Forums

For those of you unable to attend the hackathon you might be interested
to know that we have prepared a new distribution of libSBML 3.0.0 which
we are calling the "libSBML 3.0.0 Prerelease" because it is
so very nearly done, but with the Hackathon in a few days it
seems more sensible to let Hackathon people try it first
before calling it "libSBML 3.0.0 final".

This release supports the final release candidate of the
SBML Level 2 Version 3 R1 specification. In addition, among
the updates since the libSBML beta_2 release are the
following new features:

- Java, Perl and Python bindings now available (thanks Akiya!)

- Matlab binding is now available.

- Extensive code documentation and API manuals for C++ and
Java, with more coming soon.
(These will be available as direct links from the Hackathon Wiki page
http://sbml.org/wiki/Hackathon_2007 and as a separate download
shortly.)

- Many problems caught and fixed.

We've tested this on a variety of platforms, and with the
following XML parser libraries. You will need one of these
with at least the version listed:

* Expat 1.95.8
* Xerces 2.3 - 2.7 (note: 2.6 does NOT work)
* libxml2 2.6.27

The main uncertainty at this point is the SBML L2v3
specification itself. We want to issue libSBML 3.0.0 so
that it supports the specification, so are holding off the
final release pending final discussions at the Hackathon.

If you try it and want to report issues, the best way may be
to use the SourceForge bug tracking page for libSBML at

http://sourceforge.net/tracker/?group_id=71971&atid=942737

Please use the "libSBML 3.0.0 Prerelease" group for reports
dealing with this release.



Sarah Keating, Mike Hucka, Akiya Jouraku

------------------------------------------------------------




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Hello

Based on some experimental "hacking" I did last week in Newcastle, I
think the libsbml bindings currently only work for Python version 2.3
(which comes bundled with Mac OSX), not more recent versions (2.4 and 2.5).

I can provide more details if required...

This is not an urgent bug (I can revert to an older version of python),
but it would be nice to have it sorted in the future.

Thanks

Duncan

--
Duncan Hull
http://www.cs.man.ac.uk/~hulld/
+44 (0) 161 306 5139

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Dear All,

I'm using the python bindings of libsbml with no problem via Python
2.5.1 (Ubuntu 7.04)

However, I am using expat instead of xerces.

Colin

Akiya Jouraku wrote:
> Hello Duncan,
>
> Thank you for reporting the bug!
>
> Actually, I've tested only Python version 2.3.5 (OS bundled) in python
> binding for MacOSX.
> (In Linux (Fedora Core 4,5), python version 2.4 works fine.)
>
> Could you send me detailed information about the bug?
> I'll try to fix the bug.
>
> Thanks in advance,
>
> --
> Akiya Jouraku
> jouraku@symbio.jst.go.jp
>
> Duncan Hull <duncan.hull@cs.man.ac.uk> wrote
> $B!?!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1(B
>
>> Hello
>>
>> Based on some experimental "hacking" I did last week in Newcastle, I
>> think the libsbml bindings currently only work for Python version 2.3
>> (which comes bundled with Mac OSX), not more recent versions (2.4 and 2.5).
>>
>> I can provide more details if required...
>>
>> This is not an urgent bug (I can revert to an older version of python),
>> but it would be nice to have it sorted in the future.
>>
>> Thanks
>>
>> Duncan
>>
>> --
>> Duncan Hull
>> http://www.cs.man.ac.uk/~hulld/
>> +44 (0) 161 306 5139
>>
>> ____________________________________________________________
>> To manage your libsbml-discuss list subscription, visit
>> https://utils.its.caltech.edu/mailman/listinfo/libsbml-discuss
>>
>> For a web interface to the libsbml-discuss mailing list, visit
>> http://sbml.org/forums/
>>
>> For questions or feedback about the libsbml-discuss list,
>> contact sbml-team@caltech.edu.
>>
>>
> ____________________________________________________________
> To manage your libsbml-discuss list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/libsbml-discuss
>
> For a web interface to the libsbml-discuss mailing list, visit
> http://sbml.org/forums/
>
> For questions or feedback about the libsbml-discuss list,
> contact sbml-team@caltech.edu.
>
>

--
Dr Colin Gillespie
http://www.mas.ncl.ac.uk/~ncsg3/

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Hello Akiya

Akiya Jouraku wrote:
> I found that the python binding in libsbml 3.0.0 pre-release can't
> be built with Python 2.4 and 2.5 (non-system-installed Python) on
> Mac OS X (10.3 or later) due to Mac OS X specific linker problem.
> So I fixed the bug in the current CVS HEAD source.
> The fix will be included in upcoming libsbml 3.0.0 release.
>

Thanks for fixing this.

I was just getting around to digging out the bug details for you... but
it looks like you got there first!

I'll download the 3.0.0 when its out and let you know if there are any
more bugs.

Duncan

--
Duncan Hull
http://www.cs.man.ac.uk/~hulld/
+44 (0) 161 306 5139

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Hello Duncan,

I've attached a patch file for fixing the build errors of
python binding with non-system-installed python (MacPython 2.4
and 2.5. (Fink Python worked with/without this patch in my Mac
OS 10.4.9/Intel)) in libsbml 3.0.0-pre.

If you have time, could you try the patch and send me the result?
The patch can be applied as follows:

% cd /path/to/libsbml-3.0.0
% patch -p1 < /path/to/patch-libsbml3pre-macosx_python_binding

After applying the patch, please run configure with your arguments
and make.

Thanks

Akiya

Duncan Hull <duncan.hull@cs.man.ac.uk> wrote
> Hello Akiya
>
> Akiya Jouraku wrote:
> > I found that the python binding in libsbml 3.0.0 pre-release can't
> > be built with Python 2.4 and 2.5 (non-system-installed Python) on
> > Mac OS X (10.3 or later) due to Mac OS X specific linker problem.
> > So I fixed the bug in the current CVS HEAD source.
> > The fix will be included in upcoming libsbml 3.0.0 release.
> >
>
> Thanks for fixing this.
>
> I was just getting around to digging out the bug details for you... but
> it looks like you got there first!
>
> I'll download the 3.0.0 when its out and let you know if there are any
> more bugs.
>
> Duncan
>
> --
> Duncan Hull
> http://www.cs.man.ac.uk/~hulld/
> +44 (0) 161 306 5139
>
> ____________________________________________________________
> To manage your libsbml-discuss list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/libsbml-discuss
>
> For a web interface to the libsbml-discuss mailing list, visit
> http://sbml.org/forums/
>
> For questions or feedback about the libsbml-discuss list,
> contact sbml-team@caltech.edu.
>

Hello Duncan,

Thank you for your detail information.

As written in your build log, the error of distutils is due to the
mismatch between MACOSX_DEPLOYMENT_TARGET value of python (written to a
python's configuration file when python was built) and that of environment
value (I added) at libsbml's install-time.

So I've fixed the mismatch bug which could happen at install-time
on MacOSX and attached updated patch-file.

Could you try updated patch-file again, if you have time?

Thanks again.

--
Akiya Jouraku

Duncan Hull <duncan.hull@cs.man.ac.uk> wrote
$B!?!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1(B
> Hello Akiya
>
> Akiya Jouraku wrote:
> > I've attached a patch file for fixing the build errors of
> > python binding with non-system-installed python (MacPython 2.4
> > and 2.5. (Fink Python worked with/without this patch in my Mac
> > OS 10.4.9/Intel)) in libsbml 3.0.0-pre.
> >
> > If you have time, could you try the patch and send me the result?
> >
>
> It didn't quite work, maybe something to do with
>
> $MACOSX_DEPLOYMENT_TARGET mismatch: now "10.4" but "10.3" during configure
>
> more details at:
>
> http://www.cs.man.ac.uk/~hulld/macosx_libsbml_300.html
>
> Duncan
>
> --
> Duncan Hull
> http://www.cs.man.ac.uk/~hulld/
> +44 (0) 161 306 5139
>
> ____________________________________________________________
> To manage your libsbml-discuss list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/libsbml-discuss
>
> For a web interface to the libsbml-discuss mailing list, visit
> http://sbml.org/forums/
>
> For questions or feedback about the libsbml-discuss list,
> contact sbml-team@caltech.edu.
>

Hello Duncan,

Duncan Hull <duncan.hull@cs.man.ac.uk> wrote
$B!?!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1!1(B
> I get an run time error now instead :) when I call libsbml from a python
> script using
>
> import libsml
>
> Fatal Python Error: Interpreter not initialized (version mismatch?)

Could you check two environment variables PYTHONPATH and DYLD_LIBRARY_PATH?
The environment variables might be set so that old libsbml python libraries
are searched before those of libsbml-3.0.0pre with your python2.4.

Thanks,

--
Akiya Jouraku
jouraku@symbio.jst.go.jp




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Hi Max,

Thank you for your report!

(Sorry, I forgot to send previous email to libsbml-discuss).

--
Akiya Jouraku

Max Flöttmann <max.floettmann@gmail.com> wrote
> Hello Akiya,
> thank you so much! Everything is working perfectly now!
>
> Here is some system information:
> MacBook 2.16ghz
> Mac OS 10.4.9
> Python 2.5.1(installed with the .pkg file from python.org)
>
> Thanks again!
>
> Max
>
>
> Am 21.06.2007 um 18:35 schrieb Akiya Jouraku:
>
> > Hello Max,
> >
> > Thank you for your report!
> >
> > I've attached the patch file in this mail.
> > The patch can be applied as follows:
> >
> > % cd /path/to/libsbml-3.0.0
> > % patch -p1 < /path/to/patch-libsbml3pre-macosx_python_binding2
> >
> > After applying the patch, please run configure with your arguments
> > and make.
> >
> > If you have time, please let me know your environment (OS, python
> > version) and the results.
> >
> > Thanks,
> >
> > Akiya
> >
> > floettmann <max.floettmann@gmail.com> wrote
> > ／￣￣￣￣￣￣￣￣￣￣￣￣￣￣￣￣￣￣￣￣￣
> > ￣￣
> >>
> >> Hello Akiya,
> >> I don't know why, but I can't see or download the attached file.
> >> Could you please send it to me, because I have exactly the same
> >> Problem.
> >> Thanks,
> >>
> >>
> >> Max Flöttmann
> >> ____________________________________________________________
> >> To manage your libsbml-discuss list subscription, visit
> >> https://utils.its.caltech.edu/mailman/listinfo/libsbml-discuss
> >>
> >> For a web interface to the libsbml-discuss mailing list, visit
> >> http://sbml.org/forums/
> >>
> >> For questions or feedback about the libsbml-discuss list,
> >> contact sbml-team@caltech.edu.
> >>
> > diff -cr libsbml-3.0.0.old/config/python.m4 libsbml-3.0.0/config/
> > python.m4
> > *** libsbml-3.0.0.old/config/python.m4 2005-09-30
> > 08:55:12.000000000 +0900
> > --- libsbml-3.0.0/config/python.m4 2007-06-18 22:37:59.000000000 +0900
> > ***************
> > *** 4,10 ****
> > dnl Author(s) : SBML Team <sbml-team@caltech.edu>
> > dnl Organization: California Institute of Technology
> > dnl Created : 2004-06-18
> > ! dnl Revision : $Id: python.m4,v 1.10 2005/09/29 23:55:12
> > mhucka Exp $
> > dnl Source : $Source: /cvsroot/sbml/libsbml/config/
> > python.m4,v $
> > dnl
> > dnl Portions of this code originally came from the aclocal 1.7
> > --- 4,10 ----
> > dnl Author(s) : SBML Team <sbml-team@caltech.edu>
> > dnl Organization: California Institute of Technology
> > dnl Created : 2004-06-18
> > ! dnl Revision : $Id: python.m4,v 1.11 2007/06/18 10:00:01
> > ajouraku Exp $
> > dnl Source : $Source: /cvsroot/sbml/libsbml/config/
> > python.m4,v $
> > dnl
> > dnl Portions of this code originally came from the aclocal 1.7
> > ***************
> > *** 91,104 ****
> > dnl it's either the Fink version or something else, and don't use
> > dnl -framework.
> >
> > ! if test `expr "${PYTHON_PREFIX}" ':' '.*/System/Library/
> > Frameworks/.*'` -ne 0; then
> > ! dnl MacOSX-installed version of Python (we hope).
> > PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
> > ! PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload -framework Python"
> > else
> > ! dnl Fink-installed version of Python, or something else.
> > ! PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
> > ! PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload -bundle_loader ${PYTHON}"
> > fi
> > CONFIG_ADD_LDPATH(${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload)
> > ;;
> > --- 91,117 ----
> > dnl it's either the Fink version or something else, and don't use
> > dnl -framework.
> >
> > ! macosx_version=`sw_vers -productVersion | cut -d"." -f1,2`
> > ! if test ${macosx_version} '>' 10.2; then
> > ! dnl According to configure.in of Python source code, -
> > undefined dynamic_lookup
> > ! dnl should be used for 10.3 or later. Actually, the option is
> > needed to avoid
> > ! dnl undefined symbols error when building a Python binding
> > library with non-system-installed
> > ! dnl Python on 10.3 or later.
> > ! dnl Also, according to the man page of ld, environment
> > variable MACOSX_DEPLOYMENT_TARGET
> > ! dnl must be set to 10.3 or higher to use -undefined
> > dynamic_lookup.
> > ! dnl Currently, the environment variables is set in src/binding/
> > python/Makefile.in.
> > PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
> > ! PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload -undefined dynamic_lookup"
> > else
> > ! if test `expr "${PYTHON_PREFIX}" ':' '.*/System/Library/
> > Frameworks/.*'` -ne 0; then
> > ! dnl MacOSX-installed version of Python (we hope).
> > ! PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
> > ! PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload -F/System/Library/Frameworks -framework Python"
> > ! else
> > ! dnl Fink-installed version of Python, or something else.
> > ! PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
> > ! PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload -bundle_loader ${PYTHON}"
> > ! fi
> > fi
> > CONFIG_ADD_LDPATH(${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload)
> > ;;
> > diff -cr libsbml-3.0.0.old/configure libsbml-3.0.0/configure
> > *** libsbml-3.0.0.old/configure 2007-06-05 18:39:16.000000000 +0900
> > --- libsbml-3.0.0/configure 2007-06-18 22:37:54.000000000 +0900
> > ***************
> > *** 1,5 ****
> > #! /bin/sh
> > ! # From configure.ac Revision: 1.66 .
> > # Guess values for system-dependent variables and create Makefiles.
> > # Generated by GNU Autoconf 2.59 for libSBML 3.0.0.
> > #
> > --- 1,5 ----
> > #! /bin/sh
> > ! # From configure.ac Revision: 1.67 .
> > # Guess values for system-dependent variables and create Makefiles.
> > # Generated by GNU Autoconf 2.59 for libSBML 3.0.0.
> > #
> > ***************
> > *** 3674,3685 ****
> > case $host in
> > *darwin*)
> >
> > ! if test `expr "${PYTHON_PREFIX}" ':' '.*/System/Library/
> > Frameworks/.*'` -ne 0; then
> > ! PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
> > ! PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload -framework Python"
> > else
> > ! PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/${PYTHON_NAME}"
> > ! PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload -bundle_loader ${PYTHON}"
> > fi
> >
> > RUN_LDPATH="$RUN_LDPATH:${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload"
> > --- 3674,3691 ----
> > case $host in
> > *darwin*)
> >
> > ! macosx_version=`sw_vers -productVersion | cut -d"." -f1,2`
> > ! if test ${macosx_version} '>' 10.2; then
> > ! PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/
> > include/${PYTHON_NAME}"
> > ! PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload -undefined dynamic_lookup"
> > else
> > ! if test `expr "${PYTHON_PREFIX}" ':' '.*/System/Library/
> > Frameworks/.*'` -ne 0; then
> > ! PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/$
> > {PYTHON_NAME}"
> > ! PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload -F/System/Library/Frameworks -framework Python"
> > ! else
> > ! PYTHON_CPPFLAGS="-I${PYTHON_PREFIX}/include/$
> > {PYTHON_NAME}"
> > ! PYTHON_LDFLAGS="-L${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload -bundle_loader ${PYTHON}"
> > ! fi
> > fi
> >
> > RUN_LDPATH="$RUN_LDPATH:${PYTHON_PREFIX}/lib/${PYTHON_NAME}/lib-
> > dynload"
> > ***************
> > *** 4648,4654 ****
> > else
> > ac_cv_FUNC_LISPEXIT=no-exit
> > for ex in "sb-ext:quit :unix-status" "lisp:exit" "excl:exit"
> > "sys:exit" "ext:quit" "unix:unix-exit" "no-exit" ; do
> > ! echo "configure:4651 trying $ex ..." >&5
> > echo "(ignore-errors ($ex 127))"|$LISP 2>&5 1>&5
> > if test "$?" = "127" ; then
> > ac_cv_FUNC_LISPEXIT=$ex
> > --- 4654,4660 ----
> > else
> > ac_cv_FUNC_LISPEXIT=no-exit
> > for ex in "sb-ext:quit :unix-status" "lisp:exit" "excl:exit"
> > "sys:exit" "ext:quit" "unix:unix-exit" "no-exit" ; do
> > ! echo "configure:4657 trying $ex ..." >&5
> > echo "(ignore-errors ($ex 127))"|$LISP 2>&5 1>&5
> > if test "$?" = "127" ; then
> > ac_cv_FUNC_LISPEXIT=$ex
> > diff -cr libsbml-3.0.0.old/src/bindings/python/Makefile.in
> > libsbml-3.0.0/src/bindings/python/Makefile.in
> > *** libsbml-3.0.0.old/src/bindings/python/Makefile.in 2007-06-05
> > 19:07:03.000000000 +0900
> > --- libsbml-3.0.0/src/bindings/python/Makefile.in 2007-06-20
> > 03:05:51.000000000 +0900
> > ***************
> > *** 4,10 ****
> > ## \brief Makefile template for libsbml Python bindings
> > ## \author Mike Hucka
> > ##
> > ! ## $Id: Makefile.in,v 1.19 2007/06/05 08:32:42 mhucka Exp $
> > ## $Source: /cvsroot/sbml/libsbml/src/bindings/python/
> > Makefile.in,v $
> > ##
> >
> > --- 4,10 ----
> > ## \brief Makefile template for libsbml Python bindings
> > ## \author Mike Hucka
> > ##
> > ! ## $Id: Makefile.in,v 1.21 2007/06/18 10:12:20 ajouraku Exp $
> > ## $Source: /cvsroot/sbml/libsbml/src/bindings/python/
> > Makefile.in,v $
> > ##
> >
> > ***************
> > *** 79,84 ****
> > --- 79,88 ----
> > ifeq "$(HOST_TYPE)" "darwin"
> > # MacOS X note: this MUST remain .so even though we use .dylib
> > for libsbml.
> > libraries = _libsbml.so
> > + # environment variable MACOSX_DEPLOYMENT_TARGET must be set to
> > 10.3 or later
> > + # to use -undefined dynamic_lookup.
> > + macosx_version=$(shell sw_vers -productVersion | cut -d"." -f1,2)
> > + export MACOSX_DEPLOYMENT_TARGET=${macosx_version}
> > else
> > libraries = _libsbml.$(SHAREDLIBEXT)
> > endif
> > ***************
> > *** 122,127 ****
> > --- 126,141 ----
> > extra_LIBS += @LIBXML_LIBS@
> > endif
> >
> > + # -fno-strict-aliasing option is added to CXXFLAGS when using GCC.
> > + # As written in the SWIG Manual (section 20.2.4), SWIG generated
> > code could cause
> > + # crash problems when compiled by GCC with -fstrict-aliasing
> > option (automatically
> > + # enabled when using -O2 or higher optimization in GCC 3 or
> > later) and the option
> > + # should be disabled by adding -fno-strict-aliasing option.
> > +
> > + ifeq (GCC,$(findstring GCC,$(shell $(CXX) --version)))
> > + CXXFLAGS += -fno-strict-aliasing
> > + endif
> > +
> > # For Linux/Unix LD_LIBRARY_PATH *may* need to contain one or
> > more library
> > # paths to libsbml.so, libxerces-c.so and/or libexpat.so and/or the
> > # libsbml.so _libsbml.so generated by this Makfile. (For BSD/
> > MacOS X
> > ***************
> > *** 286,292 ****
> > --- 300,310 ----
> > #
> > ----------------------------------------------------------------------
> > -------
> >
> > install: setup.py create-build-dir
> > + ifeq "$(HOST_TYPE)" "darwin"
> > + env MACOSX_DEPLOYMENT_TARGET='' $(PYTHON) setup.py install --
> > skip-build --prefix=$(prefix)
> > + else
> > $(PYTHON) setup.py install --skip-build --prefix=$(prefix)
> > + endif
> >
> > installcheck:
> >
>
> --------------------------
> My public PGP key:
> http://page.mi.fu-berlin.de/~floettma/gpg-key-max.gpg
>
>
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Hello Max,

floettmann <max.floettmann@gmail.com> wrote
> Now that I installed the python bindings sucessfully I'm making
> changes to my code to solve problems with the new features of
> libSBML 3.0. I'm a bit confused by the new annotation features and
> XMLNode Classes. Is there a documentation for the python bindings
> like the one for version
> 2.4.3(http://www.sbml.org/software/libsbml/docs/python/)?

I attached a similar documentation file for the python bindings
in libsbml-3.0.0prerelease. (It may have a few glitches.)
The file was generated by pydoc command as follows:

% pydoc -w /path/to/libsbml.py
=> libsbml.html is generated in current directory.

(You may need to set DYLD_LIBRARY_PATH on MacOSX
in order to load required libraries for _libsbm.so.)

API documentation pages will be updated at the time of next release.

Thanks,

--
Akiya Jouraku

Attachment: libsbml-3_0_0pre-api-python-doc.zip (Size: 235.98KB, Downloaded 267 time(s))