#include "dmtool/DynamicModuleInfo.hpp"
+
+/**
+  DynamicModuleDescriptor is a POD class that holds the information about
+  the module.
+ */
+struct DynamicModuleDescriptor
+{
+    typedef void* (*AllocatorType)();
+    typedef const DynamicModuleInfo* (*InfoLoaderType)();
+    typedef void (*ModuleInitializerType)();
+
+    const char* moduleName;
+    AllocatorType allocator;
+    InfoLoaderType infoLoader;
+    ModuleInitializerType moduleInitializer;
+};
+
+#endif /* __DYNAMIC_MODULE_DESCRIPTOR_HPP */


Property changes on: ecell3/branches/ecell-3.1/dmtool/DynamicModuleDescriptor.hpp
___________________________________________________________________
Added: svn:mime-type
   + text/plain
Added: svn:eol-style
   + native

Added: ecell3/branches/ecell-3.1/dmtool/DynamicModuleInfo.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DynamicModuleInfo.hpp	                        (rev 0)
+++ ecell3/branches/ecell-3.1/dmtool/DynamicModuleInfo.hpp	2008-10-19 05:06:49 UTC (rev 3214)
@@ -0,0 +1,57 @@
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//       This file is part of the E-Cell System
+//
+//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 2005-2008 The Molecular Sciences Institute
+//
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//
+// E-Cell System is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public
+// License as published by the Free Software Foundation; either
+// version 2 of the License, or (at your option) any later version.
+// 
+// E-Cell System is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+// See the GNU General Public License for more details.
+// 
+// You should have received a copy of the GNU General Public
+// License along with E-Cell System -- see the file COPYING.
+// If not, write to the Free Software Foundation, Inc.,
+// 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+// 
+//END_HEADER
+
+#ifndef __DYNAMIC_MODULE_INFO_HPP
+#define __DYNAMIC_MODULE_INFO_HPP
+
+#include <string>
+#include <utility>
+
+/**
+  DynamicModuleInfo defines an interface that provides the meta-information
+  that can be used to annotate the module.
+ */
+class DynamicModuleInfo
+{
+public:
+    class EntryIterator
+    {
+    public:
+        virtual ~EntryIterator() {}
+
+        virtual bool next() = 0;
+
+        virtual std::pair< std::string, const void* > current() = 0;
+    };
+
+public:
+    virtual ~DynamicModuleInfo() {}
+    virtual const void* getInfoField( std::string const& aFieldName ) const = 0;
+    virtual EntryIterator* getInfoFields() const = 0;
+};
+
+#endif /* __DYNAMIC_MODULE_INFO_HPP */


Property changes on: ecell3/branches/ecell-3.1/dmtool/DynamicModuleInfo.hpp
___________________________________________________________________
Added: svn:mime-type
   + text/plain
Added: svn:eol-style
   + native

Modified: ecell3/branches/ecell-3.1/dmtool/Makefile.am
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/Makefile.am	2008-10-14 10:12:22 UTC (rev 3213)
+++ ecell3/branches/ecell-3.1/dmtool/Makefile.am	2008-10-19 05:06:49 UTC (rev 3214)
@@ -1,6 +1,12 @@
-AUTOMAKE_OPTIONS=foreign
+AUTOMAKE_OPTIONS = foreign
 
-pkginclude_HEADERS=DynamicModule.hpp ModuleMaker.hpp DMObject.hpp
+pkginclude_HEADERS = \
+	DynamicModule.hpp\
+	DynamicModuleInfo.hpp\
+	DynamicModuleDescriptor.hpp\
+	DMException.hpp\
+	ModuleMaker.hpp\
+	DMObject.hpp 
 
 bin_SCRIPTS = dmcompile
 

Modified: ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp	2008-10-14 10:12:22 UTC (rev 3213)
+++ ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp	2008-10-19 05:06:49 UTC (rev 3214)
@@ -1,9 +1,9 @@
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 //
-//       This file is part of the E-Cell System
+//             This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
-//       Copyright (C) 2005-2008 The Molecular Sciences Institute
+//             Copyright (C) 1996-2008 Keio University
+//             Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 //
@@ -31,18 +31,14 @@
 
 #include <iostream>
 #include <map>
+#include <set>
 #include <string>
-#include <assert.h>
+#include <cassert>
 #include "ltdl.h"
 #include "DynamicModule.hpp"
 
-/// doc needed
-
-#define DynamicModuleEntry( T )\
-addClass( new Module( std::string( #T ), &T::createInstance, &T::getClassInfoPtr ) );
-
 /**
-   A base class for ModuleMakers
+     A base class for ModuleMakers
  */
 
 class ModuleMaker
@@ -50,377 +46,256 @@
 
 public:
 
-  ModuleMaker() 
-    : 
-    theNumberOfInstances( 0 ) 
-  {
-    ; // do nothing
-  }
+    ModuleMaker()
+    {
+        ; // do nothing
+    }
 
-  virtual ~ModuleMaker() 
-  {
-    ; // do nothing
-  }
+    virtual ~ModuleMaker() 
+    {
+        ; // do nothing
+    }
 
-  static void setSearchPath( const std::string& path )
-  {
-    int error = lt_dlsetsearchpath( path.c_str() );
-    if( error != 0 )
-      {
-	throw DMException( lt_dlerror() );
-      }
-  }
+    void setSearchPath( const std::string& path )
+    {
+        theSearchPath.clear();
+        for ( std::string::size_type i( 0 ), end( path.size() ), next( 0 );
+              i < end; i = next + 1 )
+        {
+            next = path.find( PATH_SEPARATOR, i );
+            next = next == std::string::npos ? end: next;
+            if ( next > i )
+            {
+                theSearchPath.insert( path.substr( i, next - i ) );
+            }
+        }
+    }
 
-  static const std::string getSearchPath()
-  {
-    const char* aSearchPath( lt_dlgetsearchpath() );
-    if( aSearchPath == 0 )
-      {
-	return "";
-      }
-    else
-      {
-	return aSearchPath;
-      }
-  }
+    const std::string getSearchPath() const
+    {
+        typedef std::set< std::string > StringSet;
+        std::string retval;
 
-  /**
-    Initializes the dynamic module facility.
-    Applications that use this library must call this function
-    prior to any operation involved with the facility.
-    @return true on error, false otherwise.
-   */
-  static bool initialize()
-  {
-    return lt_dlinit() > 0 ? true: false;
-  }
+        for ( StringSet::const_iterator i( theSearchPath.begin() );
+              i != theSearchPath.end(); ++i )
+        {
+            retval += (*i);
+            retval += PATH_SEPARATOR; 
+        }
+        if ( !retval.empty() )
+            retval.resize( retval.size() - 1 );
+        return retval;
+    }
 
-  /**
-    Finalizes the dynamic module facility.
-    Applications that use this library must call this function when
-    the facility is no longer necessary so that allocated resources
-    can be reclaimed.
-    @return true on error, false otherwise.
-   */
-  static void finalize()
-  {
-    lt_dl...
 
[truncated message content]

[Ecell-cvs] SF.net SVN: ecell:[3220] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-19 14:46:52

Revision: 3220
          http://ecell.svn.sourceforge.net/ecell/?rev=3220&view=rev
Author:   moriyoshi
Date:     2008-10-19 14:46:45 +0000 (Sun, 19 Oct 2008)

Log Message:
-----------
* Fixing win32 build.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/build/msvc/dist.wsf
    ecell3/branches/ecell-3.1/build/msvc/ecell.sln
    ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj
    ecell3/branches/ecell-3.1/build/msvc/libemc.vcproj
    ecell3/branches/ecell-3.1/build/msvc/model-editor.vcproj
    ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj
    ecell3/branches/ecell-3.1/build/msvc/session-monitor.vcproj
    ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
    ecell3/branches/ecell-3.1/dmtool/DynamicModuleDescriptor.hpp
    ecell3/branches/ecell-3.1/dmtool/DynamicModuleInfo.hpp
    ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlot.hpp

Removed Paths:
-------------
    ecell3/branches/ecell-3.1/build/msvc/pyecs.vcproj

Property Changed:
----------------
    ecell3/branches/ecell-3.1/ecell/dm/

Modified: ecell3/branches/ecell-3.1/build/msvc/dist.wsf
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/ecell.sln
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj	2008-10-19 14:33:40 UTC (rev 3219)
+++ ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj	2008-10-19 14:46:45 UTC (rev 3220)
@@ -48,7 +48,7 @@
 				Name="VCCLCompilerTool"
 				Optimization="0"
 				AdditionalIncludeDirectories="..\..\libltdl;..\..\osdep\win32;..\..;..\..\ecell;..\..\ecell\libecs;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE)"
-				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;DM_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
 				MinimalRebuild="true"
 				ExceptionHandling="1"
 				BasicRuntimeChecks="3"
@@ -134,7 +134,7 @@
 				Name="VCCLCompilerTool"
 				Optimization="0"
 				AdditionalIncludeDirectories="..\..\libltdl;..\..\osdep\win32;..\..;..\..\ecell;..\..\ecell\libecs;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE)"
-				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;DM_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
 				MinimalRebuild="true"
 				ExceptionHandling="1"
 				BasicRuntimeChecks="3"
@@ -219,7 +219,7 @@
 			<Tool
 				Name="VCCLCompilerTool"
 				AdditionalIncludeDirectories="..\..\libltdl;..\..\osdep\win32;..\..;..\..\ecell;..\..\ecell\libecs;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE)"
-				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
+				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;DM_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
 				ExceptionHandling="1"
 				RuntimeLibrary="2"
 				UsePrecompiledHeader="0"
@@ -305,7 +305,7 @@
 			<Tool
 				Name="VCCLCompilerTool"
 				AdditionalIncludeDirectories="..\..\libltdl;..\..\osdep\win32;..\..;..\..\ecell;..\..\ecell\libecs;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE)"
-				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
+				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;DM_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
 				ExceptionHandling="1"
 				RuntimeLibrary="2"
 				UsePrecompiledHeader="0"
@@ -450,26 +450,14 @@
 				>
 			</File>
 			<File
-				RelativePath="..\..\ecell\libecs\Polymorph.cpp"
-				>
-			</File>
-			<File
 				RelativePath="..\..\ecell\libecs\Process.cpp"
 				>
 			</File>
 			<File
-				RelativePath="..\..\ecell\libecs\ProcessMaker.cpp"
-				>
-			</File>
-			<File
 				RelativePath="..\..\ecell\libecs\PropertiedClass.cpp"
 				>
 			</File>
 			<File
-				RelativePath="..\..\ecell\libecs\PropertiedObjectMaker.cpp"
-				>
-			</File>
-			<File
 				RelativePath="..\..\ecell\libecs\PropertyInterface.cpp"
 				>
 			</File>
@@ -486,18 +474,10 @@
 				>
 			</File>
 			<File
-				RelativePath="..\..\ecell\libecs\StepperMaker.cpp"
-				>
-			</File>
-			<File
 				RelativePath="..\..\ecell\libecs\System.cpp"
 				>
 			</File>
 			<File
-				RelativePath="..\..\ecell\libecs\SystemMaker.cpp"
-				>
-			</File>
-			<File
 				RelativePath="..\..\ecell\libecs\SystemStepper.cpp"
 				>
 			</File>
@@ -510,10 +490,6 @@
 				>
 			</File>
 			<File
-				RelativePath="..\..\ecell\libecs\VariableMaker.cpp"
-				>
-			</File>
-			<File
 				RelativePath="..\..\ecell\libecs\VariableReference.cpp"
 				>
 			</File>
@@ -660,6 +636,10 @@
 				>
 			</File>
 			<File
+				RelativePath="..\..\ecell\libecs\PropertyAttributes.hpp"
+				>
+			</File>
+			<File
 				RelativePath="..\..\ecell\libecs\PropertyInterface.hpp"
 				>
 			</File>
@@ -725,10 +705,6 @@
 			Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav"
 			UniqueIdentifier="{67DA6AB6-F800-4c08-8B7A-83BB121AAD01}"
 			>
-			<File
-				RelativePath=".\ecs.rct"
-				>
-			</File>
 		</Filter>
 		<Filter
 			Name="Templates"

Modified: ecell3/branches/ecell-3.1/build/msvc/libemc.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/libemc.vcproj	2008-10-19 14:33:40 UTC (rev 3219)
+++ ecell3/branches/ecell-3.1/build/msvc/libemc.vcproj	2008-10-19 14:46:45 UTC (rev 3220)
@@ -361,10 +361,6 @@
 				RelativePath="..\..\ecell\libemc\SimulatorImplementation.cpp"
 				>
 			</File>
-			<File
-				RelativePath="..\..\ecell\libemc\SimulatorMaker.cpp"
-				>
-			</File>
 		</Filter>
 		<Filter
 			Name="Header Files"
@@ -387,10 +383,6 @@
 				RelativePath="..\..\ecell\libemc\SimulatorImplementation.hpp"
 				>
 			</File>
-			<File
-				RelativePath="..\..\ecell\libemc\SimulatorMaker.hpp"
-				>
-			</File>
 		</Filter>
 		<Filter
 			Name="Resource Files"

Modified: ecell3/branches/ecell-3.1/build/msvc/model-editor.vcproj
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj	2008-10-19 14:33:40 UTC (rev 3219)
+++ ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj	2008-10-19 14:46:45 UTC (rev 3220)
@@ -298,6 +298,10 @@
 				UniqueIdentifier="{4FC737F1-C7A5-4376-A066-2A32D752A2FF}"
 				>
 				<File
+					RelativePath="..\..\ecell\pyecell\ecell\_ecs.cpp"
+					>
+				</File>
+				<File
 					RelativePath="..\..\ecell\pyecell\ecell\_tableio.c"
 					>
 					<FileConfiguration
@@ -376,10 +380,26 @@
 					>
 				</File>
 				<File
+					RelativePath="..\..\ecell\pyecell\ecell\ecs.py"
+					>
+				</File>
+				<File
+					RelativePath="..\..\ecell\pyecell\ecell\ecs_constants.py"
+					>
+				</File>
+				<File
+					RelativePath="..\..\ecell\pyecell\ecell\ecssupport.py"
+					>
+				</File>
+				<File
 					RelativePath="..\..\ecell\pyecell\ecell\em.py"
 					>
 				</File>
 				<File
+					RelativePath="..\..\ecell\pyecell\ecell\emc.py"
+					>
+				</File>
+				<File
 					RelativePath="..\..\ecell\pyecell\ecell\eml.py"
 					>
 				</File>
@@ -625,7 +645,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)config.py"
 					/>
 				</FileConfiguration>
@@ -635,7 +655,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)config.py"
 					/>
 				</FileConfiguration>
@@ -645,7 +665,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)config.py"
 					/>
 				</FileConfiguration>
@@ -655,7 +675,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)config.py"
 					/>
 				</FileConfiguration>
@@ -669,7 +689,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-em2eml"
 					/>
 				</FileConfiguration>
@@ -679,7 +699,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-em2eml"
 					/>
 				</FileConfiguration>
@@ -689,7 +709,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-em2eml"
 					/>
 				</FileConfiguration>
@@ -699,7 +719,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-em2eml"
 					/>
 				</FileConfiguration>
@@ -713,7 +733,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-eml2em"
 					/>
 				</FileConfiguration>
@@ -723,7 +743,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-eml2em"
 					/>
 				</FileConfiguration>
@@ -733,7 +753,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-eml2em"
 					/>
 				</FileConfiguration>
@@ -743,7 +763,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-eml2em"
 					/>
 				</FileConfiguration>
@@ -757,7 +777,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-eml2sbml"
 					/>
 				</FileConfiguration>
@@ -767,7 +787,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-eml2sbml"
 					/>
 				</FileConfiguration>
@@ -777,7 +797,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-eml2sbml"
 					/>
 				</FileConfiguration>
@@ -787,7 +807,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-eml2sbml"
 					/>
 				</FileConfiguration>
@@ -801,7 +821,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-sbml2eml"
 					/>
 				</FileConfiguration>
@@ -811,7 +831,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-sbml2eml"
 					/>
 				</FileConfiguration>
@@ -821,7 +841,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-sbml2eml"
 					/>
 				</FileConfiguration>
@@ -831,7 +851,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-sbml2eml"
 					/>
 				</FileConfiguration>
@@ -845,7 +865,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-session-manager"
 					/>
 				</FileConfiguration>
@@ -855,7 +875,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-session-manager"
 					/>
 				</FileConfiguration>
@@ -865,7 +885,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-session-manager"
 					/>
 				</FileConfiguration>
@@ -875,7 +895,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-session-manager"
 					/>
 				</FileConfiguration>
@@ -889,7 +909,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-session"
 					/>
 				</FileConfiguration>
@@ -899,7 +919,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-session"
 					/>
 				</FileConfiguration>
@@ -909,7 +929,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-session"
 					/>
 				</FileConfiguration>
@@ -919,7 +939,7 @@
 					<Tool
 						Name="VCCustomBuildTool"
 						Description="Generating $(InputFileName)..."
-						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+						CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 						Outputs="$(InputDir)ecell3-session"
 					/>
 				</FileConfiguration>
@@ -934,7 +954,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -944,7 +964,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -954,7 +974,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -964,7 +984,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -978,7 +998,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Generating setup.py..."
-					CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+					CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 					Outputs="$(ProjectDir)..\..\ecell\pyecell\setup.py"
 				/>
 			</FileConfiguration>
@@ -988,7 +1008,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Generating setup.py..."
-					CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;"
+					CommandLine="cscript &quot;$(ProjectDir)\gen_file.wsf&quot; &quot;$(OutDir)&quot; &quot;$(ProjectDir)\..\..&quot; &quot;$(InputDir)$(InputName)&quot;&#x0D;&#x0A;"
 					Outputs="$(ProjectDir)..\..\ecell\pyecell\setup.py"
 				/>
 			</F...
 
[truncated message content]

[Ecell-cvs] SF.net SVN: ecell:[3222] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-19 15:45:50

Revision: 3222
          http://ecell.svn.sourceforge.net/ecell/?rev=3222&view=rev
Author:   moriyoshi
Date:     2008-10-19 15:45:40 +0000 (Sun, 19 Oct 2008)

Log Message:
-----------
* More win32 fixes.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/build/msvc/dm/ConstantFluxProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/DAEStepper.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/DecayFluxProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/ESSYNSStepper.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionAlgebraicProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionAssignmentProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionFluxProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/FixedDAE1Stepper.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/FixedODE1Stepper.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/FluxDistributionStepper.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/GMAProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/GillespieProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/MassActionFluxProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/MichaelisUniUniFluxProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/ODE23Stepper.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/ODE45Stepper.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/ODEStepper.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/PingPongBiBiFluxProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/PythonFluxProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/PythonProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/QuasiDynamicFluxProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/SSystemProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/TauLeapProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/TauLeapStepper.vcproj
    ecell3/branches/ecell-3.1/build/msvc/ecell.sln
    ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj
    ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
    ecell3/branches/ecell-3.1/ecell/dm/FluxDistributionStepper.hpp
    ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/ConstantFluxProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/ConstantFluxProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/ConstantFluxProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\ConstantFluxProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/DAEStepper.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/DAEStepper.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/DAEStepper.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\DAEStepper.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/DecayFluxProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/DecayFluxProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/DecayFluxProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\DecayFluxProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/ESSYNSStepper.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/ESSYNSStepper.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/ESSYNSStepper.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\ESSYNSStepper.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionAlgebraicProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionAlgebraicProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionAlgebraicProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -364,15 +364,6 @@
 				>
 			</File>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\ExpressionAlgebraicProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionAssignmentProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionAssignmentProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionAssignmentProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -364,15 +364,6 @@
 				>
 			</File>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\ExpressionAssignmentProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionFluxProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionFluxProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/ExpressionFluxProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -364,15 +364,6 @@
 				>
 			</File>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\ExpressionFluxProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/FixedDAE1Stepper.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/FixedDAE1Stepper.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/FixedDAE1Stepper.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -360,15 +360,6 @@
 				>
 			</File>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\FixedDAE1Stepper.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/FixedODE1Stepper.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/FixedODE1Stepper.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/FixedODE1Stepper.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -360,15 +360,6 @@
 				>
 			</File>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\FixedODE1Stepper.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/FluxDistributionStepper.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/FluxDistributionStepper.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/FluxDistributionStepper.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -64,9 +64,9 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib"
+				AdditionalDependencies="ecs.lib gsl.lib QuasiDynamicFluxProcess.lib"
 				LinkIncremental="2"
-				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
+				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(SolutionDir)$(PlatformName)\$(ConfigurationName)\dm;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
 				GenerateDebugInformation="true"
 				SubSystem="2"
 				TargetMachine="1"
@@ -143,9 +143,9 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib"
+				AdditionalDependencies="ecs.lib gsl.lib QuasiDynamicFluxProcess.lib"
 				LinkIncremental="2"
-				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
+				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(SolutionDir)$(PlatformName)\$(ConfigurationName)\dm;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
 				GenerateDebugInformation="true"
 				SubSystem="2"
 				TargetMachine="17"
@@ -219,9 +219,9 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib"
+				AdditionalDependencies="ecs.lib gsl.lib QuasiDynamicFluxProcess.lib"
 				LinkIncremental="1"
-				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
+				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(SolutionDir)$(PlatformName)\$(ConfigurationName)\dm;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
 				GenerateDebugInformation="true"
 				SubSystem="2"
 				OptimizeReferences="2"
@@ -298,9 +298,9 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib"
+				AdditionalDependencies="ecs.lib gsl.lib QuasiDynamicFluxProcess.lib"
 				LinkIncremental="1"
-				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
+				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(SolutionDir)$(PlatformName)\$(ConfigurationName)\dm;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
 				GenerateDebugInformation="true"
 				SubSystem="2"
 				OptimizeReferences="2"
@@ -359,13 +359,8 @@
 				RelativePath="..\..\..\ecell\dm\FluxDistributionStepper.hpp"
 				>
 			</File>
-		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
 			<File
-				RelativePath="..\..\..\ecell\dm\FluxDistributionStepper.desc"
-				DeploymentContent="true"
+				RelativePath="..\..\..\ecell\dm\QuasiDynamicFluxProcess.hpp"
 				>
 			</File>
 		</Filter>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/GMAProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/GMAProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/GMAProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\GMAProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/GillespieProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/GillespieProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/GillespieProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -360,15 +360,6 @@
 				>
 			</File>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\GillespieProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/MassActionFluxProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/MassActionFluxProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/MassActionFluxProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\MassActionFluxProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/MichaelisUniUniFluxProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/MichaelisUniUniFluxProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/MichaelisUniUniFluxProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\MichaelisUniUniFluxProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/ODE23Stepper.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/ODE23Stepper.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/ODE23Stepper.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\ODE23Stepper.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/ODE45Stepper.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/ODE45Stepper.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/ODE45Stepper.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -358,15 +358,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\ODE45Stepper.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/ODEStepper.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/ODEStepper.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/ODEStepper.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\ODEStepper.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/PingPongBiBiFluxProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/PingPongBiBiFluxProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/PingPongBiBiFluxProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\PingPongBiBiFluxProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/PythonFluxProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/PythonFluxProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/PythonFluxProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\PythonFluxProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/PythonProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/PythonProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/PythonProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -362,15 +362,6 @@
 				>
 			</File>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\PythonProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/QuasiDynamicFluxProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/QuasiDynamicFluxProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/QuasiDynamicFluxProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\QuasiDynamicFluxProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/SSystemProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/SSystemProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/SSystemProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -356,15 +356,6 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\SSystemProcess.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/TauLeapProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/TauLeapProcess.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/TauLeapProcess.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -355,13 +355,8 @@
 			Filter="h;hpp;hxx;hm;inl;inc;xsd"
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
-		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
 			<File
-				RelativePath="..\..\..\ecell\dm\TauLeapProcess.desc"
-				DeploymentContent="true"
+				RelativePath="..\..\..\ecell\dm\TauLeapProcess.hpp"
 				>
 			</File>
 		</Filter>

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/TauLeapStepper.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/TauLeapStepper.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/TauLeapStepper.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -64,9 +64,9 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib"
+				AdditionalDependencies="ecs.lib gsl.lib GillespieProcess.lib"
 				LinkIncremental="2"
-				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
+				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(SolutionDir)$(PlatformName)\$(ConfigurationName)\dm;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
 				GenerateDebugInformation="true"
 				SubSystem="2"
 				TargetMachine="1"
@@ -143,9 +143,9 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib"
+				AdditionalDependencies="ecs.lib gsl.lib GillespieProcess.lib"
 				LinkIncremental="2"
-				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
+				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(SolutionDir)$(PlatformName)\$(ConfigurationName)\dm;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
 				GenerateDebugInformation="true"
 				SubSystem="2"
 				TargetMachine="17"
@@ -219,9 +219,9 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib"
+				AdditionalDependencies="ecs.lib gsl.lib GillespieProcess.lib"
 				LinkIncremental="1"
-				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
+				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(SolutionDir)$(PlatformName)\$(ConfigurationName)\dm;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
 				GenerateDebugInformation="true"
 				SubSystem="2"
 				OptimizeReferences="2"
@@ -298,9 +298,9 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib"
+				AdditionalDependencies="ecs.lib gsl.lib GillespieProcess.lib"
 				LinkIncremental="1"
-				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
+				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(SolutionDir)$(PlatformName)\$(ConfigurationName)\dm;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
 				GenerateDebugInformation="true"
 				SubSystem="2"
 				OptimizeReferences="2"
@@ -364,15 +364,6 @@
 				>
 			</File>
 		</Filter>
-		<Filter
-			Name="Descriptor Files"
-			>
-			<File
-				RelativePath="..\..\..\ecell\dm\TauLeapStepper.desc"
-				DeploymentContent="true"
-				>
-			</File>
-		</Filter>
 	</Files>
 	<Globals>
 	</Globals>

Modified: ecell3/branches/ecell-3.1/build/msvc/ecell.sln
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
@@ -48,7 +48,7 @@
 				Name="VCCLCompilerTool"
 				Optimization="0"
 				AdditionalIncludeDirectories="..\..\libltdl;..\..\osdep\win32;..\..;..\..\ecell;..\..\ecell\libecs;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE)"
-				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;DM_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
 				MinimalRebuild="true"
 				ExceptionHandling="1"
 				BasicRuntimeChecks="3"
@@ -134,7 +134,7 @@
 				Name="VCCLCompilerTool"
 				Optimization="0"
 				AdditionalIncludeDirectories="..\..\libltdl;..\..\osdep\win32;..\..;..\..\ecell;..\..\ecell\libecs;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE)"
-				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;DM_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
+				PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
 				MinimalRebuild="true"
 				ExceptionHandling="1"
 				BasicRuntimeChecks="3"
@@ -219,7 +219,7 @@
 			<Tool
 				Name="VCCLCompilerTool"
 				AdditionalIncludeDirectories="..\..\libltdl;..\..\osdep\win32;..\..;..\..\ecell;..\..\ecell\libecs;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE)"
-				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;DM_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
+				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
 				ExceptionHandling="1"
 				RuntimeLibrary="2"
 				UsePrecompiledHeader="0"
@@ -305,7 +305,7 @@
 			<Tool
 				Name="VCCLCompilerTool"
 				AdditionalIncludeDirectories="..\..\libltdl;..\..\osdep\win32;..\..;..\..\ecell;..\..\ecell\libecs;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE)"
-				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;DM_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
+				PreprocessorDefinitions="WIN32;NDEBUG;_WINDOWS;_USRDLL;LIBECS_EXPORTS;GSL_DLL;HAVE_CONFIG_H;__STDC__=1;_WIN32_WINNT=0x500"
 				ExceptionHandling="1"
 				RuntimeLibrary="2"
 				UsePrecompiledHeader="0"

Modified: ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DMObject.hpp	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/dmtool/DMObject.hpp	2008-10-19 15:45:40 UTC (rev 3222)
@@ -29,11 +29,11 @@
 #define __DMOBJECT_HPP
 
 #ifdef WIN32
-#if defined( DM_EXPORTS ) || defined( DLL_EXPORT )
+#ifndef DM_IMPORTS
 #define DM_IF __declspec(dllexport)
 #else
 #define DM_IF __declspec(dllimport)
-#endif /* DM_EXPORTS */
+#endif /* !DM_IMPORTS */
 #else
 #define DM_IF
 #endif /* WIN32 */

Modified: ecell3/branches/ecell-3.1/ecell/dm/FluxDistributionStepper.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/dm/FluxDistributionStepper.hpp	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/ecell/dm/FluxDistributionStepper.hpp	2008-10-19 15:45:40 UTC (rev 3222)
@@ -52,9 +52,11 @@
 #include "Interpolant.hpp"
 #include "libecs/Stepper.hpp"
 #include "libecs/DifferentialStepper.hpp"
+
+#define DM_IMPORTS
 #include "QuasiDynamicFluxProcess.hpp"
+#undef DM_IMPORTS
 
-
 USE_LIBECS;
 
 LIBECS_DM_CLASS( FluxDistributionStepper, DifferentialStepper )

Modified: ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.cpp	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.cpp	2008-10-19 15:45:40 UTC (rev 3222)
@@ -32,7 +32,7 @@
 #include <gsl/gsl_randist.h>
 
 #include "TauLeapStepper.hpp"
- 
+
 LIBECS_DM_INIT( TauLeapStepper, Stepper );
 
 void TauLeapStepper::initialize()

Modified: ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.hpp	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.hpp	2008-10-19 15:45:40 UTC (rev 3222)
@@ -37,11 +37,13 @@
 #define NOMINMAX
 #endif /* WIN32 */
 
-#include "GillespieProcess.hpp"
-
 #include "libecs/DifferentialStepper.hpp"
 #include "libecs/libecs.hpp"
 
+#define DM_IMPORTS
+#include "GillespieProcess.hpp"
+#undef DM_IMPORTS
+
 USE_LIBECS;
 
 DECLARE_CLASS( GillespieProcess );

Modified: ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp	2008-10-19 15:22:22 UTC (rev 3221)
+++ ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp	2008-10-19 15:45:40 UTC (rev 3222)
@@ -90,9 +90,16 @@
 #define LIBECS_DM_INIT_STATIC( CLASSNAME, DMTYPE ) \
   template class PropertyInterface<CLASSNAME>;\
   char CLASSNAME::thePropertyInterface[sizeof(libecs::PropertyInterface<CLASSNAME>)]; \
-  char CLASSNAME::theDMTypeName[] = #DMTYPE;
+  char CLASSNAME::theDMTypeName[] = #DMTYPE; \
+  libecs::PropertyInterface<CLASSNAME>& CLASSNAME::_getPropertyInterface() \
+  { \
+    return *reinterpret_cast< libecs::PropertyInterface<CLASSNAME>* >( thePropertyInterface ); \
+  } \
+  void CLASSNAME::initializeModule() \
+  { \
+    new(thePropertyInterface) libecs::PropertyInterface<CLASSNAME>( #CLASSNAME, theDMTypeName ); \
+  }
 
-
   ///@internal
 #define LIBECS_DM_OBJECT_DEF( CLASSNAME, DMTYPE )\
   typedef DMTYPE _LIBECS_DMTYPE_;\
@@ -106,11 +113,9 @@
 private:\
  static char thePropertyInterface[sizeof(libecs::PropertyInterface<CLASSNAME>)]; \
  static char theDMTypeName[]; \
- static libecs::PropertyInterface<CLASSNAME>& _getPropertyInterface() \
- { \
-   return *reinterpret_cast< libecs::PropertyInterface<CLASSNAME>* >( thePropertyInterface ); \
- } \
+ static libecs::PropertyInterface<CLASSNAME>& _getPropertyInterface(); \
 public:\
+ static void initializeModule(); \
  virtual PropertySlotBaseCptr getPropertySlot( libecs::StringCref aPropertyName ) const \
  { \
   return _getPropertyInterface().getPropertySlot( aPropertyName ); \
@@ -151,10 +156,6 @@
  static const DynamicModuleInfo* getClassInfoPtr()\
  {\
   return static_cast<const DynamicModuleInfo*>( &_getPropertyInterface() );\
- } \
- static void ini...
 
[truncated message content]

[Ecell-cvs] SF.net SVN: ecell:[3223] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-19 16:35:34

Revision: 3223
          http://ecell.svn.sourceforge.net/ecell/?rev=3223&view=rev
Author:   moriyoshi
Date:     2008-10-19 16:35:20 +0000 (Sun, 19 Oct 2008)

Log Message:
-----------
* Win32 fixes. (more to come)

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/build/msvc/dist.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dist.wsf
    ecell3/branches/ecell-3.1/build/msvc/ecell.sln
    ecell3/branches/ecell-3.1/build/msvc/model-editor.vcproj
    ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj
    ecell3/branches/ecell-3.1/build/msvc/session-monitor.vcproj
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp

Modified: ecell3/branches/ecell-3.1/build/msvc/dist.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dist.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
+++ ecell3/branches/ecell-3.1/build/msvc/dist.vcproj	2008-10-19 16:35:20 UTC (rev 3223)
@@ -294,7 +294,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Preparing files to be distributed..."
-					CommandLine="SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages\numpy\core\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;SET LIBDIR=\lib&#x0D;&#x0A;SET BOOST_PYTHON_LIB_NAME=boost_python-gd&#x0D;&#x0A;cscript &quot;$(InputPath)&quot; -g &quot;$(SolutionDir)\$(PlatformName)\$(ConfigurationName)&quot; &quot;$(SolutionDir)..\..&quot; &quot;$(OutDir)&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp&quot;"
+					CommandLine="SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET PYTHONPATH=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages;$(PYTHONPATH)&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages\numpy\core\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;SET LIBDIR=\lib&#x0D;&#x0A;SET BOOST_PYTHON_LIB_NAME=boost_python-gd&#x0D;&#x0A;cscript &quot;$(InputPath)&quot; -g &quot;$(SolutionDir)\$(PlatformName)\$(ConfigurationName)&quot; &quot;$(SolutionDir)..\..&quot; &quot;$(OutDir)&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -304,7 +304,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Preparing files to be distributed..."
-					CommandLine="SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages\numpy\core\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64);%LIB%&#x0D;&#x0A;SET LIBDIR=\lib&#x0D;&#x0A;SET BOOST_PYTHON_LIB_NAME=boost_python-gd&#x0D;&#x0A;cscript &quot;$(InputPath)&quot; -g &quot;$(SolutionDir)\$(PlatformName)\$(ConfigurationName)&quot; &quot;$(SolutionDir)..\..&quot; &quot;$(OutDir)&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp&quot;"
+					CommandLine="SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET PYTHONPATH=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages;$(PYTHONPATH)&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages\numpy\core\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64);%LIB%&#x0D;&#x0A;SET LIBDIR=\lib&#x0D;&#x0A;SET BOOST_PYTHON_LIB_NAME=boost_python-gd&#x0D;&#x0A;cscript &quot;$(InputPath)&quot; -g &quot;$(SolutionDir)\$(PlatformName)\$(ConfigurationName)&quot; &quot;$(SolutionDir)..\..&quot; &quot;$(OutDir)&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -314,7 +314,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Preparing files to be distributed..."
-					CommandLine="SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages\numpy\core\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;SET LIBDIR=\lib&#x0D;&#x0A;cscript &quot;$(InputPath)&quot; &quot;$(SolutionDir)\$(PlatformName)\$(ConfigurationName)&quot; &quot;$(SolutionDir)..\..&quot; &quot;$(OutDir)&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp&quot;"
+					CommandLine="SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET PYTHONPATH=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages;$(PYTHONPATH)&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages\numpy\core\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;SET LIBDIR=\lib&#x0D;&#x0A;cscript &quot;$(InputPath)&quot; &quot;$(SolutionDir)\$(PlatformName)\$(ConfigurationName)&quot; &quot;$(SolutionDir)..\..&quot; &quot;$(OutDir)&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -324,7 +324,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Preparing files to be distributed..."
-					CommandLine="SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages\numpy\core\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64);%LIB%&#x0D;&#x0A;SET LIBDIR=\lib&#x0D;&#x0A;cscript &quot;$(InputPath)&quot; &quot;$(SolutionDir)\$(PlatformName)\$(ConfigurationName)&quot; &quot;$(SolutionDir)..\..&quot; &quot;$(OutDir)&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp&quot;"
+					CommandLine="SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET PYTHONPATH=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages;$(PYTHONPATH)&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages\numpy\core\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64);%LIB%&#x0D;&#x0A;SET LIBDIR=\lib&#x0D;&#x0A;cscript &quot;$(InputPath)&quot; &quot;$(SolutionDir)\$(PlatformName)\$(ConfigurationName)&quot; &quot;$(SolutionDir)..\..&quot; &quot;$(OutDir)&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>

Modified: ecell3/branches/ecell-3.1/build/msvc/dist.wsf
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/ecell.sln
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/model-editor.vcproj
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj	2008-10-19 15:45:40 UTC (rev 3222)
+++ ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj	2008-10-19 16:35:20 UTC (rev 3223)
@@ -300,6 +300,14 @@
 				<File
 					RelativePath="..\..\ecell\pyecell\ecell\_ecs.cpp"
 					>
+					<FileConfiguration
+						Name="Release|Win32"
+						ExcludedFromBuild="true"
+						>
+						<Tool
+							Name="VCCLCompilerTool"
+						/>
+					</FileConfiguration>
 				</File>
 				<File
 					RelativePath="..\..\ecell\pyecell\ecell\_tableio.c"
@@ -954,7 +962,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -964,7 +972,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -974,7 +982,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -984,7 +992,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>

Modified: ecell3/branches/ecell-3.1/build/msvc/session-monitor.vcproj
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp	2008-10-19 15:45:40 UTC (rev 3222)
+++ ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp	2008-10-19 16:35:20 UTC (rev 3223)
@@ -98,6 +98,47 @@
   void CLASSNAME::initializeModule() \
   { \
     new(thePropertyInterface) libecs::PropertyInterface<CLASSNAME>( #CLASSNAME, theDMTypeName ); \
+  } \
+  PropertySlotBaseCptr CLASSNAME::getPropertySlot( libecs::StringCref aPropertyName ) const \
+  { \
+    return _getPropertyInterface().getPropertySlot( aPropertyName ); \
+  } \
+  void CLASSNAME::setProperty( libecs::StringCref aPropertyName, libecs::PolymorphCref aValue ) \
+  { \
+    return _getPropertyInterface().setProperty( *this, aPropertyName, aValue ); \
+  } \
+  const libecs::Polymorph CLASSNAME::getProperty( libecs::StringCref aPropertyName ) const \
+  { \
+    return _getPropertyInterface().getProperty( *this, aPropertyName ); \
+  } \
+  void CLASSNAME::loadProperty( libecs::StringCref aPropertyName, libecs::PolymorphCref aValue ) \
+  { \
+    return _getPropertyInterface().loadProperty( *this, aPropertyName, aValue ); \
+  } \
+  const libecs::Polymorph CLASSNAME::saveProperty( libecs::StringCref aPropertyName ) const \
+  { \
+   return _getPropertyInterface().saveProperty( *this, aPropertyName ); \
+  } \
+  const libecs::StringVector CLASSNAME::getPropertyList() const \
+  { \
+   return _getPropertyInterface().getPropertyList( *this ); \
+  } \
+  libecs::PropertySlotProxyPtr CLASSNAME::createPropertySlotProxy( libecs::StringCref aPropertyName ) \
+  { \
+   return _getPropertyInterface().createPropertySlotProxy( *this, aPropertyName ); \
+  } \
+  const libecs::PropertyAttributes \
+  CLASSNAME::getPropertyAttributes( libecs::StringCref aPropertyName ) const \
+  { \
+   return _getPropertyInterface().getPropertyAttributes( *this, aPropertyName ); \
+  } \
+  const libecs::PropertyInterfaceBase& CLASSNAME::getPropertyInterface() const \
+  {\
+   return _getPropertyInterface(); \
+  } \
+  const DynamicModuleInfo* CLASSNAME::getClassInfoPtr()\
+  {\
+   return static_cast<const DynamicModuleInfo*>( &_getPropertyInterface() );\
   }
 
   ///@internal
@@ -116,47 +157,16 @@
  static libecs::PropertyInterface<CLASSNAME>& _getPropertyInterface(); \
 public:\
  static void initializeModule(); \
- virtual PropertySlotBaseCptr getPropertySlot( libecs::StringCref aPropertyName ) const \
- { \
-  return _getPropertyInterface().getPropertySlot( aPropertyName ); \
- } \
- virtual void setProperty( libecs::StringCref aPropertyName, libecs::PolymorphCref aValue ) \
- { \
-  return _getPropertyInterface().setProperty( *this, aPropertyName, aValue ); \
- } \
- virtual const libecs::Polymorph getProperty( libecs::StringCref aPropertyName ) const \
- { \
-  return _getPropertyInterface().getProperty( *this, aPropertyName ); \
- } \
- virtual void loadProperty( libecs::StringCref aPropertyName, libecs::PolymorphCref aValue ) \
- { \
-  return _getPropertyInterface().loadProperty( *this, aPropertyName, aValue ); \
- } \
- virtual const libecs::Polymorph saveProperty( libecs::StringCref aPropertyName ) const \
- { \
-  return _getPropertyInterface().saveProperty( *this, aPropertyName ); \
- } \
- virtual const libecs::StringVector getPropertyList() const \
- { \
-  return _getPropertyInterface().getPropertyList( *this ); \
- } \
- virtual libecs::PropertySlotProxyPtr createPropertySlotProxy( libecs::StringCref aPropertyName ) \
- { \
-  return _getPropertyInterface().createPropertySlotProxy( *this, aPropertyName ); \
- } \
- virtual const libecs::PropertyAttributes \
- getPropertyAttributes( libecs::StringCref aPropertyName ) const \
- { \
-  return _getPropertyInterface().getPropertyAttributes( *this, aPropertyName ); \
- } \
- virtual const libecs::PropertyInterfaceBase& getPropertyInterface() const \
- {\
-  return _getPropertyInterface(); \
- } \
- static const DynamicModuleInfo* getClassInfoPtr()\
- {\
-  return static_cast<const DynamicModuleInfo*>( &_getPropertyInterface() );\
- }
+ static const DynamicModuleInfo* getClassInfoPtr(); \
+ virtual PropertySlotBaseCptr getPropertySlot( libecs::StringCref aPropertyName ) const; \
+ virtual void setProperty( libecs::StringCref aPropertyName, libecs::PolymorphCref aValue ); \
+ virtual const libecs::Polymorph getProperty( libecs::StringCref aPropertyName ) const; \
+ virtual void loadProperty( libecs::StringCref aPropertyName, libecs::PolymorphCref aValue ); \
+ virtual const libecs::Polymorph saveProperty( libecs::StringCref aPropertyName ) const; \
+ virtual const libecs::StringVector getPropertyList() const; \
+ virtual libecs::PropertySlotProxyPtr createPropertySlotProxy( libecs::StringCref aPropertyName ); \
+ virtual const libecs::PropertyAttributes getPropertyAttributes( libecs::StringCref aPropertyName ) const; \
+ virtual const libecs::PropertyInterfaceBase& getPropertyInterface() const;
  //
 
 


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[Ecell-cvs] SF.net SVN: ecell:[3224] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-20 04:19:24

Revision: 3224
          http://ecell.svn.sourceforge.net/ecell/?rev=3224&view=rev
Author:   moriyoshi
Date:     2008-10-20 04:19:14 +0000 (Mon, 20 Oct 2008)

Log Message:
-----------
* Win32 build fix (nearly completed)

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/build/msvc/dist.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dist.wsf
    ecell3/branches/ecell-3.1/build/msvc/ecell.sln
    ecell3/branches/ecell-3.1/build/msvc/model-editor.vcproj
    ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj
    ecell3/branches/ecell-3.1/build/msvc/session-monitor.vcproj
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/setup.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/setup.py

Modified: ecell3/branches/ecell-3.1/build/msvc/dist.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dist.vcproj	2008-10-19 16:35:20 UTC (rev 3223)
+++ ecell3/branches/ecell-3.1/build/msvc/dist.vcproj	2008-10-20 04:19:14 UTC (rev 3224)
@@ -314,7 +314,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Preparing files to be distributed..."
-					CommandLine="SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET PYTHONPATH=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages;$(PYTHONPATH)&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages\numpy\core\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;SET LIBDIR=\lib&#x0D;&#x0A;cscript &quot;$(InputPath)&quot; &quot;$(SolutionDir)\$(PlatformName)\$(ConfigurationName)&quot; &quot;$(SolutionDir)..\..&quot; &quot;$(OutDir)&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
+					CommandLine="SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET PYTHONPATH=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages;%PYTHONPATH%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib\site-packages\numpy\core\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;SET LIBDIR=\lib&#x0D;&#x0A;cscript &quot;$(InputPath)&quot; &quot;$(SolutionDir)\$(PlatformName)\$(ConfigurationName)&quot; &quot;$(SolutionDir)..\..&quot; &quot;$(OutDir)&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(PlatformName)\$(ConfigurationName)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>

Modified: ecell3/branches/ecell-3.1/build/msvc/dist.wsf
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/ecell.sln
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/model-editor.vcproj
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj	2008-10-19 16:35:20 UTC (rev 3223)
+++ ecell3/branches/ecell-3.1/build/msvc/pyecell.vcproj	2008-10-20 04:19:14 UTC (rev 3224)
@@ -364,6 +364,10 @@
 					>
 				</File>
 				<File
+					RelativePath="..\..\ecell\pyecell\ecell\config.py"
+					>
+				</File>
+				<File
 					RelativePath="..\..\ecell\pyecell\ecell\convertEML2SBML.py"
 					>
 				</File>
@@ -962,7 +966,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(ProjectDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -972,7 +976,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%;%LIB64%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(ProjectDir)..\..\ecell\pyecell\setup.py&quot; build -g -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -982,7 +986,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(ProjectDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>
@@ -992,7 +996,7 @@
 				<Tool
 					Name="VCCustomBuildTool"
 					Description="Running distutils..."
-					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(SolutionDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;&#x0D;&#x0A;"
+					CommandLine="cd &quot;$(ProjectDir)..\..\ecell\pyecell&quot;&#x0D;&#x0A;SET MSSDK=1&#x0D;&#x0A;SET DISTUTILS_USE_SDK=1&#x0D;&#x0A;SET SYSCONFDIR=etc&#x0D;&#x0A;SET DATAROOTDIR=share&#x0D;&#x0A;SET DATADIR=%DATAROOTDIR%&#x0D;&#x0A;SET INCLTDL=/I$(SolutionDir)\..\..\libltdl&#x0D;&#x0A;SET LIBDIR=lib&#x0D;&#x0A;SET INCLUDE=$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\include;$(INCLUDE);%INCLUDE%&#x0D;&#x0A;SET LIB=$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB);%LIB%;%LIB64%&#x0D;&#x0A;&quot;$(PYTHONHOME)\python&quot; &quot;$(ProjectDir)..\..\ecell\pyecell\setup.py&quot; build -b &quot;$(OutDir)\$(ProjectName).build&quot; &amp;&amp; ECHO &quot;1&quot; &gt; &quot;$(OutDir)\$(ProjectName).stamp&quot;"
 					Outputs="$(OutDir)\$(ProjectName).stamp"
 				/>
 			</FileConfiguration>

Modified: ecell3/branches/ecell-3.1/build/msvc/session-monitor.vcproj
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/ecell/frontend/model-editor/setup.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/frontend/model-editor/setup.py	2008-10-19 16:35:20 UTC (rev 3223)
+++ ecell3/branches/ecell-3.1/ecell/frontend/model-editor/setup.py	2008-10-20 04:19:14 UTC (rev 3224)
@@ -6,6 +6,14 @@
 from distutils.core import setup, Extension
 import ecell.config as config
 
+def relative( basePath, path ):
+	separators = os.sep + ( os.altsep or "" )
+	commonPrefix = os.path.commonprefix( [ basePath, path ] )
+	if len( basePath[ len( commonPrefix ): ].rstrip( separators ) ) != 0:
+		return path
+	else:
+		return path[ len( commonPrefix ): ].lstrip( separators )
+
 resources = glob(
     os.path.join( os.path.dirname( __file__ ), 'glade', '*' ) )
 
@@ -22,8 +30,8 @@
     packages = [ 'ecell.ui.model_editor' ],
     scripts = [ 'ecell3-model-editor' ],
     data_files = [
-        ( config.conf_dir, [ 'model-editor.ini' ] ),
-        ( os.path.join( config.data_dir, 'model-editor', 'glade' ), resources ),
-        ( os.path.join( config.lib_dir, 'model-editor', 'plugins' ), plugins ),
+        ( relative( config.prefix, config.conf_dir ), [ 'model-editor.ini' ] ),
+        ( os.path.join( relative( config.prefix, config.data_dir ), 'model-editor', 'glade' ), resources ),
+        ( os.path.join( relative( config.prefix, config.lib_dir ), 'model-editor', 'plugins' ), plugins ),
         ]
     )

Modified: ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/setup.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/setup.py	2008-10-19 16:35:20 UTC (rev 3223)
+++ ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/setup.py	2008-10-20 04:19:14 UTC (rev 3224)
@@ -6,6 +6,14 @@
 from distutils.core import setup, Extension
 import ecell.config as config
 
+def relative( basePath, path ):
+	separators = os.sep + ( os.altsep or "" )
+	commonPrefix = os.path.commonprefix( [ basePath, path ] )
+	if len( basePath[ len( commonPrefix ): ].rstrip( separators ) ) != 0:
+		return path
+	else:
+		return path[ len( commonPrefix ): ].lstrip( separators )
+
 resources = glob(
     os.path.join( os.path.dirname( __file__ ), 'glade', '*' ) )
 
@@ -22,8 +30,8 @@
     packages = [ 'ecell.ui', 'ecell.ui.osogo' ],
     scripts = [ 'ecell3-session-monitor' ],
     data_files = [
-        ( config.conf_dir, [ 'osogo.ini' ] ),
-        ( os.path.join( config.data_dir, 'session-monitor', 'glade' ), resources ),
-        ( os.path.join( config.lib_dir, 'session-monitor', 'plugins' ), plugins ),
+        ( relative( config.prefix, config.conf_dir ), [ 'osogo.ini' ] ),
+        ( os.path.join( relative( config.prefix, config.data_dir ), 'session-monitor', 'glade' ), resources ),
+        ( os.path.join( relative( config.prefix, config.lib_dir), 'session-monitor', 'plugins' ), plugins ),
         ]
     )


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3248] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-23 18:44:28

Revision: 3248
          http://ecell.svn.sourceforge.net/ecell/?rev=3248&view=rev
Author:   moriyoshi
Date:     2008-10-23 18:44:13 +0000 (Thu, 23 Oct 2008)

Log Message:
-----------
* libecs changes:
  * Fix indent / coding style.
  * Fix doxygen comments.
  * Remove $...$ placeholders as they may contain localized characters
    which are troublesome in VC++.
  * Remove obsolete FluxProcess.
  * Document macros in EcsObject.hpp.
  * Make Polymorph accept boost::tuple<> and const char *.
  * Remove setAvg() / setMin() / setMax() from DataPoint.
  * Add Logger::Policy class and remove methods that accept polymorph tuples
    that contain the policy information.
  * Make Process::setVariableReference() only accept VariableReference
    instead of scatterd arguments for consistency with getVariableReference().
  * Make Process::registerVariableReference() have the same signature as
    the previous version of Process::setVariableReference().
  * Remove LoggerBroker::setModel() in favor of dependency injection in
    initialization.
  * And more tiny changes.
* libemc changes:
  * Fix indent / conding style.
  * Remove obsolete FluxProcess.
  The same changes were applied to SimulatorImplementation and LocalSimulatorImplementation accordingly.
  * Rename Simulator::isEntityExist() to Simulator::entityExists().
  * Remove Simulator::getLoggerMinimumInterval() and
    Simulator::setLoggerMinimumInterval() in favor of setLoggerPolicy().

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj
    ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteEventStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteEventStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteTimeStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteTimeStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DynamicPriorityQueue.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/EcsObject.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/EcsObject.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/EcsObjectMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Entity.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Entity.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/EntityType.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/EntityType.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/EventScheduler.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Exceptions.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Exceptions.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/FullID.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/FullID.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Interpolant.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Interpolant.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Logger.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Logger.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/LoggerAdapter.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/LoggerAdapter.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/LoggerBroker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/LoggerBroker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Makefile.am
    ecell3/branches/ecell-3.1/ecell/libecs/MethodProxy.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Model.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Model.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PassiveStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PassiveStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PhysicalLogger.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PhysicalLogger.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Polymorph.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Process.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Process.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/ProcessEvent.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertyAttributes.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertyInterface.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertyInterface.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlot.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlot.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxy.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxy.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxyLoggerAdapter.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Stepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Stepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/StepperEvent.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/System.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/System.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/SystemStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/SystemStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Util.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Util.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Variable.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Variable.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/VariableReference.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/VariableReference.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/convertTo.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/libecs.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/libecs.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/osif.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.hpp
    ecell3/branches/ecell-3.1/ecell/libemc/Simulator.hpp
    ecell3/branches/ecell-3.1/ecell/libemc/SimulatorImplementation.hpp
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/_ecs.cpp

Removed Paths:
-------------
    ecell3/branches/ecell-3.1/ecell/libecs/FluxProcess.hpp

Modified: ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj	2008-10-23 18:24:55 UTC (rev 3247)
+++ ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj	2008-10-23 18:44:13 UTC (rev 3248)
@@ -572,10 +572,6 @@
 				>
 			</File>
 			<File
-				RelativePath="..\..\ecell\libecs\FluxProcess.hpp"
-				>
-			</File>
-			<File
 				RelativePath="..\..\ecell\libecs\FullID.hpp"
 				>
 			</File>

Modified: ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.cpp	2008-10-23 18:24:55 UTC (rev 3247)
+++ ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.cpp	2008-10-23 18:44:13 UTC (rev 3248)
@@ -25,6 +25,7 @@
 // 
 //END_HEADER
 //
+
 #ifdef HAVE_CONFIG_H
 #include "ecell_config.h"
 #endif /* HAVE_CONFIG_H */
@@ -34,5 +35,5 @@
 
 namespace libecs
 {
-  LIBECS_DM_INIT_STATIC( ContinuousProcess, Process );
+LIBECS_DM_INIT_STATIC( ContinuousProcess, Process );
 }

Modified: ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.hpp	2008-10-23 18:24:55 UTC (rev 3247)
+++ ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.hpp	2008-10-23 18:44:13 UTC (rev 3248)
@@ -28,36 +28,39 @@
 #include "libecs/libecs.hpp"
 #include "libecs/Process.hpp"
 
+/**
+   @addtogroup entities
+   @ingroup libecs
+   @{
+ */
 namespace libecs
 {
 
-  LIBECS_DM_CLASS( ContinuousProcess, Process )
-  {
+LIBECS_DM_CLASS( ContinuousProcess, Process )
+{
 
-  public:
+public:
+    LIBECS_DM_OBJECT_ABSTRACT( ContinuousProcess )
+    {
+        INHERIT_PROPERTIES( Process );
+    }
 
-    LIBECS_DM_OBJECT_ABSTRACT( ContinuousProcess )
-      {
-	INHERIT_PROPERTIES( Process );
-      }
-  
     ContinuousProcess()
-      {
-	; // do nothing
-      }
-  
+    {
+        ; // do nothing
+    }
+
     virtual ~ContinuousProcess()
-      {
-	;
-      }
+    {
+        ;
+    }
 
     virtual const bool isContinuous() const
     {
-      return true;
+        return true;
     }
+};
 
-  protected:
-  
-  };
+} // namespace libecs
 
-}
+/** @} */

Modified: ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.cpp	2008-10-23 18:24:55 UTC (rev 3247)
+++ ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.cpp	2008-10-23 18:44:13 UTC (rev 3248)
@@ -27,6 +27,7 @@
 //
 // written by Gabor Bereczki <gab...@ta...>
 // 24/03/2002
+
 #ifdef HAVE_CONFIG_H
 #include "ecell_config.h"
 #endif /* HAVE_CONFIG_H */
@@ -35,156 +36,136 @@
 
 namespace libecs
 {
-  
-
-  DataPointRef DataPoint::operator= ( LongDataPointCref aLongDataPoint )
-  {
-    setTime( aLongDataPoint.getTime() );
-    setValue ( aLongDataPoint.getValue() );
-    return *this;
-  }
-
-  
-  DataPointAggregator::DataPointAggregator()
-    :
-    theAccumulator( -1.0, 0.0 ),
-    theCollector ( -1.0, 0.0 ),
-    thePreviousPoint( 1.0, 0.0 )
-  {
+DataPointAggregator::DataPointAggregator()
+    : theAccumulator( -1.0, 0.0 ),
+      theCollector ( -1.0, 0.0 ),
+      thePreviousPoint( 1.0, 0.0 )
+{
     ; //do nothing
-  }
-  
+}
 
-  DataPointAggregator::DataPointAggregator( LongDataPointCref aDataPoint )
-  {
+
+DataPointAggregator::DataPointAggregator( LongDataPointCref aDataPoint )
+{
     store( aDataPoint );
-  }
-  
+}
 
-  DataPointAggregator::~DataPointAggregator()
-  {
+
+DataPointAggregator::~DataPointAggregator()
+{
     ; // do nothing
-  }
-  
-  
-  void DataPointAggregator::store( LongDataPointCref aDataPoint )
-  {
+}
+
+
+void DataPointAggregator::store( LongDataPointCref aDataPoint )
+{
     theAccumulator = aDataPoint;
     thePreviousPoint = aDataPoint;
     theCollector.setTime( -1.0 );
-  }
-  
-  
-  bool DataPointAggregator::stockpile( LongDataPointRef aTarget, 
-				       LongDataPointCref aNewPoint )
-  {
+}
+
+
+bool DataPointAggregator::stockpile( LongDataPointRef aTarget, 
+                                     LongDataPointCref aNewPoint )
+{
     //if target empty, simply store
     //return true
     if( aTarget.getTime() == -1.0 )
-      {
-	aTarget = aNewPoint;
-	return true;
-      }
+    {
+        aTarget = aNewPoint;
+        return true;
+    }
     
     // if target not empty and time is the same
     // calculate MinMax, store Avg
     //return true
     if( aTarget.getTime() == aNewPoint.getTime() )
-      {
-	calculateMinMax( aTarget, aNewPoint );
-	aTarget.setAvg( aNewPoint.getAvg() );
-	aTarget.setValue( aNewPoint.getValue() );
-	return true;
-      }
+    {
+        calculateMinMax( aTarget, aNewPoint );
+        aTarget.setAvg( aNewPoint.getAvg() );
+        aTarget.setValue( aNewPoint.getValue() );
+        return true;
+    }
     
     //if target time is below newtime
     //return false
     return false;
-  }
-  
-  
-  void DataPointAggregator::aggregate( LongDataPointCref aNewPoint )
-  {
+}
+
+
+void DataPointAggregator::aggregate( LongDataPointCref aNewPoint )
+{
     // first try to put it into accumulator
     if ( ! stockpile( theAccumulator, aNewPoint ) )
-      {
-	// then try to put it into collector
-	if (! stockpile( theCollector, aNewPoint ) )
-	  {
-	    // then calculate
-	    calculate( aNewPoint );
-	    theCollector = aNewPoint;
-	    calculateMinMax( theAccumulator, theCollector );
-	  }
-	else
-	  {
-	    calculateMinMax( theAccumulator, theCollector );
-	  }
-      }
-  }
-  
-  
-  LongDataPointCref DataPointAggregator::getData()
-  {
+    {
+        // then try to put it into collector
+        if (! stockpile( theCollector, aNewPoint ) )
+        {
+            // then calculate
+            calculate( aNewPoint );
+            theCollector = aNewPoint;
+            calculateMinMax( theAccumulator, theCollector );
+        }
+        else
+        {
+            calculateMinMax( theAccumulator, theCollector );
+        }
+    }
+}
+
+
+LongDataPointCref DataPointAggregator::getData()
+{
     return theAccumulator;
-  }
-  
-  
-  inline void
-  DataPointAggregator::calculateMinMax( LongDataPointRef aTarget,
-                                        LongDataPointCref aNewPoint )
-  {
+}
+
+
+inline void
+DataPointAggregator::calculateMinMax( LongDataPointRef aTarget,
+                                      LongDataPointCref aNewPoint )
+{
     // accu min
-    
     if( aTarget.getMin() > aNewPoint.getMin() )
-      {
-	aTarget.setMin ( aNewPoint.getMin() );
-      }
+    {
+        aTarget.setMin ( aNewPoint.getMin() );
+    }
     
     // accu max
     if( aTarget.getMax() < aNewPoint.getMax() )
-      {
-	aTarget.setMax ( aNewPoint.getMax() );
-      }
-    
-  }
-  
-  
-  void DataPointAggregator::calculate( LongDataPointCref aNewPoint )
-  {
+    {
+        aTarget.setMax ( aNewPoint.getMax() );
+    }
+}
+
+
+void DataPointAggregator::calculate( LongDataPointCref aNewPoint )
+{
     // accu avg
     theAccumulator.setAvg
-      ( ( theCollector.getAvg() *
-	  ( aNewPoint.getTime() - theCollector.getTime() ) +
-	  theAccumulator.getAvg() * 
-	  ( theCollector.getTime() - theAccumulator.getTime() ) ) 
-	/ ( aNewPoint.getTime() - theAccumulator.getTime() ) );
-  }
-  
-  void DataPointAggregator::beginNextPoint()
-  {
-    //	theAccumulator = thePreviousPoint;
-    //	thePreviousPoint = theCollector;
-    
+        ( ( theCollector.getAvg() *
+                ( aNewPoint.getTime() - theCollector.getTime() ) +
+                theAccumulator.getAvg() * 
+                ( theCollector.getTime() - theAccumulator.getTime() ) ) 
+            / ( aNewPoint.getTime() - theAccumulator.getTime() ) );
+}
+
+void DataPointAggregator::beginNextPoint()
+{
     store( theCollector );
-  }
-  
-  
-  LongDataPoint DataPointAggregator::getLastPoint()
-  {
+}
+
+
+LongDataPoint DataPointAggregator::getLastPoint()
+{
     //if collector empty return Accu
     if (theCollector.getTime() == -1.0 )
-      {
-	return theAccumulator;
-      }
+    {
+        return theAccumulator;
+    }
     else
-      {
-	return theCollector;
-      }
-  }
-  
-  
-  
-} // namespace libecs
+    {
+        return theCollector;
+    }
+}
 
-
+} // namespace libecs

Modified: ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.hpp	2008-10-23 18:24:55 UTC (rev 3247)
+++ ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.hpp	2008-10-23 18:44:13 UTC (rev 3248)
@@ -35,281 +35,269 @@
 #include "libecs/libecs.hpp"
 #include "libecs/Polymorph.hpp"
 
+/**
+   @addtogroup logging
+   @{
+ */
 namespace libecs
 {
 
-  /** @addtogroup logging
-   *@{
-   */
+class LongDataPoint;
+class DataPoint;
 
-  /** \file */
-
-  class LongDataPoint;
-  class DataPoint;
-
-
-
-  /**
-
-  */
-
-  class DataPoint
-  {
-
-  public:
+class DataPoint
+{
+public:
     class EarlinessOrdering
     {
     public:
-      bool operator()(const DataPoint& x, const DataPoint& y)
-      {
-        return x.getTime() < y.getTime();
-      }
+        bool operator()(const DataPoint& x, const DataPoint& y)
+        {
+            return x.getTime() < y.getTime();
+        }
     };
 
     class LatenessOrdering
     {
     public:
-      bool operator()(const DataPoint& x, const DataPoint& y)
-      {
-        return x.getTime() > y.getTime();
-      }
+        bool operator()(const DataPoint& x, const DataPoint& y)
+        {
+            return x.getTime() > y.getTime();
+        }
     };
 
-  public:
-
+public:
     DataPoint()
-      :
-      theTime ( 0.0 ),
-      theValue( 0.0 )
+        : theTime ( 0.0 ),
+          theValue( 0.0 )
     {
-      ; // do nothing
+        ; // do nothing
     }
 
     DataPoint( RealParam aTime, RealParam aValue )
-      :
-      theTime ( aTime ),
-      theValue( aValue )   
+        : theTime ( aTime ),
+          theValue( aValue )     
     {
-      ; //do nothing
+        ; //do nothing
     }
 
-
-
     ~DataPoint()
     {
-      ; // do nothing
+        ; // do nothing
     }
 
+
     const Real getTime() const
     {
-      return theTime;
+        return theTime;
     }
 
+
     const Real getValue() const
     {
-      return theValue;
+        return theValue;
     }
 
+
     const Real getAvg() const
     {
-      return theValue;
+        return theValue;
     }
 
+
     const Real getMin() const
     {
-      return theValue;
+        return theValue;
     }
 
+
     const Real getMax() const
     {
-      return theValue;
+        return theValue;
     }
 
 
     void setTime( RealParam aReal )
     {
-      theTime = aReal;
+        theTime = aReal;
     }
 
+
     void setValue( RealParam aReal )
     {
-      theValue = aReal;
+        theValue = aReal;
     }
 
-    void setAvg( RealParam aReal )
-    {
-      ;
-    }
 
-    void setMin( RealParam aReal )
-    {
-      ;
-    }
-
-    void setMax( RealParam aReal )
-    {
-      ;
-    }
-
     static const size_t getElementSize()
     {
-      return sizeof( Real );
+        return sizeof( Real );
     }
 
+
     static const int getElementNumber()
     {
-      return 2;
+        return 2;
     }
 
+
     DataPointRef operator= ( LongDataPointCref aLongDataPoint );
 
+
     bool operator==( const DataPoint& that ) const
     {
-        return theTime == that.theTime &&
-               theValue == that.theValue;
+        return theTime == that.theTime && theValue == that.theValue;
     }
 
-  protected:
+protected:
 
     Real theTime;
     Real theValue;
 
-  };
+};
 
 
 
-  class LongDataPoint 
-    :
-    public DataPoint
-  {
+class LongDataPoint: public DataPoint
+{
 
-  public:
-
+public:
     LongDataPoint() //constructor with no arguments
-      :
-    theAvg( 0.0 ),
-    theMin( 0.0 ),
-    theMax( 0.0 )
+        : theAvg( 0.0 ),
+          theMin( 0.0 ),
+          theMax( 0.0 )
     {
-      ; // do nothing
+        ; // do nothing
     }
 
 
     LongDataPoint( RealParam aTime, RealParam aValue )//constructor with 2 args
-      :
-    DataPoint( aTime, aValue ),
-    theAvg( aValue ),
-    theMin( aValue ),
-    theMax( aValue )
+        : DataPoint( aTime, aValue ),
+          theAvg( aValue ),
+          theMin( aValue ),
+          theMax( aValue )
     {
-      ; // do nothing
+        ; // do nothing
     }
 
     LongDataPoint( RealParam aTime, RealParam aValue, 
-		   RealParam anAvg,
-		   RealParam aMax, 
-		   RealParam aMin ) //constructor with 5 args
-      :
-    DataPoint( aTime, aValue ),
-    theAvg( anAvg ),
-    theMin( aMin ),
-    theMax( aMax )
+                   RealParam anAvg, RealParam aMax, 
+                   RealParam aMin ) //constructor with 5 args
+        : DataPoint( aTime, aValue ),
+          theAvg( anAvg ),
+          theMin( aMin ),
+          theMax( aMax )
     {
-      ; // do nothing
+        ; // do nothing
     }
 
 
     LongDataPoint( DataPointCref aDataPoint ) // constructor from DP2
-      :
-    DataPoint( aDataPoint ),
-    theAvg( aDataPoint.getAvg() ),
-    theMin( aDataPoint.getMin() ),
-    theMax( aDataPoint.getMax() )
+        : DataPoint( aDataPoint ),
+          theAvg( aDataPoint.getAvg() ),
+          theMin( aDataPoint.getMin() ),
+          theMax( aDataPoint.getMax() )
     {
-      ; // do nothing
+        ; // do nothing
     }
+
     
     ~LongDataPoint()
     {
-      ; // do nothing
+        ; // do nothing
     }
+
     
     const Real getTime() const
     {
-      return theTime;
+        return theTime;
     }
+
     
     const Real getValue() const
     {
-      return theValue;
+        return theValue;
     }
+
     
     const Real getAvg() const
     {
-      return theAvg;
+        return theAvg;
     }
+
     
     const Real getMin() const
     {
-      return theMin;
+        return theMin;
     }
 
+
     const Real getMax() const
     {
-      return theMax;
+        return theMax;
     }
 
 
     void setTime( RealParam aReal )
     {
-      theTime = aReal;
+        theTime = aReal;
     }
 
+
     void setValue( RealParam aReal )
     {
-      theValue = aReal;
+        theValue = aReal;
     }
 
+
     void setAvg( RealParam aReal )
     {
-      theAvg = aReal;
+        theAvg = aReal;
     }
 
+
     void setMin( RealParam aReal )
     {
-      theMin = aReal;
+        theMin = aReal;
     }
 
-    void setMax( RealParam aReal )
 
+    void setMax( RealParam aReal )
     {
-      theMax = aReal;
+        theMax = aReal;
     }
 
+
     static const size_t getElementSize()
     {
-      return sizeof( Real );
+        return sizeof( Real );
     }
 
+
     static const int getElementNumber()
     {
-      return 5;
+        return 5;
     }
 
-  protected:
-
+protected:
     Real theAvg;
     Real theMin;
     Real theMax;
+};
 
-  };
 
+inline DataPoint& DataPoint::operator=( LongDataPoint const& aLongDataPoint )
+{
+    setTime( aLongDataPoint.getTime() );
+    setValue( aLongDataPoint.getValue() );
+    return *this;
+}
 
-  class DataPointAggregator
-  {
+
+class DataPointAggregator
+{
+public:
     
-  public:
-    
     DataPointAggregator();
     
     DataPointAggregator( LongDataPointCref );
@@ -325,7 +313,7 @@
     
     LongDataPoint getLastPoint();
     
-  private:
+private:
     void store( LongDataPointCref );
     
     bool stockpile( LongDataPointRef, LongDataPointCref );
@@ -335,13 +323,10 @@
     LongDataPoint theAccumulator;
     LongDataPoint theCollector;
     LongDataPoint thePreviousPoint;
-    
-  };
-  
-  
-  //@}
-  
+};
+
 } // namespace libecs
 
+/** @} */
 
 #endif /* __DATAPOINT_HPP */

Modified: ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.cpp	2008-10-23 18:24:55 UTC (rev 3247)
+++ ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.cpp	2008-10-23 18:44:13 UTC (rev 3248)
@@ -27,103 +27,98 @@
 //
 // written by Gabor Bereczki <gab...@ta...>
 // 14/04/2002
+
 #ifdef HAVE_CONFIG_H
 #include "ecell_config.h"
 #endif /* HAVE_CONFIG_H */
 
 #include "DataPointVector.hpp"
-#include <assert.h>
+#include <cassert>
 
 namespace libecs
 {
-  DataPointVector::~DataPointVector()
-  {
+
+DataPointVector::~DataPointVector()
+{
     if( thePointSize==2 )
-      {
-	delete[] theRawArray;
-      }
+    {
+        delete[] theRawArray;
+    }
     else
-      {
-	delete[] theRawArrayLong;
-      }
-  }
+    {
+        delete[] theRawArrayLong;
+    }
+}
 
-
-
-  DataPointVector::DataPointVector( DataPointVectorIterator aLength, 
-				    int aPointSize ) 
-    :
-    theSize( aLength ),
-    thePointSize( aPointSize )
-  {
+DataPointVector::DataPointVector( DataPointVectorIterator aLength, 
+                                  int aPointSize ) 
+    : theSize( aLength ),
+      thePointSize( aPointSize )
+{
     // init the appropriate array
 
     if( thePointSize == 2 )
-      {
-	theRawArray = new DataPoint[ aLength ];
-      }
+    {
+        theRawArray = new DataPoint[ aLength ];
+    }
     else
-      {
-	theRawArrayLong = new LongDataPoint[ aLength ];
-      }
-  }
+    {
+        theRawArrayLong = new LongDataPoint[ aLength ];
+    }
+}
 
 
-  size_t DataPointVector::getElementSize() const
-  {
+size_t DataPointVector::getElementSize() const
+{
     if( thePointSize == 2 )
-      {
-	return sizeof(DataPoint);
-      }
+    {
+        return sizeof(DataPoint);
+    }
     return sizeof(LongDataPoint);
-  }
+}
 
 
-
-
-
-  DataPointRef DataPointVector::asShort( DataPointVectorIterator aPosition )
-  {
+DataPointRef DataPointVector::asShort( DataPointVectorIterator aPosition )
+{
     assert (thePointSize == 2);
     return theRawArray[ aPosition ];
-  }
+}
 
-  DataPointCref 
-  DataPointVector::asShort( DataPointVectorIterator aPosition ) const
-  {
+DataPointCref 
+DataPointVector::asShort( DataPointVectorIterator aPosition ) const
+{
     assert (thePointSize == 2);
     return theRawArray[ aPosition ];
-  }
+}
 
-  LongDataPointRef DataPointVector::asLong( DataPointVectorIterator aPosition )
-  {
+LongDataPointRef DataPointVector::asLong( DataPointVectorIterator aPosition )
+{
     assert (thePointSize == 5);
     return theRawArrayLong[ aPosition ];
-  }
+}
 
 
-  LongDataPointCref 
-  DataPointVector::asLong( DataPointVectorIterator aPosition ) const
-  {
+LongDataPointCref 
+DataPointVector::asLong( DataPointVectorIterator aPosition ) const
+{
     assert (thePointSize == 5);
     return theRawArrayLong[ aPosition ];
-  }
+}
 
 
-  const void* DataPointVector::getRawArray() const
-  {
+const void* DataPointVector::getRawArray() const
+{
     if (thePointSize == 2)
-      {
-	return (void*) theRawArray;
-      }
+    {
+        return (void*) theRawArray;
+    }
     return (void*) theRawArrayLong;
 
-  }
+}
 
-  Integer DataPointVector::getPointSize()
-  {
-      return DataPointVector::thePointSize;
-  }
-} // namespace libecs
+Integer DataPointVector::getPointSize()
+{
+    return DataPointVector::thePointSize;
+}
 
-
+} // namespace libecs

Modified: ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.hpp	2008-10-23 18:24:55 UTC (rev 3247)
+++ ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.hpp	2008-10-23 18:44:13 UTC (rev 3248)
@@ -37,25 +37,21 @@
 #include <sys/types.h>
 
 
+/**
+   @addtogroup logging
+   @{
+*/
+
 namespace libecs
 {
 
-  /** @addtogroup logging
-   *@{
-   */
+DECLARE_TYPE( size_t, DataPointVectorIterator );
 
-  /** @file */
+DECLARE_SHAREDPTR( DataPointVector );
 
-
-  DECLARE_TYPE( size_t, DataPointVectorIterator );
-
-  DECLARE_SHAREDPTR( DataPointVector );
-
-  class LIBECS_API DataPointVector
-  {
-
-  public:
-
+class LIBECS_API DataPointVector
+{
+public:
     DataPointVector( DataPointVectorIterator, int aPointSize );
 
     ~DataPointVector();
@@ -70,27 +66,26 @@
 
     DataPointVectorIterator getSize() const
     {
-      return theSize;
+        return theSize;
     }
 
     size_t getElementSize() const;
-	
+            
     DataPointVectorIterator begin() const
     {
-      return 0;
+        return 0;
     }
-	
+            
     DataPointVectorIterator end() const
     {
-      return getSize();
+        return getSize();
     }
-	
+            
     const void* getRawArray() const;
 
     Integer getPointSize();
 
-  private:
-
+private:
     DataPointVectorIterator theSize;
 
     Integer thePointSize;
@@ -98,12 +93,10 @@
     DataPoint* theRawArray;
 
     LongDataPoint* theRawArrayLong;
+};
 
-  };
-
-  //@}
-
 } // namespace libecs
 
+/** @} */
 
 #endif /* __DATAPOINTVECTOR_HPP */

Modified: ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.cpp	2008-10-23 18:24:55 UTC (rev 3247)
+++ ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.cpp	2008-10-23 18:44:13 UTC (rev 3248)
@@ -28,6 +28,7 @@
 // written by Koichi Takahashi <sh...@e-...>,
 // E-Cell Project.
 //
+
 #ifdef HAVE_CONFIG_H
 #include "ecell_config.h"
 #endif /* HAVE_CONFIG_H */
@@ -50,193 +51,190 @@
 namespace libecs
 {
 
-  LIBECS_DM_INIT_STATIC( DifferentialStepper, Stepper );
-  LIBECS_DM_INIT_STATIC( AdaptiveDifferentialStepper, Stepper );
+LIBECS_DM_INIT_STATIC( DifferentialStepper, Stepper );
+LIBECS_DM_INIT_STATIC( AdaptiveDifferentialStepper, Stepper );
 
-  DifferentialStepper::DifferentialStepper()
-    :
-    theNextStepInterval( 0.001 ),
-    theTolerableStepInterval( 0.001 ),
-    theStateFlag( true )
-  {
+DifferentialStepper::DifferentialStepper()
+    : theNextStepInterval( 0.001 ),
+      theTolerableStepInterval( 0.001 ),
+      theStateFlag( true )
+{
     ; // do nothing
-  }
+}
 
-  DifferentialStepper::~DifferentialStepper()
-  {
+
+DifferentialStepper::~DifferentialStepper()
+{
     ; // do nothing
-  }
+}
 
-  void DifferentialStepper::initialize()
-  {
+
+void DifferentialStepper::initialize()
+{
     Stepper::initialize();
 
     createInterpolants();
 
     theTaylorSeries.resize( boost::extents[ getStage() ][
-            static_cast< RealMatrix::index >(
-                getReadOnlyVariableOffset() ) ] );
+                                static_cast< RealMatrix::index >(
+                                    getReadOnlyVariableOffset() ) ] );
 
-    // should registerProcess be overrided?
+    // XXX: should go into registerProcess?
+    /*
     if ( getDiscreteProcessOffset() < theProcessVector.size() )
-      {
-	for ( ProcessVectorConstIterator
-		i( theProcessVector.begin() + getDiscreteProcessOffset() );
-	      i < theProcessVector.end(); ++i )
-	  {
-	    // XXX: To be addressed later.
-	    // std::cerr << "WARNING: Process [" << (*i)->getID() << "] is not continuous." << std::endl;
-	  }
-      }
+    {
+        for ( ProcessVectorConstIterator i(
+                theProcessVector.begin() + getDiscreteProcessOffset() );
+                i < theProcessVector.end(); ++i )
+        {
+            std::cerr << "WARNING: Process [" << (*i)->getID() << "] is not continuous." << std::endl;
+        }
+    }
+    */
 
     initializeVariableReferenceList();
+}
 
-    // should create another method for property slot ?
-    //    setNextStepInterval( getStepInterval() );
 
-    //    theStateFlag = false;
-  }
+void DifferentialStepper::initializeVariableReferenceList()
+{
+    const ProcessVector::size_type aDiscreteProcessOffset(
+            getDiscreteProcessOffset() );
 
-  void DifferentialStepper::initializeVariableReferenceList()
-  {
-    const ProcessVector::size_type 
-      aDiscreteProcessOffset( getDiscreteProcessOffset() );
-
     theVariableReferenceListVector.clear();
     theVariableReferenceListVector.resize( aDiscreteProcessOffset );
     
     for ( ProcessVector::size_type i( 0 ); i < aDiscreteProcessOffset; ++i )
-      {
-	ProcessPtr const aProcess( ...
 
[truncated message content]

[Ecell-cvs] SF.net SVN: ecell:[3256] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-10-23 19:29:31

Revision: 3256
          http://ecell.svn.sourceforge.net/ecell/?rev=3256&view=rev
Author:   moriyoshi
Date:     2008-10-23 19:29:29 +0000 (Thu, 23 Oct 2008)

Log Message:
-----------
* Forgot to commit these files.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj
    ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Makefile.am
    ecell3/branches/ecell-3.1/ecell/libecs/Polymorph.hpp

Added Paths:
-----------
    ecell3/branches/ecell-3.1/ecell/libecs/AdaptiveDifferentialStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/AdaptiveDifferentialStepper.hpp

Modified: ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj	2008-10-23 19:25:24 UTC (rev 3255)
+++ ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj	2008-10-23 19:29:29 UTC (rev 3256)
@@ -374,6 +374,10 @@
 			UniqueIdentifier="{4FC737F1-C7A5-4376-A066-2A32D752A2FF}"
 			>
 			<File
+				RelativePath="..\..\ecell\libecs\AdaptiveDifferentialStepper.cpp"
+				>
+			</File>
+			<File
 				RelativePath="..\..\ecell\libecs\ContinuousProcess.cpp"
 				>
 			</File>
@@ -504,6 +508,10 @@
 			UniqueIdentifier="{93995380-89BD-4b04-88EB-625FBE52EBFB}"
 			>
 			<File
+				RelativePath="..\..\ecell\libecs\AdaptiveDifferentialStepper.hpp"
+				>
+			</File>
+			<File
 				RelativePath="..\..\ecell\libecs\AssocVector.h"
 				>
 			</File>

Copied: ecell3/branches/ecell-3.1/ecell/libecs/AdaptiveDifferentialStepper.cpp (from rev 3248, ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.cpp)
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/AdaptiveDifferentialStepper.cpp	                        (rev 0)
+++ ecell3/branches/ecell-3.1/ecell/libecs/AdaptiveDifferentialStepper.cpp	2008-10-23 19:29:29 UTC (rev 3256)
@@ -0,0 +1,125 @@
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//       This file is part of the E-Cell System
+//
+//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 2005-2008 The Molecular Sciences Institute
+//
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//
+// E-Cell System is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public
+// License as published by the Free Software Foundation; either
+// version 2 of the License, or (at your option) any later version.
+// 
+// E-Cell System is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+// See the GNU General Public License for more details.
+// 
+// You should have received a copy of the GNU General Public
+// License along with E-Cell System -- see the file COPYING.
+// If not, write to the Free Software Foundation, Inc.,
+// 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+// 
+//END_HEADER
+//
+// written by Koichi Takahashi <sh...@e-...>,
+// E-Cell Project.
+//
+
+#ifdef HAVE_CONFIG_H
+#include "ecell_config.h"
+#endif /* HAVE_CONFIG_H */
+
+#include "AdaptiveDifferentialStepper.hpp"
+
+namespace libecs
+{
+LIBECS_DM_INIT_STATIC( AdaptiveDifferentialStepper, Stepper );
+
+AdaptiveDifferentialStepper::AdaptiveDifferentialStepper()
+    : theTolerance( 1.0e-6 ),
+      theAbsoluteToleranceFactor( 1.0 ),
+      theStateToleranceFactor( 1.0 ),
+      theDerivativeToleranceFactor( 1.0 ),
+      theEpsilonChecked( 0 ),
+      theAbsoluteEpsilon( 0.1 ),
+      theRelativeEpsilon( 0.1 ),
+      safety( 0.9 ),
+      theMaxErrorRatio( 1.0 )
+{
+    // use more narrow range
+    setMinStepInterval( 1e-100 );
+    setMaxStepInterval( 1e+10 );
+}
+
+AdaptiveDifferentialStepper::~AdaptiveDifferentialStepper()
+{
+    ; // do nothing
+}
+
+
+void AdaptiveDifferentialStepper::initialize()
+{
+    DifferentialStepper::initialize();
+}
+
+void AdaptiveDifferentialStepper::step()
+{
+    theStateFlag = false;
+
+    clearVariables();
+
+    setStepInterval( getNextStepInterval() );
+
+    while ( !calculate() )
+    {
+        const Real anExpectedStepInterval( safety * getStepInterval() 
+                                           * pow( getMaxErrorRatio(),
+                                                  -1.0 / getOrder() ) );
+
+        if ( anExpectedStepInterval > getMinStepInterval() )
+        {
+            // shrink it if the error exceeds 110%
+            setStepInterval( anExpectedStepInterval );
+        }
+        else
+        {
+            setStepInterval( getMinStepInterval() );
+
+            // this must return false,
+            // so theTolerableStepInterval does NOT LIMIT the error.
+            THROW_EXCEPTION( SimulationError,
+                             "The error-limit step interval of Stepper ["
+                             + getID() + "] is too small." );
+
+            calculate();
+            break;
+        }
+    }
+
+    // an extra calculation for resetting the activities of processes
+    fireProcesses();
+
+    setTolerableStepInterval( getStepInterval() );
+
+    theStateFlag = true;
+
+    // grow it if error is 50% less than desired
+    const Real maxError( getMaxErrorRatio() );
+    if ( maxError < 0.5 )
+    {
+        const Real aNewStepInterval( getTolerableStepInterval() * safety
+                                     * pow( maxError,
+                                            -1.0 / ( getOrder() + 1 ) ) );
+        setNextStepInterval( aNewStepInterval );
+    }
+    else 
+    {
+        setNextStepInterval( getTolerableStepInterval() );
+    }
+}
+
+} // namespace libecs


Property changes on: ecell3/branches/ecell-3.1/ecell/libecs/AdaptiveDifferentialStepper.cpp
___________________________________________________________________
Added: svn:mime-type
   + text/plain
Added: svn:keywords
   + Id Author Date Revision
Added: svn:eol-style
   + native

Copied: ecell3/branches/ecell-3.1/ecell/libecs/AdaptiveDifferentialStepper.hpp (from rev 3248, ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.hpp)
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/AdaptiveDifferentialStepper.hpp	                        (rev 0)
+++ ecell3/branches/ecell-3.1/ecell/libecs/AdaptiveDifferentialStepper.hpp	2008-10-23 19:29:29 UTC (rev 3256)
@@ -0,0 +1,195 @@
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//       This file is part of the E-Cell System
+//
+//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 2005-2008 The Molecular Sciences Institute
+//
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//
+// E-Cell System is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public
+// License as published by the Free Software Foundation; either
+// version 2 of the License, or (at your option) any later version.
+// 
+// E-Cell System is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+// See the GNU General Public License for more details.
+// 
+// You should have received a copy of the GNU General Public
+// License along with E-Cell System -- see the file COPYING.
+// If not, write to the Free Software Foundation, Inc.,
+// 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+// 
+//END_HEADER
+//
+// written by Koichi Takahashi <sh...@e-...>,
+// E-Cell Project.
+//
+
+#ifndef __ADAPTIVEDIFFERENTIALSTEPPER_HPP
+#define __ADAPTIVEDIFFERENTIALSTEPPER_HPP
+
+#include "libecs/DifferentialStepper.hpp"
+
+/**
+   ADAPTIVE STEPSIZE DIFFERENTIAL EQUATION SOLVER
+   @addtogroup stepper
+   @{
+*/
+namespace libecs
+{
+DECLARE_CLASS( AdaptiveDifferentialStepper );
+
+LIBECS_DM_CLASS( AdaptiveDifferentialStepper, DifferentialStepper )
+{
+public:
+    LIBECS_DM_OBJECT_ABSTRACT( AdaptiveDifferentialStepper )
+    {
+        INHERIT_PROPERTIES( DifferentialStepper );
+
+        PROPERTYSLOT_SET_GET( Real, Tolerance );
+        PROPERTYSLOT_SET_GET( Real, AbsoluteToleranceFactor );
+        PROPERTYSLOT_SET_GET( Real, StateToleranceFactor );
+        PROPERTYSLOT_SET_GET( Real, DerivativeToleranceFactor );
+
+        PROPERTYSLOT( Integer, IsEpsilonChecked,
+                      &AdaptiveDifferentialStepper::setEpsilonChecked,
+                      &AdaptiveDifferentialStepper::isEpsilonChecked );
+        PROPERTYSLOT_SET_GET( Real, AbsoluteEpsilon );
+        PROPERTYSLOT_SET_GET( Real, RelativeEpsilon );
+
+        PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, MaxErrorRatio );
+    }
+
+public:
+    AdaptiveDifferentialStepper();
+
+    virtual ~AdaptiveDifferentialStepper();
+
+    /**
+       Adaptive stepsize control.
+
+       These methods are for handling the standerd error control objects.
+    */
+    SET_METHOD( Real, Tolerance )
+    {
+        theTolerance = value;
+    }
+
+    GET_METHOD( Real, Tolerance )
+    {
+        return theTolerance;
+    }
+
+    SET_METHOD( Real, AbsoluteToleranceFactor )
+    {
+        theAbsoluteToleranceFactor = value;
+    }
+
+    GET_METHOD( Real, AbsoluteToleranceFactor )
+    {
+        return theAbsoluteToleranceFactor;
+    }
+
+    SET_METHOD( Real, StateToleranceFactor )
+    {
+        theStateToleranceFactor = value;
+    }
+
+    GET_METHOD( Real, StateToleranceFactor )
+    {
+        return theStateToleranceFactor;
+    }
+
+    SET_METHOD( Real, DerivativeToleranceFactor )
+    {
+        theDerivativeToleranceFactor = value;
+    }
+
+    GET_METHOD( Real, DerivativeToleranceFactor )
+    {
+        return theDerivativeToleranceFactor;
+    }
+
+    SET_METHOD( Real, MaxErrorRatio )
+    {
+        theMaxErrorRatio = value;
+    }
+
+    GET_METHOD( Real, MaxErrorRatio )
+    {
+        return theMaxErrorRatio;
+    }
+
+    /**
+       check difference in one step
+    */
+    SET_METHOD( Integer, EpsilonChecked )
+    {
+        if ( value > 0 ) {
+            theEpsilonChecked = true;
+        }
+        else {
+            theEpsilonChecked = false;
+        }
+    }
+
+    const Integer isEpsilonChecked() const
+    {
+        return theEpsilonChecked;
+    }
+
+    SET_METHOD( Real, AbsoluteEpsilon )
+    {
+        theAbsoluteEpsilon = value;
+    }
+
+    GET_METHOD( Real, AbsoluteEpsilon )
+    {
+        return theAbsoluteEpsilon;
+    }
+
+    SET_METHOD( Real, RelativeEpsilon )
+    {
+        theRelativeEpsilon = value;
+    }
+
+    GET_METHOD( Real, RelativeEpsilon )
+    {
+        return theRelativeEpsilon;
+    }
+
+    virtual void initialize();
+
+    virtual void step();
+
+    virtual bool calculate() = 0;
+
+    virtual GET_METHOD( Integer, Stage )
+    { 
+        return 2;
+    }
+
+private:
+
+    Real safety;
+    Real theTolerance;
+    Real theAbsoluteToleranceFactor;
+    Real theStateToleranceFactor;
+    Real theDerivativeToleranceFactor;
+
+    bool theEpsilonChecked;
+    Real theAbsoluteEpsilon;
+    Real theRelativeEpsilon;
+
+    Real theMaxErrorRatio;
+};
+
+} // namespace libecs
+
+/** @} */
+
+#endif /* __ADAPTIVEDIFFERENTIALSTEPPER_HPP */


Property changes on: ecell3/branches/ecell-3.1/ecell/libecs/AdaptiveDifferentialStepper.hpp
___________________________________________________________________
Added: svn:mime-type
   + text/plain
Added: svn:keywords
   + Id Author Date Revision
Added: svn:eol-style
   + native

Modified: ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.cpp	2008-10-23 19:25:24 UTC (rev 3255)
+++ ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.cpp	2008-10-23 19:29:29 UTC (rev 3256)
@@ -50,9 +50,7 @@
 
 namespace libecs
 {
-
 LIBECS_DM_INIT_STATIC( DifferentialStepper, Stepper );
-LIBECS_DM_INIT_STATIC( AdaptiveDifferentialStepper, Stepper );
 
 DifferentialStepper::DifferentialStepper()
     : theNextStepInterval( 0.001 ),
@@ -388,90 +386,4 @@
     return aValue;
 }
 
-
-////////////////////////// AdaptiveDifferentialStepper
-
-AdaptiveDifferentialStepper::AdaptiveDifferentialStepper()
-    : theTolerance( 1.0e-6 ),
-      theAbsoluteToleranceFactor( 1.0 ),
-      theStateToleranceFactor( 1.0 ),
-      theDerivativeToleranceFactor( 1.0 ),
-      theEpsilonChecked( 0 ),
-      theAbsoluteEpsilon( 0.1 ),
-      theRelativeEpsilon( 0.1 ),
-      safety( 0.9 ),
-      theMaxErrorRatio( 1.0 )
-{
-    // use more narrow range
-    setMinStepInterval( 1e-100 );
-    setMaxStepInterval( 1e+10 );
-}
-
-AdaptiveDifferentialStepper::~AdaptiveDifferentialStepper()
-{
-    ; // do nothing
-}
-
-
-void AdaptiveDifferentialStepper::initialize()
-{
-    DifferentialStepper::initialize();
-}
-
-void AdaptiveDifferentialStepper::step()
-{
-    theStateFlag = false;
-
-    clearVariables();
-
-    setStepInterval( getNextStepInterval() );
-
-    while ( !calculate() )
-    {
-        const Real anExpectedStepInterval( safety * getStepInterval() 
-                                           * pow( getMaxErrorRatio(),
-                                                  -1.0 / getOrder() ) );
-
-        if ( anExpectedStepInterval > getMinStepInterval() )
-        {
-            // shrink it if the error exceeds 110%
-            setStepInterval( anExpectedStepInterval );
-        }
-        else
-        {
-            setStepInterval( getMinStepInterval() );
-
-            // this must return false,
-            // so theTolerableStepInterval does NOT LIMIT the error.
-            THROW_EXCEPTION( SimulationError,
-                             "The error-limit step interval of Stepper ["
-                             + getID() + "] is too small." );
-
-            calculate();
-            break;
-        }
-    }
-
-    // an extra calculation for resetting the activities of processes
-    fireProcesses();
-
-    setTolerableStepInterval( getStepInterval() );
-
-    theStateFlag = true;
-
-    // grow it if error is 50% less than desired
-    const Real maxError( getMaxErrorRatio() );
-    if ( maxError < 0.5 )
-    {
-        const Real aNewStepInterval( getTolerableStepInterval() * safety
-                                     * pow( maxError,
-                                            -1.0 / ( getOrder() + 1 ) ) );
-        setNextStepInterval( aNewStepInterval );
-    }
-    else 
-    {
-        setNextStepInterval( getTolerableStepInterval() );
-    }
-}
-
 } // namespace libecs

Modified: ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.hpp	2008-10-23 19:25:24 UTC (rev 3255)
+++ ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.hpp	2008-10-23 19:29:29 UTC (rev 3256)
@@ -184,165 +184,6 @@
     Real theTolerableStepInterval;
 };
 
-
-/**
-     ADAPTIVE STEPSIZE DIFFERENTIAL EQUATION SOLVER
-
-
-*/
-
-DECLARE_CLASS( AdaptiveDifferentialStepper );
-
-LIBECS_DM_CLASS( AdaptiveDifferentialStepper, DifferentialStepper )
-{
-
-public:
-
-    LIBECS_DM_OBJECT_ABSTRACT( AdaptiveDifferentialStepper )
-    {
-        INHERIT_PROPERTIES( DifferentialStepper );
-
-        PROPERTYSLOT_SET_GET( Real, Tolerance );
-        PROPERTYSLOT_SET_GET( Real, AbsoluteToleranceFactor );
-        PROPERTYSLOT_SET_GET( Real, StateToleranceFactor );
-        PROPERTYSLOT_SET_GET( Real, DerivativeToleranceFactor );
-
-        PROPERTYSLOT( Integer, IsEpsilonChecked,
-                      &AdaptiveDifferentialStepper::setEpsilonChecked,
-                      &AdaptiveDifferentialStepper::isEpsilonChecked );
-        PROPERTYSLOT_SET_GET( Real, AbsoluteEpsilon );
-        PROPERTYSLOT_SET_GET( Real, RelativeEpsilon );
-
-        PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, MaxErrorRatio );
-    }
-
-public:
-
-    AdaptiveDifferentialStepper();
-
-    virtual ~AdaptiveDifferentialStepper();
-
-    /**
-       Adaptive stepsize control.
-
-       These methods are for handling the standerd error control objects.
-    */
-
-    SET_METHOD( Real, Tolerance )
-    {
-        theTolerance = value;
-    }
-
-    GET_METHOD( Real, Tolerance )
-    {
-        return theTolerance;
-    }
-
-    SET_METHOD( Real, AbsoluteToleranceFactor )
-    {
-        theAbsoluteToleranceFactor = value;
-    }
-
-    GET_METHOD( Real, AbsoluteToleranceFactor )
-    {
-        return theAbsoluteToleranceFactor;
-    }
-
-    SET_METHOD( Real, StateToleranceFactor )
-    {
-        theStateToleranceFactor = value;
-    }
-
-    GET_METHOD( Real, StateToleranceFactor )
-    {
-        return theStateToleranceFactor;
-    }
-
-    SET_METHOD( Real, DerivativeToleranceFactor )
-    {
-        theDerivativeToleranceFactor = value;
-    }
-
-    GET_METHOD( Real, DerivativeToleranceFactor )
-    {
-        return theDerivativeToleranceFactor;
-    }
-
-    SET_METHOD( Real, MaxErrorRatio )
-    {
-        theMaxErrorRatio = value;
-    }
-
-    GET_METHOD( Real, MaxErrorRatio )
-    {
-        return theMaxErrorRatio;
-    }
-
-    /**
-       check difference in one step
-    */
-
-    SET_METHOD( Integer, EpsilonChecked )
-    {
-        if ( value > 0 ) {
-            theEpsilonChecked = true;
-        }
-        else {
-            theEpsilonChecked = false;
-        }
-    }
-
-    const Integer isEpsilonChecked() const
-    {
-        return theEpsilonChecked;
-    }
-
-    SET_METHOD( Real, AbsoluteEpsilon )
-    {
-        theAbsoluteEpsilon = value;
-    }
-
-    GET_METHOD( Real, AbsoluteEpsilon )
-    {
-        return theAbsoluteEpsilon;
-    }
-
-    SET_METHOD( Real, RelativeEpsilon )
-    {
-        theRelativeEpsilon = value;
-    }
-
-    GET_METHOD( Real, RelativeEpsilon )
-    {
-        return theRelativeEpsilon;
-    }
-
-    virtual void initialize();
-
-    virtual void step();
-
-    virtual bool calculate() = 0;
-
-    virtual GET_METHOD( Integer, Stage )
-    { 
-        return 2;
-    }
-
-private:
-
-    Real safety;
-    Real theTolerance;
-    Real theAbsoluteToleranceFactor;
-    Real theStateToleranceFactor;
-    Real theDerivativeToleranceFactor;
-
-    bool theEpsilonChecked;
-    Real theAbsoluteEpsilon;
-    Real theRelativeEpsilon;
-
-    Real theMaxErrorRatio;
-};
-
 } // namespace libecs
 
 /** @} */

Modified: ecell3/branches/ecell-3.1/ecell/libecs/Makefile.am
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/Makefile.am	2008-10-23 19:25:24 UTC (rev 3255)
+++ ecell3/branches/ecell-3.1/ecell/libecs/Makefile.am	2008-10-23 19:29:29 UTC (rev 3256)
@@ -32,6 +32,7 @@
 Variable.cpp\
 Stepper.cpp\
 DifferentialStepper.cpp\
+AdaptiveDifferentialStepper.cpp\
 DiscreteTimeStepper.cpp\
 DiscreteEventStepper.cpp\
 PassiveStepper.cpp\
@@ -73,6 +74,7 @@
 StepperEvent.hpp\
 EventScheduler.hpp\
 DifferentialStepper.hpp\
+AdaptiveDifferentialStepper.hpp\
 DiscreteTimeStepper.hpp\
 DiscreteEventStepper.hpp\
 PassiveStepper.hpp\

Modified: ecell3/branches/ecell-3.1/ecell/libecs/Polymorph.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/Polymorph.hpp	2008-10-23 19:25:24 UTC (rev 3255)
+++ ecell3/branches/ecell-3.1/ecell/libecs/Polymorph.hpp	2008-10-23 19:29:29 UTC (rev 3256)
@@ -300,7 +300,7 @@
             throw std::bad_alloc();
         }
 
-        return new(ptr) PolymorphValue( sptr );
+        return new(ptr) PolymorphValue( sptr, sz );
     }
 
     static Handle create( String const& aValue )
@@ -408,14 +408,9 @@
     explicit PolymorphValue( Real aValue )
         : theType( REAL ), theRefCount( 0 ), theRealValue( aValue ) {}
 
-    explicit PolymorphValue( const char* sptr,
-                             std::size_t sz = static_cast< std::size_t >( -1 ) )
+    explicit PolymorphValue( const char* sptr, std::size_t sz )
         : theType( STRING ), theRefCount( 0 )
     {
-        if ( sz == static_cast< std::size_t >( -1 ) )
-        {
-            sz = std::strlen( sptr );
-        }
         theStringValue.theLength = sz;
         std::memcpy( theStringValue.ptr, sptr, sz );
         theStringValue.ptr[ sz ] = '\0';


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[Ecell-cvs] SF.net SVN: ecell:[3278] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-11-06 09:49:52

Revision: 3278
          http://ecell.svn.sourceforge.net/ecell/?rev=3278&view=rev
Author:   moriyoshi
Date:     2008-11-06 09:49:49 +0000 (Thu, 06 Nov 2008)

Log Message:
-----------
* Rename ecell.SessionManager to ecell.session_manager

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-session-manager.in

Added Paths:
-----------
    ecell3/branches/ecell-3.1/doc/samples/session_manager/
    ecell3/branches/ecell-3.1/doc/samples/session_manager/README
    ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.globus.py
    ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.py
    ecell3/branches/ecell-3.1/doc/samples/session_manager/model.em
    ecell3/branches/ecell-3.1/doc/samples/session_manager/runsession.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus2Proxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus4Proxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LSFProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LocalProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/SGEProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/SessionManager.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Util.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/__init__.py

Removed Paths:
-------------
    ecell3/branches/ecell-3.1/doc/samples/session_manager/README
    ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.globus.py
    ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.py
    ecell3/branches/ecell-3.1/doc/samples/session_manager/model.em
    ecell3/branches/ecell-3.1/doc/samples/session_manager/runsession.py
    ecell3/branches/ecell-3.1/doc/samples/sessionmanager/
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus2Proxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus4Proxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LSFProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LocalProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/SGEProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/SessionManager.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Util.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/__init__.py

Deleted: ecell3/branches/ecell-3.1/doc/samples/session_manager/README
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/sessionmanager/README	2008-10-26 13:53:04 UTC (rev 3260)
+++ ecell3/branches/ecell-3.1/doc/samples/session_manager/README	2008-11-06 09:49:49 UTC (rev 3278)
@@ -1,35 +0,0 @@
-%Id: README,v 1.0 2003/09/03 19:02 sugi Exp %
-
-
-
-=== About ===
-
-This is a very simple example of E-Cell Session Manager Script (EMS)
-for SessionManager. SessionManager concurrently runs script files,
-including ESS files or other script files(sh,python,etc.).
-
-
-=== Files and directories ===
-
-README:                     This file
-runsession.py:              Script file for E-Cell Session
-ems.py:                     Script file for E-Cell Session Manager
-simple.em:                  Model file(EM file) 
-
-
-=== Running this script ===
-
-1. Convert the .em file to .eml file.
-
-   % ecell3-em2eml simple.em
-   % ls simple.eml
-   simple.eml
-
-2. Run esm file.
-
-   % ecell3-session-manager ems.py
-
-   Environment and Cuncurrency could be specified as bellow.
-
-   % ecell3-session-manager --environment=SGE --concurrency=5 ems.py
-

Copied: ecell3/branches/ecell-3.1/doc/samples/session_manager/README (from rev 3277, ecell3/branches/ecell-3.1/doc/samples/sessionmanager/README)
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/session_manager/README	                        (rev 0)
+++ ecell3/branches/ecell-3.1/doc/samples/session_manager/README	2008-11-06 09:49:49 UTC (rev 3278)
@@ -0,0 +1,35 @@
+%Id: README,v 1.0 2003/09/03 19:02 sugi Exp %
+
+
+
+=== About ===
+
+This is a very simple example of E-Cell Session Manager Script (EMS)
+for SessionManager. SessionManager concurrently runs script files,
+including ESS files or other script files(sh,python,etc.).
+
+
+=== Files and directories ===
+
+README:                     This file
+runsession.py:              Script file for E-Cell Session
+ems.py:                     Script file for E-Cell Session Manager
+simple.em:                  Model file(EM file) 
+
+
+=== Running this script ===
+
+1. Convert the .em file to .eml file.
+
+   % ecell3-em2eml simple.em
+   % ls simple.eml
+   simple.eml
+
+2. Run esm file.
+
+   % ecell3-session-manager ems.py
+
+   Environment and Cuncurrency could be specified as bellow.
+
+   % ecell3-session-manager --environment=SGE --concurrency=5 ems.py
+


Property changes on: ecell3/branches/ecell-3.1/doc/samples/session_manager/README
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Added: svn:mime-type
   + text/plain
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   + Author Date Id Revision
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   + native

Deleted: ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.globus.py
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.globus.py	2008-10-26 13:53:04 UTC (rev 3260)
+++ ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.globus.py	2008-11-06 09:49:49 UTC (rev 3278)
@@ -1,53 +0,0 @@
-#
-# This is a sample script file of EMS ( E-Cell Session Manager script )
-# for Globus
-#
-
-import os
-
-setEnvironment('Globus2')  
-
-setTmpDirRemovable(False)  # not delete tmp directory
-
-setConcurrency(2) # set concurrency
-
-# -------------------------------
-# set up SystemProxy's properties
-
-aSystemProxy = getSystemProxy()
-
-aSystemProxy.setPassword('your_passwd')  # password for globus gate-keeper
-aSystemProxy.gridProxyInit()      # initialize gate-keeper
-
-# create a list of hosts on which jobs are conducted.
-aHostList = ['host1.domain',
-             'host2.domain']
-aSystemProxy.setHosts(aHostList) # set the host list
-
-# -------------------------------
-
-MODEL_FILE = 'model.eml'
-ESS_FILE = 'runsession.py'
-
-# Register jobs.
-
-aJobIDList = []
-
-for i in xrange(0,2):
-	
-	VALUE_OF_S = i * 1000
-	aParameterDict = { 'MODEL_FILE': MODEL_FILE, 'VALUE_OF_S': VALUE_OF_S }
-
-	#registerEcellSession( ESS file, parameters, files that ESS uses )
-	aJobID = registerEcellSession( ESS_FILE, aParameterDict, [ MODEL_FILE, ])
-	aJobIDList.append( aJobID ) # Memorize the job IDs in aJobIDList.
-
-# Run the registered jobs.
-
-run()
-
-for aJobID in aJobIDList: 
-
-	print " --- job id = %s ---" %aJobID
-	print getStdout( aJobID )  # Print the output of each job. 
-

Copied: ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.globus.py (from rev 3277, ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.globus.py)
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.globus.py	                        (rev 0)
+++ ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.globus.py	2008-11-06 09:49:49 UTC (rev 3278)
@@ -0,0 +1,47 @@
+#
+# This is a sample script file of EMS ( E-Cell Session Manager script )
+# for Globus
+#
+
+import os
+
+setEnvironment('Globus4')
+
+setTmpDirRemovable(False)  # not delete tmp directory
+
+setConcurrency(2) # set concurrency
+
+# -------------------------------
+# set up SystemProxy's properties
+
+aSystemProxy = getSystemProxy()
+aSystemProxy.setLocalHostName( 'myhost.example.com' )
+aSystemProxy.setFactoryEndpoint( 'https://endpoint.example.com:8443/wsrf/services/ManagedJobFactoryService' )
+
+# -------------------------------
+
+MODEL_FILE = 'model.eml'
+ESS_FILE = 'runsession.py'
+
+# Register jobs.
+
+aJobIDList = []
+
+for i in xrange(0,2):
+	
+	VALUE_OF_S = i * 1000
+	aParameterDict = { 'MODEL_FILE': MODEL_FILE, 'VALUE_OF_S': VALUE_OF_S }
+
+	#registerEcellSession( ESS file, parameters, files that ESS uses )
+	aJobID = registerEcellSession( ESS_FILE, aParameterDict, [ MODEL_FILE, ])
+	aJobIDList.append( aJobID ) # Memorize the job IDs in aJobIDList.
+
+# Run the registered jobs.
+
+run()
+
+for aJobID in aJobIDList: 
+
+	print " --- job id = %s ---" %aJobID
+	print getStdout( aJobID )  # Print the output of each job. 
+


Property changes on: ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.globus.py
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Added: svn:mime-type
   + text/plain
Added: svn:keywords
   + Author Date Id Revision
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   + native

Deleted: ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.py
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.py	2008-10-26 13:53:04 UTC (rev 3260)
+++ ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.py	2008-11-06 09:49:49 UTC (rev 3278)
@@ -1,32 +0,0 @@
-#
-# This is a sample script file of EMS ( E-Cell Session Manager script )
-#
-
-import os
-
-MODEL_FILE = 'model.eml'
-ESS_FILE = 'runsession.py'
-
-# Register jobs.
-
-aJobIDList = []
-
-for i in xrange(0,5):
-	
-	VALUE_OF_S = i * 1000
-	aParameterDict = { 'MODEL_FILE': MODEL_FILE, 'VALUE_OF_S': VALUE_OF_S }
-
-	#registerEcellSession( ESS file, parameters, files that ESS uses )
-	aJobID = registerEcellSession( ESS_FILE, aParameterDict, [ MODEL_FILE, ])
-	aJobIDList.append( aJobID ) # Memorize the job IDs in aJobIDList.
-
-# Run the registered jobs.
-
-run()
-
-for aJobID in aJobIDList: 
-
-	print " --- job id = %s ---" %aJobID
-	print getStdout( aJobID )  # Print the output of each job. 
-
-

Copied: ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.py (from rev 3277, ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.py)
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.py	                        (rev 0)
+++ ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.py	2008-11-06 09:49:49 UTC (rev 3278)
@@ -0,0 +1,30 @@
+#
+# This is a sample script file of EMS ( E-Cell Session Manager script )
+#
+
+import os
+
+MODEL_FILE = 'model.eml'
+ESS_FILE = 'runsession.py'
+
+# Register jobs.
+
+aJobIDList = []
+
+for i in xrange(0,5):
+	
+	VALUE_OF_S = i * 1000
+	aParameterDict = { 'MODEL_FILE': MODEL_FILE, 'VALUE_OF_S': VALUE_OF_S }
+
+	#registerEcellSession( ESS file, parameters, files that ESS uses )
+	aJobID = registerEcellSession( ESS_FILE, aParameterDict, [ MODEL_FILE, ])
+	aJobIDList.append( aJobID ) # Memorize the job IDs in aJobIDList.
+
+# Run the registered jobs.
+
+run()
+
+for aJobID in aJobIDList: 
+
+	print " --- job id = %s ---" % aJobID
+	print getStdout( aJobID )  # Print the output of each job. 


Property changes on: ecell3/branches/ecell-3.1/doc/samples/session_manager/ems.py
___________________________________________________________________
Added: svn:mime-type
   + text/plain
Added: svn:keywords
   + Author Date Id Revision
Added: svn:eol-style
   + native

Deleted: ecell3/branches/ecell-3.1/doc/samples/session_manager/model.em
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/sessionmanager/model.em	2008-10-26 13:53:04 UTC (rev 3260)
+++ ecell3/branches/ecell-3.1/doc/samples/session_manager/model.em	2008-11-06 09:49:49 UTC (rev 3278)
@@ -1,46 +0,0 @@
-#
-# A very simple model with one michaelis-uni-uni reaction.
-#
-
-# Stepper FixedODE1Stepper( DE1 )
-Stepper ODEStepper( DE1 )
-{
-	# no property
-}
-
-System System( / )
-{
-	StepperID	DE1;
-
-	Variable Variable( SIZE )
-	{
-		Value	1e-18;
-	}
-
-	Variable Variable( S )
-	{
-		Value	1000000;
-	}
-	
-	Variable Variable( P )
-	{
-		Value	0;
-	}
-	
-	Variable Variable( E )
-	{
-		Value	1000;
-	}
-	
-	Process MichaelisUniUniFluxProcess( E )
-	{
-		VariableReferenceList	[ S0 :.:S -1 ]
- 					[ P0 :.:P 1 ]
-					[ C0 :.:E 0 ];
-		KmS	1;
-		KcF	10;
-	}
-
-	
-}
-

Copied: ecell3/branches/ecell-3.1/doc/samples/session_manager/model.em (from rev 3277, ecell3/branches/ecell-3.1/doc/samples/sessionmanager/model.em)
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/session_manager/model.em	                        (rev 0)
+++ ecell3/branches/ecell-3.1/doc/samples/session_manager/model.em	2008-11-06 09:49:49 UTC (rev 3278)
@@ -0,0 +1,46 @@
+#
+# A very simple model with one michaelis-uni-uni reaction.
+#
+
+# Stepper FixedODE1Stepper( DE1 )
+Stepper ODEStepper( DE1 )
+{
+	# no property
+}
+
+System System( / )
+{
+	StepperID	DE1;
+
+	Variable Variable( SIZE )
+	{
+		Value	1e-18;
+	}
+
+	Variable Variable( S )
+	{
+		Value	1000000;
+	}
+	
+	Variable Variable( P )
+	{
+		Value	0;
+	}
+	
+	Variable Variable( E )
+	{
+		Value	1000;
+	}
+	
+	Process MichaelisUniUniFluxProcess( E )
+	{
+		VariableReferenceList	[ S0 :.:S -1 ]
+ 					[ P0 :.:P 1 ]
+					[ C0 :.:E 0 ];
+		KmS	1;
+		KcF	10;
+	}
+
+	
+}
+


Property changes on: ecell3/branches/ecell-3.1/doc/samples/session_manager/model.em
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Added: svn:mime-type
   + text/plain
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   + Author Date Id Revision
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   + native

Deleted: ecell3/branches/ecell-3.1/doc/samples/session_manager/runsession.py
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/sessionmanager/runsession.py	2008-10-26 13:53:04 UTC (rev 3260)
+++ ecell3/branches/ecell-3.1/doc/samples/session_manager/runsession.py	2008-11-06 09:49:49 UTC (rev 3278)
@@ -1,11 +0,0 @@
-loadModel( MODEL_FILE )                # Load the model.
-
-S = createEntityStub( 'Variable:/:S' ) # Create a stub object of 
-
-S[ 'Value' ] = VALUE_OF_S              # Set the value VALUE_OF_S given by the 
-                                       # ESM script.
-
-run( 200 )                             # Run the simulation for 200 seconds.
-
-message( S[ 'Value' ] )                # Print the value of 'Variable:/:S'.
-

Copied: ecell3/branches/ecell-3.1/doc/samples/session_manager/runsession.py (from rev 3277, ecell3/branches/ecell-3.1/doc/samples/sessionmanager/runsession.py)
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/session_manager/runsession.py	                        (rev 0)
+++ ecell3/branches/ecell-3.1/doc/samples/session_manager/runsession.py	2008-11-06 09:49:49 UTC (rev 3278)
@@ -0,0 +1,10 @@
+loadModel( MODEL_FILE )                # Load the model.
+
+S = createEntityStub( 'Variable:/:S' ) # Create a stub object of 
+
+S[ 'Value' ] = VALUE_OF_S              # Set the value VALUE_OF_S given by the 
+                                       # ESM script.
+
+run( 200 )                             # Run the simulation for 200 seconds.
+
+print S[ 'Value' ]                     # Print the value of 'Variable:/:S'.


Property changes on: ecell3/branches/ecell-3.1/doc/samples/session_manager/runsession.py
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Added: svn:mime-type
   + text/plain
Added: svn:keywords
   + Author Date Id Revision
Added: svn:eol-style
   + native

Deleted: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/Constants.py	2008-10-26 13:53:04 UTC (rev 3260)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py	2008-11-06 09:49:49 UTC (rev 3278)
@@ -1,63 +0,0 @@
-#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-#
-#       This file is part of the E-Cell System
-#
-#       Copyright (C) 1996-2008 Keio University
-#       Copyright (C) 2005-2008 The Molecular Sciences Institute
-#
-#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-#
-#
-# E-Cell System is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public
-# License as published by the Free Software Foundation; either
-# version 2 of the License, or (at your option) any later version.
-# 
-# E-Cell System is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU General Public License for more details.
-# 
-# You should have received a copy of the GNU General Public
-# License along with E-Cell System -- see the file COPYING.
-# If not, write to the Free Software Foundation, Inc.,
-# 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
-# 
-#END_HEADER
-#
-# Designed by Koichi Takahashi <sh...@e-...>
-# Programmed by Masahiro Sugimoto <ms...@sf...>
-
-ECELL3_PYTHON = 'ecell3-python'
-ECELL3_SESSION = 'ecell3-session'
-
-DEFAULT_STDOUT = 'stdout'
-DEFAULT_STDERR = 'stderr'
-
-SYSTEM_PROXY = 'SystemProxy'
-SESSION_PROXY = 'SessionProxy'
-
-DEFAULT_TMP_DIRECTORY = 'tmp'
-DEFAULT_ENVIRONMENT = 'Local'
-
-# job status
-QUEUED       = 0
-RUN          = 1
-FINISHED     = 2
-ERROR        = 3
-
-STATUS = {
-    QUEUED:   'QUEUED',
-    RUN:      'RUN',
-    FINISHED: 'FINISHED',
-    ERROR:    'ERROR',
-    }
-
-INTERESTING_ENV_VARS = (
-    'ECELL3_PREFIX',
-    'ECELL3_DM_PATH',
-    'LTDL_LIBRARY_PATH',
-    'LD_LIBRARY_PATH',
-    'PYTHONPATH',
-    'PATH', # XXX: better not include this one?
-    )

Copied: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py (from rev 3277, ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/Constants.py)
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py	                        (rev 0)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py	2008-11-06 09:49:49 UTC (rev 3278)
@@ -0,0 +1,63 @@
+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+#
+#       This file is part of the E-Cell System
+#
+#       Copyright (C) 1996-2008 Keio University
+#       Copyright (C) 2005-2008 The Molecular Sciences Institute
+#
+#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+#
+#
+# E-Cell System is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public
+# License as published by the Free Software Foundation; either
+# version 2 of the License, or (at your option) any later version.
+# 
+# E-Cell System is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public
+# License along with E-Cell System -- see the file COPYING.
+# If not, write to the Free Software Foundation, Inc.,
+# 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+# 
+#END_HEADER
+#
+# Designed by Koichi Takahashi <sh...@e-...>
+# Programmed by Masahiro Sugimoto <ms...@sf...>
+
+ECELL3_PYTHON = 'ecell3-python'
+ECELL3_SESSION = 'ecell3-session'
+
+DEFAULT_STDOUT = 'stdout'
+DEFAULT_STDERR = 'stderr'
+
+SYSTEM_PROXY = 'SystemProxy'
+SESSION_PROXY = 'SessionProxy'
+
+DEFAULT_TMP_DIRECTORY = 'tmp'
+DEFAULT_ENVIRONMENT = 'Local'
+
+# job status
+QUEUED       = 0
+RUN          = 1
+FINISHED     = 2
+ERROR        = 3
+
+STATUS = {
+    QUEUED:   'QUEUED',
+    RUN:      'RUN',
+    FINISHED: 'FINISHED',
+    ERROR:    'ERROR',
+    }
+
+INTERESTING_ENV_VARS = (
+    'ECELL3_PREFIX',
+    'ECELL3_DM_PATH',
+    'LTDL_LIBRARY_PATH',
+    'LD_LIBRARY_PATH',
+    'PYTHONPATH',
+    'PATH', # XXX: better not include this one?
+    )


Property changes on: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py
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Added: svn:mime-type
   + text/plain
Added: svn:eol-style
   + native

Deleted: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus2Proxy.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/Globus2Proxy.py	2008-10-26 13:53:04 UTC (rev 3260)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus2Proxy.py	2008-11-06 09:49:49 UTC (rev 3278)
@@ -1,272 +0,0 @@
-#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-#
-#       This file is part of the E-Cell System
-#
-#       Copyright (C) 1996-2008 Keio University
-#       Copyright (C) 2005-2008 The Molecular Sciences Institute
-#
-#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
-#
-#
-# E-Cell System is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public
-# License as published by the Free Software Foundation; either
-# version 2 of the License, or (at your option) any later version.
-# 
-# E-Cell System is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU General Public License for more details.
-# 
-# You should have received a copy of the GNU General Public
-# License along with E-Cell System -- see the file COPYING.
-# If not, write to the Free Software Foundation, Inc.,
-# 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
-# 
-#END_HEADER
-#
-# Designed by Koichi Takahashi <sh...@e-...>
-# Programmed by Masahiro Sugimoto <ms...@sf...>
-
-# imports standard modules
-import sys
-import os
-import time
-import signal
-import re
-import popen2
-
-
-# imports ecell modules
-from ecell.SessionManager.Util import *
-from ecell.SessionManager.SessionManager import *
-from ecell.SessionManager.Constants import *
-
-GRID_INFO_SEARCH = 'grid-info-search'
-GLOBUS_JOB_RUN='globus-job-run'
-GLOBUS_JOB_SUBMIT='globus-job-submit'
-GLOBUS_JOB_GET_STATUS='globus-job-status'
-GLOBUS_JOB_GET_OUTPUT='globus-job-get-output'
-GLOBUS_JOB_CLEAN='globus-job-clean'
-GLOBUS_URL_COPY='globus-url-copy'
-MKDIR='/bin/mkdir'
-RM='/bin/rm'
-
-class SessionProxy( AbstractSessionProxy ):
-    def __init__( self, dispatcher, jobID ):
-        AbstractSessionProxy.__init__( self, dispatcher, jobID )
-
-        # initialize parameter
-        self.__theContactString = None
-
-        # initialize script name
-        # if current shell is '/bin/tcsh', set 'script.tcsh' 
-        self.__theTmpScriptFileName = "script." \
-                + os.path.basename( getCurrentShell() )
-        self.__theCpu = None
-
-    def getContactString( self ):
-        '''return job id 
-        '''
-        return self.__theContactString 
-
-    def __submitSessionProxy( self, args, environmentVars = {}, dir = None ):
-        _args = [
-            GLOBUS_JOB_RUN,
-            self.__theCpu
-            ]
-        if dir != None:
-            _args.extend( ( '-dir', dir ) )
-        for i in environmentVars:
-            _args.extend( ( '-env', '%s=%s' % i ) )
-        _args.extend( args )
-        stdout, stdin = popen2.popen2( args )
-        stdin.close()
-        return stdout.read()
-
-    def __transferFiles( self, destCpu, files, dest ):
-        for file in files:
-            aLocalFile  = "file://" + file.replace( os.sep, '/' )
-            aRemoteFile = "gsiftp://" + destCpu + '/' \
-                    + dest.replace( os.sep, '/' ) \
-                    + os.path.basename( file )
-            os.spawnlp( os.P_WAIT, GLOBUS_URL_COPY,
-                GLOBUS_URL_COPY, aLocalFile, aRemoteFile )
-
-    def run( self ):
-        '''run process
-        Return None
-        '''
-        if not AbstractSessionProxy.run( self ):
-            return False
-
-        self.__theCpu = self.getSystemProxy().getFreeCpu()
-
-        aCwd = os.getcwd()
-        try:
-            os.chdir( self.getJobDirectory() )
-            self.__submitSessionProxy( ( MKDIR, '-p',
-                    os.path.abspath( self.getJobDirectory() ) ) )
-
-            files = [ self.getScriptFileName() ] 
-            files.extend( self.getExtraFileList() )
-            self.__transferFiles( self.__theCpu, map( os.path.abspath, files ),
-                    self.getJobDirectory() )
-            self.__theContactString = self.__submitSessionProxy( (
-                self.getInterpreter(),
-                '-stdin', '-s', self.getScriptFileName() ),
-                self.getEnvironmentVariables(),
-                self.getJobDirectory() )
-        finally:
-            os.chdir( aCwd )
-        return True
-
-    def getCpu( self ):
-        '''Return cpu name
-        Return str : cpu name
-        '''
-
-        return self.__theCpu
-
-    def __cancel( self ):
-        raiseExceptionOnError( RuntineError,
-            pollForOutputs( popen2.Popen3(
-                ( GLOBUS_JOB_CLEAN, self.__theContactString ), True ) )
-            )
-
-    def stop( self ):
-        '''stop the job
-        Return None
-        '''
-
-        # When this job is running, stop it.
-        if self.getStatus() == RUN:
-            self.__cancel()
-
-        # set error status
-        self.setStatus(ERROR) 
-
-class SystemProxy( AbstractSystemProxy ):
-    '''Globus2SystemProxy'''
-    def __init__( self, sessionManager ):
-        '''Constructor
-        sessionManager -- the reference to SessionManager
-        '''
-
-        # calls superclass's constructor
-        AbstractSystemProxy.__init__( self, sessionManager )
-
-        self.__theIdentity = None
-        self.__theHostList = []
-        self.__theFreeCpuList = None
-        self._updateStatus()
-
-    def __del__( self ):
-        '''When Globus2SystemProxy exits, this method id called.
-        Remove tmp root directory on remote hosts.
-        '''
-
-        for aHost in self.__theHostList:
-            if aHost != self.getLocalHost():
-                self.__submitSessionProxy( aHost, RM, "-rf",
-                        self.getSessionManager().getTmpRootDir(),
-                        dir = os.getcwd() )
-
-    def setHosts( self, hostlist ):
-        '''Set host names on which the jobs will be conducted
-        hostlist(list of str) -- list of host name
-        Return None
-        '''
-        self.__theHostList = list( hostlist )
-
-    def getDefaultConcurrency( self ):
-        '''returns default cpus
-        Return int : the number of cpus
-        '''
-        return 1
-
-    def _createSessionProxy( self ):
-        '''creates and returns new SessionProxy instance
-        Return SessionProxy
-        '''
-        return SessionProxy( self, self.getNextJobID() )
-
-    def getFreeCpuList( self ):
-        '''Return free cpus
-        Return list of str : cpu names
-        '''
-        if self.__theFreeCpuList == None:
-            self._updateStatus()
-        return self.__theFreeCpuList
-
-    def getFreeCpu( self ):
-        if self.__theFreeCpuList == None:
-            self._updateStatus()
-        return self.__theFreeCpuList.pop()
-
-    def _updateStatus( self ):
-        '''update jobs's status
-        Return None
-        '''
-        freeCpuList = []
-        for aHost in self.__theHostList:
-            stdout, stdin, stderr = popen2.popen3( (
-                GRID_INFO_SEARCH,
-                '-h', aHost,
-                'objectClass=MdsCpu'
-                'Mds-Cpu-Free-1minX100'
-                ) )
-            stdin.close()
-            for aLine in stdout:
-                m = re.match( r'Mds-Cpu-Free-1minX100:\s*(\d+)', aLine )
-                if m != None:
-                    aFreeCpu = int( m.groups( 0 ) )
-                    if aFreeCpu > 60:
-                        freeCpuList.append( aHost )
-                    break
-            stdout.close()
-        self.__theFreeCpuList = freeCpuList
-
-        for job in self.getSessionProxies():
-            stdout, stdin = popen2.popen2(
-                ( GLOBUS_JOB_GET_STATUS, job.getContactString() ) )
-            stdin.close()
-            status = stdout.readline()[:-1]
-
-            # if the status is done, copy remote output files
-            # to local machine.
-            if status == 'DONE' and job.getStatus() != FINISHED:
-                job.setStatus( FINISHED ) 
-
-                # save current directory
-                aCwd = os.getcwd()
-                try:
-                    os.chdir( job.getJobDirectory() )
-
-                    dest = open(
-                        os.path.join( os.getcwd(), job.getStdoutFileName() ),
-                            'wb' )
-
-                    try:
-                        stdout, stdin = popen2.popen2(
-                            ( GLOBUS_JOB_GET_OUTPUT, job.getContactString() ) )
-                        stdin.close() 
-                        copyfileobj( stdout, dest )
-                    finally:
-                        close( dest )
-
-                    dest = open(
-                        os.path.join( os.getcwd(), job.getStderrtFileName() ),
-                            'wb' )
-
-                    try:
-                        stdout, stdin = popen2.popen2(
-                            ( GLOBUS_JOB_GET_OUTPUT, '-err',
-                              job.getContactString() ) )
-                        stdin.close() 
-                        copyfileobj( stdout, dest )
-                    finally:
-                        close( dest )
-                finally:
-                    os.chdir( aCwd )
-

Copied: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus2Proxy.py (from rev 3277, ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/Globus2Proxy.py)
======================================================...
 
[truncated message content]

[Ecell-cvs] SF.net SVN: ecell:[3285] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-11-10 19:26:28

Revision: 3285
          http://ecell.svn.sourceforge.net/ecell/?rev=3285&view=rev
Author:   moriyoshi
Date:     2008-11-10 19:26:25 +0000 (Mon, 10 Nov 2008)

Log Message:
-----------
* Take care of package revision.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/build/msvc/info.js
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/config.py.in

Modified: ecell3/branches/ecell-3.1/build/msvc/info.js
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/info.js	2008-11-10 19:19:29 UTC (rev 3284)
+++ ecell3/branches/ecell-3.1/build/msvc/info.js	2008-11-10 19:26:25 UTC (rev 3285)
@@ -26,6 +26,7 @@
     version: {
         major: buildInfo.env.ECELL_MAJOR_VERSION,
         minor: buildInfo.env.ECELL_MINOR_VERSION,
-        micro: buildInfo.env.ECELL_MICRO_VERSION
+        micro: buildInfo.env.ECELL_MICRO_VERSION,
+        revision: buildInfo.env.ECELL_PACKAGE_REVISION
     }
 };

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/config.py.in
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/config.py.in	2008-11-10 19:19:29 UTC (rev 3284)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/config.py.in	2008-11-10 19:26:25 UTC (rev 3285)
@@ -62,7 +62,8 @@
 version_info = {
     'major': @ECELL_MAJOR_VERSION@,
     'minor': @ECELL_MINOR_VERSION@,
-    'micro': @ECELL_MICRO_VERSION@
+    'micro': @ECELL_MICRO_VERSION@,
+    'revision': '@ECELL_PACKAGE_REVISION@'
 }
 
 prefix = '''@PREFIX@'''


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[Ecell-cvs] SF.net SVN: ecell:[3297] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-11-28 05:06:28

Revision: 3297
          http://ecell.svn.sourceforge.net/ecell/?rev=3297&view=rev
Author:   moriyoshi
Date:     2008-11-28 05:06:23 +0000 (Fri, 28 Nov 2008)

Log Message:
-----------
* Forgot to add these,

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj
    ecell3/branches/ecell-3.1/ecell/libecs/Makefile.am

Modified: ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj	2008-11-21 10:48:36 UTC (rev 3296)
+++ ecell3/branches/ecell-3.1/build/msvc/libecs.vcproj	2008-11-28 05:06:23 UTC (rev 3297)
@@ -584,6 +584,10 @@
 				>
 			</File>
 			<File
+				RelativePath="..\..\ecell\libecs\Handle.hpp"
+				>
+			</File>
+			<File
 				RelativePath="..\..\ecell\libecs\Interpolant.hpp"
 				>
 			</File>

Modified: ecell3/branches/ecell-3.1/ecell/libecs/Makefile.am
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/Makefile.am	2008-11-21 10:48:36 UTC (rev 3296)
+++ ecell3/branches/ecell-3.1/ecell/libecs/Makefile.am	2008-11-28 05:06:23 UTC (rev 3297)
@@ -99,7 +99,8 @@
 MethodProxy.hpp\
 EcsObjectMaker.hpp\
 PropertySlotProxyLoggerAdapter.hpp\
-PropertyAttributes.hpp
+PropertyAttributes.hpp\
+Handle.hpp
 
 noinst_HEADERS=\
 osif.h\


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[Ecell-cvs] SF.net SVN: ecell:[3298] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-12-03 20:12:02

Revision: 3298
          http://ecell.svn.sourceforge.net/ecell/?rev=3298&view=rev
Author:   moriyoshi
Date:     2008-12-03 20:11:55 +0000 (Wed, 03 Dec 2008)

Log Message:
-----------
* Win32 build fix.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/build/msvc/dist.wsf
    ecell3/branches/ecell-3.1/build/msvc/dm/PythonFluxProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/dm/PythonProcess.vcproj
    ecell3/branches/ecell-3.1/build/msvc/model-editor.vcproj
    ecell3/branches/ecell-3.1/build/msvc/session-monitor.vcproj
    ecell3/branches/ecell-3.1/ecell/pyecell/setup.py.in

Modified: ecell3/branches/ecell-3.1/build/msvc/dist.wsf
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/PythonFluxProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/PythonFluxProcess.vcproj	2008-11-28 05:06:23 UTC (rev 3297)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/PythonFluxProcess.vcproj	2008-12-03 20:11:55 UTC (rev 3298)
@@ -64,7 +64,7 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib python25_d.lib boost_python-gd.lib"
+				AdditionalDependencies="ecs.lib python*_d.lib $(BOOST_PYTHON_LIB_NAME)-gd.lib"
 				LinkIncremental="2"
 				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
 				GenerateDebugInformation="true"
@@ -143,7 +143,7 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib python25_d.lib boost_python-gd.lib"
+				AdditionalDependencies="ecs.lib python*_d.lib $(BOOST_PYTHON_LIB_NAME)-gd.lib"
 				LinkIncremental="2"
 				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
 				GenerateDebugInformation="true"
@@ -219,7 +219,7 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib python25.lib boost_python.lib"
+				AdditionalDependencies="ecs.lib python*.lib $(BOOST_PYTHON_LIB_NAME).lib"
 				LinkIncremental="1"
 				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
 				GenerateDebugInformation="true"
@@ -298,7 +298,7 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib python25.lib boost_python.lib"
+				AdditionalDependencies="ecs.lib python*.lib $(BOOST_PYTHON_LIB_NAME).lib"
 				LinkIncremental="1"
 				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
 				GenerateDebugInformation="true"

Modified: ecell3/branches/ecell-3.1/build/msvc/dm/PythonProcess.vcproj
===================================================================
--- ecell3/branches/ecell-3.1/build/msvc/dm/PythonProcess.vcproj	2008-11-28 05:06:23 UTC (rev 3297)
+++ ecell3/branches/ecell-3.1/build/msvc/dm/PythonProcess.vcproj	2008-12-03 20:11:55 UTC (rev 3298)
@@ -64,7 +64,7 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib python25_d.lib boost_python-gd.lib"
+				AdditionalDependencies="ecs.lib gsl.lib python*_d.lib $(BOOST_PYTHON_LIB_NAME)-gd.lib"
 				LinkIncremental="2"
 				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
 				IgnoreDefaultLibraryNames=""
@@ -144,7 +144,7 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib python25_d.lib boost_python-gd.lib"
+				AdditionalDependencies="ecs.lib gsl.lib python*_d.lib $(BOOST_PYTHON_LIB_NAME)-gd.lib"
 				LinkIncremental="2"
 				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
 				IgnoreDefaultLibraryNames=""
@@ -221,7 +221,7 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib python25.lib boost_python.lib"
+				AdditionalDependencies="ecs.lib gsl.lib python*.lib $(BOOST_PYTHON_LIB_NAME).lib"
 				LinkIncremental="1"
 				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB)"
 				GenerateDebugInformation="true"
@@ -300,7 +300,7 @@
 			/>
 			<Tool
 				Name="VCLinkerTool"
-				AdditionalDependencies="ecs.lib gsl.lib python25.lib boost_python.lib"
+				AdditionalDependencies="ecs.lib gsl.lib python*.lib $(BOOST_PYTHON_LIB_NAME).lib"
 				LinkIncremental="1"
 				AdditionalLibraryDirectories="$(SolutionDir)$(PlatformName)\$(ConfigurationName);$(ECELL_STAGING_HOME)\$(PlatformName)\$(ConfigurationName)\lib;$(LIB64)"
 				GenerateDebugInformation="true"

Modified: ecell3/branches/ecell-3.1/build/msvc/model-editor.vcproj
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/build/msvc/session-monitor.vcproj
===================================================================
(Binary files differ)

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/setup.py.in
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/setup.py.in	2008-11-28 05:06:23 UTC (rev 3297)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/setup.py.in	2008-12-03 20:11:55 UTC (rev 3298)
@@ -5,11 +5,11 @@
 from numpy.distutils.core import setup, Extension
 
 include_dirs = [
-    '@DMTOOL_INCLUDE_DIR@',
+    r'@DMTOOL_INCLUDE_DIR@',
     os.environ['INCLTDL'][2:],
-    '@top_srcdir@',
-    '@top_srcdir@/libecs',
-    '@top_srcdir@/libemc',
+    r'@top_srcdir@',
+    r'@top_srcdir@/libecs',
+    r'@top_srcdir@/libemc',
     ]
 
 common_libraries = [
@@ -17,7 +17,7 @@
     'gsl'
     ]
 
-ecell_staging_home = '@abs_top_builddir@/tmp'
+ecell_staging_home = r'@abs_top_builddir@/tmp'
 
 setup(
     name = 'E-Cell',


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[Ecell-cvs] SF.net SVN: ecell:[3300] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-12-05 09:17:51

Revision: 3300
          http://ecell.svn.sourceforge.net/ecell/?rev=3300&view=rev
Author:   moriyoshi
Date:     2008-12-05 09:17:47 +0000 (Fri, 05 Dec 2008)

Log Message:
-----------
* Rename StaticModuleMaker<> to ModuleMaker<> and remove the old
  ModuleMaker base class.
* Introduce SharedModuleMakerBase that is the base class of
  SharedModuleMaker<> in place of ModuleMaker.
* Purge SharedDynamicModule and SharedModuleMaker into SharedDynamicModule.hpp
  and SharedModuleMaker.hpp respectively in order to remove unwanted
  dependencies on libltdl.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/NEWS
    ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp
    ecell3/branches/ecell-3.1/dmtool/Makefile.am
    ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/EcsObjectMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Model.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Model.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/libecs.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/libecs.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/tests/LoggerBroker_test.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/tests/Process_test.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/tests/System_test.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.hpp

Added Paths:
-----------
    ecell3/branches/ecell-3.1/dmtool/SharedDynamicModule.hpp
    ecell3/branches/ecell-3.1/dmtool/SharedModuleMaker.hpp

Modified: ecell3/branches/ecell-3.1/NEWS
===================================================================
--- ecell3/branches/ecell-3.1/NEWS	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/NEWS	2008-12-05 09:17:47 UTC (rev 3300)
@@ -18,6 +18,23 @@
    - Two GUI frontends (session-monitor and model-editor) were renewed to be
      two packages of python modules, ecell.ui.osogo and ecell.ui.model_editor.
 
+ * dmtool changes
+
+   - ModuleMaker class is removed and StaticModuleMaker<> template class is
+     renamed to ModuleMaker<>.
+
+   - Added SharedModuleMakerBase class that is the base class of
+     SharedModuleMaker<> template classes.  Initialization and finalization
+     static methods are moved from ModuleMaker to it.
+
+   - SharedModuleMakerBase provides a couple of instance methods,
+     setSearchPath() and getSearchPath() which sets or gets the path used when.
+     looking up for a shared module.
+
+   - Purged SharedDynamicModule and SharedModuleMaker into
+     SharedDynamicModule.hpp and SharedModuleMaker.hpp respectively, in order
+     to remove unwanted dependencies on libltdl.
+
  * libecs changes
 
    - Thoroughly overhauled DM/PropertiedClass ABI. Backwards binary

Modified: ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -30,7 +30,6 @@
 
 #include "dmtool/DMException.hpp"
 #include "dmtool/DynamicModuleDescriptor.hpp"
-#include <ltdl.h>
 
 /// doc needed
 
@@ -142,60 +141,4 @@
     }
 };
 
-/**
-   SharedDynamicModule loads a class from a shared object file
-   and instantiate objects of the loaded class.
-   It opens and loads a shared object(.so) file into memory
-   when constructed. It closes the file when deleted.
-
-   The shared object must have the following (in "C" signature):
-     - __dm_info                      - a DynamicModuleDescriptor
-                                        which holds the module information.
- */
-
-template < class T, class DMAllocator = typename SimpleAllocatorDef< T >::type >
-class SharedDynamicModule : public DynamicModule< T, DMAllocator >
-{
-public:
-
-    typedef DynamicModule< T, DMAllocator > Base;    
-
-public:
-
-    SharedDynamicModule( DynamicModuleDescriptor const& desc,
-                         const std::string& fileName,
-                         lt_dlhandle handle )
-        : DynamicModule< T, DMAllocator >(
-            desc, DM_TYPE_SHARED,
-            reinterpret_cast< typename Base::FileNameGetterType >(
-                &SharedDynamicModule::getFileName ),
-            reinterpret_cast< typename Base::FinalizerType >(
-                &SharedDynamicModule::finalize ) )
-    {
-        ; // do nothing
-    }
-
-private:
-
-    void finalize()
-    {
-        if( this->theHandle )
-        {
-            lt_dlclose( this->theHandle );
-            this->theHandle = 0;
-        }
-    }
-
-
-    const char* getFileName() const
-    {
-        return theFileName.c_str();
-    }
-
-private:
-
-    lt_dlhandle theHandle;
-    std::string theFileName;
-};
-
 #endif /* __DYNAMICMODULE_HPP */

Modified: ecell3/branches/ecell-3.1/dmtool/Makefile.am
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/Makefile.am	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/dmtool/Makefile.am	2008-12-05 09:17:47 UTC (rev 3300)
@@ -6,6 +6,8 @@
 	DynamicModuleDescriptor.hpp\
 	DMException.hpp\
 	ModuleMaker.hpp\
+	SharedDynamicModule.hpp\
+	SharedModuleMaker.hpp\
 	DMObject.hpp 
 
 bin_SCRIPTS = dmcompile

Modified: ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -34,108 +34,16 @@
 #include <set>
 #include <string>
 #include <cassert>
-#include "ltdl.h"
 
 #include "DynamicModule.hpp"
 
 /**
-     A base class for ModuleMakers
- */
-
-class ModuleMaker
-{
-
-public:
-
-    ModuleMaker()
-    {
-        ; // do nothing
-    }
-
-    virtual ~ModuleMaker() 
-    {
-        ; // do nothing
-    }
-
-    void setSearchPath( const std::string& path )
-    {
-        theSearchPath.clear();
-        for ( std::string::size_type i( 0 ), end( path.size() ), next( 0 );
-              i < end; i = next + 1 )
-        {
-            next = path.find( PATH_SEPARATOR, i );
-            next = next == std::string::npos ? end: next;
-            if ( next > i )
-            {
-                theSearchPath.insert( path.substr( i, next - i ) );
-            }
-        }
-    }
-
-    const std::string getSearchPath() const
-    {
-        typedef std::set< std::string > StringSet;
-        std::string retval;
-
-        for ( StringSet::const_iterator i( theSearchPath.begin() );
-              i != theSearchPath.end(); ++i )
-        {
-            retval += (*i);
-            retval += PATH_SEPARATOR; 
-        }
-        if ( !retval.empty() )
-            retval.resize( retval.size() - 1 );
-        return retval;
-    }
-
-    /**
-        Initializes the dynamic module facility.
-        Applications that use this library must call this function
-        prior to any operation involved with the facility.
-        @return true on error, false otherwise.
-     */
-    static bool initialize()
-    {
-        if ( lt_dlinit() > 0 )
-            return true;
-
-        if ( lt_dlsetsearchpath("") > 0 )
-        {
-            lt_dlexit();
-            return true;
-        }
-
-        return false;
-    }
-
-    /**
-        Finalizes the dynamic module facility.
-        Applications that use this library must call this function when
-        the facility is no longer necessary so that allocated resources
-        can be reclaimed.
-        @return true on error, false otherwise.
-     */
-    static void finalize()
-    {
-        lt_dlexit();
-    }
-
-public:
-    static const char PATH_SEPARATOR = LT_PATHSEP_CHAR;
-
-protected:
-
-    std::set< std::string > theSearchPath;
-};
-
-
-/**
-    StaticModuleMaker is used to instantiate
+    ModuleMaker is used to instantiate
     various subclasses of certain template parameter class T. 
 */
 
 template<class T, class DMAllocator = typename SimpleAllocatorDef< T >::type >
-class StaticModuleMaker : public ModuleMaker
+class ModuleMaker 
 {
 
 public:
@@ -146,12 +54,12 @@
 
 public: 
 
-    StaticModuleMaker()
+    ModuleMaker()
     {
         ; // do nothing
     }
 
-    virtual ~StaticModuleMaker()
+    virtual ~ModuleMaker()
     {
         for( ModuleMapIterator i = this->theModuleMap.begin();
              i != this->theModuleMap.end(); ++i )
@@ -193,102 +101,4 @@
 
 };
 
-/**
-    SharedModuleMaker dynamically instantiates various classes of 
-    objects encapsulated in shared object(.so) file.
-    @sa StaticClassModuleMaker, SharedDynamicModule
-*/
-
-template<class T, class DMAllocator = typename SimpleAllocatorDef< T >::type >
-class SharedModuleMaker : public StaticModuleMaker< T, DMAllocator >
-{
-public:
-    typedef StaticModuleMaker< T, DMAllocator > Base;
-    typedef DynamicModule< T, DMAllocator > Module;
-    typedef SharedDynamicModule< T, DMAllocator > SharedModule;
-
-    SharedModuleMaker()
-    {
-        ; // do nothing
-    }
-
-    virtual ~SharedModuleMaker()
-    {
-        ; // do nothing
-    }
-
-    virtual const Module& getModule( const std::string& aClassName, bool forceReload = false )
-    {
-        if ( forceReload ) 
-        {
-            typename Base::ModuleMap::iterator i( this->theModuleMap.find( aClassName ) );
-            if ( i != this->theModuleMap.end() &&
-                 (*i).second->getType() == DM_TYPE_SHARED )
-            {
-                this->theModuleMap.erase( i );
-                delete i->second;
-            }
-        }
-
-        if ( this->theModuleMap.find( aClassName ) == this->theModuleMap.end() )
-        {
-            loadModule( aClassName );
-        }
-
-        return *this->theModuleMap[ aClassName ];
-    }
-
-
-protected:
-    void loadModule( const std::string& aClassname )
-    {
-        typedef std::set< std::string > StringSet;
-
-        std::string filename;
-
-        lt_dlhandle handle( 0 );
-        {
-            std::string error;
-
-            for ( StringSet::const_iterator i( this->theSearchPath.begin() );
-                  i != this->theSearchPath.end(); ++i )
-            {
-                filename = (*i) + '/' + aClassname;
-                handle = lt_dlopenext( filename.c_str() );
-                if ( handle ) 
-                {
-                    break;
-                }
-                if ( error.empty() )
-                {
-                    error = lt_dlerror();
-                }
-                else
-                {
-                    if ( error != lt_dlerror() )
-                    {
-                        error = "various reasons";
-                    }
-                }
-            }
-
-            if ( !handle )
-            {
-                throw DMException( "Failed to find or load a DM ["
-                                   + aClassname + "]: " + error );
-            }
-        }
-
-        DynamicModuleDescriptor* desc(
-                reinterpret_cast< DynamicModuleDescriptor* >(
-                    lt_dlsym( handle, "__dm_descriptor" ) ) );
-        if ( !desc )
-        {
-            throw DMException( "[" + filename + "] is not a valid DM file." );
-        }
-
-        addClass( new SharedModule( *desc, filename, handle ) );
-    }
-};
-
 #endif /* __MODULEMAKER_HPP */

Copied: ecell3/branches/ecell-3.1/dmtool/SharedDynamicModule.hpp (from rev 3299, ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp)
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/SharedDynamicModule.hpp	                        (rev 0)
+++ ecell3/branches/ecell-3.1/dmtool/SharedDynamicModule.hpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -0,0 +1,90 @@
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//       This file is part of the E-Cell System
+//
+//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 2005-2008 The Molecular Sciences Institute
+//
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//
+// E-Cell System is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public
+// License as published by the Free Software Foundation; either
+// version 2 of the License, or (at your option) any later version.
+// 
+// E-Cell System is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+// See the GNU General Public License for more details.
+// 
+// You should have received a copy of the GNU General Public
+// License along with E-Cell System -- see the file COPYING.
+// If not, write to the Free Software Foundation, Inc.,
+// 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+// 
+//END_HEADER
+
+#ifndef __SHAREDDYNAMICMODULE_HPP
+#define __SHAREDDYNAMICMODULE_HPP
+
+#include "dmtool/DynamicModule.hpp"
+#include <ltdl.h>
+
+/**
+   SharedDynamicModule loads a class from a shared object file
+   and instantiate objects of the loaded class.
+   It opens and loads a shared object(.so) file into memory
+   when constructed. It closes the file when deleted.
+
+   The shared object must have the following (in "C" signature):
+     - __dm_info                      - a DynamicModuleDescriptor
+                                        which holds the module information.
+ */
+
+template < class T, class DMAllocator = typename SimpleAllocatorDef< T >::type >
+class SharedDynamicModule : public DynamicModule< T, DMAllocator >
+{
+public:
+
+    typedef DynamicModule< T, DMAllocator > Base;    
+
+public:
+
+    SharedDynamicModule( DynamicModuleDescriptor const& desc,
+                         const std::string& fileName,
+                         lt_dlhandle handle )
+        : DynamicModule< T, DMAllocator >(
+            desc, DM_TYPE_SHARED,
+            reinterpret_cast< typename Base::FileNameGetterType >(
+                &SharedDynamicModule::getFileName ),
+            reinterpret_cast< typename Base::FinalizerType >(
+                &SharedDynamicModule::finalize ) )
+    {
+        ; // do nothing
+    }
+
+private:
+
+    void finalize()
+    {
+        if( this->theHandle )
+        {
+            lt_dlclose( this->theHandle );
+            this->theHandle = 0;
+        }
+    }
+
+
+    const char* getFileName() const
+    {
+        return theFileName.c_str();
+    }
+
+private:
+
+    lt_dlhandle theHandle;
+    std::string theFileName;
+};
+
+#endif /* __SHAREDDYNAMICMODULE_HPP */


Property changes on: ecell3/branches/ecell-3.1/dmtool/SharedDynamicModule.hpp
___________________________________________________________________
Added: svn:executable
   + *
Added: svn:mime-type
   + text/plain
Added: svn:keywords
   + Id Author Date Revision
Added: svn:eol-style
   + native

Added: ecell3/branches/ecell-3.1/dmtool/SharedModuleMaker.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/SharedModuleMaker.hpp	                        (rev 0)
+++ ecell3/branches/ecell-3.1/dmtool/SharedModuleMaker.hpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -0,0 +1,208 @@
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//       This file is part of the E-Cell System
+//
+//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 2005-2008 The Molecular Sciences Institute
+//
+//::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+//
+//
+// E-Cell System is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public
+// License as published by the Free Software Foundation; either
+// version 2 of the License, or (at your option) any later version.
+// 
+// E-Cell System is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+// See the GNU General Public License for more details.
+// 
+// You should have received a copy of the GNU General Public
+// License along with E-Cell System -- see the file COPYING.
+// If not, write to the Free Software Foundation, Inc.,
+// 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+// 
+//END_HEADER
+
+
+#ifndef __SHAREDMODULEMAKER_HPP
+#define __SHAREDMODULEMAKER_HPP
+
+#include "ModuleMaker.hpp"
+#include "SharedDynamicModule.hpp"
+#include "ltdl.h"
+
+class SharedModuleMakerBase
+{
+public:
+    void setSearchPath( const std::string& path )
+    {
+        theSearchPath.clear();
+        for ( std::string::size_type i( 0 ), end( path.size() ), next( 0 );
+              i < end; i = next + 1 )
+        {
+            next = path.find( PATH_SEPARATOR, i );
+            next = next == std::string::npos ? end: next;
+            if ( next > i )
+            {
+                theSearchPath.insert( path.substr( i, next - i ) );
+            }
+        }
+    }
+
+    const std::string getSearchPath() const
+    {
+        typedef std::set< std::string > StringSet;
+        std::string retval;
+
+        for ( StringSet::const_iterator i( theSearchPath.begin() );
+              i != theSearchPath.end(); ++i )
+        {
+            retval += (*i);
+            retval += PATH_SEPARATOR; 
+        }
+        if ( !retval.empty() )
+            retval.resize( retval.size() - 1 );
+        return retval;
+    }
+    /**
+        Initializes the dynamic module facility.
+        Applications that use this library must call this function
+        prior to any operation involved with the facility.
+        @return true on error, false otherwise.
+     */
+    static bool initialize()
+    {
+        if ( lt_dlinit() > 0 )
+            return true;
+
+        if ( lt_dlsetsearchpath("") > 0 )
+        {
+            lt_dlexit();
+            return true;
+        }
+
+        return false;
+    }
+
+    /**
+        Finalizes the dynamic module facility.
+        Applications that use this library must call this function when
+        the facility is no longer necessary so that allocated resources
+        can be reclaimed.
+        @return true on error, false otherwise.
+     */
+    static void finalize()
+    {
+        lt_dlexit();
+    }
+
+public:
+    static const char PATH_SEPARATOR = LT_PATHSEP_CHAR;
+
+
+protected:
+    std::set< std::string > theSearchPath;
+};
+
+/**
+    SharedModuleMaker dynamically instantiates various classes of 
+    objects encapsulated in shared object(.so) file.
+    @sa StaticClassModuleMaker, SharedDynamicModule
+*/
+
+template<class T, class DMAllocator = typename SimpleAllocatorDef< T >::type >
+class SharedModuleMaker : public ModuleMaker< T, DMAllocator >,
+                          public SharedModuleMakerBase
+{
+public:
+    typedef ModuleMaker< T, DMAllocator > Base;
+    typedef DynamicModule< T, DMAllocator > Module;
+    typedef SharedDynamicModule< T, DMAllocator > SharedModule;
+
+    SharedModuleMaker()
+    {
+        ; // do nothing
+    }
+
+    virtual ~SharedModuleMaker()
+    {
+        ; // do nothing
+    }
+
+    virtual const Module& getModule( const std::string& aClassName, bool forceReload = false )
+    {
+        if ( forceReload ) 
+        {
+            typename Base::ModuleMap::iterator i( this->theModuleMap.find( aClassName ) );
+            if ( i != this->theModuleMap.end() &&
+                 (*i).second->getType() == DM_TYPE_SHARED )
+            {
+                this->theModuleMap.erase( i );
+                delete i->second;
+            }
+        }
+
+        if ( this->theModuleMap.find( aClassName ) == this->theModuleMap.end() )
+        {
+            loadModule( aClassName );
+        }
+
+        return *this->theModuleMap[ aClassName ];
+    }
+
+
+protected:
+    void loadModule( const std::string& aClassname )
+    {
+        typedef std::set< std::string > StringSet;
+
+        std::string filename;
+
+        lt_dlhandle handle( 0 );
+        {
+            std::string error;
+
+            for ( StringSet::const_iterator i( this->theSearchPath.begin() );
+                  i != this->theSearchPath.end(); ++i )
+            {
+                filename = (*i) + '/' + aClassname;
+                handle = lt_dlopenext( filename.c_str() );
+                if ( handle ) 
+                {
+                    break;
+                }
+                if ( error.empty() )
+                {
+                    error = lt_dlerror();
+                }
+                else
+                {
+                    if ( error != lt_dlerror() )
+                    {
+                        error = "various reasons";
+                    }
+                }
+            }
+
+            if ( !handle )
+            {
+                throw DMException( "Failed to find or load a DM ["
+                                   + aClassname + "]: " + error );
+            }
+        }
+
+        DynamicModuleDescriptor* desc(
+                reinterpret_cast< DynamicModuleDescriptor* >(
+                    lt_dlsym( handle, "__dm_descriptor" ) ) );
+        if ( !desc )
+        {
+            throw DMException( "[" + filename + "] is not a valid DM file." );
+        }
+
+        addClass( new SharedModule( *desc, filename, handle ) );
+    }
+};
+
+#endif /* __SHAREDMODULEMAKER_HPP */


Property changes on: ecell3/branches/ecell-3.1/dmtool/SharedModuleMaker.hpp
___________________________________________________________________
Added: svn:executable
   + *
Added: svn:mime-type
   + text/plain
Added: svn:eol-style
   + native

Modified: ecell3/branches/ecell-3.1/ecell/libecs/EcsObjectMaker.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/EcsObjectMaker.hpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/ecell/libecs/EcsObjectMaker.hpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -45,7 +45,7 @@
 class EcsObjectMaker 
 {
 public:
-    typedef StaticModuleMaker< EcsObject > Backend;
+    typedef ModuleMaker< EcsObject > Backend;
     typedef T_ DMType;
 
 public:

Modified: ecell3/branches/ecell-3.1/ecell/libecs/Model.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/Model.cpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/ecell/libecs/Model.cpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -33,6 +33,8 @@
 #include "ecell_config.h"
 #endif /* HAVE_CONFIG_H */
 
+#include "dmtool/SharedModuleMaker.hpp"
+
 #include "Util.hpp"
 #include "EntityType.hpp"
 #include "LoggerBroker.hpp"
@@ -50,7 +52,9 @@
 namespace libecs
 {
 
-Model::Model( StaticModuleMaker< EcsObject >& maker )
+const char Model::PATH_SEPARATOR = SharedModuleMakerBase::PATH_SEPARATOR;
+
+Model::Model( ModuleMaker< EcsObject >& maker )
     : theCurrentTime( 0.0 ),
       theNextHandleVal( 0 ),
       theLoggerBroker( *this ),
@@ -330,12 +334,28 @@
 
 void Model::setDMSearchPath( const std::string& path )
 {
-    theEcsObjectMaker.setSearchPath( path );
+    SharedModuleMakerBase* smmbase(
+        dynamic_cast< SharedModuleMakerBase* >( &theEcsObjectMaker ) );
+    if ( !smmbase )
+    {
+        THROW_EXCEPTION( IllegalOperation,
+                         "The ModuleMaker assigned to this model is not a "
+                         "SharedModuleMaker.");
+    }
+    smmbase->setSearchPath( path );
 }
 
 const std::string Model::getDMSearchPath() const
 {
-    return theEcsObjectMaker.getSearchPath();
+    SharedModuleMakerBase const* smmbase(
+        dynamic_cast< SharedModuleMakerBase const* >( &theEcsObjectMaker ) );
+    if ( !smmbase )
+    {
+        THROW_EXCEPTION( IllegalOperation,
+                         "The ModuleMaker assigned to this model is not a "
+                         "SharedModuleMaker.");
+    }
+    return smmbase->getSearchPath();
 }
 
 void Model::registerBuiltinModules()

Modified: ecell3/branches/ecell-3.1/ecell/libecs/Model.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/Model.hpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/ecell/libecs/Model.hpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -74,7 +74,7 @@
     typedef EcsObjectMaker< Variable > VariableMaker;
     typedef EcsObjectMaker< Process > ProcessMaker;
 public:
-    Model( StaticModuleMaker< EcsObject >& maker );
+    Model( ModuleMaker< EcsObject >& maker );
     ~Model();
     /**
        Initialize the whole model.
@@ -285,7 +285,7 @@
     static void initializeSystems( SystemPtr const aSystem );
 
 public:
-    static const char PATH_SEPARATOR = ModuleMaker::PATH_SEPARATOR;
+    static const char PATH_SEPARATOR;
 
 private:
 
@@ -307,7 +307,7 @@
 
     StepperMap                      theStepperMap;
 
-    StaticModuleMaker< EcsObject >& theEcsObjectMaker;
+    ModuleMaker< EcsObject >&       theEcsObjectMaker;
     StepperMaker                    theStepperMaker;
     SystemMaker                     theSystemMaker;
     VariableMaker                   theVariableMaker;

Modified: ecell3/branches/ecell-3.1/ecell/libecs/libecs.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/libecs.cpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/ecell/libecs/libecs.cpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -39,6 +39,7 @@
 
 #include "libecs.hpp"
 #include "EcsObject.hpp"
+#include "dmtool/SharedModuleMaker.hpp"
 
 namespace libecs
 {
@@ -59,21 +60,21 @@
     else
         isInitialized = true;
 
-    if ( ModuleMaker::initialize() )
+    if ( SharedModuleMakerBase::initialize() )
     {
         return false;
     }
 #if defined( WIN32 ) && !defined( __CYGWIN__ )
     if ( libecs_win32_init() )
     {
-        ModuleMaker::finalize();
+        SharedModuleMaker::finalize();
         return false;
     }
 #endif
     return true;
 }
 
-StaticModuleMaker< EcsObject >* createDefaultModuleMaker()
+ModuleMaker< EcsObject >* createDefaultModuleMaker()
 {
     return new SharedModuleMaker< EcsObject >();
 }
@@ -89,7 +90,7 @@
 #if defined( WIN32 ) && !defined( __CYGWIN__ )
     libecs_win32_fini();
 #endif
-    ModuleMaker::finalize();
+    SharedModuleMakerBase::finalize();
 }
 
 const int getMajorVersion()

Modified: ecell3/branches/ecell-3.1/ecell/libecs/libecs.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/libecs.hpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/ecell/libecs/libecs.hpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -59,7 +59,7 @@
 
 LIBECS_API bool initialize();
 LIBECS_API void finalize();
-LIBECS_API StaticModuleMaker< EcsObject >* createDefaultModuleMaker();
+LIBECS_API ModuleMaker< EcsObject >* createDefaultModuleMaker();
 
 // Forward declarations.
 } // namespace libecs

Modified: ecell3/branches/ecell-3.1/ecell/libecs/tests/LoggerBroker_test.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/tests/LoggerBroker_test.cpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/ecell/libecs/tests/LoggerBroker_test.cpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -51,7 +51,7 @@
 {
     using namespace libecs;
 
-    StaticModuleMaker< EcsObject > mmaker;
+    ModuleMaker< EcsObject > mmaker;
     Model model( mmaker );
 
     BOOST_CHECK_THROW(
@@ -65,7 +65,7 @@
 {
     using namespace libecs;
 
-    StaticModuleMaker< EcsObject > mmaker;
+    ModuleMaker< EcsObject > mmaker;
 
     Model model( mmaker );
 

Modified: ecell3/branches/ecell-3.1/ecell/libecs/tests/Process_test.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/tests/Process_test.cpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/ecell/libecs/tests/Process_test.cpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -69,7 +69,7 @@
 
 BOOST_AUTO_TEST_CASE(testInstantiation)
 {
-    StaticModuleMaker< EcsObject > mmaker;
+    ModuleMaker< EcsObject > mmaker;
     DM_NEW_STATIC( &mmaker, EcsObject, MockProcess );
     
     MockProcess* proc = reinterpret_cast< MockProcess * >( mmaker.getModule( "MockProcess" ).getAllocator()() );
@@ -81,7 +81,7 @@
 {
     using namespace libecs;
 
-    StaticModuleMaker< EcsObject > mmaker;
+    ModuleMaker< EcsObject > mmaker;
     DM_NEW_STATIC( &mmaker, EcsObject, MockProcess );
     DM_NEW_STATIC( &mmaker, EcsObject, Variable );
     DM_NEW_STATIC( &mmaker, EcsObject, System );
@@ -107,7 +107,7 @@
 {
     using namespace libecs;
 
-    StaticModuleMaker< EcsObject > mmaker;
+    ModuleMaker< EcsObject > mmaker;
     DM_NEW_STATIC( &mmaker, EcsObject, MockProcess );
     DM_NEW_STATIC( &mmaker, EcsObject, PassiveStepper );
 

Modified: ecell3/branches/ecell-3.1/ecell/libecs/tests/System_test.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/tests/System_test.cpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/ecell/libecs/tests/System_test.cpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -49,7 +49,7 @@
 {
     using namespace libecs;
 
-    StaticModuleMaker< EcsObject > mmaker;
+    ModuleMaker< EcsObject > mmaker;
     DM_NEW_STATIC( &mmaker, EcsObject, System );
     
     System* sys = reinterpret_cast< System * >( mmaker.getModule( "System" ).getAllocator()() );
@@ -61,7 +61,7 @@
 {
     using namespace libecs;
 
-    StaticModuleMaker< EcsObject > mmaker;
+    ModuleMaker< EcsObject > mmaker;
     DM_NEW_STATIC( &mmaker, EcsObject, System );
     DM_NEW_STATIC( &mmaker, EcsObject, Variable );
     

Modified: ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.cpp	2008-12-04 06:34:16 UTC (rev 3299)
+++ ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.cpp	2008-12-05 09:17:47 UTC (rev 3300)
@@ -719,7 +719,7 @@
 
 const libecs::PolymorphVector LocalSimulatorImplementation::getDMInfo() const
 {
-    typedef StaticModuleMaker< libecs::EcsObject ...
 
[truncated message content]

[Ecell-cvs] SF.net SVN: ecell:[3302] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-12-11 14:11:35

Revision: 3302
          http://ecell.svn.sourceforge.net/ecell/?rev=3302&view=rev
Author:   moriyoshi
Date:     2008-12-11 14:11:30 +0000 (Thu, 11 Dec 2008)

Log Message:
-----------
* Thorough overhaul.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/dmtool/dmcompile.in
    ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in

Modified: ecell3/branches/ecell-3.1/dmtool/dmcompile.in
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/dmcompile.in	2008-12-10 10:15:53 UTC (rev 3301)
+++ ecell3/branches/ecell-3.1/dmtool/dmcompile.in	2008-12-11 14:11:30 UTC (rev 3302)
@@ -1,12 +1,14 @@
 #!/usr/bin/env python
 
-# usage: dcompile cfile [[cflags]... ]
+# usage: dmcompile cfile [[cflags]... ]
 
 import sys
 import os
 import glob
-import string
 import getopt
+from distutils.ccompiler import new_compiler
+from distutils.errors import CompileError, LinkError
+from distutils.util import split_quoted
 
 # prefix='@prefix@'
 # exec_prefix='@exec_prefix@'
@@ -15,99 +17,119 @@
 ORIG_CPPFLAGS = '@CPPFLAGS@'
 ORIG_LDFLAGS = '@LDFLAGS@'
 SHLEXT = os.popen('echo @LTDL_SHLIB_EXT@').readline().rstrip()
-CXX = '@CXX@'
 CXXSUFFIX = '.cpp'
 CXXFLAGS = os.environ.get('CXXFLAGS','')
+CPPFLAGS = os.environ.get('CPPFLAGS','')
 LDFLAGS =  os.environ.get('LDFLAGS','')
-VERBOSE = False
 
+progname = os.path.basename( sys.argv[0] )
+
 def help():
-    ext = os.path.basename( sys.argv[0] )
-    aProgramName, ext = os.path.splitext( ext )
+    global progname
     print '''
-%s -- Compile dynamic modules for E-Cell Simulation Environment Version 3
+%(progname)s -- Compile dynamic modules for E-Cell Simulation Environment Version 3
 
 Usage:
-       %s [-v|--verbose] <source.cpp> [compile options]
-       %s [-h|--help]
-    '''% ( aProgramName, aProgramName, aProgramName )
+       %(progname)s [-v|--verbose] [-o file|--output=file] <compiler / linker options> source.cpp
+       %(progname)s [-h|--help]
 
+Acceptable compiler / linker options:
+       -Dname=value
+       -Iincludedir
+       -Llibdir
+       -llib
+    ''' % dict( progname = progname )
+
 def msg( outstr ):
-    print "E-Cell3 dmcompile: " + outstr
+    global progname
+    print "%s: %s" % ( progname, outstr )
 
-def execute( cmdstr ):
-    if VERBOSE:
-	print cmdstr
-    return os.system( cmdstr )
+def main():
+    opts , args = getopt.gnu_getopt( sys.argv[1:], "hvI:L:l:o:D:", ["help", "verbose", "output=" ])
+  
+    include_dirs = []
+    library_dirs = []
+    libs = []
+    macros = []
+    out = None
+    verbose = False
 
-def compile( CXX, CXXCOMPILEFLAGS, SRC ):
-    return execute( CXX + ' ' + CXXCOMPILEFLAGS + ' -fPIC -c ' + SRC )
-
-def link( CXX, CPPFLAGS, OBJ, SOBJ, LDFLAGS ):
-	cflags = CPPFLAGS
-	if sys.platform == 'darwin':
-			cflags = cflags + ' -dynamiclib -install_name ' + SOBJ
-	else:
-			cflags = cflags + ' -shared -Wl,-soname=\"' + SOBJ + '\" ' 
-
-	return execute( CXX + ' ' + cflags + ' ' + OBJ + ' -o ' + SOBJ + ' ' + LDFLAGS)
-
-def cleanup( OBJ ):
-    if os.path.isfile( OBJ ):
-	os.remove( OBJ )
-    
-def main():
-    opts , args = getopt.getopt( sys.argv[1:], "hv", ["help", "verbose"])   
-    global VERBOSE
-    
     for anOption, anArg in opts:
-
-	# print help message
-        if anOption in ( "-h", '--help' ):
+        # print help message
+        if anOption in ( '-h', '--help' ):
             help()
-            sys.exit(0)
-      
-  	# be verbose
-        if anOption in ( "-v", '--verbose'):
-	    VERBOSE = True
+            return 0
+        elif anOption in ( '-v', '--verbose'):
+            verbose = True
+        elif anOption == '-I':
+            include_dirs.append( anArg )
+        elif anOption == '-D':
+            macros.append( anArg.split('=') )
+        elif anOption == '-L':
+            library_dirs.append( anArg )
+        elif anOption == '-l':
+            libs.append( anArg )
+        elif anOption in ( '-o', '--output' ):
+            out = anArg
 
+
     # check if source file is given
     if len( args ) < 1:
-	help()
-	msg( "Error: source file was not given." )
-	sys.exit(1)
+        help()
+        msg( "no source file was given." )
+        return 255 
 
-    # check if source file is valid
-    if len( glob.glob ( args[0].replace( '\"', '' ) ) ) < 1:
-	msg( "Error: source file "+ args[0] + " was not found." )
-	sys.exit(1)
-		
-    SRC = args[0]
-    ext = os.path.basename(SRC)
-    CLASSNAME, ext = os.path.splitext( ext.replace( '\"', '' ) )
-    OBJ = CLASSNAME + '.o'
-    SOBJ = CLASSNAME + SHLEXT
-    if len(args) > 0:
-        ARGS = ' \"' + string.join( args[1:], '\" \"' ) + '\"'
+    if out == None:
+        if len( args ) == 1:
+            out, dummy  = os.path.splitext( args[ 0 ] )
+            out += SHLEXT
+        else:
+            msg( "specify the output filename." )
+            return 255 
     else:
-        ARGS = ' '
+        path_without_ext, ext = os.path.splitext( out )
+        if ext == '':
+            out = path_without_ext + SHLEXT
 
-	# compiler: use env + autoconf + plus anything that was given on the cmd line (?) -- FIXME
-    CXXCOMPILEFLAGS = CXXFLAGS + ' ' + ORIG_CXXFLAGS + ' ' + ORIG_CPPFLAGS + ' ' + ARGS
-
+    # compiler: use env + autoconf + plus anything that was given on the cmd line (?) -- FIXME
+    cxxflags = split_quoted( ORIG_CXXFLAGS ) + \
+        split_quoted( CXXFLAGS )
+    cppflags = split_quoted( ORIG_CPPFLAGS ) + \
+        split_quoted( CPPFLAGS )
     # linker: use env + autoconf (?) -- FIXME
-    LINKFLAGS = LDFLAGS + ' ' + ORIG_LDFLAGS
-    
-    if compile( CXX, CXXCOMPILEFLAGS, "\"" + SRC + "\"" ) or not os.path.isfile( OBJ ):
-	msg( "Error: The compiler failed to create " + OBJ )
-	sys.exit(1)
-	
-    if link( CXX, CXXCOMPILEFLAGS, '\"' + OBJ + '\"' , '\"' + SOBJ + '\"', LINKFLAGS ) or not os.path.isfile( SOBJ ):
-	msg( "Error: The compiler failed to create " + SOBJ )
-	sys.exit(1)
-    
-    cleanup( OBJ )
+    ldflags = split_quoted( ORIG_LDFLAGS ) + \
+        split_quoted( LDFLAGS )
 
+    compiler = new_compiler( verbose = verbose )
+    if verbose:
+        old_spawn = compiler.spawn
+        def new_spawn( self, cmd ):
+            print ' '.join( cmd )
+            old_spawn( cmd )
+        compiler.__class__.spawn = new_spawn
+    map( compiler.add_include_dir, include_dirs )
+    map( compiler.add_library_dir, library_dirs )
+    map( compiler.add_library, libs )
+    map( lambda args: compiler.define_macro( *args ), macros )
+
+    objects = None
+    try:
+        objects = compiler.compile( args, extra_preargs = cxxflags + cppflags )
+    except CompileError, e:
+        msg( "failed to compile the specified source files: " + repr( e ) )
+        return 1 
+
+    try:
+        try:
+            compiler.link( output_filename = out,
+                    target_desc = compiler.SHARED_LIBRARY,
+                    objects = objects, extra_preargs = ldflags )
+        except LinkError, e:
+            msg( "failed to link the object files: " + repr( e ) )
+            return 1 
+    finally:
+        map( os.unlink, objects )
+
 if __name__ == '__main__':
-	main()
+    sys.exit( main() )
 

Modified: ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in
===================================================================
--- ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in	2008-12-10 10:15:53 UTC (rev 3301)
+++ ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in	2008-12-11 14:11:30 UTC (rev 3302)
@@ -1,4 +1,4 @@
-#!/usr/bin/env @prefix@/bin/ecell3-python
+#!/usr/bin/env python
 #
 # ecell3-dmc  - a program to compile and/or docify dynamic module in 
 #               E-Cell Simulation Environment Version 3
@@ -11,25 +11,27 @@
 
 import sys
 import os
-import glob
 import getopt
-import string
+import operator
+from glob import glob
+from distutils.util import split_quoted
+    
+DMCOMPILE = 'dmcompile'
+CLASS_NAME_MACRO_NAME = '_ECELL3_DM_CLASSNAME'
 
+progname = os.path.basename( sys.argv[ 0 ] )
+
 def usage():
-    ext = os.path.basename( sys.argv[0] )
-    aProgramName, ext = os.path.splitext( ext )
     print '''
 %s -- Compile dynamic modules for E-Cell Simulation Environment Version 3.
 
 Usage:
     %s [options] [sourcefile(s)]
     %s [-h] or [--help]
-    '''% ( aProgramName, aProgramName, aProgramName )
+    ''' % dict( progname = progname )
 
 def help():
     usage()
-    ext = os.path.basename( sys.argv[0] )
-    aProgramName, ext = os.path.splitext( ext )
     print '''
 %s options:
     --no-stdinclude          Don't set standard include file path.
@@ -47,29 +49,28 @@
 Written by:
     Tomoya Kitayama <to...@e-...>
     Satya Arjunan <sa...@tt...>
-    '''% ( aProgramName )
+    ''' % dict( progname = progname )
 
 def msg( outstr ):
-    print "E-Cell3 ecell3-dmc: " + outstr
+    global progname
+    print "%s: %s" % ( progname, outstr )
 
 def main():
 
     # -------------------------------------
     # initialize file names
     # -------------------------------------
-    prefix = os.environ['ECELL3_PREFIX']
-    ecell3dir = os.environ['ECELL_DIRNAME']
-    BOOST_LIBRARIES = os.environ['BOOST_LIBRARIES']
+    prefix = r'''@PREFIX@'''
+    ecell3dir = r'''@ECELL_DIRNAME@'''
+    BOOST_LIBRARIES = r'''-lboost_python'''
     exec_prefix = prefix
     BINDIR = exec_prefix + os.sep + 'bin'
-    STDLIBDIR = '-L\"' + exec_prefix + os.sep + 'lib\"'
+    STDLIBDIRS = [ '-L' + exec_prefix + os.sep + 'lib' ]
     ECELL_INCLUDE = prefix + os.sep + 'include' + os.sep + ecell3dir
     LIBECS_INCLUDE = ECELL_INCLUDE + os.sep + 'libecs'
-    STDINCLUDE = [ '\"-I' + prefix + os.sep + 'include\"',
-                   '\"-I' + ECELL_INCLUDE + '\"',
-                   '\"-I' + LIBECS_INCLUDE + '\"',
-                   os.environ['PYTHON_INCLUDES'] ]
-    DMCOMPILE = os.path.abspath( BINDIR + os.sep + 'dmcompile' )
+    STDINCLUDE = [ '-I' + prefix + os.sep + 'include',
+                   '-I' + ECELL_INCLUDE,
+                   '-I' + LIBECS_INCLUDE ]
     SRC = None
 
 
@@ -88,11 +89,11 @@
     NO_STDINCLUDE = False
     NO_STDLIBDIR = False
     NO_DEFINE_CXXFLAGS = False
-    LDFLAGS = ''
+    LDFLAGS = []
     CXXFLAGS = []
     CXXCOMPILEFLAGS = []
-    PYTHON = None
     cmdList = []
+    dmcompile = DMCOMPILE
 
     # -------------------------------------
     # check argument
@@ -102,7 +103,7 @@
         # print help message
         if anOption in ( "-h", '--help' ):
             help()
-            sys.exit( -1 )
+            return 255
       
         # be verbose
         if anOption in ( "-v", '--verbose'):
@@ -118,85 +119,72 @@
 
         # set ldflags
         if anOption == "--ldflags":
-            LDFLAGS = LDFLAGS + ' ' + anArg
+            LDFLAGS.extend( split_quoted( LDFLAGS ) )
 
         # set no-define-cxxflags
         if anOption == "--no-define-cxxflags":
             NO_DEFINE_CXXFLAGS = True
-            CXXFLAGS = anArg.split()
+            CXXFLAGS.extend( split_quoted( anArg ) )
 
         # set cxxflags
         if anOption == "--cxxflags":
-            CXXCOMPILEFLAGS.extend( CXXFLAGS )
-            CXXCOMPILEFLAGS.extend( anArg.split() )
+            CXXFLAGS.extend( split_quoted( anArg ) )
 
         # set cxxflags
         if anOption == "--dmcompile":
-            DMCOMPILE = os.path.abspath( anArg + os.sep + 'dmcompile' )
+            if os.path.isdir( anArg ):
+                dmcompile = os.path.join( anArg, DMCOMPILE )
+            else:
+                dmcompile = anArg
 
     # check if source file is given
     if len( args ) < 1:
         help()
-        msg( "Error: source file was not given." )
-        sys.exit( 1 )
+        msg( "no source file is given." )
+        return 1
 
-    if os.name == 'nt':
-        PYTHON_WIN_VERSION = ( '%d%d' )%( sys.version_info[:2] )
-        ADDFLAGS = ' -Wl,--enable-runtime-pseudo-reloc -Wl,-s -lpython' + \
-                   PYTHON_WIN_VERSION
-    elif sys.platform == 'darwin':
-        ADDFLAGS = ' -Wl,-undefined,dynamic_lookup'
-    else:
-        ADDFLAGS = ''
-        cmdList.append( sys.executable )
-
     cmdList.append( DMCOMPILE )
 
     if VERBOSE:
         cmdList.append( '-v' )
 
     # on MS-Windows, command line doesn't expand *.cpp automatically
-    FILELIST = []
-    for arg in args:
-        FILELIST.extend( glob.glob( arg ) )
+    srcs = reduce( operator.add, map( glob, args ) )
 
     # check if source file is valid
-    if len( FILELIST ) < 1:
-        msg( "Error: source file "+ args[0] + " was not found." )
-        sys.exit( 1 )    
+    if len( srcs ) < 1:
+        msg( "source file "+ args[0] + " was not found." )
+        return 1
 
     if NO_STDINCLUDE:
         STDINCLUDE = []
 
     if not NO_STDLIBDIR:
-        LDFLAGS = LDFLAGS + ' ' + STDLIBDIR
-        
-    LDFLAGS = LDFLAGS + ADDFLAGS + ' -lecs -lgsl ' + BOOST_LIBRARIES
-    os.environ['LDFLAGS'] = LDFLAGS
+        LDFLAGS.extend( STDLIBDIRS )
+  
+    LDFLAGS.append( '-lecs' )
+    LDFLAGS.append( '-lgsl' )
+    LDFLAGS.extend( split_quoted( BOOST_LIBRARIES ) )
 
-    if NO_DEFINE_CXXFLAGS:
-        os.environ['CXXFLAGS'] = CXXFLAGS.join()
+    cmdList.extend( STDINCLUDE )
+    cmdList.extend( CXXFLAGS )
+    cmdList.extend( LDFLAGS )
 
-    for SRC in FILELIST:
-        ext = os.path.basename(SRC)
-        CLASSNAME, ext = os.path.splitext(ext)
-        CLASSNAMEDEFINE = '-D_ECELL3_DM_CLASSNAME=' + CLASSNAME
-        argList = []
-        argList.append( cmdList[0] )
-        argList.extend( cmdList[1:] )
-        argList.extend( [ SRC, CLASSNAMEDEFINE ] )
-        argList.extend( STDINCLUDE )
-        argList.extend( CXXCOMPILEFLAGS )
+    for src in srcs:
+        ext = os.path.basename( src )
+        classname, ext = os.path.splitext( ext )
+        argList = cmdList + [ '-D%s=%s' % ( CLASS_NAME_MACRO_NAME, classname ), src ]
 
         if VERBOSE:
-            print string.join( argList[0:] )
+            print ' '.join( argList[0:] )
             
         # Need to us os.spawnv because of problems in MS-Windows with os.sytem
         # when the dmcompile path contains whitespaces even if we force quotes
-        ret = os.spawnv( os.P_WAIT, cmdList[0], argList )
-        if not ret == 0:
-            sys.exit( 1 )
+        ret = os.spawnvp( os.P_WAIT, cmdList[0], argList )
+        if ret != 0:
+            msg( '%s returned error status: %d' % ( cmdList[0], ret ) )
+            return 1
+    return 0
 
 if __name__ == '__main__':
-    main()
-    sys.exit( 0 )
+    sys.exit( main() )


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[Ecell-cvs] SF.net SVN: ecell:[3303] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-12-11 15:49:04

Revision: 3303
          http://ecell.svn.sourceforge.net/ecell/?rev=3303&view=rev
Author:   moriyoshi
Date:     2008-12-11 15:49:00 +0000 (Thu, 11 Dec 2008)

Log Message:
-----------
* Fix for darwin

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/dmtool/configure.in
    ecell3/branches/ecell-3.1/dmtool/dmcompile.in
    ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in

Modified: ecell3/branches/ecell-3.1/dmtool/configure.in
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/configure.in	2008-12-11 14:11:30 UTC (rev 3302)
+++ ecell3/branches/ecell-3.1/dmtool/configure.in	2008-12-11 15:49:00 UTC (rev 3303)
@@ -77,6 +77,7 @@
 dnl
 dnl Create the top-level Makefile.
 dnl
-AC_OUTPUT(Makefile dmcompile,chmod +x dmcompile)
+AC_CONFIG_FILES(dmcompile, [chmod +x dmcompile])
+AC_CONFIG_FILES(Makefile)
+AC_OUTPUT
 
-

Modified: ecell3/branches/ecell-3.1/dmtool/dmcompile.in
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/dmcompile.in	2008-12-11 14:11:30 UTC (rev 3302)
+++ ecell3/branches/ecell-3.1/dmtool/dmcompile.in	2008-12-11 15:49:00 UTC (rev 3303)
@@ -6,6 +6,7 @@
 import os
 import glob
 import getopt
+from distutils.sysconfig import get_config_var
 from distutils.ccompiler import new_compiler
 from distutils.errors import CompileError, LinkError
 from distutils.util import split_quoted
@@ -34,6 +35,11 @@
        %(progname)s [-h|--help]
 
 Acceptable compiler / linker options:
+       -g
+       -W[warning options]
+       -f[compiler-specific-option]
+       -m[architecture-specific-option]
+       -O[optimizatin-option] 
        -Dname=value
        -Iincludedir
        -Llibdir
@@ -45,7 +51,9 @@
     print "%s: %s" % ( progname, outstr )
 
 def main():
-    opts , args = getopt.gnu_getopt( sys.argv[1:], "hvI:L:l:o:D:", ["help", "verbose", "output=" ])
+    global ORIG_CXXFLAGS, ORIG_CPPFLAGS, ORIG_LDFLAGS, SHLEXT, \
+           CXXSUFFIX, CXXFLAGS, CPPFLAGS, LDFLAGS
+    opts , args = getopt.gnu_getopt( sys.argv[1:], "hvI:L:l:o:D:f:m:O:W:g", ["help", "verbose", "output=" ])
   
     include_dirs = []
     library_dirs = []
@@ -61,6 +69,8 @@
             return 0
         elif anOption in ( '-v', '--verbose'):
             verbose = True
+        elif anOption in ( '-f', '-m', '-g', '-O', '-W' ):
+            CXXFLAGS += ' ' + anOption + anArg
         elif anOption == '-I':
             include_dirs.append( anArg )
         elif anOption == '-D':
@@ -119,11 +129,23 @@
         msg( "failed to compile the specified source files: " + repr( e ) )
         return 1 
 
+    if sys.platform == 'darwin':
+        compiler.linker_so = [ arg for arg in compiler.linker_so if arg != '-shard' ]
+
+    dlflags = []
+    dlflags.extend(
+        split_quoted(
+            get_config_var( 'LDSHARED' ).replace(
+                get_config_var( 'LINKCC' ), '' ).replace(
+                    get_config_var( 'LDFLAGS' ), '' ) ) )
+
     try:
         try:
             compiler.link( output_filename = out,
-                    target_desc = compiler.SHARED_LIBRARY,
-                    objects = objects, extra_preargs = ldflags )
+                    target_desc = compiler.SHARED_OBJECT,
+                    objects = objects,
+                    extra_preargs = ldflags + dlflags,
+                    target_lang = 'c++' )
         except LinkError, e:
             msg( "failed to link the object files: " + repr( e ) )
             return 1 

Modified: ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in
===================================================================
--- ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in	2008-12-11 14:11:30 UTC (rev 3302)
+++ ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in	2008-12-11 15:49:00 UTC (rev 3303)
@@ -119,7 +119,7 @@
 
         # set ldflags
         if anOption == "--ldflags":
-            LDFLAGS.extend( split_quoted( LDFLAGS ) )
+            LDFLAGS.extend( split_quoted( anArg ) )
 
         # set no-define-cxxflags
         if anOption == "--no-define-cxxflags":
@@ -143,7 +143,7 @@
         msg( "no source file is given." )
         return 1
 
-    cmdList.append( DMCOMPILE )
+    cmdList.append( dmcompile )
 
     if VERBOSE:
         cmdList.append( '-v' )


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3313] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2008-12-15 09:39:53

Revision: 3313
          http://ecell.svn.sourceforge.net/ecell/?rev=3313&view=rev
Author:   moriyoshi
Date:     2008-12-15 09:39:47 +0000 (Mon, 15 Dec 2008)

Log Message:
-----------
* Merge from branch.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/dmtool/configure.in
    ecell3/branches/ecell-3.1/dmtool/dmcompile.in
    ecell3/branches/ecell-3.1/doc/Makefile.am
    ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.globus.py
    ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.py
    ecell3/branches/ecell-3.1/doc/samples/sessionmanager/runsession.py
    ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in
    ecell3/branches/ecell-3.1/ecell/libecs/PropertyInterface.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlot.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxy.hpp

Modified: ecell3/branches/ecell-3.1/dmtool/configure.in
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/configure.in	2008-12-15 09:22:47 UTC (rev 3312)
+++ ecell3/branches/ecell-3.1/dmtool/configure.in	2008-12-15 09:39:47 UTC (rev 3313)
@@ -77,6 +77,7 @@
 dnl
 dnl Create the top-level Makefile.
 dnl
-AC_OUTPUT(Makefile dmcompile,chmod +x dmcompile)
+AC_CONFIG_FILES(dmcompile, [chmod +x dmcompile])
+AC_CONFIG_FILES(Makefile)
+AC_OUTPUT
 
-

Modified: ecell3/branches/ecell-3.1/dmtool/dmcompile.in
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/dmcompile.in	2008-12-15 09:22:47 UTC (rev 3312)
+++ ecell3/branches/ecell-3.1/dmtool/dmcompile.in	2008-12-15 09:39:47 UTC (rev 3313)
@@ -1,12 +1,15 @@
 #!/usr/bin/env python
 
-# usage: dcompile cfile [[cflags]... ]
+# usage: dmcompile cfile [[cflags]... ]
 
 import sys
 import os
 import glob
-import string
 import getopt
+from distutils.sysconfig import get_config_var
+from distutils.ccompiler import new_compiler
+from distutils.errors import CompileError, LinkError
+from distutils.util import split_quoted
 
 # prefix='@prefix@'
 # exec_prefix='@exec_prefix@'
@@ -15,99 +18,140 @@
 ORIG_CPPFLAGS = '@CPPFLAGS@'
 ORIG_LDFLAGS = '@LDFLAGS@'
 SHLEXT = os.popen('echo @LTDL_SHLIB_EXT@').readline().rstrip()
-CXX = '@CXX@'
 CXXSUFFIX = '.cpp'
 CXXFLAGS = os.environ.get('CXXFLAGS','')
+CPPFLAGS = os.environ.get('CPPFLAGS','')
 LDFLAGS =  os.environ.get('LDFLAGS','')
-VERBOSE = False
 
+progname = os.path.basename( sys.argv[0] )
+
 def help():
-    ext = os.path.basename( sys.argv[0] )
-    aProgramName, ext = os.path.splitext( ext )
+    global progname
     print '''
-%s -- Compile dynamic modules for E-Cell Simulation Environment Version 3
+%(progname)s -- Compile dynamic modules for E-Cell Simulation Environment Version 3
 
 Usage:
-       %s [-v|--verbose] <source.cpp> [compile options]
-       %s [-h|--help]
-    '''% ( aProgramName, aProgramName, aProgramName )
+       %(progname)s [-v|--verbose] [-o file|--output=file] <compiler / linker options> source.cpp
+       %(progname)s [-h|--help]
 
+Acceptable compiler / linker options:
+       -g
+       -W[warning options]
+       -f[compiler-specific-option]
+       -m[architecture-specific-option]
+       -O[optimizatin-option] 
+       -Dname=value
+       -Iincludedir
+       -Llibdir
+       -llib
+    ''' % dict( progname = progname )
+
 def msg( outstr ):
-    print "E-Cell3 dmcompile: " + outstr
+    global progname
+    print "%s: %s" % ( progname, outstr )
 
-def execute( cmdstr ):
-    if VERBOSE:
-	print cmdstr
-    return os.system( cmdstr )
+def main():
+    global ORIG_CXXFLAGS, ORIG_CPPFLAGS, ORIG_LDFLAGS, SHLEXT, \
+           CXXSUFFIX, CXXFLAGS, CPPFLAGS, LDFLAGS
+    opts , args = getopt.gnu_getopt( sys.argv[1:], "hvI:L:l:o:D:f:m:O:W:g", ["help", "verbose", "output=" ])
+  
+    include_dirs = []
+    library_dirs = []
+    libs = []
+    macros = []
+    out = None
+    verbose = False
 
-def compile( CXX, CXXCOMPILEFLAGS, SRC ):
-    return execute( CXX + ' ' + CXXCOMPILEFLAGS + ' -fPIC -c ' + SRC )
-
-def link( CXX, CPPFLAGS, OBJ, SOBJ, LDFLAGS ):
-	cflags = CPPFLAGS
-	if sys.platform == 'darwin':
-			cflags = cflags + ' -dynamiclib -install_name ' + SOBJ
-	else:
-			cflags = cflags + ' -shared -Wl,-soname=\"' + SOBJ + '\" ' 
-
-	return execute( CXX + ' ' + cflags + ' ' + OBJ + ' -o ' + SOBJ + ' ' + LDFLAGS)
-
-def cleanup( OBJ ):
-    if os.path.isfile( OBJ ):
-	os.remove( OBJ )
-    
-def main():
-    opts , args = getopt.getopt( sys.argv[1:], "hv", ["help", "verbose"])   
-    global VERBOSE
-    
     for anOption, anArg in opts:
-
-	# print help message
-        if anOption in ( "-h", '--help' ):
+        # print help message
+        if anOption in ( '-h', '--help' ):
             help()
-            sys.exit(0)
-      
-  	# be verbose
-        if anOption in ( "-v", '--verbose'):
-	    VERBOSE = True
+            return 0
+        elif anOption in ( '-v', '--verbose'):
+            verbose = True
+        elif anOption in ( '-f', '-m', '-g', '-O', '-W' ):
+            CXXFLAGS += ' ' + anOption + anArg
+        elif anOption == '-I':
+            include_dirs.append( anArg )
+        elif anOption == '-D':
+            macros.append( anArg.split('=') )
+        elif anOption == '-L':
+            library_dirs.append( anArg )
+        elif anOption == '-l':
+            libs.append( anArg )
+        elif anOption in ( '-o', '--output' ):
+            out = anArg
 
+
     # check if source file is given
     if len( args ) < 1:
-	help()
-	msg( "Error: source file was not given." )
-	sys.exit(1)
+        help()
+        msg( "no source file was given." )
+        return 255 
 
-    # check if source file is valid
-    if len( glob.glob ( args[0].replace( '\"', '' ) ) ) < 1:
-	msg( "Error: source file "+ args[0] + " was not found." )
-	sys.exit(1)
-		
-    SRC = args[0]
-    ext = os.path.basename(SRC)
-    CLASSNAME, ext = os.path.splitext( ext.replace( '\"', '' ) )
-    OBJ = CLASSNAME + '.o'
-    SOBJ = CLASSNAME + SHLEXT
-    if len(args) > 0:
-        ARGS = ' \"' + string.join( args[1:], '\" \"' ) + '\"'
+    if out == None:
+        if len( args ) == 1:
+            out, dummy  = os.path.splitext( args[ 0 ] )
+            out += SHLEXT
+        else:
+            msg( "specify the output filename." )
+            return 255 
     else:
-        ARGS = ' '
+        path_without_ext, ext = os.path.splitext( out )
+        if ext == '':
+            out = path_without_ext + SHLEXT
 
-	# compiler: use env + autoconf + plus anything that was given on the cmd line (?) -- FIXME
-    CXXCOMPILEFLAGS = CXXFLAGS + ' ' + ORIG_CXXFLAGS + ' ' + ORIG_CPPFLAGS + ' ' + ARGS
-
+    # compiler: use env + autoconf + plus anything that was given on the cmd line (?) -- FIXME
+    cxxflags = split_quoted( ORIG_CXXFLAGS ) + \
+        split_quoted( CXXFLAGS )
+    cppflags = split_quoted( ORIG_CPPFLAGS ) + \
+        split_quoted( CPPFLAGS )
     # linker: use env + autoconf (?) -- FIXME
-    LINKFLAGS = LDFLAGS + ' ' + ORIG_LDFLAGS
-    
-    if compile( CXX, CXXCOMPILEFLAGS, "\"" + SRC + "\"" ) or not os.path.isfile( OBJ ):
-	msg( "Error: The compiler failed to create " + OBJ )
-	sys.exit(1)
-	
-    if link( CXX, CXXCOMPILEFLAGS, '\"' + OBJ + '\"' , '\"' + SOBJ + '\"', LINKFLAGS ) or not os.path.isfile( SOBJ ):
-	msg( "Error: The compiler failed to create " + SOBJ )
-	sys.exit(1)
-    
-    cleanup( OBJ )
+    ldflags = split_quoted( ORIG_LDFLAGS ) + \
+        split_quoted( LDFLAGS )
 
+    compiler = new_compiler( verbose = verbose )
+    if verbose:
+        old_spawn = compiler.spawn
+        def new_spawn( self, cmd ):
+            print ' '.join( cmd )
+            old_spawn( cmd )
+        compiler.__class__.spawn = new_spawn
+    map( compiler.add_include_dir, include_dirs )
+    map( compiler.add_library_dir, library_dirs )
+    map( compiler.add_library, libs )
+    map( lambda args: compiler.define_macro( *args ), macros )
+
+    objects = None
+    try:
+        objects = compiler.compile( args, extra_preargs = cxxflags + cppflags )
+    except CompileError, e:
+        msg( "failed to compile the specified source files: " + repr( e ) )
+        return 1 
+
+    if sys.platform == 'darwin':
+        compiler.linker_so = [ arg for arg in compiler.linker_so if arg != '-shard' ]
+
+    dlflags = []
+    dlflags.extend(
+        split_quoted(
+            get_config_var( 'LDSHARED' ).replace(
+                get_config_var( 'LINKCC' ), '' ).replace(
+                    get_config_var( 'LDFLAGS' ), '' ) ) )
+
+    try:
+        try:
+            compiler.link( output_filename = out,
+                    target_desc = compiler.SHARED_OBJECT,
+                    objects = objects,
+                    extra_preargs = ldflags + dlflags,
+                    target_lang = 'c++' )
+        except LinkError, e:
+            msg( "failed to link the object files: " + repr( e ) )
+            return 1 
+    finally:
+        map( os.unlink, objects )
+
 if __name__ == '__main__':
-	main()
+    sys.exit( main() )
 

Modified: ecell3/branches/ecell-3.1/doc/Makefile.am
===================================================================
--- ecell3/branches/ecell-3.1/doc/Makefile.am	2008-12-15 09:22:47 UTC (rev 3312)
+++ ecell3/branches/ecell-3.1/doc/Makefile.am	2008-12-15 09:39:47 UTC (rev 3313)
@@ -8,7 +8,7 @@
 _htmldir = $(htmldir)/api
 _html_DATA = api/*
 
-api/*: ecell3.doxy
+api/index.html: ecell3.doxy
 	doxygen ecell3.doxy
 
 clean-local:

Modified: ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.globus.py
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.globus.py	2008-12-15 09:22:47 UTC (rev 3312)
+++ ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.globus.py	2008-12-15 09:39:47 UTC (rev 3313)
@@ -5,7 +5,7 @@
 
 import os
 
-setEnvironment('Globus2')  
+setEnvironment('Globus4')
 
 setTmpDirRemovable(False)  # not delete tmp directory
 
@@ -15,15 +15,9 @@
 # set up SystemProxy's properties
 
 aSystemProxy = getSystemProxy()
+aSystemProxy.setLocalHostName( 'myhost.example.com' )
+aSystemProxy.setFactoryEndpoint( 'https://endpoint.example.com:8443/wsrf/services/ManagedJobFactoryService' )
 
-aSystemProxy.setPassword('your_passwd')  # password for globus gate-keeper
-aSystemProxy.gridProxyInit()      # initialize gate-keeper
-
-# create a list of hosts on which jobs are conducted.
-aHostList = ['host1.domain',
-             'host2.domain']
-aSystemProxy.setHosts(aHostList) # set the host list
-
 # -------------------------------
 
 MODEL_FILE = 'model.eml'

Modified: ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.py
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.py	2008-12-15 09:22:47 UTC (rev 3312)
+++ ecell3/branches/ecell-3.1/doc/samples/sessionmanager/ems.py	2008-12-15 09:39:47 UTC (rev 3313)
@@ -26,7 +26,5 @@
 
 for aJobID in aJobIDList: 
 
-	print " --- job id = %s ---" %aJobID
+	print " --- job id = %s ---" % aJobID
 	print getStdout( aJobID )  # Print the output of each job. 
-
-

Modified: ecell3/branches/ecell-3.1/doc/samples/sessionmanager/runsession.py
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/sessionmanager/runsession.py	2008-12-15 09:22:47 UTC (rev 3312)
+++ ecell3/branches/ecell-3.1/doc/samples/sessionmanager/runsession.py	2008-12-15 09:39:47 UTC (rev 3313)
@@ -7,5 +7,4 @@
 
 run( 200 )                             # Run the simulation for 200 seconds.
 
-message( S[ 'Value' ] )                # Print the value of 'Variable:/:S'.
-
+print S[ 'Value' ]                     # Print the value of 'Variable:/:S'.

Modified: ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in
===================================================================
--- ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in	2008-12-15 09:22:47 UTC (rev 3312)
+++ ecell3/branches/ecell-3.1/ecell/bin/ecell3-dmc.in	2008-12-15 09:39:47 UTC (rev 3313)
@@ -1,4 +1,4 @@
-#!/usr/bin/env @prefix@/bin/ecell3-python
+#!/usr/bin/env python
 #
 # ecell3-dmc  - a program to compile and/or docify dynamic module in 
 #               E-Cell Simulation Environment Version 3
@@ -11,25 +11,27 @@
 
 import sys
 import os
-import glob
 import getopt
-import string
+import operator
+from glob import glob
+from distutils.util import split_quoted
+    
+DMCOMPILE = 'dmcompile'
+CLASS_NAME_MACRO_NAME = '_ECELL3_DM_CLASSNAME'
 
+progname = os.path.basename( sys.argv[ 0 ] )
+
 def usage():
-    ext = os.path.basename( sys.argv[0] )
-    aProgramName, ext = os.path.splitext( ext )
     print '''
 %s -- Compile dynamic modules for E-Cell Simulation Environment Version 3.
 
 Usage:
     %s [options] [sourcefile(s)]
     %s [-h] or [--help]
-    '''% ( aProgramName, aProgramName, aProgramName )
+    ''' % dict( progname = progname )
 
 def help():
     usage()
-    ext = os.path.basename( sys.argv[0] )
-    aProgramName, ext = os.path.splitext( ext )
     print '''
 %s options:
     --no-stdinclude          Don't set standard include file path.
@@ -47,29 +49,28 @@
 Written by:
     Tomoya Kitayama <to...@e-...>
     Satya Arjunan <sa...@tt...>
-    '''% ( aProgramName )
+    ''' % dict( progname = progname )
 
 def msg( outstr ):
-    print "E-Cell3 ecell3-dmc: " + outstr
+    global progname
+    print "%s: %s" % ( progname, outstr )
 
 def main():
 
     # -------------------------------------
     # initialize file names
     # -------------------------------------
-    prefix = os.environ['ECELL3_PREFIX']
-    ecell3dir = os.environ['ECELL_DIRNAME']
-    BOOST_LIBRARIES = os.environ['BOOST_LIBRARIES']
+    prefix = r'''@PREFIX@'''
+    ecell3dir = r'''@ECELL_DIRNAME@'''
+    BOOST_LIBRARIES = r'''-lboost_python'''
     exec_prefix = prefix
     BINDIR = exec_prefix + os.sep + 'bin'
-    STDLIBDIR = '-L\"' + exec_prefix + os.sep + 'lib\"'
+    STDLIBDIRS = [ '-L' + exec_prefix + os.sep + 'lib' ]
     ECELL_INCLUDE = prefix + os.sep + 'include' + os.sep + ecell3dir
     LIBECS_INCLUDE = ECELL_INCLUDE + os.sep + 'libecs'
-    STDINCLUDE = [ '\"-I' + prefix + os.sep + 'include\"',
-                   '\"-I' + ECELL_INCLUDE + '\"',
-                   '\"-I' + LIBECS_INCLUDE + '\"',
-                   os.environ['PYTHON_INCLUDES'] ]
-    DMCOMPILE = os.path.abspath( BINDIR + os.sep + 'dmcompile' )
+    STDINCLUDE = [ '-I' + prefix + os.sep + 'include',
+                   '-I' + ECELL_INCLUDE,
+                   '-I' + LIBECS_INCLUDE ]
     SRC = None
 
 
@@ -88,11 +89,11 @@
     NO_STDINCLUDE = False
     NO_STDLIBDIR = False
     NO_DEFINE_CXXFLAGS = False
-    LDFLAGS = ''
+    LDFLAGS = []
     CXXFLAGS = []
     CXXCOMPILEFLAGS = []
-    PYTHON = None
     cmdList = []
+    dmcompile = DMCOMPILE
 
     # -------------------------------------
     # check argument
@@ -102,7 +103,7 @@
         # print help message
         if anOption in ( "-h", '--help' ):
             help()
-            sys.exit( -1 )
+            return 255
       
         # be verbose
         if anOption in ( "-v", '--verbose'):
@@ -118,85 +119,72 @@
 
         # set ldflags
         if anOption == "--ldflags":
-            LDFLAGS = LDFLAGS + ' ' + anArg
+            LDFLAGS.extend( split_quoted( anArg ) )
 
         # set no-define-cxxflags
         if anOption == "--no-define-cxxflags":
             NO_DEFINE_CXXFLAGS = True
-            CXXFLAGS = anArg.split()
+            CXXFLAGS.extend( split_quoted( anArg ) )
 
         # set cxxflags
         if anOption == "--cxxflags":
-            CXXCOMPILEFLAGS.extend( CXXFLAGS )
-            CXXCOMPILEFLAGS.extend( anArg.split() )
+            CXXFLAGS.extend( split_quoted( anArg ) )
 
         # set cxxflags
         if anOption == "--dmcompile":
-            DMCOMPILE = os.path.abspath( anArg + os.sep + 'dmcompile' )
+            if os.path.isdir( anArg ):
+                dmcompile = os.path.join( anArg, DMCOMPILE )
+            else:
+                dmcompile = anArg
 
     # check if source file is given
     if len( args ) < 1:
         help()
-        msg( "Error: source file was not given." )
-        sys.exit( 1 )
+        msg( "no source file is given." )
+        return 1
 
-    if os.name == 'nt':
-        PYTHON_WIN_VERSION = ( '%d%d' )%( sys.version_info[:2] )
-        ADDFLAGS = ' -Wl,--enable-runtime-pseudo-reloc -Wl,-s -lpython' + \
-                   PYTHON_WIN_VERSION
-    elif sys.platform == 'darwin':
-        ADDFLAGS = ' -Wl,-undefined,dynamic_lookup'
-    else:
-        ADDFLAGS = ''
-        cmdList.append( sys.executable )
+    cmdList.append( dmcompile )
 
-    cmdList.append( DMCOMPILE )
-
     if VERBOSE:
         cmdList.append( '-v' )
 
     # on MS-Windows, command line doesn't expand *.cpp automatically
-    FILELIST = []
-    for arg in args:
-        FILELIST.extend( glob.glob( arg ) )
+    srcs = reduce( operator.add, map( glob, args ) )
 
     # check if source file is valid
-    if len( FILELIST ) < 1:
-        msg( "Error: source file "+ args[0] + " was not found." )
-        sys.exit( 1 )    
+    if len( srcs ) < 1:
+        msg( "source file "+ args[0] + " was not found." )
+        return 1
 
     if NO_STDINCLUDE:
         STDINCLUDE = []
 
     if not NO_STDLIBDIR:
-        LDFLAGS = LDFLAGS + ' ' + STDLIBDIR
-        
-    LDFLAGS = LDFLAGS + ADDFLAGS + ' -lecs -lgsl ' + BOOST_LIBRARIES
-    os.environ['LDFLAGS'] = LDFLAGS
+        LDFLAGS.extend( STDLIBDIRS )
+  
+    LDFLAGS.append( '-lecs' )
+    LDFLAGS.append( '-lgsl' )
+    LDFLAGS.extend( split_quoted( BOOST_LIBRARIES ) )
 
-    if NO_DEFINE_CXXFLAGS:
-        os.environ['CXXFLAGS'] = CXXFLAGS.join()
+    cmdList.extend( STDINCLUDE )
+    cmdList.extend( CXXFLAGS )
+    cmdList.extend( LDFLAGS )
 
-    for SRC in FILELIST:
-        ext = os.path.basename(SRC)
-        CLASSNAME, ext = os.path.splitext(ext)
-        CLASSNAMEDEFINE = '-D_ECELL3_DM_CLASSNAME=' + CLASSNAME
-        argList = []
-        argList.append( cmdList[0] )
-        argList.extend( cmdList[1:] )
-        argList.extend( [ SRC, CLASSNAMEDEFINE ] )
-        argList.extend( STDINCLUDE )
-        argList.extend( CXXCOMPILEFLAGS )
+    for src in srcs:
+        ext = os.path.basename( src )
+        classname, ext = os.path.splitext( ext )
+        argList = cmdList + [ '-D%s=%s' % ( CLASS_NAME_MACRO_NAME, classname ), src ]
 
         if VERBOSE:
-            print string.join( argList[0:] )
+            print ' '.join( argList[0:] )
             
         # Need to us os.spawnv because of problems in MS-Windows with os.sytem
         # when the dmcompile path contains whitespaces even if we force quotes
-        ret = os.spawnv( os.P_WAIT, cmdList[0], argList )
-        if not ret == 0:
-            sys.exit( 1 )
+        ret = os.spawnvp( os.P_WAIT, cmdList[0], argList )
+        if ret != 0:
+            msg( '%s returned error status: %d' % ( cmdList[0], ret ) )
+            return 1
+    return 0
 
 if __name__ == '__main__':
-    main()
-    sys.exit( 0 )
+    sys.exit( main() )

Modified: ecell3/branches/ecell-3.1/ecell/libecs/PropertyInterface.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/PropertyInterface.hpp	2008-12-15 09:22:47 UTC (rev 3312)
+++ ecell3/branches/ecell-3.1/ecell/libecs/PropertyInterface.hpp	2008-12-15 09:39:47 UTC (rev 3313)
@@ -88,11 +88,10 @@
 
   public:
 
-    typedef PropertySlot<T> PropertySlot_;
-    DECLARE_TYPE( PropertySlot_, PropertySlot );
+    DECLARE_TYPE( PropertySlot<T>, PropertySlotType );
 
-    DECLARE_ASSOCVECTOR_TEMPLATE( String, PropertySlotPtr,
-				  std::less<const String>, PropertySlotMap );
+    DECLARE_ASSOCVECTOR_TEMPLATE( String, PropertySlotTypePtr,
+				  std::less<const String>, PropertySlotTypeMap );
 
     DECLARE_ASSOCVECTOR_TEMPLATE( String, Polymorph,
 				  std::less<const String>, PolymorphAssocVector);
@@ -184,9 +183,9 @@
        @return a borrowed pointer to the PropertySlot with that name.
     */
 
-    static PropertySlotPtr getPropertySlot( StringCref aPropertyName )
+    static PropertySlotTypePtr getPropertySlot( StringCref aPropertyName )
     {
-      PropertySlotMapConstIterator i( findPropertySlot( aPropertyName ) );
+      PropertySlotTypeMapConstIterator i( findPropertySlot( aPropertyName ) );
 
       if( i == thePropertySlotMap.end() )
 	{
@@ -202,7 +201,7 @@
     {
       try
 	{
-	  PropertySlotPtr aPropertySlot( getPropertySlot( aPropertyName ) );
+	  PropertySlotTypePtr aPropertySlot( getPropertySlot( aPropertyName ) );
 	  return new ConcretePropertySlotProxy<T>( anObject, *aPropertySlot );
 	}
       catch( NoSlotCref )
@@ -227,7 +226,7 @@
     static void setProperty( T& anObject, StringCref aPropertyName, 
 			     PolymorphCref aValue )
     {
-      PropertySlotMapConstIterator 
+      PropertySlotTypeMapConstIterator 
 	aPropertySlotMapIterator( findPropertySlot( aPropertyName ) );
       
       if( aPropertySlotMapIterator != thePropertySlotMap.end() )
@@ -255,7 +254,7 @@
     static const Polymorph getProperty( const T& anObject,
 					StringCref aPropertyName )
     {
-      PropertySlotMapConstIterator 
+      PropertySlotTypeMapConstIterator 
 	aPropertySlotMapIterator( findPropertySlot( aPropertyName ) );
       
       if( aPropertySlotMapIterator != thePropertySlotMap.end() )
@@ -272,12 +271,12 @@
     static void loadProperty( T& anObject, StringCref aPropertyName, 
 			      PolymorphCref aValue )
     {
-      PropertySlotMapConstIterator 
+      PropertySlotTypeMapConstIterator 
 	aPropertySlotMapIterator( findPropertySlot( aPropertyName ) );
 
       if( aPropertySlotMapIterator != thePropertySlotMap.end() )
 	{
-	  PropertySlotPtr aPropertySlotPtr( aPropertySlotMapIterator->second );
+	  PropertySlotTypePtr aPropertySlotPtr( aPropertySlotMapIterator->second );
 
 	  if( aPropertySlotPtr->isLoadable() )
 	    {
@@ -298,12 +297,12 @@
     static const Polymorph
     saveProperty( const T& anObject, StringCref aPropertyName )
     {
-      PropertySlotMapConstIterator 
+      PropertySlotTypeMapConstIterator 
 	aPropertySlotMapIterator( findPropertySlot( aPropertyName ) );
 
       if( aPropertySlotMapIterator != thePropertySlotMap.end() )
 	{
-	  PropertySlotPtr aPropertySlotPtr( aPropertySlotMapIterator->second );
+	  PropertySlotTypePtr aPropertySlotPtr( aPropertySlotMapIterator->second );
 	  if( aPropertySlotPtr->isSavable() )
 	    {
 	      return aPropertySlotPtr->savePolymorph( anObject );
@@ -325,7 +324,7 @@
       PolymorphVector aVector1, aVector2;
       // aVector.reserve( thePropertySlotMap.size() );
       
-      for( PropertySlotMapConstIterator i( thePropertySlotMap.begin() ); 
+      for( PropertySlotTypeMapConstIterator i( thePropertySlotMap.begin() ); 
 	   i != thePropertySlotMap.end() ; ++i )
 	{
 	  aVector1.push_back( i->first );
@@ -347,7 +346,7 @@
 
     
     static void 
-    registerPropertySlot( StringCref aName, PropertySlotPtr aPropertySlotPtr )
+    registerPropertySlot( StringCref aName, PropertySlotTypePtr aPropertySlotPtr )
     {
       if( findPropertySlot( aName ) != thePropertySlotMap.end() )
 	{
@@ -364,7 +363,7 @@
     static const Polymorph
     getPropertyAttributes( const T& anObject, StringCref aPropertyName )
     {
-      PropertySlotMapConstIterator i( findPropertySlot( aPropertyName ) );
+      PropertySlotTypeMapConstIterator i( findPropertySlot( aPropertyName ) );
 
       if( i != thePropertySlotMap.end() )
 	{
@@ -413,7 +412,7 @@
     }
     */
 
-    static PropertySlotMapCref getPropertySlotMap()
+    static PropertySlotTypeMapCref getPropertySlotMap()
     {
       return thePropertySlotMap;
     }
@@ -465,7 +464,7 @@
 
   private:
 
-    static PropertySlotMapConstIterator 
+    static PropertySlotTypeMapConstIterator 
     findPropertySlot( StringCref aPropertyName )
     {
       return thePropertySlotMap.find( aPropertyName );
@@ -473,7 +472,7 @@
 
   private:
 
-    static PropertySlotMap  thePropertySlotMap;
+    static PropertySlotTypeMap  thePropertySlotMap;
 
     static PolymorphAssocVector theInfoMap;
   };
@@ -482,7 +481,7 @@
   // This is necessary for the static data member of 
   // the PropertyInterface template class to be instantiated
   // when the class is specialized (in LIBECS_DM_INIT_STATIC()).
-  template< class T > typename libecs::PropertyInterface< T>::PropertySlotMap
+  template< class T > typename libecs::PropertyInterface< T>::PropertySlotTypeMap
     libecs::PropertyInterface< T>::thePropertySlotMap;
   template< class T > typename libecs::PropertyInterface< T>::PolymorphAssocVector
     libecs::PropertyInterface< T>::theInfoMap;

Modified: ecell3/branches/ecell-3.1/ecell/libecs/PropertySlot.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/PropertySlot.hpp	2008-12-15 09:22:47 UTC (rev 3312)
+++ ecell3/branches/ecell-3.1/ecell/libecs/PropertySlot.hpp	2008-12-15 09:39:47 UTC (rev 3313)
@@ -289,8 +289,7 @@
   };
 
   template
-  < 
-    class T,
+  < class T,
     typename SlotType_
   >
   class LoadSaveConcretePropertySlot
@@ -302,20 +301,20 @@
 
     DECLARE_TYPE( SlotType_, SlotType );
 
-    typedef ConcretePropertySlot<T,SlotType> ConcretePropertySlot;
+    typedef ConcretePropertySlot<T,SlotType> ConcretePropertySlotType;
 
-    typedef typename ConcretePropertySlot::SetType SetType;
-    typedef typename ConcretePropertySlot::GetType GetType;
+    typedef typename ConcretePropertySlotType::SetType SetType;
+    typedef typename ConcretePropertySlotType::GetType GetType;
 
-    typedef typename ConcretePropertySlot::SetMethodPtr SetMethodPtr;
-    typedef typename ConcretePropertySlot::GetMethodPtr GetMethodPtr;
+    typedef typename ConcretePropertySlotType::SetMethodPtr SetMethodPtr;
+    typedef typename ConcretePropertySlotType::GetMethodPtr GetMethodPtr;
 
     DM_IF LoadSaveConcretePropertySlot( const SetMethodPtr aSetMethodPtr,
 				  const GetMethodPtr aGetMethodPtr,
 				  const SetMethodPtr aLoadMethodPtr,
 				  const GetMethodPtr aSaveMethodPtr )
       :
-      ConcretePropertySlot( aSetMethodPtr, aGetMethodPtr ),
+      ConcretePropertySlotType( aSetMethodPtr, aGetMethodPtr ),
       theLoadMethodPtr( SetMethod( aLoadMethodPtr ) ),
       theSaveMethodPtr( GetMethod( aSaveMethodPtr ) )
     {

Modified: ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxy.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxy.hpp	2008-12-15 09:22:47 UTC (rev 3312)
+++ ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxy.hpp	2008-12-15 09:39:47 UTC (rev 3313)
@@ -162,11 +162,10 @@
 
   public:
 
-    typedef PropertySlot<T> PropertySlot_;
-    DECLARE_TYPE( PropertySlot_, PropertySlot );
+    DECLARE_TYPE( PropertySlot<T>, PropertySlotType );
 
     DM_IF ConcretePropertySlotProxy( T& anObject, 
-			       PropertySlotRef aPropertySlot )
+			       PropertySlotTypeRef aPropertySlot )
       :
       theObject( anObject ),
       thePropertySlot( aPropertySlot )
@@ -223,7 +222,7 @@
     DM_IF ConcretePropertySlotProxy();
 
     T&               theObject;
-    PropertySlotRef  thePropertySlot;
+    PropertySlotTypeRef  thePropertySlot;
 
   };
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3372] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2009-02-04 08:29:29

Revision: 3372
          http://ecell.svn.sourceforge.net/ecell/?rev=3372&view=rev
Author:   moriyoshi
Date:     2009-02-04 08:29:23 +0000 (Wed, 04 Feb 2009)

Log Message:
-----------
* Bundle libtool's m4 script.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/autogen.sh

Added Paths:
-----------
    ecell3/branches/ecell-3.1/m4/
    ecell3/branches/ecell-3.1/m4/libtool.m4
    ecell3/branches/ecell-3.1/m4/ltdl.m4

Modified: ecell3/branches/ecell-3.1/autogen.sh
===================================================================
--- ecell3/branches/ecell-3.1/autogen.sh	2009-02-04 08:20:52 UTC (rev 3371)
+++ ecell3/branches/ecell-3.1/autogen.sh	2009-02-04 08:29:23 UTC (rev 3372)
@@ -43,11 +43,12 @@
 
 for dir in . libltdl dmtool ecell
   do 
+  top_srcdir=`echo $dir | sed -e 's#\([^./][^/]*\|\.[^/][^/]*\)\(/\|$\)#..\2#g'`
   echo -n "Running autotools for $dir ... "
   (cd $dir; \
   { if [ -r configure.ac.in ]; then echo -n 'configure.ac ' && sed -e "s/@ECELL_VERSION_NUMBER@/$ECELL_VERSION_NUMBER/g" configure.ac.in > configure.ac; fi } && \
   { echo -n 'libtoolize '; $LIBTOOLIZE -c --force --automake; } && \
-  { echo -n 'aclocal '; aclocal; } && \
+  { echo -n 'aclocal '; aclocal -I$top_srcdir/m4; } && \
   { echo -n 'autoheader '; autoheader -f ; } && \
   { echo -n 'automake ';  automake -c --add-missing --gnu $am_opt; } && \
   { echo -n 'autoconf '; autoconf; } && \

Added: ecell3/branches/ecell-3.1/m4/libtool.m4
===================================================================
--- ecell3/branches/ecell-3.1/m4/libtool.m4	                        (rev 0)
+++ ecell3/branches/ecell-3.1/m4/libtool.m4	2009-02-04 08:29:23 UTC (rev 3372)
@@ -0,0 +1,6656 @@
+# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*-
+## Copyright 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007,
+## 2008  Free Software Foundation, Inc.
+## Originally by Gordon Matzigkeit <go...@gn...>, 1996
+##
+## This file is free software; the Free Software Foundation gives
+## unlimited permission to copy and/or distribute it, with or without
+## modifications, as long as this notice is preserved.
+
+# serial 52 AC_PROG_LIBTOOL
+
+
+# AC_PROVIDE_IFELSE(MACRO-NAME, IF-PROVIDED, IF-NOT-PROVIDED)
+# -----------------------------------------------------------
+# If this macro is not defined by Autoconf, define it here.
+m4_ifdef([AC_PROVIDE_IFELSE],
+         [],
+         [m4_define([AC_PROVIDE_IFELSE],
+	         [m4_ifdef([AC_PROVIDE_$1],
+		           [$2], [$3])])])
+
+
+# AC_PROG_LIBTOOL
+# ---------------
+AC_DEFUN([AC_PROG_LIBTOOL],
+[AC_REQUIRE([_AC_PROG_LIBTOOL])dnl
+dnl If AC_PROG_CXX has already been expanded, run AC_LIBTOOL_CXX
+dnl immediately, otherwise, hook it in at the end of AC_PROG_CXX.
+  AC_PROVIDE_IFELSE([AC_PROG_CXX],
+    [AC_LIBTOOL_CXX],
+    [define([AC_PROG_CXX], defn([AC_PROG_CXX])[AC_LIBTOOL_CXX
+  ])])
+dnl And a similar setup for Fortran 77 support
+  AC_PROVIDE_IFELSE([AC_PROG_F77],
+    [AC_LIBTOOL_F77],
+    [define([AC_PROG_F77], defn([AC_PROG_F77])[AC_LIBTOOL_F77
+])])
+
+dnl Quote A][M_PROG_GCJ so that aclocal doesn't bring it in needlessly.
+dnl If either AC_PROG_GCJ or A][M_PROG_GCJ have already been expanded, run
+dnl AC_LIBTOOL_GCJ immediately, otherwise, hook it in at the end of both.
+  AC_PROVIDE_IFELSE([AC_PROG_GCJ],
+    [AC_LIBTOOL_GCJ],
+    [AC_PROVIDE_IFELSE([A][M_PROG_GCJ],
+      [AC_LIBTOOL_GCJ],
+      [AC_PROVIDE_IFELSE([LT_AC_PROG_GCJ],
+	[AC_LIBTOOL_GCJ],
+      [ifdef([AC_PROG_GCJ],
+	     [define([AC_PROG_GCJ], defn([AC_PROG_GCJ])[AC_LIBTOOL_GCJ])])
+       ifdef([A][M_PROG_GCJ],
+	     [define([A][M_PROG_GCJ], defn([A][M_PROG_GCJ])[AC_LIBTOOL_GCJ])])
+       ifdef([LT_AC_PROG_GCJ],
+	     [define([LT_AC_PROG_GCJ],
+		defn([LT_AC_PROG_GCJ])[AC_LIBTOOL_GCJ])])])])
+])])# AC_PROG_LIBTOOL
+
+
+# _AC_PROG_LIBTOOL
+# ----------------
+AC_DEFUN([_AC_PROG_LIBTOOL],
+[AC_REQUIRE([AC_LIBTOOL_SETUP])dnl
+AC_BEFORE([$0],[AC_LIBTOOL_CXX])dnl
+AC_BEFORE([$0],[AC_LIBTOOL_F77])dnl
+AC_BEFORE([$0],[AC_LIBTOOL_GCJ])dnl
+
+# This can be used to rebuild libtool when needed
+LIBTOOL_DEPS="$ac_aux_dir/ltmain.sh"
+
+# Always use our own libtool.
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+AC_SUBST(LIBTOOL)dnl
+
+# Prevent multiple expansion
+define([AC_PROG_LIBTOOL], [])
+])# _AC_PROG_LIBTOOL
+
+
+# AC_LIBTOOL_SETUP
+# ----------------
+AC_DEFUN([AC_LIBTOOL_SETUP],
+[AC_PREREQ(2.50)dnl
+AC_REQUIRE([AC_ENABLE_SHARED])dnl
+AC_REQUIRE([AC_ENABLE_STATIC])dnl
+AC_REQUIRE([AC_ENABLE_FAST_INSTALL])dnl
+AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_CANONICAL_BUILD])dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([AC_PROG_LD])dnl
+AC_REQUIRE([AC_PROG_LD_RELOAD_FLAG])dnl
+AC_REQUIRE([AC_PROG_NM])dnl
+
+AC_REQUIRE([AC_PROG_LN_S])dnl
+AC_REQUIRE([AC_DEPLIBS_CHECK_METHOD])dnl
+# Autoconf 2.13's AC_OBJEXT and AC_EXEEXT macros only works for C compilers!
+AC_REQUIRE([AC_OBJEXT])dnl
+AC_REQUIRE([AC_EXEEXT])dnl
+dnl
+AC_LIBTOOL_SYS_MAX_CMD_LEN
+AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE
+AC_LIBTOOL_OBJDIR
+
+AC_REQUIRE([_LT_AC_SYS_COMPILER])dnl
+_LT_AC_PROG_ECHO_BACKSLASH
+
+case $host_os in
+aix3*)
+  # AIX sometimes has problems with the GCC collect2 program.  For some
+  # reason, if we set the COLLECT_NAMES environment variable, the problems
+  # vanish in a puff of smoke.
+  if test "X${COLLECT_NAMES+set}" != Xset; then
+    COLLECT_NAMES=
+    export COLLECT_NAMES
+  fi
+  ;;
+esac
+
+# Sed substitution that helps us do robust quoting.  It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed='sed -e 1s/^X//'
+[sed_quote_subst='s/\([\\"\\`$\\\\]\)/\\\1/g']
+
+# Same as above, but do not quote variable references.
+[double_quote_subst='s/\([\\"\\`\\\\]\)/\\\1/g']
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+# Constants:
+rm="rm -f"
+
+# Global variables:
+default_ofile=libtool
+can_build_shared=yes
+
+# All known linkers require a `.a' archive for static linking (except MSVC,
+# which needs '.lib').
+libext=a
+ltmain="$ac_aux_dir/ltmain.sh"
+ofile="$default_ofile"
+with_gnu_ld="$lt_cv_prog_gnu_ld"
+
+AC_CHECK_TOOL(AR, ar, false)
+AC_CHECK_TOOL(RANLIB, ranlib, :)
+AC_CHECK_TOOL(STRIP, strip, :)
+
+old_CC="$CC"
+old_CFLAGS="$CFLAGS"
+
+# Set sane defaults for various variables
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+test -z "$AS" && AS=as
+test -z "$CC" && CC=cc
+test -z "$LTCC" && LTCC=$CC
+test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS
+test -z "$DLLTOOL" && DLLTOOL=dlltool
+test -z "$LD" && LD=ld
+test -z "$LN_S" && LN_S="ln -s"
+test -z "$MAGIC_CMD" && MAGIC_CMD=file
+test -z "$NM" && NM=nm
+test -z "$SED" && SED=sed
+test -z "$OBJDUMP" && OBJDUMP=objdump
+test -z "$RANLIB" && RANLIB=:
+test -z "$STRIP" && STRIP=:
+test -z "$ac_objext" && ac_objext=o
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+  case $host_os in
+  openbsd*)
+    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+    ;;
+  *)
+    old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+    ;;
+  esac
+  old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+
+_LT_CC_BASENAME([$compiler])
+
+# Only perform the check for file, if the check method requires it
+case $deplibs_check_method in
+file_magic*)
+  if test "$file_magic_cmd" = '$MAGIC_CMD'; then
+    AC_PATH_MAGIC
+  fi
+  ;;
+esac
+
+_LT_REQUIRED_DARWIN_CHECKS
+
+AC_PROVIDE_IFELSE([AC_LIBTOOL_DLOPEN], enable_dlopen=yes, enable_dlopen=no)
+AC_PROVIDE_IFELSE([AC_LIBTOOL_WIN32_DLL],
+enable_win32_dll=yes, enable_win32_dll=no)
+
+AC_ARG_ENABLE([libtool-lock],
+    [AC_HELP_STRING([--disable-libtool-lock],
+	[avoid locking (might break parallel builds)])])
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+AC_ARG_WITH([pic],
+    [AC_HELP_STRING([--with-pic],
+	[try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
+    [pic_mode="$withval"],
+    [pic_mode=default])
+test -z "$pic_mode" && pic_mode=default
+
+# Use C for the default configuration in the libtool script
+tagname=
+AC_LIBTOOL_LANG_C_CONFIG
+_LT_AC_TAGCONFIG
+])# AC_LIBTOOL_SETUP
+
+
+# _LT_AC_SYS_COMPILER
+# -------------------
+AC_DEFUN([_LT_AC_SYS_COMPILER],
+[AC_REQUIRE([AC_PROG_CC])dnl
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+])# _LT_AC_SYS_COMPILER
+
+
+# _LT_CC_BASENAME(CC)
+# -------------------
+# Calculate cc_basename.  Skip known compiler wrappers and cross-prefix.
+AC_DEFUN([_LT_CC_BASENAME],
+[for cc_temp in $1""; do
+  case $cc_temp in
+    compile | *[[\\/]]compile | ccache | *[[\\/]]ccache ) ;;
+    distcc | *[[\\/]]distcc | purify | *[[\\/]]purify ) ;;
+    \-*) ;;
+    *) break;;
+  esac
+done
+cc_basename=`$echo "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+])
+
+
+# _LT_COMPILER_BOILERPLATE
+# ------------------------
+# Check for compiler boilerplate output or warnings with
+# the simple compiler test code.
+AC_DEFUN([_LT_COMPILER_BOILERPLATE],
+[AC_REQUIRE([LT_AC_PROG_SED])dnl
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$rm conftest*
+])# _LT_COMPILER_BOILERPLATE
+
+
+# _LT_LINKER_BOILERPLATE
+# ----------------------
+# Check for linker boilerplate output or warnings with
+# the simple link test code.
+AC_DEFUN([_LT_LINKER_BOILERPLATE],
+[AC_REQUIRE([LT_AC_PROG_SED])dnl
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$rm -r conftest*
+])# _LT_LINKER_BOILERPLATE
+
+# _LT_REQUIRED_DARWIN_CHECKS
+# --------------------------
+# Check for some things on darwin
+AC_DEFUN([_LT_REQUIRED_DARWIN_CHECKS],[
+  case $host_os in
+    rhapsody* | darwin*)
+    AC_CHECK_TOOL([DSYMUTIL], [dsymutil], [:])
+    AC_CHECK_TOOL([NMEDIT], [nmedit], [:])
+
+    AC_CACHE_CHECK([for -single_module linker flag],[lt_cv_apple_cc_single_mod],
+      [lt_cv_apple_cc_single_mod=no
+      if test -z "${LT_MULTI_MODULE}"; then
+   # By default we will add the -single_module flag. You can override
+   # by either setting the environment variable LT_MULTI_MODULE
+   # non-empty at configure time, or by adding -multi_module to the
+   # link flags.
+   echo "int foo(void){return 1;}" > conftest.c
+   $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+     -dynamiclib ${wl}-single_module conftest.c
+   if test -f libconftest.dylib; then
+     lt_cv_apple_cc_single_mod=yes
+     rm -rf libconftest.dylib*
+   fi
+   rm conftest.c
+      fi])
+    AC_CACHE_CHECK([for -exported_symbols_list linker flag],
+      [lt_cv_ld_exported_symbols_list],
+      [lt_cv_ld_exported_symbols_list=no
+      save_LDFLAGS=$LDFLAGS
+      echo "_main" > conftest.sym
+      LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym"
+      AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])],
+   [lt_cv_ld_exported_symbols_list=yes],
+   [lt_cv_ld_exported_symbols_list=no])
+   LDFLAGS="$save_LDFLAGS"
+    ])
+    case $host_os in
+    rhapsody* | darwin1.[[0123]])
+      _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;;
+    darwin1.*)
+     _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+    darwin*)
+      # if running on 10.5 or later, the deployment target defaults
+      # to the OS version, if on x86, and 10.4, the deployment
+      # target defaults to 10.4. Don't you love it?
+      case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
+   10.0,*86*-darwin8*|10.0,*-darwin[[91]]*)
+     _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+   10.[[012]]*)
+     _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+   10.*)
+     _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+      esac
+    ;;
+  esac
+    if test "$lt_cv_apple_cc_single_mod" = "yes"; then
+      _lt_dar_single_mod='$single_module'
+    fi
+    if test "$lt_cv_ld_exported_symbols_list" = "yes"; then
+      _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym'
+    else
+      _lt_dar_export_syms="~$NMEDIT -s \$output_objdir/\${libname}-symbols.expsym \${lib}"
+    fi
+    if test "$DSYMUTIL" != ":"; then
+      _lt_dsymutil="~$DSYMUTIL \$lib || :"
+    else
+      _lt_dsymutil=
+    fi
+    ;;
+  esac
+])
+
+# _LT_AC_SYS_LIBPATH_AIX
+# ----------------------
+# Links a minimal program and checks the executable
+# for the system default hardcoded library path. In most cases,
+# this is /usr/lib:/lib, but when the MPI compilers are used
+# the location of the communication and MPI libs are included too.
+# If we don't find anything, use the default library path according
+# to the aix ld manual.
+AC_DEFUN([_LT_AC_SYS_LIBPATH_AIX],
+[AC_REQUIRE([LT_AC_PROG_SED])dnl
+AC_LINK_IFELSE(AC_LANG_PROGRAM,[
+lt_aix_libpath_sed='
+    /Import File Strings/,/^$/ {
+	/^0/ {
+	    s/^0  *\(.*\)$/\1/
+	    p
+	}
+    }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+  aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi],[])
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+])# _LT_AC_SYS_LIBPATH_AIX
+
+
+# _LT_AC_SHELL_INIT(ARG)
+# ----------------------
+AC_DEFUN([_LT_AC_SHELL_INIT],
+[ifdef([AC_DIVERSION_NOTICE],
+	     [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)],
+	 [AC_DIVERT_PUSH(NOTICE)])
+$1
+AC_DIVERT_POP
+])# _LT_AC_SHELL_INIT
+
+
+# _LT_AC_PROG_ECHO_BACKSLASH
+# --------------------------
+# Add some code to the start of the generated configure script which
+# will find an echo command which doesn't interpret backslashes.
+AC_DEFUN([_LT_AC_PROG_ECHO_BACKSLASH],
+[_LT_AC_SHELL_INIT([
+# Check that we are running under the correct shell.
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+case X$ECHO in
+X*--fallback-echo)
+  # Remove one level of quotation (which was required for Make).
+  ECHO=`echo "$ECHO" | sed 's,\\\\\[$]\\[$]0,'[$]0','`
+  ;;
+esac
+
+echo=${ECHO-echo}
+if test "X[$]1" = X--no-reexec; then
+  # Discard the --no-reexec flag, and continue.
+  shift
+elif test "X[$]1" = X--fallback-echo; then
+  # Avoid inline document here, it may be left over
+  :
+elif test "X`($echo '\t') 2>/dev/null`" = 'X\t' ; then
+  # Yippee, $echo works!
+  :
+else
+  # Restart under the correct shell.
+  exec $SHELL "[$]0" --no-reexec ${1+"[$]@"}
+fi
+
+if test "X[$]1" = X--fallback-echo; then
+  # used as fallback echo
+  shift
+  cat <<EOF
+[$]*
+EOF
+  exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$ECHO"; then
+if test "X${echo_test_string+set}" != Xset; then
+# find a string as large as possible, as long as the shell can cope with it
+  for cmd in 'sed 50q "[$]0"' 'sed 20q "[$]0"' 'sed 10q "[$]0"' 'sed 2q "[$]0"' 'echo test'; do
+    # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+    if (echo_test_string=`eval $cmd`) 2>/dev/null &&
+       echo_test_string=`eval $cmd` &&
+       (test "X$echo_test_string" = "X$echo_test_string") 2>/dev/null
+    then
+      break
+    fi
+  done
+fi
+
+if test "X`($echo '\t') 2>/dev/null`" = 'X\t' &&
+   echo_testing_string=`($echo "$echo_test_string") 2>/dev/null` &&
+   test "X$echo_testing_string" = "X$echo_test_string"; then
+  :
+else
+  # The Solaris, AIX, and Digital Unix default echo programs unquote
+  # backslashes.  This makes it impossible to quote backslashes using
+  #   echo "$something" | sed 's/\\/\\\\/g'
+  #
+  # So, first we look for a working echo in the user's PATH.
+
+  lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+  for dir in $PATH /usr/ucb; do
+    IFS="$lt_save_ifs"
+    if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+       test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+       echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+       test "X$echo_testing_string" = "X$echo_test_string"; then
+      echo="$dir/echo"
+      break
+    fi
+  done
+  IFS="$lt_save_ifs"
+
+  if test "X$echo" = Xecho; then
+    # We didn't find a better echo, so look for alternatives.
+    if test "X`(print -r '\t') 2>/dev/null`" = 'X\t' &&
+       echo_testing_string=`(print -r "$echo_test_string") 2>/dev/null` &&
+       test "X$echo_testing_string" = "X$echo_test_string"; then
+      # This shell has a builtin print -r that does the trick.
+      echo='print -r'
+    elif (test -f /bin/ksh || test -f /bin/ksh$ac_exeext) &&
+	 test "X$CONFIG_SHELL" != X/bin/ksh; then
+      # If we have ksh, try running configure again with it.
+      ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+      export ORIGINAL_CONFIG_SHELL
+      CONFIG_SHELL=/bin/ksh
+      export CONFIG_SHELL
+      exec $CONFIG_SHELL "[$]0" --no-reexec ${1+"[$]@"}
+    else
+      # Try using printf.
+      echo='printf %s\n'
+      if test "X`($echo '\t') 2>/dev/null`" = 'X\t' &&
+	 echo_testing_string=`($echo "$echo_test_string") 2>/dev/null` &&
+	 test "X$echo_testing_string" = "X$echo_test_string"; then
+	# Cool, printf works
+	:
+      elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+	   test "X$echo_testing_string" = 'X\t' &&
+	   echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+	   test "X$echo_testing_string" = "X$echo_test_string"; then
+	CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+	export CONFIG_SHELL
+	SHELL="$CONFIG_SHELL"
+	export SHELL
+	echo="$CONFIG_SHELL [$]0 --fallback-echo"
+      elif echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+	   test "X$echo_testing_string" = 'X\t' &&
+	   echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+	   test "X$echo_testing_string" = "X$echo_test_string"; then
+	echo="$CONFIG_SHELL [$]0 --fallback-echo"
+      else
+	# maybe with a smaller string...
+	prev=:
+
+	for cmd in 'echo test' 'sed 2q "[$]0"' 'sed 10q "[$]0"' 'sed 20q "[$]0"' 'sed 50q "[$]0"'; do
+	  if (test "X$echo_test_string" = "X`eval $cmd`") 2>/dev/null
+	  then
+	    break
+	  fi
+	  prev="$cmd"
+	done
+
+	if test "$prev" != 'sed 50q "[$]0"'; then
+	  echo_test_string=`eval $prev`
+	  export echo_test_string
+	  exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "[$]0" ${1+"[$]@"}
+	else
+	  # Oops.  We lost completely, so just stick with echo.
+	  echo=echo
+	fi
+      fi
+    fi
+  fi
+fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+ECHO=$echo
+if test "X$ECHO" = "X$CONFIG_SHELL [$]0 --fallback-echo"; then
+   ECHO="$CONFIG_SHELL \\\$\[$]0 --fallback-echo"
+fi
+
+AC_SUBST(ECHO)
+])])# _LT_AC_PROG_ECHO_BACKSLASH
+
+
+# _LT_AC_LOCK
+# -----------
+AC_DEFUN([_LT_AC_LOCK],
+[AC_ARG_ENABLE([libtool-lock],
+    [AC_HELP_STRING([--disable-libtool-lock],
+	[avoid locking (might break parallel builds)])])
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+  # Find out which ABI we are using.
+  echo 'int i;' > conftest.$ac_ext
+  if AC_TRY_EVAL(ac_compile); then
+    case `/usr/bin/file conftest.$ac_objext` in
+    *ELF-32*)
+      HPUX_IA64_MODE="32"
+      ;;
+    *ELF-64*)
+      HPUX_IA64_MODE="64"
+      ;;
+    esac
+  fi
+  rm -rf conftest*
+  ;;
+*-*-irix6*)
+  # Find out which ABI we are using.
+  echo '[#]line __oline__ "configure"' > conftest.$ac_ext
+  if AC_TRY_EVAL(ac_compile); then
+   if test "$lt_cv_prog_gnu_ld" = yes; then
+    case `/usr/bin/file conftest.$ac_objext` in
+    *32-bit*)
+      LD="${LD-ld} -melf32bsmip"
+      ;;
+    *N32*)
+      LD="${LD-ld} -melf32bmipn32"
+      ;;
+    *64-bit*)
+      LD="${LD-ld} -melf64bmip"
+      ;;
+    esac
+   else
+    case `/usr/bin/file conftest.$ac_objext` in
+    *32-bit*)
+      LD="${LD-ld} -32"
+      ;;
+    *N32*)
+      LD="${LD-ld} -n32"
+      ;;
+    *64-bit*)
+      LD="${LD-ld} -64"
+      ;;
+    esac
+   fi
+  fi
+  rm -rf conftest*
+  ;;
+
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+s390*-*linux*|sparc*-*linux*)
+  # Find out which ABI we are using.
+  echo 'int i;' > conftest.$ac_ext
+  if AC_TRY_EVAL(ac_compile); then
+    case `/usr/bin/file conftest.o` in
+    *32-bit*)
+      case $host in
+        x86_64-*kfreebsd*-gnu)
+          LD="${LD-ld} -m elf_i386_fbsd"
+          ;;
+        x86_64-*linux*)
+          LD="${LD-ld} -m elf_i386"
+          ;;
+        ppc64-*linux*|powerpc64-*linux*)
+          LD="${LD-ld} -m elf32ppclinux"
+          ;;
+        s390x-*linux*)
+          LD="${LD-ld} -m elf_s390"
+          ;;
+        sparc64-*linux*)
+          LD="${LD-ld} -m elf32_sparc"
+          ;;
+      esac
+      ;;
+    *64-bit*)
+      case $host in
+        x86_64-*kfreebsd*-gnu)
+          LD="${LD-ld} -m elf_x86_64_fbsd"
+          ;;
+        x86_64-*linux*)
+          LD="${LD-ld} -m elf_x86_64"
+          ;;
+        ppc*-*linux*|powerpc*-*linux*)
+          LD="${LD-ld} -m elf64ppc"
+          ;;
+        s390*-*linux*)
+          LD="${LD-ld} -m elf64_s390"
+          ;;
+        sparc*-*linux*)
+          LD="${LD-ld} -m elf64_sparc"
+          ;;
+      esac
+      ;;
+    esac
+  fi
+  rm -rf conftest*
+  ;;
+
+*-*-sco3.2v5*)
+  # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+  SAVE_CFLAGS="$CFLAGS"
+  CFLAGS="$CFLAGS -belf"
+  AC_CACHE_CHECK([whether the C compiler needs -belf], lt_cv_cc_needs_belf,
+    [AC_LANG_PUSH(C)
+     AC_TRY_LINK([],[],[lt_cv_cc_needs_belf=yes],[lt_cv_cc_needs_belf=no])
+     AC_LANG_POP])
+  if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+    # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+    CFLAGS="$SAVE_CFLAGS"
+  fi
+  ;;
+sparc*-*solaris*)
+  # Find out which ABI we are using.
+  echo 'int i;' > conftest.$ac_ext
+  if AC_TRY_EVAL(ac_compile); then
+    case `/usr/bin/file conftest.o` in
+    *64-bit*)
+      case $lt_cv_prog_gnu_ld in
+      yes*) LD="${LD-ld} -m elf64_sparc" ;;
+      *)
+        if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
+	  LD="${LD-ld} -64"
+	fi
+	;;
+      esac
+      ;;
+    esac
+  fi
+  rm -rf conftest*
+  ;;
+
+AC_PROVIDE_IFELSE([AC_LIBTOOL_WIN32_DLL],
+[*-*-cygwin* | *-*-mingw* | *-*-pw32*)
+  AC_CHECK_TOOL(DLLTOOL, dlltool, false)
+  AC_CHECK_TOOL(AS, as, false)
+  AC_CHECK_TOOL(OBJDUMP, objdump, false)
+  ;;
+  ])
+esac
+
+need_locks="$enable_libtool_lock"
+
+])# _LT_AC_LOCK
+
+
+# AC_LIBTOOL_COMPILER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+#		[OUTPUT-FILE], [ACTION-SUCCESS], [ACTION-FAILURE])
+# ----------------------------------------------------------------
+# Check whether the given compiler option works
+AC_DEFUN([AC_LIBTOOL_COMPILER_OPTION],
+[AC_REQUIRE([LT_AC_PROG_SED])
+AC_CACHE_CHECK([$1], [$2],
+  [$2=no
+  ifelse([$4], , [ac_outfile=conftest.$ac_objext], [ac_outfile=$4])
+   echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+   lt_compiler_flag="$3"
+   # Insert the option either (1) after the last *FLAGS variable, or
+   # (2) before a word containing "conftest.", or (3) at the end.
+   # Note that $ac_compile itself does not contain backslashes and begins
+   # with a dollar sign (not a hyphen), so the echo should work correctly.
+   # The option is referenced via a variable to avoid confusing sed.
+   lt_compile=`echo "$ac_compile" | $SED \
+   -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+   -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+   -e 's:$: $lt_compiler_flag:'`
+   (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+   (eval "$lt_compile" 2>conftest.err)
+   ac_status=$?
+   cat conftest.err >&AS_MESSAGE_LOG_FD
+   echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+   if (exit $ac_status) && test -s "$ac_outfile"; then
+     # The compiler can only warn and ignore the option if not recognized
+     # So say no if there are warnings other than the usual output.
+     $echo "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+     $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+     if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+       $2=yes
+     fi
+   fi
+   $rm conftest*
+])
+
+if test x"[$]$2" = xyes; then
+    ifelse([$5], , :, [$5])
+else
+    ifelse([$6], , :, [$6])
+fi
+])# AC_LIBTOOL_COMPILER_OPTION
+
+
+# AC_LIBTOOL_LINKER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+#                          [ACTION-SUCCESS], [ACTION-FAILURE])
+# ------------------------------------------------------------
+# Check whether the given compiler option works
+AC_DEFUN([AC_LIBTOOL_LINKER_OPTION],
+[AC_REQUIRE([LT_AC_PROG_SED])dnl
+AC_CACHE_CHECK([$1], [$2],
+  [$2=no
+   save_LDFLAGS="$LDFLAGS"
+   LDFLAGS="$LDFLAGS $3"
+   echo "$lt_simple_link_test_code" > conftest.$ac_ext
+   if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+     # The linker can only warn and ignore the option if not recognized
+     # So say no if there are warnings
+     if test -s conftest.err; then
+       # Append any errors to the config.log.
+       cat conftest.err 1>&AS_MESSAGE_LOG_FD
+       $echo "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+       $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+       if diff conftest.exp conftest.er2 >/dev/null; then
+         $2=yes
+       fi
+     else
+       $2=yes
+     fi
+   fi
+   $rm -r conftest*
+   LDFLAGS="$save_LDFLAGS"
+])
+
+if test x"[$]$2" = xyes; then
+    ifelse([$4], , :, [$4])
+else
+    ifelse([$5], , :, [$5])
+fi
+])# AC_LIBTOOL_LINKER_OPTION
+
+
+# AC_LIBTOOL_SYS_MAX_CMD_LEN
+# --------------------------
+AC_DEFUN([AC_LIBTOOL_SYS_MAX_CMD_LEN],
+[# find the maximum length of command line arguments
+AC_MSG_CHECKING([the maximum length of command line arguments])
+AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl
+  i=0
+  teststring="ABCD"
+
+  case $build_os in
+  msdosdjgpp*)
+    # On DJGPP, this test can blow up pretty badly due to problems in libc
+    # (any single argument exceeding 2000 bytes causes a buffer overrun
+    # during glob expansion).  Even if it were fixed, the result of this
+    # check would be larger than it should be.
+    lt_cv_sys_max_cmd_len=12288;    # 12K is about right
+    ;;
+
+  gnu*)
+    # Under GNU Hurd, this test is not required because there is
+    # no limit to the length of command line arguments.
+    # Libtool will interpret -1 as no limit whatsoever
+    lt_cv_sys_max_cmd_len=-1;
+    ;;
+
+  cygwin* | mingw*)
+    # On Win9x/ME, this test blows up -- it succeeds, but takes
+    # about 5 minutes as the teststring grows exponentially.
+    # Worse, since 9x/ME are not pre-emptively multitasking,
+    # you end up with a "frozen" computer, even though with patience
+    # the test eventually succeeds (with a max line length of 256k).
+    # Instead, let's just punt: use the minimum linelength reported by
+    # all of the supported platforms: 8192 (on NT/2K/XP).
+    lt_cv_sys_max_cmd_len=8192;
+    ;;
+
+  amigaos*)
+    # On AmigaOS with pdksh, this test takes hours, literally.
+    # So we just punt and use a minimum line length of 8192.
+    lt_cv_sys_max_cmd_len=8192;
+    ;;
+
+  netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+    # This has been around since 386BSD, at least.  Likely further.
+    if test -x /sbin/sysctl; then
+      lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+    elif test -x /usr/sbin/sysctl; then
+      lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+    else
+      lt_cv_sys_max_cmd_len=65536	# usable default for all BSDs
+    fi
+    # And add a safety zone
+    lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+    lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+    ;;
+
+  interix*)
+    # We know the value 262144 and hardcode it with a safety zone (like BSD)
+    lt_cv_sys_max_cmd_len=196608
+    ;;
+
+  osf*)
+    # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+    # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+    # nice to cause kernel panics so lets avoid the loop below.
+    # First set a reasonable default.
+    lt_cv_sys_max_cmd_len=16384
+    #
+    if test -x /sbin/sysconfig; then
+      case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+        *1*) lt_cv_sys_max_cmd_len=-1 ;;
+      esac
+    fi
+    ;;
+  sco3.2v5*)
+    lt_cv_sys_max_cmd_len=102400
+    ;;
+  sysv5* | sco5v6* | sysv4.2uw2*)
+    kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+    if test -n "$kargmax"; then
+      lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[[ 	]]//'`
+    else
+      lt_cv_sys_max_cmd_len=32768
+    fi
+    ;;
+  *)
+    lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
+    if test -n "$lt_cv_sys_max_cmd_len"; then
+      lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+      lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+    else
+      SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+      while (test "X"`$SHELL [$]0 --fallback-echo "X$teststring" 2>/dev/null` \
+	       = "XX$teststring") >/dev/null 2>&1 &&
+	      new_result=`expr "X$teststring" : ".*" 2>&1` &&
+	      lt_cv_sys_max_cmd_len=$new_result &&
+	      test $i != 17 # 1/2 MB should be enough
+      do
+        i=`expr $i + 1`
+        teststring=$teststring$teststring
+      done
+      teststring=
+      # Add a significant safety factor because C++ compilers can tack on massive
+      # amounts of additional arguments before passing them to the linker.
+      # It appears as though 1/2 is a usable...
 
[truncated message content]

[Ecell-cvs] SF.net SVN: ecell:[3382] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2009-02-05 05:04:22

Revision: 3382
          http://ecell.svn.sourceforge.net/ecell/?rev=3382&view=rev
Author:   moriyoshi
Date:     2009-02-05 05:04:18 +0000 (Thu, 05 Feb 2009)

Log Message:
-----------
* Merge from the branch.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus2Proxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus4Proxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LSFProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LocalProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/SGEProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/SessionManager.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Util.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/__init__.py

Added Paths:
-----------
    ecell3/branches/ecell-3.1/doc/samples/session_manager/
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/

Removed Paths:
-------------
    ecell3/branches/ecell-3.1/doc/samples/sessionmanager/
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/Constants.py	2009-02-04 08:29:23 UTC (rev 3372)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Constants.py	2009-02-05 05:04:18 UTC (rev 3382)
@@ -2,7 +2,7 @@
 #
 #       This file is part of the E-Cell System
 #
-#       Copyright (C) 1996-2008 Keio University
+#       Copyright (C) 1996-2009 Keio University
 #       Copyright (C) 2005-2008 The Molecular Sciences Institute
 #
 #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus2Proxy.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/Globus2Proxy.py	2009-02-04 08:29:23 UTC (rev 3372)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus2Proxy.py	2009-02-05 05:04:18 UTC (rev 3382)
@@ -2,7 +2,7 @@
 #
 #       This file is part of the E-Cell System
 #
-#       Copyright (C) 1996-2008 Keio University
+#       Copyright (C) 1996-2009 Keio University
 #       Copyright (C) 2005-2008 The Molecular Sciences Institute
 #
 #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -38,9 +38,9 @@
 
 
 # imports ecell modules
-from ecell.SessionManager.Util import *
-from ecell.SessionManager.SessionManager import *
-from ecell.SessionManager.Constants import *
+from ecell.session_manager.Util import *
+from ecell.session_manager.SessionManager import *
+from ecell.session_manager.Constants import *
 
 GRID_INFO_SEARCH = 'grid-info-search'
 GLOBUS_JOB_RUN='globus-job-run'

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus4Proxy.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/Globus4Proxy.py	2009-02-04 08:29:23 UTC (rev 3372)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Globus4Proxy.py	2009-02-05 05:04:18 UTC (rev 3382)
@@ -2,7 +2,7 @@
 #
 #       This file is part of the E-Cell System
 #
-#       Copyright (C) 1996-2008 Keio University
+#       Copyright (C) 1996-2009 Keio University
 #       Copyright (C) 2005-2008 The Molecular Sciences Institute
 #
 #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -44,9 +44,9 @@
 from urlparse import urlunsplit
 
 # imports ecell modules
-from ecell.SessionManager.Util import *
-from ecell.SessionManager.SessionManager import *
-from ecell.SessionManager.Constants import *
+from ecell.session_manager.Util import *
+from ecell.session_manager.SessionManager import *
+from ecell.session_manager.Constants import *
 
 GLOBUSRUN_WS = 'globusrun-ws'
 GLOBUS_URL_COPY='globus-url-copy'
@@ -571,7 +571,8 @@
         job.directory = absJobDirectory
         job.environment.update( self.getEnvironmentVariables() )
         job.executable = self.getInterpreter()
-        job.arguments = ( self.getScriptFileName(), )
+        job.arguments = [ self.getScriptFileName() ]
+        job.arguments += self.getArguments()
 
         tmpfile = None
         tmpfile = mkstemp()
@@ -635,7 +636,7 @@
         self.setStatus( ERROR )
 
 class SystemProxy( AbstractSystemProxy ):
-    '''Globus2SystemProxy'''
+    '''Globus4SystemProxy'''
     def __init__( self, sessionManager ):
         '''Constructor
         sessionManager -- the reference to SessionManager

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LSFProxy.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/LSFProxy.py	2009-02-04 08:29:23 UTC (rev 3372)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LSFProxy.py	2009-02-05 05:04:18 UTC (rev 3382)
@@ -2,8 +2,8 @@
 #
 #       This file is part of the E-Cell System
 #
-#       Copyright (C) 1996-2007 Keio University
-#       Copyright (C) 2005-2007 The Molecular Sciences Institute
+#       Copyright (C) 1996-2009 Keio University
+#       Copyright (C) 2005-2008 The Molecular Sciences Institute
 #
 #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
 #
@@ -37,9 +37,9 @@
 from string import *
 
 # imports ecell modules
-from ecell.SessionManager.Util import *
-from ecell.SessionManager.SessionManager import *
-from ecell.SessionManager.Constants import *
+from ecell.session_manager.Util import *
+from ecell.session_manager.SessionManager import *
+from ecell.session_manager.Constants import *
 
 BSUB = 'bsub'
 BJOBS = 'bjobs'

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LocalProxy.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/LocalProxy.py	2009-02-04 08:29:23 UTC (rev 3372)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LocalProxy.py	2009-02-05 05:04:18 UTC (rev 3382)
@@ -2,7 +2,7 @@
 #
 #       This file is part of the E-Cell System
 #
-#       Copyright (C) 1996-2008 Keio University
+#       Copyright (C) 1996-2009 Keio University
 #       Copyright (C) 2005-2008 The Molecular Sciences Institute
 #
 #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -53,8 +53,9 @@
         def wait( self ):
             return os.WEXITSTATUS( os.waitpid( self.pid, 0 )[ 1 ] )
 
-from ecell.SessionManager.SessionManager import *
-from ecell.SessionManager.Util import *
+from ecell.session_manager.SessionManager import *
+from ecell.session_manager.Constants import *
+from ecell.session_manager.Util import *
 
 class SessionProxy( AbstractSessionProxy ):
     '''LocalSessionProxy class

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/SGEProxy.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/SGEProxy.py	2009-02-04 08:29:23 UTC (rev 3372)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/SGEProxy.py	2009-02-05 05:04:18 UTC (rev 3382)
@@ -2,7 +2,7 @@
 #
 #       This file is part of the E-Cell System
 #
-#       Copyright (C) 1996-2008 Keio University
+#       Copyright (C) 1996-2009 Keio University
 #       Copyright (C) 2005-2008 The Molecular Sciences Institute
 #
 #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -36,9 +36,9 @@
 import time
 from itertools import ifilter
 
-from ecell.SessionManager.Util import *
-from ecell.SessionManager.SessionManager import *
-from ecell.SessionManager.Constants import *
+from ecell.session_manager.Util import *
+from ecell.session_manager.SessionManager import *
+from ecell.session_manager.Constants import *
 
 QSUB = 'qsub'
 QSTAT = 'qstat'

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/SessionManager.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/SessionManager.py	2009-02-04 08:29:23 UTC (rev 3372)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/SessionManager.py	2009-02-05 05:04:18 UTC (rev 3382)
@@ -2,7 +2,7 @@
 #
 #       This file is part of the E-Cell System
 #
-#       Copyright (C) 1996-2008 Keio University
+#       Copyright (C) 1996-2009 Keio University
 #       Copyright (C) 2005-2008 The Molecular Sciences Institute
 #
 #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
@@ -41,8 +41,8 @@
 import inspect
 import ecell.eml
 
-from ecell.SessionManager.Constants import *
-from ecell.SessionManager.Util import *
+from ecell.session_manager.Constants import *
+from ecell.session_manager.Util import *
 
 __all__ = (
     'AbstractSessionProxy',
@@ -499,7 +499,7 @@
         
         Return str : the stdout
         '''
-        return self.__jobDict[ jobid ].getStdout()
+        return self.jobs[ jobid ].getStdout()
 
     def getStderr( self, jobid ):
         '''return the stderr of the job
@@ -508,7 +508,7 @@
         
         Return str : the stderr
         '''
-        return self.__jobDict[ jobid ].getStderr()
+        return self.jobs[ jobid ].getStderr()
 
     def getJobDirectory( self, jobid ):
         '''Return the job directory name
@@ -519,7 +519,7 @@
         '''
 
         # return the path of the job directory
-        return self.__jobDict[ jobid ].getJobDirectory()
+        return self.jobs[ jobid ].getJobDirectory()
 
     def setRetryMaxCount( self, count ):
         '''Set retry max count.
@@ -826,12 +826,10 @@
         # creates AbstractSessionProxy
         job = self.__theSystemProxy.createSessionProxy()
         job.setScriptFileName( ess )
-        job.setInterpreter( ECELL3_PYTHON )
+        job.setInterpreter( ECELL3_SESSION )
         job.setArguments(
             (
-                ECELL3_SESSION,
-                '-e', ess,
-                '--parameters', str( arguments )
+                '--parameters=' + str( arguments ),
                 ) )
         job.setEnvironmentVariable( 'ECELL3_DM_PATH', dmpath )
         for i in INTERESTING_ENV_VARS:
@@ -1134,7 +1132,7 @@
                 signal.getsignal( emitted_signum[ 0 ] )( emitted_signum,
                     inspect.currentframe() )
 
-    def stop( self, jobid=0 ):
+    def stop( self, jobid = 0 ):
         '''stop jobs.
         Change the statuses of QUEUED or RUNNING jobs to ERROR.
         About FINISHED jobs, do nothing.
@@ -1146,12 +1144,12 @@
 
         # stops all jobs
         if jobid == 0:
-            for job in self.__jobDict.values():
+            for job in self.jobs.values():
                 job.stop()
 
         # stops one job
         else:
-            self.__jobDict[jobid].stop()
+            self.jobs[jobid].stop()
 
     def stopRunningSessionProxies( self ):
         '''Stop running jobs.

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Util.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/Util.py	2009-02-04 08:29:23 UTC (rev 3372)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/Util.py	2009-02-05 05:04:18 UTC (rev 3382)
@@ -2,7 +2,7 @@
 #
 #       This file is part of the E-Cell System
 #
-#       Copyright (C) 1996-2008 Keio University
+#       Copyright (C) 1996-2009 Keio University
 #       Copyright (C) 2005-2008 The Molecular Sciences Institute
 #
 #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/__init__.py
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SessionManager/__init__.py	2009-02-04 08:29:23 UTC (rev 3372)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/__init__.py	2009-02-05 05:04:18 UTC (rev 3382)
@@ -2,7 +2,7 @@
 #
 #       This file is part of the E-Cell System
 #
-#       Copyright (C) 1996-2008 Keio University
+#       Copyright (C) 1996-2009 Keio University
 #       Copyright (C) 2005-2008 The Molecular Sciences Institute
 #
 #::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3385] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2009-02-05 05:33:56

Revision: 3385
          http://ecell.svn.sourceforge.net/ecell/?rev=3385&view=rev
Author:   moriyoshi
Date:     2009-02-05 05:33:51 +0000 (Thu, 05 Feb 2009)

Log Message:
-----------
* Forgot to fix these files.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/doc/samples/Makefile.am
    ecell3/branches/ecell-3.1/ecell/pyecell/Makefile.am

Modified: ecell3/branches/ecell-3.1/doc/samples/Makefile.am
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/Makefile.am	2009-02-05 05:05:09 UTC (rev 3384)
+++ ecell3/branches/ecell-3.1/doc/samples/Makefile.am	2009-02-05 05:33:51 UTC (rev 3385)
@@ -12,7 +12,7 @@
 	branchG \
 	ga \
 	heatshock \
-	sessionmanager \
+	session_manager \
 	simple \
 	tauleap
 

Modified: ecell3/branches/ecell-3.1/ecell/pyecell/Makefile.am
===================================================================
--- ecell3/branches/ecell-3.1/ecell/pyecell/Makefile.am	2009-02-05 05:05:09 UTC (rev 3384)
+++ ecell3/branches/ecell-3.1/ecell/pyecell/Makefile.am	2009-02-05 05:33:51 UTC (rev 3385)
@@ -49,15 +49,15 @@
 	ecell/yacc.py \
 	ecell/_tableio.c \
 	ecell/README.TableIO \
-	ecell/SessionManager/__init__.py \
-	ecell/SessionManager/Globus4Proxy.py \
-	ecell/SessionManager/LocalProxy.py \
-	ecell/SessionManager/SessionManager.py \
-	ecell/SessionManager/Constants.py \
-	ecell/SessionManager/LSFProxy.py \
-	ecell/SessionManager/Util.py \
-	ecell/SessionManager/Globus2Proxy.py \
-	ecell/SessionManager/SGEProxy.py \
+	ecell/session_manager/Constants.py \
+	ecell/session_manager/Globus2Proxy.py \
+	ecell/session_manager/Globus4Proxy.py \
+	ecell/session_manager/LSFProxy.py \
+	ecell/session_manager/LocalProxy.py \
+	ecell/session_manager/SGEProxy.py \
+	ecell/session_manager/SessionManager.py \
+	ecell/session_manager/Util.py \
+	ecell/session_manager/__init__.py \
 	ecell/analysis/ControlCoefficient.py \
 	ecell/analysis/Elasticity.py \
 	ecell/analysis/Jacobian.py \


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3386] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2009-02-05 06:01:12

Revision: 3386
          http://ecell.svn.sourceforge.net/ecell/?rev=3386&view=rev
Author:   moriyoshi
Date:     2009-02-05 06:01:04 +0000 (Thu, 05 Feb 2009)

Log Message:
-----------
* Bump year.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
    ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp
    ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
    ecell3/branches/ecell-3.1/ecell/dm/ConstantFluxProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/DAEStepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/DAEStepper.hpp
    ecell3/branches/ecell-3.1/ecell/dm/DecayFluxProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/ESSYNSProcess.hpp
    ecell3/branches/ecell-3.1/ecell/dm/ESSYNSStepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/ESSYNSStepper.hpp
    ecell3/branches/ecell-3.1/ecell/dm/ExpressionAlgebraicProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/ExpressionAssignmentProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/ExpressionCompiler.hpp
    ecell3/branches/ecell-3.1/ecell/dm/ExpressionFluxProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/ExpressionProcessBase.hpp
    ecell3/branches/ecell-3.1/ecell/dm/FixedDAE1Stepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/FixedDAE1Stepper.hpp
    ecell3/branches/ecell-3.1/ecell/dm/FixedODE1Stepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/FixedODE1Stepper.hpp
    ecell3/branches/ecell-3.1/ecell/dm/FluxDistributionStepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/FluxDistributionStepper.hpp
    ecell3/branches/ecell-3.1/ecell/dm/GMAProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/GillespieProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/GillespieProcess.hpp
    ecell3/branches/ecell-3.1/ecell/dm/JITExpressionProcessBase.hpp
    ecell3/branches/ecell-3.1/ecell/dm/MassActionFluxProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/MichaelisUniUniFluxProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/ODE23Stepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/ODE23Stepper.hpp
    ecell3/branches/ecell-3.1/ecell/dm/ODE45Stepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/ODE45Stepper.hpp
    ecell3/branches/ecell-3.1/ecell/dm/ODEStepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/ODEStepper.hpp
    ecell3/branches/ecell-3.1/ecell/dm/PingPongBiBiFluxProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/PythonFluxProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/PythonFluxProcess.hpp
    ecell3/branches/ecell-3.1/ecell/dm/PythonProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/PythonProcess.hpp
    ecell3/branches/ecell-3.1/ecell/dm/PythonProcessBase.hpp
    ecell3/branches/ecell-3.1/ecell/dm/QuasiDynamicFluxProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/QuasiDynamicFluxProcess.hpp
    ecell3/branches/ecell-3.1/ecell/dm/SSystemProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/TauLeapProcess.cpp
    ecell3/branches/ecell-3.1/ecell/dm/TauLeapProcess.hpp
    ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.cpp
    ecell3/branches/ecell-3.1/ecell/dm/TauLeapStepper.hpp
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/AboutModelEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/AutoLayout.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/AutosaveWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Buffer.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/BufferFactory.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ClassEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ClassEditorWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ClassList.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ClassPropertyList.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Clipboard.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Command.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/CommandMultiplexer.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/CommandQueue.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ComplexLine.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ComplexShape.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Config.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ConfirmWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ConnectionObject.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ConnectionObjectEditorWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Constants.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/DMInfo.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/EditorObject.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/EntityCommand.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/EntityEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/EntityList.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/EntityListTab.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Error.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/FullIDBrowserWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/GraphicalUtils.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Layout.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/LayoutBuffer.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/LayoutBufferFactory.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/LayoutCommand.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/LayoutEml.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/LayoutManager.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/LayoutXML.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/LineDescriptor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/LinePropertyComponent.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/LinePropertyEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ListWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/MEMainWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/MEVariableReferenceEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ModelEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ModelStore.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/MultiLineEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/NestedListEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ObjectEditorWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/PackingStrategy.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/PathwayCanvas.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/PathwayEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/PopupMenu.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ProcessObject.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/PropertyEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/PropertyList.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ResizeableText.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/RunTester.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Runtime.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ShapeDescriptor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ShapePluginManager.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ShapePropertyComponent.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/StepperChooser.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/StepperCommand.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/StepperEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/StepperList.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/StepperTab.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/SystemObject.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/SystemTree.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/TextObject.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Utils.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/VariableObject.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/VariableReferenceEditorComponent.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/ViewComponent.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/Window.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/ecell/ui/model_editor/opengui.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/AminoAcidVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/AnionVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/CarbohydrateVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/CationVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/DNAVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/FattyAcidVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/IonVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/LipidVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/NucleotideVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/OtherProcessSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/ProcessSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/ProteinVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/RNAVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/RibozymeVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/SmallMolVariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/SystemSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/model-editor/plugins/VariableSD.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/AboutSessionMonitor.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/BoardWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/ConfirmWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/DataGenerator.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/EntityListWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/FullPNQueue.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/GtkSessionMonitor.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/InterfaceWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/LoggerFactory.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/LoggerWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/LoggingPolicy.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/MainWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/MessageWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/ModelWalker.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/OsogoPluginManager.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/OsogoPluginWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/OsogoUtil.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/OsogoWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/Plot.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/PluginInstanceSelection.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/PluginWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/StepperWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/VariableReferenceEditor.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/ViewWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/Window.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/config.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/main.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/opengui.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/plugins/BargraphWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/plugins/DigitalWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/plugins/PropertyWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/plugins/TracerWindow.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/plugins/VariableWindow.py
    ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/ContinuousProcess.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DataPoint.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DataPointVector.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DifferentialStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteEventStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteEventStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteTimeStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/DiscreteTimeStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/DynamicPriorityQueue.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Entity.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Entity.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/EntityType.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/EntityType.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/EventScheduler.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Exceptions.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Exceptions.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/FluxProcess.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/FullID.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/FullID.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Interpolant.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Interpolant.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Logger.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Logger.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/LoggerAdapter.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/LoggerAdapter.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/LoggerBroker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/LoggerBroker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/MethodProxy.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Model.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Model.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PassiveStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PassiveStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PhysicalLogger.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PhysicalLogger.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Polymorph.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Polymorph.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Process.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Process.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/ProcessEvent.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/ProcessMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/ProcessMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedClass.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedObjectMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertiedObjectMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertyInterface.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertyInterface.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlot.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlot.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxy.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxy.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/PropertySlotProxyLoggerAdapter.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Stepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Stepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/StepperEvent.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/StepperMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/StepperMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/System.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/System.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/SystemMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/SystemMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/SystemStepper.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/SystemStepper.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/Util.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Util.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/VVector.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/VVector.h
    ecell3/branches/ecell-3.1/ecell/libecs/Variable.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/Variable.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/VariableMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/VariableMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/VariableReference.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/VariableReference.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/convertTo.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/libecs.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/libecs.hpp
    ecell3/branches/ecell-3.1/ecell/libecs/osif.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/osif.h
    ecell3/branches/ecell-3.1/ecell/libecs/tests/DataPointAggregator_test.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/tests/DynamicPriorityQueue_test.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/tests/FullID_test.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/tests/Util_test.cpp
    ecell3/branches/ecell-3.1/ecell/libecs/tests/VVector_test.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/LocalSimulatorImplementation.hpp
    ecell3/branches/ecell-3.1/ecell/libemc/Simulator.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/Simulator.hpp
    ecell3/branches/ecell-3.1/ecell/libemc/SimulatorImplementation.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/SimulatorImplementation.hpp
    ecell3/branches/ecell-3.1/ecell/libemc/SimulatorMaker.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/SimulatorMaker.hpp
    ecell3/branches/ecell-3.1/ecell/libemc/libemc.cpp
    ecell3/branches/ecell-3.1/ecell/libemc/libemc.hpp
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/DataFile.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/DataFileManager.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/ECDDataFile.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/EntityStub.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/FullID.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/LoggerStub.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/ObjectStub.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/Plugin.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/RecordingSimulator.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/SbmlFunctions.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/Session.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/StepperStub.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/__init__.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/_ecs.cpp
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/ControlCoefficient.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/Elasticity.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/Jacobian.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/MatrixIO.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/PathwayProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/SBMLExporter.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/SBMLImporter.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/Structure.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/__init__.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/ecdsupport.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/emlsupport.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/emlsupport2.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/sbmlsupport.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/util.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/convertEML2SBML.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/convertSBML2EML.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/convertSBMLFunctions.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/ecs.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/ecs_constants.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/ecssupport.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/emc.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/eml.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/emlextab.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/emparser.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/emparsetab.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/expressionlextab.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/expressionparser.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/util.py
    ecell3/branches/ecell-3.1/osdep/win32/errno.h
    ecell3/branches/ecell-3.1/osdep/win32/io_compat.c
    ecell3/branches/ecell-3.1/osdep/win32/mman.h
    ecell3/branches/ecell-3.1/osdep/win32/mman_compat.c
    ecell3/branches/ecell-3.1/osdep/win32/private.h
    ecell3/branches/ecell-3.1/osdep/win32/traits.h
    ecell3/branches/ecell-3.1/osdep/win32/unistd.h
    ecell3/branches/ecell-3.1/osdep/win32/utils.c
    ecell3/branches/ecell-3.1/osdep/win32/win32_dl_compat.h
    ecell3/branches/ecell-3.1/osdep/win32/win32_io_compat.h
    ecell3/branches/ecell-3.1/osdep/win32/win32_mman_compat.h
    ecell3/branches/ecell-3.1/osdep/win32/win32_utils.h

Modified: ecell3/branches/ecell-3.1/dmtool/DMObject.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DMObject.hpp	2009-02-05 05:33:51 UTC (rev 3385)
+++ ecell3/branches/ecell-3.1/dmtool/DMObject.hpp	2009-02-05 06:01:04 UTC (rev 3386)
@@ -2,7 +2,7 @@
 //
 //       This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 1996-2009 Keio University
 //       Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp	2009-02-05 05:33:51 UTC (rev 3385)
+++ ecell3/branches/ecell-3.1/dmtool/DynamicModule.hpp	2009-02-05 06:01:04 UTC (rev 3386)
@@ -2,7 +2,7 @@
 //
 //       This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 1996-2009 Keio University
 //       Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp
===================================================================
--- ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp	2009-02-05 05:33:51 UTC (rev 3385)
+++ ecell3/branches/ecell-3.1/dmtool/ModuleMaker.hpp	2009-02-05 06:01:04 UTC (rev 3386)
@@ -2,7 +2,7 @@
 //
 //       This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 1996-2009 Keio University
 //       Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/ecell/dm/ConstantFluxProcess.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/dm/ConstantFluxProcess.cpp	2009-02-05 05:33:51 UTC (rev 3385)
+++ ecell3/branches/ecell-3.1/ecell/dm/ConstantFluxProcess.cpp	2009-02-05 06:01:04 UTC (rev 3386)
@@ -2,7 +2,7 @@
 //
 //       This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 1996-2009 Keio University
 //       Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/ecell/dm/DAEStepper.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/dm/DAEStepper.cpp	2009-02-05 05:33:51 UTC (rev 3385)
+++ ecell3/branches/ecell-3.1/ecell/dm/DAEStepper.cpp	2009-02-05 06:01:04 UTC (rev 3386)
@@ -2,7 +2,7 @@
 //
 //       This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 1996-2009 Keio University
 //       Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/ecell/dm/DAEStepper.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/dm/DAEStepper.hpp	2009-02-05 05:33:51 UTC (rev 3385)
+++ ecell3/branches/ecell-3.1/ecell/dm/DAEStepper.hpp	2009-02-05 06:01:04 UTC (rev 3386)
@@ -2,7 +2,7 @@
 //
 //       This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 1996-2009 Keio University
 //       Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/ecell/dm/DecayFluxProcess.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/dm/DecayFluxProcess.cpp	2009-02-05 05:33:51 UTC (rev 3385)
+++ ecell3/branches/ecell-3.1/ecell/dm/DecayFluxProcess.cpp	2009-02-05 06:01:04 UTC (rev 3386)
@@ -2,7 +2,7 @@
 //
 //       This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 1996-2009 Keio University
 //       Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/ecell/dm/ESSYNSProcess.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/dm/ESSYNSProcess.hpp	2009-02-05 05:33:51 UTC (rev 3385)
+++ ecell3/branches/ecell-3.1/ecell/dm/ESSYNSProcess.hpp	2009-02-05 06:01:04 UTC (rev 3386)
@@ -2,7 +2,7 @@
 //
 //       This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 1996-2009 Keio University
 //       Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/ecell/dm/ESSYNSStepper.cpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/dm/ESSYNSStepper.cpp	2009-02-05 05:33:51 UTC (rev 3385)
+++ ecell3/branches/ecell-3.1/ecell/dm/ESSYNSStepper.cpp	2009-02-05 06:01:04 UTC (rev 3386)
@@ -2,7 +2,7 @@
 //
 //       This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 1996-2009 Keio University
 //       Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell3/branches/ecell-3.1/ecell/dm/ESSYNSStepper.hpp
===================================================================
--- ecell3/branches/ecell-3.1/ecell/dm/ESSYNSStepper.hpp	2009-02-05 05:33:51 UTC (rev 3385)
+++ ecell3/branches/ecell-3.1/ecell/dm/ESSYNSStepper.hpp	2009-02-05 06:01:04 UTC (rev 3386)
@@ -2,7 +2,7 @@
 //
 //       This file is part of the E-Cell System
 //
-//       Copyright (C) 1996-2008 Keio University
+//       Copyright (C) 1996-2009 Keio University
 //       Copyright (C) 2005-2008 The Molecular Sciences Institute
 //
 //::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Modified: ecell...
 
[truncated message content]

[Ecell-cvs] SF.net SVN: ecell:[3394] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2009-02-06 03:00:43

Revision: 3394
          http://ecell.svn.sourceforge.net/ecell/?rev=3394&view=rev
Author:   moriyoshi
Date:     2009-02-06 03:00:39 +0000 (Fri, 06 Feb 2009)

Log Message:
-----------
* RC2

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/NEWS
    ecell3/branches/ecell-3.1/ecell_version.sh

Modified: ecell3/branches/ecell-3.1/NEWS
===================================================================
--- ecell3/branches/ecell-3.1/NEWS	2009-02-06 02:59:21 UTC (rev 3393)
+++ ecell3/branches/ecell-3.1/NEWS	2009-02-06 03:00:39 UTC (rev 3394)
@@ -1,3 +1,10 @@
+ecell-3.1.107RC2: 6-Feb-2009
+
+ * Fixed a bug in ecell.Session.saveLoggerData().
+
+ * Fixed a bug in ecell.ECDDataFile.
+
+
 ecell-3.1.107RC1: 5-Feb-2009
 
  * Fixed compilation problem on newer GCC (>= 4.3).

Modified: ecell3/branches/ecell-3.1/ecell_version.sh
===================================================================
--- ecell3/branches/ecell-3.1/ecell_version.sh	2009-02-06 02:59:21 UTC (rev 3393)
+++ ecell3/branches/ecell-3.1/ecell_version.sh	2009-02-06 03:00:39 UTC (rev 3394)
@@ -1,6 +1,6 @@
 ECELL_MAJOR_VERSION=3
 ECELL_MINOR_VERSION=1
 ECELL_MICRO_VERSION=107
-ECELL_PACKAGE_REVISION=rc1
+ECELL_PACKAGE_REVISION=rc2
 ECELL_VERSION_NUMBER=${ECELL_MAJOR_VERSION}.${ECELL_MINOR_VERSION}.${ECELL_MICRO_VERSION}${ECELL_PACKAGE_REVISION}
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Ecell-cvs] SF.net SVN: ecell:[3403] ecell3/branches/ecell-3.1

From: <mor...@us...> - 2009-02-11 05:50:55

Revision: 3403
          http://ecell.svn.sourceforge.net/ecell/?rev=3403&view=rev
Author:   moriyoshi
Date:     2009-02-11 05:50:49 +0000 (Wed, 11 Feb 2009)

Log Message:
-----------
* Eliminate usage of string module.

Modified Paths:
--------------
    ecell3/branches/ecell-3.1/doc/samples/ga/ga.py
    ecell3/branches/ecell-3.1/ecell/frontend/session-monitor/ecell/ui/osogo/MainWindow.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/Elasticity.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/PathwayProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/SBMLExporter.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/SBMLImporter.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/ecdsupport.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/emlsupport.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/sbmlsupport.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/analysis/util.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/emparser.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/expressionparser.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell/session_manager/LSFProxy.py
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-em2eml.in
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-eml2em.in
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-eml2sbml.in
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-sbml2eml.in
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-session-manager.in
    ecell3/branches/ecell-3.1/ecell/pyecell/ecell3-session.in

Modified: ecell3/branches/ecell-3.1/doc/samples/ga/ga.py
===================================================================
--- ecell3/branches/ecell-3.1/doc/samples/ga/ga.py	2009-02-11 04:39:44 UTC (rev 3402)
+++ ecell3/branches/ecell-3.1/doc/samples/ga/ga.py	2009-02-11 05:50:49 UTC (rev 3403)
@@ -1,6 +1,5 @@
 # a sample of Genetic Algorithm on SessionManager
 
-from string import *
 from ConfigParser import *
 import sys
 import shutil
@@ -41,2104 +40,2104 @@
 
 # ###################################################################################
 class RCGA:
-	'''Real Coded Genetic Algorithm 
-	'''
+    '''Real Coded Genetic Algorithm 
+    '''
 
-	# ------------------------------------------------------------------
-	def __init__(self, aSetting):
-		'''Constructor
-		aSetting   -- a Setting instance (Setting)
+    # ------------------------------------------------------------------
+    def __init__(self, aSetting):
+        '''Constructor
+        aSetting   -- a Setting instance (Setting)
 
-		'''
-		self.theSetting = aSetting
+        '''
+        self.theSetting = aSetting
 
-		# Initialize parameters
-		self.theCurrentGeneration = 0
-		self.theIndividualList = []
-		self.theErFileList = None
-		self.theEliteIndividual = None
-		self.theParameterMap = None
-		self.theMutationRatio = None
-		self.theEliteImprovedFlag = False
+        # Initialize parameters
+        self.theCurrentGeneration = 0
+        self.theIndividualList = []
+        self.theErFileList = None
+        self.theEliteIndividual = None
+        self.theParameterMap = None
+        self.theMutationRatio = None
+        self.theEliteImprovedFlag = False
 
-	# end of __init__
+    # end of __init__
 
 
 
-	# ------------------------------------------------------------------
-	def initialize( self ):
-		'''executs initizalize strategy of GA as bellow.
-		- initialize random generator
-		- sets up parameter
-		- generates population
-		- write gnuplot file
+    # ------------------------------------------------------------------
+    def initialize( self ):
+        '''executs initizalize strategy of GA as bellow.
+        - initialize random generator
+        - sets up parameter
+        - generates population
+        - write gnuplot file
 
-		Return None
-		'''
+        Return None
+        '''
 
-		print START_MESSAGE
+        print START_MESSAGE
 
-		# ----------------------------------------------------------
-		# initialize random generator
-		# ----------------------------------------------------------
-		
-		random.seed(self.theSetting['RANDOM SEED'] )
-		
-		# ----------------------------------------------------------
-		# sets up parameter
-		# ----------------------------------------------------------
-		self.theParameterMap = {}
-		for aParameterLine in self.theSetting['PARAMETER']:
-			anElementList = aParameterLine
-			aParameter = anElementList[0]
-			aMin = atof(anElementList[1])
-			aMax = atof(anElementList[2])
-			aType = anElementList[3]
-			if aType == 'int':
-				aMin = int(aMin)
-				aMax = int(aMax)
-			self.theParameterMap[aParameter] = [ aMin, aMax, aType ]
+        # ----------------------------------------------------------
+        # initialize random generator
+        # ----------------------------------------------------------
+        
+        random.seed(self.theSetting['RANDOM SEED'] )
+        
+        # ----------------------------------------------------------
+        # sets up parameter
+        # ----------------------------------------------------------
+        self.theParameterMap = {}
+        for aParameterLine in self.theSetting['PARAMETER']:
+            anElementList = aParameterLine
+            aParameter = anElementList[0]
+            aMin = float(anElementList[1])
+            aMax = float(anElementList[2])
+            aType = anElementList[3]
+            if aType == 'int':
+                aMin = int(aMin)
+                aMax = int(aMax)
+            self.theParameterMap[aParameter] = [ aMin, aMax, aType ]
 
 
-		# ----------------------------------------------------------
-		# generates population
-		# ----------------------------------------------------------
-		for anIndex in xrange(0,self.theSetting['POPULATION']):
+        # ----------------------------------------------------------
+        # generates population
+        # ----------------------------------------------------------
+        for anIndex in xrange(0,self.theSetting['POPULATION']):
 
-			aCode = RealCodedIndividual( self.theSetting ) 
-			self.theIndividualList.append( aCode )
+            aCode = RealCodedIndividual( self.theSetting ) 
+            self.theIndividualList.append( aCode )
 
-		# set parameter map
-		self.theIndividualList[0].setParameterMap( self.theParameterMap )
+        # set parameter map
+        self.theIndividualList[0].setParameterMap( self.theParameterMap )
 
-		# generate population
-		for anIndividual in self.theIndividualList:
-			anIndividual.constructRandomly()
+        # generate population
+        for anIndividual in self.theIndividualList:
+            anIndividual.constructRandomly()
 
-		# ----------------------------------------------------------
-		# resume 
-		# ----------------------------------------------------------
+        # ----------------------------------------------------------
+        # resume 
+        # ----------------------------------------------------------
 
-		# when resume file is specified, read resume file
-		if self.theSetting['RESUME FILE'] != None:
+        # when resume file is specified, read resume file
+        if self.theSetting['RESUME FILE'] != None:
 
-			sys.stdout.write( "Reading resume file ... %s\n" \
-			                   %self.theSetting['RESUME FILE'] )
+            sys.stdout.write( "Reading resume file ... %s\n" \
+                               %self.theSetting['RESUME FILE'] )
 
-			# read resume data
-			aGenoType = self.readResumeFile( self.theSetting['RESUME FILE'] )
+            # read resume data
+            aGenoType = self.readResumeFile( self.theSetting['RESUME FILE'] )
 
-			# set resume data to first individual
-			self.theIndividualList[0].setGenoType(aGenoType)
+            # set resume data to first individual
+            self.theIndividualList[0].setGenoType(aGenoType)
 
 
-		# ----------------------------------------------------------
-		# write gnuplot file
-		# ----------------------------------------------------------
-		# evaluate
-		aContents  = "set ylabel \"Evaluated Value\"\n"
-		aContents += "set xlabel \"Generation\"\n"
-		aContents += "plot \"%s\" with linespoints\n" \
-		              %self.theSetting['EVALUATED VALUE FILE']
-		aContents += "pause -1"
+        # ----------------------------------------------------------
+        # write gnuplot file
+        # ----------------------------------------------------------
+        # evaluate
+        aContents  = "set ylabel \"Evaluated Value\"\n"
+        aContents += "set xlabel \"Generation\"\n"
+        aContents += "plot \"%s\" with linespoints\n" \
+                      %self.theSetting['EVALUATED VALUE FILE']
+        aContents += "pause -1"
 
-		open(self.theSetting['EVALUATED VALUE GNUPLOT'],'w').write(aContents)
+        open(self.theSetting['EVALUATED VALUE GNUPLOT'],'w').write(aContents)
 
-		# mutation
-		aContents  = "set ylabel \"Mutation ratio %\"\n"
-		aContents += "set xlabel \"Generation\"\n"
-		aContents += "plot \"%s\" with linespoints\n" \
-		              %self.theSetting['MUTATION VALUE FILE']
-		aContents += "pause -1"
+        # mutation
+        aContents  = "set ylabel \"Mutation ratio %\"\n"
+        aContents += "set xlabel \"Generation\"\n"
+        aContents += "plot \"%s\" with linespoints\n" \
+                      %self.theSetting['MUTATION VALUE FILE']
+        aContents += "pause -1"
 
-		open(self.theSetting['MUTATION VALUE GNUPLOT'],'w').write(aContents)
+        open(self.theSetting['MUTATION VALUE GNUPLOT'],'w').write(aContents)
 
 
-	# ------------------------------------------------------------------
-	def readResumeFile( self, aFile ):
-		'''read resume file
-		Return resume data (dict)
+    # ------------------------------------------------------------------
+    def readResumeFile( self, aFile ):
+        '''read resume file
+        Return resume data (dict)
         key is parameter symbol
         value is parameter value
-		'''
+        '''
 
-		aGenoType = {}
-		aSearch = re.compile('^(\S)+\s+=\s+(\S+)')
+        aGenoType = {}
+        aSearch = re.compile('^(\S)+\s+=\s+(\S+)')
 
-		aCounter = 0
+        aCounter = 0
 
-		for aLine in open(aFile,'r').readlines():
+        for aLine in open(aFile,'r').readlines():
 
-			# delete comment after #
-			anIndex = find( aLine, '#' ) 
-			if anIndex != -1:
-				aLine = aLine[:anIndex]
+            # delete comment after #
+            anIndex = aLine.find( '#' ) 
+            if anIndex != -1:
+                aLine = aLine[:anIndex]
 
 
-			# get parameter symbol and value
-			aResult = aSearch.match(aLine)
-			if aResult != None:
-				aParam, anEqual, aValue = split( aResult.group() )
-				aValue = atof( aValue )
-				aMessage = " [%s] <--- [%s]\n" %(aParam,aValue)
-				sys.stdout.write(aMessage)
-				sys.stdout.flush()
+            # get parameter symbol and value
+            aResult = aSearch.match(aLine)
+            if aResult != None:
+                aParam, anEqual, aValue = aResult.group().split()
+                aValue = float( aValue )
+                aMessage = " [%s] <--- [%s]\n" %(aParam,aValue)
+                sys.stdout.write(aMessage)
+                sys.stdout.flush()
 
-			aCounter += 1
-			aGenoType[aParam] = aValue
+            aCounter += 1
+            aGenoType[aParam] = aValue
 
-		if aCounter != len(aGenoType):
-			aMessage = "%s : same parameter is found in resume input file.\n" %(ERROR)
-			sys.stdout.write(aMessage)
-			sys.stdout.flush()
-			sys.exit(RESUMEFILE_EXIT)
+        if aCounter != len(aGenoType):
+            aMessage = "%s : same parameter is found in resume input file.\n" %(ERROR)
+            sys.stdout.write(aMessage)
+            sys.stdout.flush()
+            sys.exit(RESUMEFILE_EXIT)
 
 
-		# validate resume file.
-		aParameterMap = {}
-		copy.deepcopy( Individual.theParameterMap, aParameterMap )
+        # validate resume file.
+        aParameterMap = {}
+        copy.deepcopy( Individual.theParameterMap, aParameterMap )
 
-		aKeyDict = copy.deepcopy( Individual.theParameterMap )
+        aKeyDict = copy.deepcopy( Individual.theParameterMap )
 
-		for aType in aGenoType.keys():
-			try:
-				del aKeyDict[aType]
-			except KeyError:
-				aMessage = "%s : %s no such parameter resume input file.\n" %(ERROR, aType)
-				sys.stdout.write(aMessage)
-				sys.stdout.flush()
-				sys.exit(RESUMEFILE_EXIT)
-		
+        for aType in aGenoType.keys():
+            try:
+                del aKeyDict[aType]
+            except KeyError:
+                aMessage = "%s : %s no such parameter resume input file.\n" %(ERROR, aType)
+                sys.stdout.write(aMessage)
+                sys.stdout.flush()
+                sys.exit(RESUMEFILE_EXIT)
+        
 
-		if len(aKeyDict)!=0:
-			aMessage = "%s : %s must be set in resume input file.\n" \
-			            %(ERROR, str(aKeyDict.keys()))
-			sys.stdout.write(aMessage)
-			sys.stdout.flush()
-			sys.exit(RESUMEFILE_EXIT)
+        if len(aKeyDict)!=0:
+            aMessage = "%s : %s must be set in resume input file.\n" \
+                        %(ERROR, str(aKeyDict.keys()))
+            sys.stdout.write(aMessage)
+            sys.stdout.flush()
+            sys.exit(RESUMEFILE_EXIT)
 
-		return aGenoType
+        return aGenoType
 
 
-	# ------------------------------------------------------------------
-	def run( self ):
-		'''run a main loop of estimation
-		Return : None
-		'''
+    # ------------------------------------------------------------------
+    def run( self ):
+        '''run a main loop of estimation
+        Return : None
+        '''
 
-		while(True):
+        while(True):
 
-			self.theCurrentGeneration += 1
-			self.__executeEvaluateStrategy()
-			self.__executeEliteStrategy()
+            self.theCurrentGeneration += 1
+            self.__executeEvaluateStrategy()
+            self.__executeEliteStrategy()
 
-			# clear all jobs
-			clearJob(jobid=-1)
+            # clear all jobs
+            clearJob(jobid=-1)
 
 
-			print "[%s]\t%s" %(self.theCurrentGeneration, \
-			       self.theEliteIndividual.getEvaluatedValue())
+            print "[%s]\t%s" %(self.theCurrentGeneration, \
+                   self.theEliteIndividual.getEvaluatedValue())
 
-			#if atoi(self.theSetiting['MAX GENERATION']) <= self.theCurrentGeneration:
-			if self.theSetting['MAX GENERATION'] <= self.theCurrentGeneration:
-				print "reached max generation"
-				break
+            #if int(self.theSetiting['MAX GENERATION']) <= self.theCurrentGeneration:
+            if self.theSetting['MAX GENERATION'] <= self.theCurrentGeneration:
+                print "reached max generation"
+                break
 
-			if self.theEliteIndividual.getEvaluatedValue() <= self.theSetting['FINISH CONDITION']:
-				print "fufilled finish condition"
-				break
+            if self.theEliteIndividual.getEvaluatedValue() <= self.theSetting['FINISH CONDITION']:
+                print "fufilled finish condition"
+                break
 
-			self.__executeSelectionStrategy()
-			self.__executeCrossoverStrategy()
-			self.__executeMutationStrategy()
+            self.__executeSelectionStrategy()
+            self.__executeCrossoverStrategy()
+            self.__executeMutationStrategy()
 
 
-	# ------------------------------------------------------------------
-	def report( self ):
-		'''Display the results of GA
+    # ------------------------------------------------------------------
+    def report( self ):
+        '''Display the results of GA
 
-		Return None
-		'''
+        Return None
+        '''
 
-		print "----------------------------------------"
-		print "|   Result                             |"
-		print "----------------------------------------"
-		sys.stdout.write( "%s" %self.theEliteIndividual )
+        print "----------------------------------------"
+        print "|   Result                             |"
+        print "----------------------------------------"
+        sys.stdout.write( "%s" %self.theEliteIndividual )
 
 
-	# ------------------------------------------------------------------
-	def __executeEvaluateStrategy( self ):
-		'''Execute evaluate strategy
+    # ------------------------------------------------------------------
+    def __executeEvaluateStrategy( self ):
+        '''Execute evaluate strategy
 
-		[1] Register ess files to SessionManager
-		[2] Run ess files using SessionManager
-		[3] Wait until all ess files finish
-		[4] Read evaluated values
+        [1] Register ess files to SessionManager
+        [2] Run ess files using SessionManager
+        [3] Wait until all ess files finish
+        [4] Read evaluated values
 
-		Return None
-		'''
+        Return None
+        '''
 
-		# -----------------------------------------------------
-		# [1] Register ess files to SessionManager
-		# -----------------------------------------------------
-		anIndex = 0
-		aParameterMapList = []
-		aValueList = []
+        # -----------------------------------------------------
+        # [1] Register ess files to SessionManager
+        # -----------------------------------------------------
+        anIndex = 0
+        aParameterMapList = []
+        aValueList = []
 
-		for anIndividual in self.theIndividualList:
+        for anIndividual in self.theIndividualList:
 
-			#aParameterMap = anIndividual.getGenoType()
+            #aParameterMap = anIndividual.getGenoType()
 
-			aJobIDList = []
+            aJobIDList = []
 
-			for anIndex in xrange(0, len(self.theSetting['EXTRA DIRS']) ):
+            for anIndex in xrange(0, len(self.theSetting['EXTRA DIRS']) ):
 
-				anEssFile = self.theSetting['ESS FILE']
-				anExtraFiles = [ self.theSetting['EXTRA DIRS'][anIndex],
-				                 self.theSetting['EML FILES'][anIndex] ]
+                anEssFile = self.theSetting['ESS FILE']
+                anExtraFiles = [ self.theSetting['EXTRA DIRS'][anIndex],
+                                 self.theSetting['EML FILES'][anIndex] ]
 
-				#if self.theCurrentGeneration == 1:
-				#	if self.theSetting['RESUME FILE'] != None:
+                #if self.theCurrentGeneration == 1:
+                #    if self.theSetting['RESUME FILE'] != None:
 
-				#sys.exit(0)
+                #sys.exit(0)
 
-				anArgument = {}
+                anArgument = {}
 
-				for aKey in anIndividual.getGenoType().keys():
-					anArgument[aKey] = anIndividual.getGenoType()[aKey]
+                for aKey in anIndividual.getGenoType().keys():
+                    anArgument[aKey] = anIndividual.getGenoType()[aKey]
 
-				#print anArgument
+                #print anArgument
 
-				anArgument[self.theSetting['EML KEY']] = self.theSetting['EML FILES'][anIndex]
-				anArgument[self.theSetting['DIR KEY']] = self.theSetting['EXTRA DIRS'][anIndex]
+                anArgument[self.theSetting['EML KEY']] = self.theSetting['EML FILES'][anIndex]
+                anArgument[self.theSetting['DIR KEY']] = self.theSetting['EXTRA DIRS'][anIndex]
 
-				aJobID = registerEcellSession( anEssFile, anArgument, anExtraFiles )
+                aJobID = registerEcellSession( anEssFile, anArgument, anExtraFiles )
 
-				aJobIDList.append( aJobID )
-				anIndividual.setJobIDList( aJobIDList )
+                aJobIDList.append( aJobID )
+                anIndividual.setJobIDList( aJobIDList )
 
 
-		aJobNumber = len(getQueuedJobList())
+        aJobNumber = len(getQueuedJobList())
 
-		# -----------------------------------------------------
-		# [2] Run ess files using SessionManager
-		# -----------------------------------------------------
-		run(block=False)
+        # -----------------------------------------------------
+        # [2] Run ess files using SessionManager
+        # -----------------------------------------------------
+        run(block=False)
 
-		# -----------------------------------------------------
-		# [3] Wait until all ess files finish
-		# -----------------------------------------------------
-		aLoopCounter = 0
+        # -----------------------------------------------------
+        # [3] Wait until all ess files finish
+        # -----------------------------------------------------
+        aLoopCounter = 0
 
-		while(True):
+        while(True):
 
-			update()
-			time.sleep(1)
+            update()
+            time.sleep(1)
 
-			sys.stdout.write("\r")
-			sys.stdout.write("(%s/%s)" %(len(getFinishedJobList()),aJobNumber))
+            sys.stdout.write("\r")
+            sys.stdout.write("(%s/%s)" %(len(getFinishedJobList()),aJobNumber))
 
-			if aLoopCounter % 6 == 1:
-				sys.stdout.write(" .    ")
-			elif aLoopCounter % 6 == 2:
-				sys.stdout.write(" ..   ")
-			elif aLoopCounter % 6 == 3: 
-				sys.stdout.write(" ...  ")
-			elif aLoopCounter % 6 == 4: 
-				sys.stdout.write(" .... ")
-			elif aLoopCounter % 6 == 5: 
-				sys.stdout.write(" .....")
-			else:
-				sys.stdout.write("      ")
+            if aLoopCounter % 6 == 1:
+                sys.stdout.write(" .    ")
+            elif aLoopCounter % 6 == 2:
+                sys.stdout.write(" ..   ")
+            elif aLoopCounter % 6 == 3: 
+                sys.stdout.write(" ...  ")
+            elif aLoopCounter % 6 == 4: 
+                sys.stdout.write(" .... ")
+            elif aLoopCounter % 6 == 5: 
+                sys.stdout.write(" .....")
+            else:
+                sys.stdout.write("      ")
 
-			sys.stdout.flush()
-			aLoopCounter += 1
+            sys.stdout.flush()
+            aLoopCounter += 1
 
-			if isFinished() == True:
-				sys.stdout.write("\r")
-				sys.stdout.write("(%s/%s)" %(len(getFinishedJobList()),aJobNumber))
-				sys.stdout.write(" .....")
-				break
+            if isFinished() == True:
+                sys.stdout.write("\r")
+                sys.stdout.write("(%s/%s)" %(len(getFinishedJobList()),aJobNumber))
+                sys.stdout.write(" .....")
+                break
 
 
-		# -----------------------------------------------------
-		# [4] Read evaluated values
-		# -----------------------------------------------------
-		for anIndividual in self.theIndividualList:
+        # -----------------------------------------------------
+        # [4] Read evaluated values
+        # -----------------------------------------------------
+        for anIndividual in self.theIndividualList:
 
-			anEvaluatedValue = 0
+            anEvaluatedValue = 0
 
-			for aJobID in anIndividual.getJobList():
+            for aJobID in anIndividual.getJobList():
 
-				#print aJobID
+                #print aJobID
 
-				#print getJobDirectory(aJobID)
-				aResultFile = "%s%sresult.dat" %(getJobDirectory(aJobID), os.sep)
+                #print getJobDirectory(aJobID)
+                aResultFile = "%s%sresult.dat" %(getJobDirectory(aJobID), os.sep)
 
-				if os.access(aResultFile,os.R_OK) == False:
-					sys.stdout.flush()
-					sys.stderr.write("\n%s: could not find %s. \n%s must write %s.\n" \
-					                 %(ERROR,
-					                   str(aResultFile),
-					                   getSessionProxy(aJobID).getScriptFileName(),
-					                   str(aResultFile)))
-					sys.stderr.write("see %s%s%s.\n" 
-					                 %(getJobDirectory(aJobID),
-					                   os.sep,
-					                   getStderrFileName()))
-					sys.stderr.write("If you set \'TMP REMOVABLE\' is True, change it to False and try again.\n")
-					sys.stderr.flush()
-					
-					sys.exit(SCRIPTFILE_EXIT)
-	
-				aResult = open( aResultFile, 'r').read()
-				aResult = atof(aResult)
-				anEvaluatedValue += aResult
+                if os.access(aResultFile,os.R_OK) == False:
+                    sys.stdout.flush()
+                    sys.stderr.write("\n%s: could not find %s. \n%s must write %s.\n" \
+                                     %(ERROR,
+                                       str(aResultFile),
+                                       getSessionProxy(aJobID).getScriptFileName(),
+                                       str(aResultFile)))
+                    sys.stderr.write("see %s%s%s.\n" 
+                                     %(getJobDirectory(aJobID),
+                                       os.sep,
+                                       getStderrFileName()))
+                    sys.stderr.write("If you set \'TMP REMOVABLE\' is True, change it to False and try again.\n")
+                    sys.stderr.flush()
+                    
+                    sys.exit(SCRIPTFILE_EXIT)
+    
+                aResult = open( aResultFile, 'r').read()
+                aResult = float(aResult)
+                anEvaluatedValue += aResult
 
-			anEvaluatedValue /= len(anIndividual.getJobList())
-			anIndividual.setEvaluatedValue(anEvaluatedValue)
+            anEvaluatedValue /= len(anIndividual.getJobList())
+            anIndividual.setEvaluatedValue(anEvaluatedValue)
 
 
-	# ------------------------------------------------------------------
-	def __executeEliteStrategy( self ):
-		'''Execute elite strategy
+    # ------------------------------------------------------------------
+    def __executeEliteStrategy( self ):
+        '''Execute elite strategy
 
-		[1] Find the inidividual who has best evaluated value as elite
-		[2] Save elite individual
-		Return None
-		'''
+        [1] Find the inidividual who has best evaluated value as elite
+        [2] Save elite individual
+        Return None
+        '''
 
 
-		# --------------------------------------------------------------
-		# [1] Find the inidividual who has best evaluated value as elite
-		# --------------------------------------------------------------
-		aValueList = []
-		for anIndividual in self.theIndividualList:
-			aValueList.append(anIndividual.getEvaluatedValue())
+        # --------------------------------------------------------------
+        # [1] Find the inidividual who has best evaluated value as elite
+        # --------------------------------------------------------------
+        aValueList = []
+        for anIndividual in self.theIndividualList:
+            aValueList.append(anIndividual.getEvaluatedValue())
 
 
-		self.theIndividualList.sort()
-		aMinValue = self.theIndividualList[0].getEvaluatedValue()
+        self.theIndividualList.sort()
+        aMinValue = self.theIndividualList[0].getEvaluatedValue()
 
-		aMinIndex = 0
-		for aValue in aValueList:
-			if aValue == aMinValue:
-				break
-			else:
-				pass
-			aMinIndex += 1
+        aMinIndex = 0
+        for aValue in aValueList:
+            if aValue == aMinValue:
+                break
+            else:
+                pass
+            aMinIndex += 1
 
 
-		# --------------------------------------------------------------
-		# [2] Save elite individual
-		# --------------------------------------------------------------
-		# First generation,
-		if type(self.theEliteIndividual) == type(None):
+        # --------------------------------------------------------------
+        # [2] Save elite individual
+        # --------------------------------------------------------------
+        # First generation,
+        if type(self.theEliteIndividual) == type(None):
 
-			# -----------------------------------------------------
-			# save elite individual
-			# -----------------------------------------------------
-			self.theEliteIndividual = copy.deepcopy( self.theIndividualList[0] )
-			self.theEliteImprovedFlag = True
+            # -----------------------------------------------------
+            # save elite individual
+            # -----------------------------------------------------
+            self.theEliteIndividual = copy.deepcopy( self.theIndividualList[0] )
+            self.theEliteImprovedFlag = True
 
 
-			# -----------------------------------------------------
-			# copy the directories related to elite individual
-			# -----------------------------------------------------
-			for aJobID in self.theEliteIndividual.getJobList():
-				aSrcDir = getSessionProxy(aJobID).getJobDirectory()
+            # -----------------------------------------------------
+            # copy the directories related to elite individual
+            # -----------------------------------------------------
+            for aJobID in self.theEliteIndividual.getJobList():
+                aSrcDir = getSessionProxy(aJobID).getJobDirectory()
 
-				aDstDir = "%s%s%s" %(self.theSetting['ELITE DIR'],\
-				                     os.sep,\
-				                     os.path.basename(aSrcDir[:-len(os.sep)]))
-				shutil.copytree(aSrcDir,aDstDir)
+                aDstDir = "%s%s%s" %(self.theSetting['ELITE DIR'],\
+                                     os.sep,\
+                                     os.path.basename(aSrcDir[:-len(os.sep)]))
+                shutil.copytree(aSrcDir,aDstDir)
 
-		# Second generation or after
-		else:
+        # Second generation or after
+        else:
 
-			# -----------------------------------------------------
-			# When the best individual is better than the elite,
-			# save best evaluation value as the elite's value
-			# -----------------------------------------------------
-			if self.theIndividualList[0] < self.theEliteIndividual:
+            # -----------------------------------------------------
+            # When the best individual is better than the elite,
+            # save best evaluation value as the elite's value
+            # -----------------------------------------------------
+            if self.theIndividualList[0] < self.theEliteIndividual:
 
-				# ---------------------
-				# save elite individual
-				# ---------------------
-				self.theEliteIndividual = copy.deepcopy( self.theIndividualList[0] )
-				self.theEliteImprovedFlag = True
+                # ---------------------
+                # save elite individual
+                # ---------------------
+                self.theEliteIndividual = copy.deepcopy( self.theIndividualList[0] )
+                self.theEliteImprovedFlag = True
 
-				# ---------------------
-				# delete elite directory
-				# ---------------------
-				#print os.listdir(self.theSetting['ELITE DIR'])
-				for aDir in os.listdir(self.theSetting['ELITE DIR']):
-					if aDir == '.' or aDir == '..':
-						continue
-					aDir = "%s%s%s" %(self.theSetting['ELITE DIR'],
-					                  os.sep,
-					                  aDir)
-					shutil.rmtree(aDir)
+                # ---------------------
+...
 
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