sbml-svn Mailing List for Systems Biology Markup Language (SBML)

Revision: 26322
          http://sourceforge.net/p/sbml/code/26322
Author:   luciansmith
Date:     2022-07-13 17:10:40 +0000 (Wed, 13 Jul 2022)
Log Message:
-----------
Remove everything and point to new locations on github.

Added Paths:
-----------
    trunk/specifications/README.txt

Removed Paths:
-------------
    trunk/specifications/RelaxNG/
    trunk/specifications/sbml-level-1/
    trunk/specifications/sbml-level-2/
    trunk/specifications/sbml-level-3/

Added: trunk/specifications/README.txt
===================================================================
--- trunk/specifications/README.txt	                        (rev 0)
+++ trunk/specifications/README.txt	2022-07-13 17:10:40 UTC (rev 26322)
@@ -0,0 +1,12 @@
+All of the sources for the SBML specifications have been moved to github in the following repository:
+
+https://github.com/sbmlteam/sbml-specifications
+
+In addition, the 'project' files needed to compile the TeX documents have also been moved to github:
+
+https://github.com/sbmlteam/specifications-tex
+https://github.com/sbmlteam/specifications-bib
+
+Please update any links you may have to point at the new locations.
+
+Previous versions of these files may still be obtained here (by checking out a previous revision of the code), and are also available at github, where the history of the specs was migrated along with the source.

Revision: 26321
          http://sourceforge.net/p/sbml/code/26321
Author:   luciansmith
Date:     2022-07-13 17:06:03 +0000 (Wed, 13 Jul 2022)
Log Message:
-----------
Remove everything and point to new locations on github.

Modified Paths:
--------------
    trunk/sbmlvalidator/README.txt

Removed Paths:
-------------
    trunk/sbmlvalidator/LICENSE.html
    trunk/sbmlvalidator/LICENSE.txt
    trunk/sbmlvalidator/build.xml
    trunk/sbmlvalidator/validator/
    trunk/sbmlvalidator/validator_servlet/
    trunk/sbmlvalidator/validator_ui/
    trunk/sbmlvalidator/validator_ws/
    trunk/sbmlvalidator/validator_wsClient/

Deleted: trunk/sbmlvalidator/LICENSE.html
===================================================================
--- trunk/sbmlvalidator/LICENSE.html	2022-07-13 17:03:56 UTC (rev 26320)
+++ trunk/sbmlvalidator/LICENSE.html	2022-07-13 17:06:03 UTC (rev 26321)
@@ -1,201 +0,0 @@
-<!-- 
- This file uses only basic HTML formatting because it is also
- included by machine-generated documentation files.  Do not add
- more HTML formatting because it may break the documentation-
- generation system code in ./docs/src/ .
--->
-
-The majority of libSBML is copyrighted as follows:
-
-<ul>
-
-<li> Copyright &copy; 2013-2016 jointly by the following organizations:<br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK<br>
-    3. University of Heidelberg, Heidelberg, Germany<br>
-
-<li> Copyright &copy; 2009-2013 jointly by the following organizations:<br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK<br>
-
-<li> Copyright &copy; 2006-2008 by the California Institute of Technology,
-    Pasadena, CA, USA 
-
-<li> Copyright &copy; 2002-2005 jointly by the following organizations: <br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. Japan Science and Technology Agency, Japan
-</ul>
-
-<p>
-Portions of the source code comprising libSBML were copyrighted and
-contributed by third parties, and placed under the same LGPL 2.1
-license as the rest of libSBML. The following are their copyright
-statements:
-
-<ul>
-
-<li> Copyright &copy; 2004-2008 by European Media Laboratories
-Research gGmbH, Heidelberg, Germany (for the "SBML Layout" code
-and associated examples.)
-
-</ul>
-    
-<p>
-LibSBML is free software; you can redistribute it and/or modify 
-it under the terms of the GNU Lesser General Public License as
-published by the Free Software Foundation; either version 2.1 of
-the License, or any later version.
-
-<p>
-This software 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.  The software
-and documentation provided hereunder is on an "as is" basis, and
-the copyright holders have no obligations to provide maintenance,
-support, updates, enhancements or modifications.  In no event
-shall the copyright holders be liable to any party for direct,
-indirect, special, incidental or consequential damages, including
-lost profits, arising out of the use of this software and its
-documentation, even if the copyright holders have been advised of
-the possibility of such damage.  See the GNU Lesser General Public
-License for more details.
-
-<p>
-You should have received a copy of the GNU Lesser General Public
-License along with this library in the file named "COPYING.txt"
-included with the software distribution.  A copy is also
-available online at the Internet address
-  <a href="http://sbml.org/software/libsbml/COPYING.html">
-    http://sbml.org/software/libsbml/COPYING.html</a> for your
-convenience.  You may also write to obtain a copy from the Free
-Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
-MA 02110-1301, USA.
-
-
-<h2>Third-party software incorporated into both the libSBML
-binary and source-code distributions</h2>
-
-LibSBML incorporates an open-source compression library written by
-a third party.  The following is information about the copyright
-and distribution terms of this library:
-
-<ul>
-  <li> <em>MiniZip1.01e</em>, copyright &copy; 1998-2005
-    Gilles Vollant, released under terms compatible with the LGPL.
-    Please see the file src/sbml/compress/00README.txt for more
-    information about MiniZip 1.01e and its license terms.</li>
-
-</ul>
-
-
-<h2>Additional third-party software incorporated only into
-the libSBML source code distribution</h2>
-
-<p>
-Additional software is used to produce the documentation of
-libSBML.  The binary distributions of libSBML do not include this
-software; they are only present in the source code distribution
-and the libSBML documentation archives.
-
-<ul>
-  <li> <em>Argparse 1.2.1</em>, copyright &copy; 2006-2009 Steven J. Bethard
-  (ste...@gm...) and distributed under the Python Software
-  Foundation License version 2.  Code downloaded from
-  <a href="http://code.google.com/p/argparse">http://code.google.com/p/argparse</a>
-  on 2012-02-10.</li>
-
-  <li> <em>Google Code Prettify</em>, distributed under the terms
-    of the Apache License Version 2.0, January 2004.  Code
-    downloaded from <a href="http://code.google.com/p/google-code-prettify/">
-    http://code.google.com/p/google-code-prettify</a> on 2013-10-16.</li>
-
-  <li> <em>PrettyTable</em>, copyright &copy; 2009-2013 Luke Maurits,
-  distributed under the following BSD-derivative license:
-
-<blockquote>
-    Copyright (c) 2009-2013 Luke Maurits (lu...@ma...)
-    All rights reserved.<br>
-    With contributions from:<br>
-    <ul>
-     <li style="margin-top: 0.25em; margin-bottom: 0.25em"> Chris Clark
-     <li style="margin-top: 0.25em; margin-bottom: 0.25em"> Christoph Robbert
-     <li style="margin-top: 0.25em; margin-bottom: 0.25em"> Klein Stephane
-     <li style="margin-top: 0.25em; margin-bottom: 0.25em"> "maartendb"
-    </ul>
-    Redistribution and use in source and binary forms, with or
-    without modification, are permitted provided that the
-    following conditions are met:
-    <ul>
-    <li> Redistributions of source code must retain the above
-      copyright notice, this list of conditions and the
-      following disclaimer. 
-
-    <li> Redistributions in binary form must reproduce the above
-      copyright notice, this list of conditions and the
-      following disclaimer in the documentation and/or other
-      materials provided with the distribution.
-
-    <li> The name of the author may not be used to endorse or
-      promote products derived from this software without
-      specific prior written permission.
-    </ul>
-    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
-    CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
-    INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-    MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
-    CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
-    NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
-    HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-    OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-</blockquote>
-
-  <li> <em>ExcludeDoclet</em>, copyright &copy; 2004 by Sun
-Microsystems, Inc., and distributed under the following
-open-source terms:
-
-<blockquote>
-   Copyright 2004 Sun Microsystems, Inc. All Rights Reserved.
-   <p>
-   Redistribution and use in source and binary forms, with or
-   without modification, are permitted provided that the
-   following conditions are met:
-   <ul>
-   <li> Redistribution of source code must retain the above
-   copyright notice, this list of conditions and the following
-   disclaimer.
-
-   <li> Redistribution in binary form must reproduce the above
-   copyright notice, this list of conditions and the following
-   disclaimer in the documentation and/or other materials provided
-   with the distribution. Neither the name of Sun Microsystems,
-   Inc. nor the names of contributors may be used to endorse or
-   promote products derived from this software without specific
-   prior written permission.
-   </ul>
-
-   This software is provided "AS IS," without a warranty of any
-   kind. ALL EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND
-   WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY,
-   FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT, ARE
-   HEREBY EXCLUDED. SUN MICROSYSTEMS, INC. ("SUN") AND ITS
-   LICENSORS SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED BY
-   LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THIS
-   SOFTWARE OR ITS DERIVATIVES. IN NO EVENT WILL SUN OR ITS
-   LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR
-   FOR DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR
-   PUNITIVE DAMAGES, HOWEVER CAUSED AND REGARDLESS OF THE THEORY
-   OF LIABILITY, ARISING OUT OF THE USE OF OR INABILITY TO USE
-   THIS SOFTWARE, EVEN IF SUN HAS BEEN ADVISED OF THE POSSIBILITY
-   OF SUCH DAMAGES.<br>
-   <p>
-   You acknowledge that this software is not designed, licensed
-   or intended for use in the design, construction, operation or
-   maintenance of any nuclear facility.
-</blockquote>
-
-</ul>

Deleted: trunk/sbmlvalidator/LICENSE.txt
===================================================================
--- trunk/sbmlvalidator/LICENSE.txt	2022-07-13 17:03:56 UTC (rev 26320)
+++ trunk/sbmlvalidator/LICENSE.txt	2022-07-13 17:06:03 UTC (rev 26321)
@@ -1,167 +0,0 @@
-           Licensing and Distribution Terms for libSBML
-
-The majority of libSBML is copyrighted as follows:
-
-* Copyright (C) 2013-2016 jointly by the following organizations:
-  1. California Institute of Technology, Pasadena, CA, USA
-  2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-  3. University of Heidelberg, Heidelberg, Germany
-
-* Copyright (C) 2009-2013 jointly by the following organizations: 
-  1. California Institute of Technology, Pasadena, CA, USA
-  2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- 
-* Copyright (C) 2006-2008 by the California Institute of Technology,
-    Pasadena, CA, USA 
- 
-* Copyright (C) 2002-2005 jointly by the following organizations: 
-  1. California Institute of Technology, Pasadena, CA, USA
-  2. Japan Science and Technology Agency, Japan
-
-Portions of the source code comprising libSBML were copyrighted
-and contributed by third parties, and placed under the same LGPL
-2.1 license as the rest of libSBML. The following are their
-copyright statements:
-
-* Copyright (C) 2004-2008 by European Media Laboratories Research
-  gGmbH, Heidelberg, Germany.  (For the "SBML Layout" code.)
-
-LibSBML is free software; you can redistribute it and/or modify 
-it under the terms of the GNU Lesser General Public License as
-published by the Free Software Foundation; either version 2.1 of
-the License, or any later version.
-
-This software 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.  The software
-and documentation provided hereunder is on an "as is" basis, and
-the copyright holders have no obligations to provide maintenance,
-support, updates, enhancements or modifications.  In no event
-shall the copyright holders be liable to any party for direct,
-indirect, special, incidental or consequential damages, including
-lost profits, arising out of the use of this software and its
-documentation, even if the copyright holders have been advised of
-the possibility of such damage.  See the GNU Lesser General Public
-License for more details.
-
-You should have received a copy of the GNU Lesser General Public
-License along with this library in the file named "COPYING.txt"
-included with the software distribution.  A copy is also
-available online at the Internet address
-http://sbml.org/software/libsbml/COPYING.html for your
-convenience.  You may also write to obtain a copy from the Free
-Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
-MA 02110-1301,  USA.
-
-
-     Third-party software incorporated into both the libSBML
-               binary and source-code distributions
-
-LibSBML incorporates an open-source compression library written by
-a third party.  The following is information about the copyright
-and distribution terms of this library:
-
-* MiniZip 1.01e, copyright (C) 1998-2005 Gilles Vollant, released 
-  under terms compatible with the LGPL.  Please see the file
-  src/sbml/compress/00README.txt for more information about
-  MiniZip 1.01e and its license terms.
-
-
-        Additional third-party software incorporated only
-            into the libSBML source code distribution
-
-Additional software is used to produce the documentation of
-libSBML.  The binary distributions of libSBML do not include this
-software; they are only present in the source code distribution
-and the libSBML documentation archives.
-
-* Argparse 1.2.1, copyright (C) 2006-2009 Steven J. Bethard
-  <ste...@gm...> and distributed under the Python Software
-  Foundation License version 2.  Code downloaded from 
-  http://code.google.com/p/argparse/ on 2012-02-10.
-
-* Google Code Prettify, distributed under the terms of the
-  Apache License Version 2.0, January 2004.  Code downloaded from 
-  http://code.google.com/p/google-code-prettify/ on 2013-10-16.
-
-* PrettyTable, copyright (C) 2009-2013 Luke Maurits, distributed
-  under the following BSD-derivative license:
-
-    Copyright (c) 2009-2013 Luke Maurits <lu...@ma...>
-    All rights reserved.
-    With contributions from:
-     * Chris Clark
-     * Christoph Robbert
-     * Klein Stephane
-     * "maartendb"
-    
-    Redistribution and use in source and binary forms, with or
-    without modification, are permitted provided that the
-    following conditions are met:
-
-    * Redistributions of source code must retain the above
-      copyright notice, this list of conditions and the
-      following disclaimer. 
-
-    * Redistributions in binary form must reproduce the above
-      copyright notice, this list of conditions and the
-      following disclaimer in the documentation and/or other
-      materials provided with the distribution.
-
-    * The name of the author may not be used to endorse or
-      promote products derived from this software without
-      specific prior written permission.
-
-    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
-    CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
-    INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-    MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-    DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
-    CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
-    NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-    LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
-    HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-    CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-    OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-* ExcludeDoclet, copyright (C) 2004 by Sun Microsystems, Inc., and
-  distributed under the following open-source terms:
-
-   Copyright 2004 Sun Microsystems, Inc. All Rights Reserved.
-
-   Redistribution and use in source and binary forms, with or
-   without modification, are permitted provided that the
-   following conditions are met:
-
-    - Redistribution of source code must retain the above
-   copyright notice, this list of conditions and the following
-   disclaimer.
-
-   - Redistribution in binary form must reproduce the above
-   copyright notice, this list of conditions and the following
-   disclaimer in the documentation and/or other materials provided
-   with the distribution. Neither the name of Sun Microsystems,
-   Inc. nor the names of contributors may be used to endorse or
-   promote products derived from this software without specific
-   prior written permission.
-
-   This software is provided "AS IS," without a warranty of any
-   kind. ALL EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND
-   WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY,
-   FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT, ARE
-   HEREBY EXCLUDED. SUN MICROSYSTEMS, INC. ("SUN") AND ITS
-   LICENSORS SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED BY
-   LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THIS
-   SOFTWARE OR ITS DERIVATIVES. IN NO EVENT WILL SUN OR ITS
-   LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR
-   FOR DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR
-   PUNITIVE DAMAGES, HOWEVER CAUSED AND REGARDLESS OF THE THEORY
-   OF LIABILITY, ARISING OUT OF THE USE OF OR INABILITY TO USE
-   THIS SOFTWARE, EVEN IF SUN HAS BEEN ADVISED OF THE POSSIBILITY
-   OF SUCH DAMAGES.
-
-   You acknowledge that this software is not designed, licensed
-   or intended for use in the design, construction, operation or
-   maintenance of any nuclear facility.

Modified: trunk/sbmlvalidator/README.txt
===================================================================
--- trunk/sbmlvalidator/README.txt	2022-07-13 17:03:56 UTC (rev 26320)
+++ trunk/sbmlvalidator/README.txt	2022-07-13 17:06:03 UTC (rev 26321)
@@ -1,99 +1,7 @@
+The SBML Validator code has been moved to github in the following repository:
 
-                        Online SBML Validator
+https://github.com/sbmlteam/sbmlvalidator
 
-	    Frank Bergmann, Ben Bornstein, Sarah Keating, 
-                   Akiya Jouraku and Michael Hucka
+Please update any links you may have to point at the new locations.
 
-    Mailing lists and online web forums for discussing SBML are at
-                        http://sbml.org/Forums
-
-        To contact the core developers directly, send email to
-                        sbm...@ca...
-
-   ,---------------------------------------------------------------.
-  | Table of contents                                               |
-  | 1. Introduction                                                 |
-  | 2. Installation                                                 |
-  | 3. Licensing and distribution                                   |
-  | 4. Acknowledgments                                              |
-   `---------------------------------------------------------------'
-
-
-1. Introduction
-======================================================================
-
-This is the source code to the Online SBML Validator running at
-http://sbml.org/Facilities/Validator .  This facility allows users to
-upload SBML files and have them tested for adherence to the syntax and
-other rules defined by the SBML specifications.  The validation is
-actually performed by libSBML (http://sbml.org/Software/libSBML) for
-core SBML and accepted SBML Level 3 packages, and by a RELAX NG
-validation engine for unofficial, draft SBML Level 3 package
-definitions.  The code you see here is the system that permits files
-to be uploaded to the server and processed to produce a report of the
-results.
-
-
-2. Installation
-======================================================================
-
-Information forthcoming ....
-
-
-
-3. LICENSING AND DISTRIBUTION
-======================================================================
-
-Copyright (C) 2011-2016 jointly by the following organizations:
-    1. California Institute of Technology, Pasadena, CA, USA
-    2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
-    3. University of Heidelberg, Heidelberg, Germany
-
-Copyright (C) 2009-2011 jointly by the following organizations:
-    1. California Institute of Technology, Pasadena, CA, USA
-    2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
-
-Copyright (C) 2006-2008 by the California Institute of Technology,
-    Pasadena, CA, USA
-
-Copyright (C) 2002-2005 jointly by the following organizations:
-    1. California Institute of Technology, Pasadena, CA, USA
-    2. Japan Science and Technology Agency, Japan
-
-This library is free software; you can redistribute it and/or modify
-it under the terms of the GNU Lesser General Public License as
-published by the Free Software Foundation.  A copy of the license
-agreement is provided in the file named "LICENSE.txt" included with
-this software distribution and also available online as
-http://sbml.org/software/libsbml/license.html
-
-
-4. ACKNOWLEDGMENTS
-======================================================================
-
-This system has undergone many revisions.  It was originally written
-by Ben Borenstein, and later (around 2014-2016) overhauled
-significantly by Frank Bergmann.
-
-This and other projects of the SBML Team have been supported by the
-following organizations: the National Institutes of Health (USA) under
-grants R01 GM070923 and R01 GM077671; the International Joint Research
-Program of NEDO (Japan); the JST ERATO-SORST Program (Japan); the
-Japanese Ministry of Agriculture; the Japanese Ministry of Education,
-Culture, Sports, Science and Technology; the BBSRC e-Science
-Initiative (UK); the DARPA IPTO Bio-Computation Program (USA); the
-Army Research Office's Institute for Collaborative Biotechnologies
-(USA); the Air Force Office of Scientific Research (USA); the
-California Institute of Technology (USA); the University of
-Hertfordshire (UK); the Molecular Sciences Institute (USA); the
-Systems Biology Institute (Japan); and Keio University (Japan).
-
-
------------------------------------------------
-File author: M. Hucka, F. Bergmann
------------------------------------------------
-
-# The following is for [X]Emacs users.  Please leave in place.
-# Local Variables:
-# fill-column: 70
-# End:
+Previous versions of these files may still be obtained here (by checking out a previous revision of the code), and are also available at github, where the history of the code was migrated along with the source.

Deleted: trunk/sbmlvalidator/build.xml
===================================================================
--- trunk/sbmlvalidator/build.xml	2022-07-13 17:03:56 UTC (rev 26320)
+++ trunk/sbmlvalidator/build.xml	2022-07-13 17:06:03 UTC (rev 26321)
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<project basedir="." default="default" name="validator">
-    <property environment="env"/>
-    <property name="validator.location" value="validator"/>
-    <property name="validator_ui.location" value="validator_ui"/>
-    <property name="validator_servlet.location" value="validator_servlet"/>
-    <property name="validator_ws.location" value="validator_ws"/>
-    <property name="validator_wsClient.location" value="validator_wsClient"/>
-    <target name="clean">
-        <ant antfile="build.xml" dir="${validator.location}" inheritAll="false" target="clean"/>
-        <ant antfile="build.xml" dir="${validator_ui.location}" inheritAll="false" target="clean"/>
-        <ant antfile="build.xml" dir="${validator_servlet.location}" inheritAll="false" target="clean"/>
-        <ant antfile="build.xml" dir="${validator_ws.location}" inheritAll="false" target="clean"/>
-        <ant antfile="build.xml" dir="${validator_wsClient.location}" inheritAll="false" target="clean"/>
-    </target>
-    <target depends="clean" name="cleanall"/>
-    <target name="build">
-        <ant antfile="build.xml" dir="${validator.location}" inheritAll="false" target="build"/>
-        <ant antfile="build.xml" dir="${validator_ui.location}" inheritAll="false" target="build"/>
-        <ant antfile="build.xml" dir="${validator_servlet.location}" inheritAll="false" target="build"/>
-        <ant antfile="build.xml" dir="${validator_ws.location}" inheritAll="false" target="build"/>
-        <ant antfile="build.xml" dir="${validator_wsClient.location}" inheritAll="false" target="build"/>
-    </target>
-	<target name="default">
-        <ant antfile="build.xml" dir="${validator.location}" inheritAll="false" />
-        <ant antfile="build.xml" dir="${validator_ui.location}" inheritAll="false" />
-        <ant antfile="build.xml" dir="${validator_servlet.location}" inheritAll="false" />
-        <ant antfile="build.xml" dir="${validator_ws.location}" inheritAll="false" />
-        <ant antfile="build.xml" dir="${validator_wsClient.location}" inheritAll="false" />
-    </target>
-</project>

Revision: 26320
          http://sourceforge.net/p/sbml/code/26320
Author:   luciansmith
Date:     2022-07-13 17:03:56 +0000 (Wed, 13 Jul 2022)
Log Message:
-----------
Remove everything and point to new locations on github.

Modified Paths:
--------------
    trunk/SBMLToolbox/README.txt

Removed Paths:
-------------
    trunk/SBMLToolbox/AUTHORS.txt
    trunk/SBMLToolbox/COPYING.html
    trunk/SBMLToolbox/COPYING.txt
    trunk/SBMLToolbox/FUNDING.txt
    trunk/SBMLToolbox/LICENSE.html
    trunk/SBMLToolbox/LICENSE.txt
    trunk/SBMLToolbox/NEWS.txt
    trunk/SBMLToolbox/VERSION.html
    trunk/SBMLToolbox/VERSION.txt
    trunk/SBMLToolbox/dev/
    trunk/SBMLToolbox/docs/
    trunk/SBMLToolbox/graphics/
    trunk/SBMLToolbox/src/
    trunk/SBMLToolbox/win32_installer/

Deleted: trunk/SBMLToolbox/AUTHORS.txt
===================================================================
--- trunk/SBMLToolbox/AUTHORS.txt	2022-07-13 17:00:19 UTC (rev 26319)
+++ trunk/SBMLToolbox/AUTHORS.txt	2022-07-13 17:03:56 UTC (rev 26320)
@@ -1,15 +0,0 @@
-	      SBMLToolbox has been primarily developed by
-
-			     Sarah Keating
-
-	    with contributions from (in alphabetical order)
-	Arsen Batagov, Ben Bornstein, Will Bryant, Bill Denney,
-     Andrew Finney, Thomas Grotkj\xE6r, Mike Hucka, Pieter Pareit, 
-                  Kieran Smallbone, Sumant Turlapati,
-		   and others in the SBML community.
-
-	For more information about SBML or SBMLToolbox, contact:
-
-			     The SBML Team
-			  http://www.sbml.org/
-		      mailto:sbm...@ca...

Deleted: trunk/SBMLToolbox/COPYING.html
===================================================================
--- trunk/SBMLToolbox/COPYING.html	2022-07-13 17:00:19 UTC (rev 26319)
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@@ -1,618 +0,0 @@
-<html>
-<body>
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-<table width="325">
-  <tr>
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-<h2 align=center>GNU LESSER GENERAL PUBLIC LICENSE</h2>
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Deleted: trunk/SBMLToolbox/COPYING.txt
===================================================================
--- trunk/SBMLToolbox/COPYING.txt	2022-07-13 17:00:19 UTC (rev 26319)
+++ trunk/SBMLToolbox/COPYING.txt	2022-07-13 17:03:56 UTC (rev 26320)
@@ -1,513 +0,0 @@
-
-
-                  GNU LESSER GENERAL PUBLIC LICENSE
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- Copyright (C) 1991, 1999 Free Software Foundation, Inc.
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Deleted: trunk/SBMLToolbox/FUNDING.txt
===================================================================
--- trunk/SBMLToolbox/FUNDING.txt	2022-07-13 17:00:19 UTC (rev 26319)
+++ trunk/SBMLToolbox/FUNDING.txt	2022-07-13 17:03:56 UTC (rev 26320)
@@ -1,11 +0,0 @@
-This and other projects of the SBML Team have been supported by the
-following organizations: the National Institutes of Health (USA) under
-grants R01 GM070923 and R01 GM077671; the International Joint Research
-Program of NEDO (Japan); the JST ERATO-SORST Program (Japan); the Japanese
-Ministry of Agriculture; the Japanese Ministry of Education, Culture,
-Sports, Science and Technology; the BBSRC e-Science Initiative (UK); the
-DARPA IPTO Bio-Computation Program (USA); the Army Research Office's
-Institute for Collaborative Biotechnologies (USA); the Air Force Office of
-Scientific Research (USA); the California Institute of Technology (USA);
-the University of Hertfordshire (UK); the Molecular Sciences Institute
-(USA); the Systems Biology Institute (Japan); and Keio University (Japan).

Deleted: trunk/SBMLToolbox/LICENSE.html
===================================================================
--- trunk/SBMLToolbox/LICENSE.html	2022-07-13 17:00:19 UTC (rev 26319)
+++ trunk/SBMLToolbox/LICENSE.html	2022-07-13 17:03:56 UTC (rev 26320)
@@ -1,54 +0,0 @@
-<!-- 
- This file uses only basic HTML formatting because it is also
- included by machine-generated documentation files.  Do not add
- more HTML formatting because it may break the documentation-
- generation system.
--->
-
-Copyright &copy; 2009-2012 jointly by the following organizations:<br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK<br>
-<p>
-Copyright &copy; 2006-2008 jointly by the following organizations:<br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. University of Hertfordshire, Hatfield, UK<br>
-<p>
-Copyright &copy; 2003-2005 jointly by the following organizations:<br>
-    1. California Institute of Technology, Pasadena, CA, USA<br>
-    2. Japan Science and Technology Agency, Japan<br>
-    3. University of Hertfordshire, Hatfield, UK<br>
-
-<p>
-SBMLToolbox is free software; you can redistribute it and/or
-modify it under the terms of the GNU Lesser General Public
-License as published by the Free Software Foundation; either
-version 2.1 of the License, or any later version.
-
-<p>
-This software 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.  The
-software and documentation provided hereunder is on an "as is"
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-and Technology Agency, or the University of Hertfordshire be
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-California Institute of Technology, the Japan Science and
-Technology Agency, and/or the University of Hertfordshire have
-been advised of the possibility of such damage.  See the GNU
-Lesser General Public License for more details.
-
-<p>
-You should have received a copy of the GNU Lesser General Public
-License along with this library in the file named "LICENSE.txt"
-included with the software distribution.  A copy is also
-available online at the Internet address
-http://sbml.org/Software/SBMLToolbox/LICENSE.html for your
-convenience.  You may also write to obtain a copy from the Free
-Softwar...
 
[truncated message content]

Revision: 26319
          http://sourceforge.net/p/sbml/code/26319
Author:   luciansmith
Date:     2022-07-13 17:00:19 +0000 (Wed, 13 Jul 2022)
Log Message:
-----------
Remove everything and point to new locations on github.

Added Paths:
-----------
    trunk/project/README.txt

Removed Paths:
-------------
    trunk/project/bib/
    trunk/project/sourceforge/
    trunk/project/tex/

Added: trunk/project/README.txt
===================================================================
--- trunk/project/README.txt	                        (rev 0)
+++ trunk/project/README.txt	2022-07-13 17:00:19 UTC (rev 26319)
@@ -0,0 +1,8 @@
+The 'project' files for SBML (which are used to build the various SBML specifications) have been moved to github, in the following two repositories:
+
+https://github.com/sbmlteam/specifications-tex
+https://github.com/sbmlteam/specifications-bib
+
+Please update any links you may have to point at the new locations.
+
+Previous versions of these files may still be obtained here (by checking out a previous revision of the code), and are also available at github, where the history of those directories was migrated along with the source.

Revision: 26318
          http://sourceforge.net/p/sbml/code/26318
Author:   luciansmith
Date:     2022-07-13 16:54:48 +0000 (Wed, 13 Jul 2022)
Log Message:
-----------
Remove everything and leave a note pointing people to the new source repository.

Modified Paths:
--------------
    trunk/libsbml/README.txt

Removed Paths:
-------------
    trunk/libsbml/AUTHORS.txt
    trunk/libsbml/CMakeLists.txt
    trunk/libsbml/COPYING.html
    trunk/libsbml/COPYING.txt
    trunk/libsbml/FUNDING.txt
    trunk/libsbml/LICENSE.html
    trunk/libsbml/LICENSE.txt
    trunk/libsbml/Makefile.in
    trunk/libsbml/NEWS.txt
    trunk/libsbml/OLD_NEWS.txt
    trunk/libsbml/README-code-from-svn.txt
    trunk/libsbml/VERSION.txt
    trunk/libsbml/VERSION_PACKAGES.ac
    trunk/libsbml/acinclude.m4
    trunk/libsbml/aclocal.m4
    trunk/libsbml/autogen.sh
    trunk/libsbml/cmake_uninstall.cmake.in
    trunk/libsbml/common.cmake
    trunk/libsbml/comp-package.cmake
    trunk/libsbml/config/
    trunk/libsbml/configure
    trunk/libsbml/configure.ac
    trunk/libsbml/dev/
    trunk/libsbml/docs/
    trunk/libsbml/examples/
    trunk/libsbml/fbc-package.cmake
    trunk/libsbml/groups-package.cmake
    trunk/libsbml/l3v2extendedmath-package.cmake
    trunk/libsbml/layout-package.cmake
    trunk/libsbml/libsbml.spec.in
    trunk/libsbml/libtoolize.sh
    trunk/libsbml/macosx/
    trunk/libsbml/multi-package.cmake
    trunk/libsbml/qual-package.cmake
    trunk/libsbml/render-package.cmake
    trunk/libsbml/src/

Deleted: trunk/libsbml/AUTHORS.txt
===================================================================
--- trunk/libsbml/AUTHORS.txt	2021-10-23 00:01:15 UTC (rev 26317)
+++ trunk/libsbml/AUTHORS.txt	2022-07-13 16:54:48 UTC (rev 26318)
@@ -1,16 +0,0 @@
-                 LibSBML 5 was primarily developed by
- 
-            Sarah Keating, Frank Bergmann, Ben Bornstein,
-            Akiya Jouraku, Lucian Smith, and Michael Hucka
-
-           with contributions from (in alphabetical order):
-     Gordon Ball, Bill Denney, Christoph Flamm, Akira Funahashi,
-     Ralph Gauges, Martin Ginkel, Alex Gutteridge, Stefan Hoops,
-    Totte Karlsson, Moriyoshi Koizumi, Ben Kovitz, Rainer Machne,
-          Nicolas Rodriguez, Fengkai Zhang and many others.
-                                     
-         For more information about SBML or libSBML, contact:
-
-                            The SBML Team
-                         http://www.sbml.org/
-                     mailto:sbm...@go...

Deleted: trunk/libsbml/CMakeLists.txt
===================================================================
--- trunk/libsbml/CMakeLists.txt	2021-10-23 00:01:15 UTC (rev 26317)
+++ trunk/libsbml/CMakeLists.txt	2022-07-13 16:54:48 UTC (rev 26318)
@@ -1,1543 +0,0 @@
-###############################################################################
-#
-# Description       : CMake build script for libSBML
-# Original author(s): Frank Bergmann <fbe...@ca...>
-# Organization      : California Institute of Technology
-#
-# This file is part of libSBML.  Please visit http://sbml.org for more
-# information about SBML, and the latest version of libSBML.
-#
-# Copyright (C) 2013-2017 jointly by the following organizations:
-#     1. California Institute of Technology, Pasadena, CA, USA
-#     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-#     3. University of Heidelberg, Heidelberg, Germany
-#
-# Copyright (C) 2009-2013 jointly by the following organizations:
-#     1. California Institute of Technology, Pasadena, CA, USA
-#     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
-#
-# Copyright (C) 2006-2008 by the California Institute of Technology,
-#     Pasadena, CA, USA
-#
-# Copyright (C) 2002-2005 jointly by the following organizations:
-#     1. California Institute of Technology, Pasadena, CA, USA
-#     2. Japan Science and Technology Agency, Japan
-#
-# This library is free software; you can redistribute it and/or modify it
-# under the terms of the GNU Lesser General Public License as published by
-# the Free Software Foundation.  A copy of the license agreement is provided
-# in the file named "LICENSE.txt" included with this software distribution
-# and also available online as http://sbml.org/software/libsbml/license.html
-#
-###############################################################################
-
-cmake_minimum_required(VERSION 2.6)
-project(libsbml)
-
-if(POLICY CMP0054)
-    cmake_policy(SET CMP0054 NEW)
-endif()
-
-if(POLICY CMP0058)
-    cmake_policy(SET CMP0058 OLD)
-endif()
-
-
-
-set(LIBSBML_ROOT_SOURCE_DIR "${CMAKE_SOURCE_DIR}" CACHE PATH
-    "Path to the libSBML root source directory")
-set(LIBSBML_ROOT_BINARY_DIR "${CMAKE_BINARY_DIR}" CACHE PATH
-    "Path to the libSBML root build directory")
-
-include (CMakeTestCCompiler)
-include (CheckCSourceCompiles)
-include (CheckCXXSourceCompiles)
-include (CheckStructHasMember)
-include (CheckLibraryExists)
-include (CheckFunctionExists)
-include (CheckCCompilerFlag)
-include (CheckCSourceRuns)
-include (CheckSymbolExists)
-include (CheckTypeSize)
-if (${CMAKE_VERSION} VERSION_GREATER 2.8.4)
-	include(GNUInstallDirs)
-else ()
-	set (CMAKE_INSTALL_DATADIR "share/libsbml/")
-	set (CMAKE_INSTALL_LIBDIR "lib")
-	set (CMAKE_INSTALL_INCLUDEDIR "include")
-	set (CMAKE_INSTALL_BINDIR "bin")
-	set (CMAKE_INSTALL_DATADIR "share")
-	set (CMAKE_INSTALL_FULL_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib")
-	set (CMAKE_INSTALL_FULL_INCLUDEDIR "${CMAKE_INSTALL_PREFIX}/include")
-endif ()
-
-###############################################################################
-#
-# Parse VERSION.txt to determine the package version
-#
-
-set(LIBSBML_VERSION_MAJOR)
-set(LIBSBML_VERSION_MINOR)
-set(LIBSBML_VERSION_PATCH)
-set(LIBSBML_VERSION_RELEASE)
-set(LIBSBML_DOTTED_VERSION)
-
-if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/VERSION.txt")
-
-    file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/VERSION.txt" VersionString NEWLINE_CONSUME)
-    string(STRIP "${VersionString}" VersionString)
-    set(LIBSBML_DOTTED_VERSION ${VersionString})
-    string(REPLACE "." ";" VersionString "${VersionString}" )
-    string(REPLACE "-" ";" VersionString "${VersionString}" )
-    list(LENGTH VersionString versionLength)
-    list(GET VersionString 0 LIBSBML_VERSION_MAJOR )
-    list(GET VersionString 1 LIBSBML_VERSION_MINOR )
-    list(GET VersionString 2 LIBSBML_VERSION_PATCH )
-
-    if(${versionLength} GREATER 3)
-        list(GET VersionString 3 LIBSBML_VERSION_RELEASE )
-    endif()
-
-endif()
-
-# version number needs to be calculated correctly
-MATH(EXPR LIBSBML_VERSION_NUMERIC "${LIBSBML_VERSION_MAJOR} * 10000 + ${LIBSBML_VERSION_MINOR} * 100 + ${LIBSBML_VERSION_PATCH}" )
-set(PACKAGE_VERSION "${LIBSBML_VERSION_MAJOR}.${LIBSBML_VERSION_MINOR}.${LIBSBML_VERSION_PATCH}${LIBSBML_VERSION_RELEASE}")
-set(PACKAGE_NAME "libSBML")
-
-set(PACKAGE_CONFIG_DIR "${CMAKE_INSTALL_LIBDIR}/cmake" CACHE PATH
-    "Path into which the cmake config files should be installed")
-
-
-# PACKAGE_VERSION gets overridden by using other packages, so setting
-# the PROJECT_VERSION, which will be used when exporting targets in
-# src/CMakeLists.txt
-set(PROJECT_VERSION ${PACKAGE_VERSION})
-
-if (WITH_DOXYGEN OR WITH_PYTHON)
-  # configure the version for documentation / bindings
-  configure_file(
-      ${CMAKE_CURRENT_SOURCE_DIR}/docs/src/common-text/libsbml-version.html.in
-      ${CMAKE_CURRENT_SOURCE_DIR}/docs/src/common-text/libsbml-version.html
-  )
-endif()
-
-# add make dist and make check target as they are already familiar for
-# everyone using the gnumake build
-add_custom_target(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
-add_custom_target(check COMMAND ${CMAKE_MAKE_PROGRAM} test)
-
-###############################################################################
-#
-# The next lines configure the parameters for packaging the binaries.
-# They can be invoked with "make package" or "nmake package" or by using
-# cpack -G zip|deb|rpm|dmg|nsis
-#
-
-include(InstallRequiredSystemLibraries)
-
-set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "An API library for reading/writing/manipulating SBML.")
-set(CPACK_PACKAGE_NAME "${PACKAGE_NAME}")
-set(CPACK_PACKAGE_VENDOR "The libSBML Team")
-set(CPACK_PACKAGE_CONTACT "LibSBML Team <lib...@go...>")
-set(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.txt")
-set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/COPYING.txt")
-set(CPACK_PACKAGE_VERSION_MAJOR "${LIBSBML_VERSION_MAJOR}")
-set(CPACK_PACKAGE_VERSION_MINOR "${LIBSBML_VERSION_MINOR}")
-set(CPACK_PACKAGE_VERSION_PATCH "${LIBSBML_VERSION_PATCH}")
-set(CPACK_RPM_PACKAGE_LICENSE "LGPL")
-set(CPACK_RPM_PACKAGE_GROUP "Libraries/Development")
-set(CPACK_DEBIAN_PACKAGE_SECTION "Libraries")
-
-set(CPACK_SOURCE_IGNORE_FILES "${CMAKE_CURRENT_BINARY_DIR};/.vs/;/.vscode/;/.svn/;/.libs/;/.deps/;/.bzr/;.*.o$;.*.lo$;.*.la$;${CPACK_SOURCE_IGNORE_FILES};/.DS_Store;/.svnignore;blib;libsbml-dist")
-
-if(UNIX)
-    set(CPACK_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
-    set(CPACK_SET_DESTDIR "ON")
-endif()
-
-if(CMAKE_SIZEOF_VOID_P EQUAL 4)
-    set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "i386")
-    set(CPACK_RPM_PACKAGE_ARCHITECTURE "i386")
-else()
-    set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "amd64")
-    set(CPACK_RPM_PACKAGE_ARCHITECTURE "x86_64")
-endif()
-
-include(CPack)
-
-
-###############################################################################
-#
-# Here we have the main configuration options for libsbml.
-#
-
-# Build static / shared library
-# option(BUILD_SHARED_LIBS  "Build shared library. (Set to OFF to build static libraries.)" OFF)
-
-# Whether to compile examples
-option(WITH_EXAMPLES "Compile the libSBML example programs."  OFF)
-
-# Which language bindings should be built
-option(WITH_CSHARP   "Generate the C# language interface for libSBML."     OFF)
-option(WITH_JAVA     "Generate the Java language interface for libSBML."   OFF)
-option(WITH_PYTHON   "Generate the Python language interface for libSBML." OFF)
-option(WITH_PERL     "Generate the Perl language interface for libSBML."   OFF)
-option(WITH_PHP      "Generate the PHP language interface for libSBML."    OFF)
-option(WITH_RUBY     "Generate the Ruby language interface for libSBML"    OFF)
-option(WITH_R        "Generate the R language interface for libSBML"       OFF)
-option(WITH_OCTAVE   "Generate the Octave language interface for libSBML." OFF)
-option(WITH_MATLAB   "Generate the MATLAB language interface for libSBML." OFF)
-option(WITH_JAVASCRIPT   "Generate the experimental Node.js language interface for libSBML." OFF)
-
-if (WITH_JAVASCRIPT)
-
-  set(_PF86 "ProgramFiles(x86)")
-  find_program(NODE_GYP_EXECUTABLE
-        NAMES node-gyp node-gyp.cmd
-        PATHS
-              /usr/local/bin
-              /opt/local/bin
-              /usr/bin
-              "$ENV{ProgramFilesProgramFiles}/nodejs/"
-              "$ENV{ProgramW6432}/nodejs/"
-        DOC "The file name of the node-gyp executable."
-        )
-
-  find_program(NODEJS_EXECUTABLE
-        NAMES node nodeexe
-        PATHS
-              /usr/local/bin
-              /opt/local/bin
-              /usr/bin
-              "$ENV{ProgramFiles}/nodejs/"
-              "$ENV{ProgramW6432}/nodejs/"
-        DOC "The file name of the nodejs executable."
-        )
-  # check that we found node-gyp
-  if (NOT NODE_GYP_EXECUTABLE)
-        message(FATAL_ERROR
-"In oder to build the JavaScript language interface, libSBML needs the
-node-gyp executable. Please set the variable named NODE_GYP_EXECUTABLE.")
-  endif()
-
-  # ensure that the swig version is high enough for javascript
-  if (SWIG_VERSION AND NOT SWIG_VERSION VERSION_GREATER 3.0.1)
-        message(FATAL_ERROR
-"SWIG version 3.0.2 or greater is needed in order to build the JavaScript
-language interface for libSBML, but only version ${SWIG_VERSION} was found.")
-  endif()
-
-endif()
-
-# Add an option to compile with all warnings shown
-option(WITH_WALL     "Compile with -Wall, so that the compiler will display all warnings." OFF)
-mark_as_advanced(WITH_WALL)
-
-if(WITH_WALL)
-    if(MSVC OR USING_INTEL)
-        add_definitions(/W4)
-        string(REPLACE "/W3" "/W4" CMAKE_C_FLAGS "${CMAKE_C_FLAGS}")
-        string(REPLACE "/W3" "/W4" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
-    else()
-        add_definitions(-Wall)
-    endif()
-endif()
-
-# Add an option to instruct libSBML to not include SBMLTypes.h and other files internally.
-option(LIBSBML_USE_STRICT_INCLUDES
-"Compile using 'strict includes' rules: libSBML header files won't
-use SBMLTypes.h, among others." OFF)
-if(LIBSBML_USE_STRICT_INCLUDES)
-  add_definitions(-DLIBSBML_USE_STRICT_INCLUDES)
-endif(LIBSBML_USE_STRICT_INCLUDES)
-mark_as_advanced(LIBSBML_USE_STRICT_INCLUDES)
-
-set(LIBSBML_BUILD_TYPE "native")
-if (CMAKE_SIZEOF_VOID_P EQUAL 4)
-  set(LIBSBML_BUILD_TYPE "32bit")
-else()
-  set(LIBSBML_BUILD_TYPE "64bit")
-endif()
-if (APPLE AND ENABLE_UNIVERSAL)
-  set(LIBSBML_BUILD_TYPE "universal")
-endif()
-
-# When allocation of memory fails or the libSBML C API is unable to open
-# a file, libSBML can exit the current process. By default this behavior
-# is disabled.
-#
-option (EXIT_ON_ERROR "Call exit(-1) in case of allocation or file error." OFF)
-mark_as_advanced(EXIT_ON_ERROR)
-
-# Use the version number in the shared library.
-#
-option (LIBSBML_SHARED_VERSION
-"Include version information into the compiled libSBML shared library." ON)
-mark_as_advanced(LIBSBML_SHARED_VERSION)
-
-# Enable the generation of unit tests. If enabled, all test runners
-# will be created and can be run with "make test" or ctest.
-# This won't work in Visual Studio 2003, so we disable this option there.
-#
-if(NOT ${CMAKE_GENERATOR} MATCHES "Visual Studio 6" AND NOT ${CMAKE_GENERATOR} MATCHES "Visual Studio 7")
-    option(WITH_CHECK
-"Compile the libSBML unit tests. (You can then run the tests with the
-command 'make test' or 'ctest'.)" OFF)
-endif()
-
-# Choose the xml parsing library to be used.
-option(WITH_EXPAT    "Use the Expat XML parser library."     OFF)
-option(WITH_LIBXML   "Use the libxml2 XML parser library."   ON )
-option(WITH_XERCES   "Use the Xerces XML parser library."    OFF)
-
-# Use C++ namespace.
-option(WITH_CPP_NAMESPACE "Use a C++ namespace for libSBML."   OFF)
-
-# Generate documentation.
-option(WITH_DOXYGEN  "Generate documentation for libSBML using Doxygen."  OFF )
-# marks as advanced, so as to hide documentation generation
-mark_as_advanced(WITH_DOXYGEN)
-
-# Re-generate the swig bindings? This really should be on by default
-# otherwise one might have the wrong wrapper code without support for
-# the libsbml packages one wants.
-option(WITH_SWIG     "Regenerate the programming language interface code
-(for Java, Python, etc.) using SWIG."  ON )
-
-# Set build type default.
-set(CMAKE_BUILD_TYPE "Release" CACHE STRING
-  "Choose the type of build to perform. The options are: None (CMAKE_CXX_FLAGS
-or CMAKE_C_FLAGS are used), Debug, Release, RelWithDebInfo, MinSizeRel.")
-if("${CMAKE_BUILD_TYPE}" STREQUAL "")
-  set(CMAKE_BUILD_TYPE "Release" CACHE STRING
-    "Choose the type of build to perform. The options are: None (CMAKE_CXX_FLAGS
-or CMAKE_C_FLAGS are used), Debug, Release, RelWithDebInfo, MinSizeRel." FORCE)
-endif()
-
-# Set the default dependency directory.
-set(LIBSBML_DEPENDENCY_DIR ${LIBSBML_ROOT_SOURCE_DIR}/dependencies/ CACHE PATH
-  "Directory containing libraries that libSBML depends upon.
-(Particularly important on Windows.)")
-if("${LIBSBML_DEPENDENCY_DIR}" STREQUAL "")
-  set(LIBSBML_DEPENDENCY_DIR ${LIBSBML_ROOT_SOURCE_DIR}/dependencies/ CACHE PATH
-    "Directory containing libraries that libSBML depends upon.
-(Particularly important on Windows.)" FORCE)
-endif()
-
-if (WITH_PYTHON)
-    # add option to enable Python API2 (with warnings)
-    option(PYTHON_USE_API2_WARNINGS   "Enable the new Python API2 with warnings."    OFF)
-endif (WITH_PYTHON)
-
-###############################################################################
-#
-# If WITH_SWIG is selected, we need to find swig
-#
-set(LIBSBML_USE_CPP_NAMESPACE OFF)
-if(WITH_CPP_NAMESPACE)
-    add_definitions(-DLIBSBML_USE_CPP_NAMESPACE=1)
-    set(LIBSBML_USE_CPP_NAMESPACE ON)
-endif()
-
-if(WITH_SWIG)
-    find_program(SWIG_EXECUTABLE
-        NAMES swig
-        PATHS
-              c:/swigwin-3.0.10
-              c:/swigwin-3.0.9
-              c:/swigwin-3.0.8
-              c:/swigwin-3.0.7
-              c:/swigwin-3.0.6
-              c:/swigwin-3.0.5
-              c:/swigwin-3.0.4
-              c:/swigwin-3.0.3
-              c:/swigwin-3.0.2
-              c:/swigwin-3.0.1
-              c:/swigwin-2.0.12
-              c:/swigwin-2.0.11
-              c:/swigwin-2.0.10
-              c:/swigwin-2.0.9
-              c:/swigwin-2.0.8
-              c:/swigwin-2.0.7
-              c:/swigwin-2.0.6
-              c:/swigwin-2.0.5
-              c:/swigwin-2.0.4
-              c:/swigwin-2.0.3
-              c:/swigwin-2.0.2
-              c:/swigwin-2.0.1
-              c:/swigwin-2.0.0
-              /usr/local/bin
-              /opt/local/bin
-              /usr/bin
-              "C:/Program Files (x86)/Swig"
-              "C:/Program Files/Swig"
-        DOC "The file name of the SWIG executable."
-        )
-    find_package(SWIG)
-    if (SWIG_FOUND AND SWIG_VERSION VERSION_LESS "2.0.4")
-      message(WARNING
-"You are using SWIG version ${SWIG_VERSION}.  We strongly recommend
-using version 2.0.4 or greater. For libSBML JavaScript support, you
-will need version 3.0.1 at minimum.")
-    endif()
-    set(SWIG_EXTRA_ARGS -DLIBSBML_COMPILED_IN_SRC)
-    add_definitions(-DLIBSBML_COMPILED_IN_SRC)
-    set(SWIG_SWIGDOCDEFINES)
-endif(WITH_SWIG)
-
-
-###############################################################################
-#
-# Locate expat if needed
-#
-
-set(LIBSBML_XML_LIBRARY)
-set(LIBSBML_XML_LIBRARY_INCLUDE)
-set(LIBSBML_XML_LIBRARY_LIBS)
-
-if(WITH_EXPAT)
-  if (NOT LIBEXPAT_LIBRARY)
-    find_library(LIBEXPAT_LIBRARY
-        NAMES libexpat.lib expat
-        PATHS ${LIBSBML_DEPENDENCY_DIR}/lib
-              /usr/lib /usr/local/lib
-              /usr/lib/i386-linux-gnu
-        DOC "The file name of the Expat library."
-                )
-
-  endif()
-
-  if (NOT LIBEXPAT_INCLUDE_DIR)
-    find_path(LIBEXPAT_INCLUDE_DIR
-        NAMES expat.h
-        PATHS ${LIBSBML_DEPENDENCY_DIR}/include
-              /usr/include /usr/local/include
-              ${CMAKE_OSX_SYSROOT}/usr/include
-        DOC "The directory containing the Expat include files."
-              )
-  endif()
-
-    add_definitions( -DUSE_EXPAT )
-    list(APPEND SWIG_EXTRA_ARGS -DUSE_EXPAT)
-
-    set(LIBSBML_XML_LIBRARY "expat")
-    set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBEXPAT_INCLUDE_DIR})
-    set(LIBSBML_XML_LIBRARY_LIBS ${LIBEXPAT_LIBRARY})
-
-    if(NOT EXISTS "${LIBEXPAT_INCLUDE_DIR}/expat.h")
-        message(FATAL_ERROR
-"The include directory specified for Expat appears to be invalid.
-It should contain the file expat.h, but it does not.")
-    else()
-        if (LIBEXPAT_INCLUDE_DIR AND EXISTS "${LIBEXPAT_INCLUDE_DIR}/expat.h")
-            file(STRINGS "${LIBEXPAT_INCLUDE_DIR}/expat.h" expat_version_str
-                 REGEX "^#[\t ]*define[\t ]+XML_(MAJOR|MINOR|MICRO)_VERSION[\t ]+[0-9]+$")
-
-            unset(EXPAT_VERSION_STRING)
-            foreach(VPART MAJOR MINOR MICRO)
-                foreach(VLINE ${expat_version_str})
-                    if(VLINE MATCHES "^#[\t ]*define[\t ]+XML_${VPART}_VERSION[\t ]+([0-9]+)$")
-                        set(EXPAT_VERSION_PART "${CMAKE_MATCH_1}")
-                        if(EXPAT_VERSION_STRING)
-                            set(EXPAT_VERSION_STRING "${EXPAT_VERSION_STRING}.${EXPAT_VERSION_PART}")
-                        else()
-                            set(EXPAT_VERSION_STRING "${EXPAT_VERSION_PART}")
-                        endif()
-                    endif()
-                endforeach()
-            endforeach()
-
-            if (EXPAT_VERSION_STRING VERSION_LESS 1.95.9)
-                     message(FATAL_ERROR
-"Expat version ${EXPAT_VERSION_STRING} is not compatible with libSBML.
-Please use a version newer than 1.95.8 or an alternate XML parser.")
-            endif()
-        endif()
-    endif()
-endif(WITH_EXPAT)
-
-
-###############################################################################
-#
-# Locate Libxml2 if needed
-#
-set(USE_LIBXML OFF)
-if(WITH_LIBXML)
-  if (NOT LIBXML_LIBRARY)
-    find_library(LIBXML_LIBRARY
-        NAMES libxml2.lib xml2
-        PATHS /usr/lib /usr/local/lib
-              ${LIBSBML_DEPENDENCY_DIR}/lib
-        DOC "The file name of the libxml2 library."
-                )
-  endif()
-
-  if (NOT LIBXML_INCLUDE_DIR)
-    find_path(LIBXML_INCLUDE_DIR
-        NAMES libxml/parser.h
-        PATHS ${LIBSBML_DEPENDENCY_DIR}/include
-              /usr/include /usr/local/include
-              /usr/include/libxml2
-              ${CMAKE_OSX_SYSROOT}/usr/include/libxml2
-              /usr/local/include/libxml2
-
-        DOC "The directory containing the libxml2 include files."
-              )
-  endif()
-
-  add_definitions( -DUSE_LIBXML )
-  list(APPEND SWIG_EXTRA_ARGS -DUSE_LIBXML)
-  set(USE_LIBXML ON)
-
-  set(LIBSBML_XML_LIBRARY "libxml2")
-  set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBXML_INCLUDE_DIR})
-  set(LIBSBML_XML_LIBRARY_LIBS ${LIBXML_LIBRARY})
-
-  if(NOT EXISTS "${LIBXML_INCLUDE_DIR}/libxml/parser.h")
-        message(FATAL_ERROR
-"The include directory specified for libxml appears to be invalid.
-It should contain the file libxml/parser.h, but it does not.")
-  endif()
-endif(WITH_LIBXML)
-
-
-###############################################################################
-#
-# Locate xerces
-#
-
-if(WITH_XERCES)
-    add_definitions( -DUSE_XERCES )
-    list(APPEND SWIG_EXTRA_ARGS -DUSE_XERCES)
-
-    find_library(XERCES_LIBRARY
-        NAMES xerces-c_3.lib xerces-c
-        PATHS /usr/lib /usr/local/lib
-              ${LIBSBML_DEPENDENCY_DIR}/lib
-        DOC "The file name of the Xerces library."
-                )
-
-    find_path(XERCES_INCLUDE_DIR
-        NAMES xercesc/parsers/XercesDOMParser.hpp
-        PATHS /usr/include /usr/local/include
-              ${CMAKE_OSX_SYSROOT}/usr/include/xercesc
-              /usr/include/xercesc
-              /usr/local/include/xercesc
-              ${LIBSBML_DEPENDENCY_DIR}/include
-        DOC "The directory containing the Xerces include files."
-              )
-
-    if (EXISTS "${XERCES_INCLUDE_DIR}/xercesc/util/XercesVersion.hpp")
-        function(_myXercesC_GET_VERSION  version_hdr)
-            file(STRINGS ${version_hdr} _contents REGEX "^[ \t]*#define XERCES_VERSION_.*")
-            if(_contents)
-                string(REGEX REPLACE ".*#define XERCES_VERSION_MAJOR[ \t]+([0-9]+).*" "\\1" XercesC_MAJOR "${_contents}")
-                string(REGEX REPLACE ".*#define XERCES_VERSION_MINOR[ \t]+([0-9]+).*" "\\1" XercesC_MINOR "${_contents}")
-                string(REGEX REPLACE ".*#define XERCES_VERSION_REVISION[ \t]+([0-9]+).*" "\\1" XercesC_PATCH "${_contents}")
-
-                if(NOT XercesC_MAJOR MATCHES "^[0-9]+$")
-                    message(FATAL_ERROR "Version parsing failed for XERCES_VERSION_MAJOR!")
-                endif()
-                if(NOT XercesC_MINOR MATCHES "^[0-9]+$")
-                    message(FATAL_ERROR "Version parsing failed for XERCES_VERSION_MINOR!")
-                endif()
-                if(NOT XercesC_PATCH MATCHES "^[0-9]+$")
-                    message(FATAL_ERROR "Version parsing failed for XERCES_VERSION_REVISION!")
-                endif()
-
-                set(XercesC_VERSION "${XercesC_MAJOR}.${XercesC_MINOR}.${XercesC_PATCH}" PARENT_SCOPE)
-            else()
-                message(FATAL_ERROR "Include file ${version_hdr} does not exist or does not contain expected version information")
-            endif()
-        endfunction()
-
-        _myXercesC_GET_VERSION("${XERCES_INCLUDE_DIR}/xercesc/util/XercesVersion.hpp")
-        if (XercesC_VERSION VERSION_EQUAL 2.6.0)
-         message(FATAL_ERROR
-"Xerces version ${XercesC_VERSION} contains known bugs
-and is not compatible with libSBML. Please use a newer version of
-Xerces or an alternate XML parser.")
-        endif()
-    endif ()
-
-    set(LIBSBML_XML_LIBRARY "xerces-c")
-    set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR})
-    set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY})
-
-    if(NOT EXISTS "${XERCES_INCLUDE_DIR}/xercesc/parsers/XercesDOMParser.hpp")
-        message(FATAL_ERROR
-"The include directory specified for Xerces appears to be invalid.
-It should contain the file xercesc/parsers/XercesDOMParser.hpp, but
-it does not.")
-    endif()
-
-endif(WITH_XERCES)
-
-###############################################################################
-#
-# Locate bz2
-#
-
-set(BZIP_INITIAL_VALUE)
-if (NOT LIBBZ_LIBRARY)
-find_library(LIBBZ_LIBRARY
-    NAMES bzip2.lib bz2 libbz2.lib
-    PATHS /usr/lib /usr/local/lib
-          ${CMAKE_OSX_SYSROOT}/usr/lib
-          ${LIBSBML_DEPENDENCY_DIR}/lib
-          NO_DEFAULT_PATH
-          NO_CMAKE_ENVIRONMENT_PATH
-          NO_CMAKE_PATH
-          NO_SYSTEM_ENVIRONMENT_PATH
-          NO_CMAKE_SYSTEM_PATH
-
-          DOC "The file name of the bzip2 library."
-)
-endif()
-if (NOT LIBBZ_LIBRARY)
-find_library(LIBBZ_LIBRARY
-    NAMES bzip2.lib bz2 libbz2.lib
-    PATHS /usr/lib /usr/local/lib
-          ${CMAKE_OSX_SYSROOT}/usr/lib
-          ${LIBSBML_DEPENDENCY_DIR}/lib
-    DOC "The file name of the bzip2 library."
-)
-endif()
-
-if(EXISTS ${LIBBZ_LIBRARY})
-    set(BZIP_INITIAL_VALUE ON)
-else()
-    set(BZIP_INITIAL_VALUE OFF)
-endif()
-
-option(WITH_BZIP2    "Enable the use of bzip2 compression."  ${BZIP_INITIAL_VALUE})
-set(USE_BZ2 OFF)
-if(WITH_BZIP2)
-
-  if (NOT LIBBZ_INCLUDE_DIR)
-    find_path(LIBBZ_INCLUDE_DIR
-        NAMES bzlib.h bzip2/bzlib.h
-        PATHS ${CMAKE_OSX_SYSROOT}/usr/include
-              /usr/include /usr/local/include
-              ${LIBSBML_DEPENDENCY_DIR}/include
-              NO_DEFAULT_PATH
-        DOC "The directory containing the bzip2 include files."
-        )
-  endif()
-
-  if (NOT LIBBZ_INCLUDE_DIR)
-      find_path(LIBBZ_INCLUDE_DIR
-        NAMES bzlib.h bzip2/bzlib.h
-        PATHS ${CMAKE_OSX_SYSROOT}/usr/include
-              /usr/include /usr/local/include
-              ${LIBSBML_DEPENDENCY_DIR}/include
-        DOC "The directory containing the bzip2 include files."
-              )
-  endif()
-
-    set(USE_BZ2 ON)
-    add_definitions( -DUSE_BZ2 )
-  list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2)
-
-    # make sure that we have a valid bzip2 library
-    check_library_exists("${LIBBZ_LIBRARY}" "BZ2_bzCompressInit" "" LIBBZ_FOUND_SYMBOL)
-    if(NOT LIBBZ_FOUND_SYMBOL)
-        # this is odd, but on windows this check always fails! must be a
-        # bug in the current cmake version so for now only issue this
-        # warning on linux
-        if(UNIX)
-            message(WARNING
-"The chosen bz2 library does not appear to be valid because it is
-missing some required symbols. Please check that ${LIBBZ_LIBRARY}
-is the bzip2 library. For details about the error, please see
-${LIBSBML_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log")
-        endif()
-    endif()
-    if(NOT EXISTS "${LIBBZ_INCLUDE_DIR}/bzlib.h")
-        message(FATAL_ERROR
-"The include directory specified for the bz2 library does not
-appear to be valid.  It should contain the file bzlib.h, but
-it does not.")
-    endif()
-
-
-endif(WITH_BZIP2)
-
-
-###############################################################################
-#
-# list of additional files to link against.
-#
-
-set(EXTRA_LIBS "" CACHE STRING
-"List of additional libraries to link against.  Separate multiple
-names using semicolons." )
-set(EXTRA_INCLUDE_DIRS "" CACHE STRING
-"List of additional include directories to use during compilation.
-Separate multiple directories using semicolons." )
-
-
-###############################################################################
-#
-# Locate zlib
-#
-
-set(ZLIB_INITIAL_VALUE)
-if (NOT LIBZ_LIBRARY)
-find_library(LIBZ_LIBRARY
-    NAMES zdll.lib z zlib.lib
-    PATHS /usr/lib /usr/local/lib
-          ${CMAKE_OSX_SYSROOT}/usr/lib
-          ${LIBSBML_DEPENDENCY_DIR}/lib
-          NO_DEFAULT_PATH
-          NO_CMAKE_ENVIRONMENT_PATH
-          NO_CMAKE_PATH
-          NO_SYSTEM_ENVIRONMENT_PATH
-          NO_CMAKE_SYSTEM_PATH
-          DOC "The file name of the zip compression library."
-    )
-endif()
-if (NOT LIBZ_LIBRARY)
-find_library(LIBZ_LIBRARY
-    NAMES zdll.lib z zlib.lib
-    PATHS /usr/lib /usr/local/lib
-          ${CMAKE_OSX_SYSROOT}/usr/lib
-          ${LIBSBML_DEPENDENCY_DIR}/lib
-    DOC "The file name of the zip compression library."
-    )
-endif()
-
-if(EXISTS ${LIBZ_LIBRARY})
-    set(ZLIB_INITIAL_VALUE ON)
-else()
-    set(ZLIB_INITIAL_VALUE OFF)
-endif()
-option(WITH_ZLIB     "Enable the use of zip compression."    ${ZLIB_INITIAL_VALUE} )
-
-set(USE_ZLIB OFF)
-if(WITH_ZLIB)
-
-  if (NOT LIBZ_INCLUDE_DIR)
-    find_path(LIBZ_INCLUDE_DIR
-        NAMES zlib.h zlib/zlib.h
-        PATHS ${CMAKE_OSX_SYSROOT}/usr/include
-              /usr/include /usr/local/include
-              ${LIBSBML_DEPENDENCY_DIR}/include
-              NO_DEFAULT_PATH
-        DOC "The directory containing the zlib include files."
-              )
-  endif()
-    if (NOT LIBZ_INCLUDE_DIR)
-        find_path(LIBZ_INCLUDE_DIR
-        NAMES zlib.h zlib/zlib.h
-        PATHS ${CMAKE_OSX_SYSROOT}/usr/include
-              /usr/include /usr/local/include
-              ${LIBSBML_DEPENDENCY_DIR}/include
-        DOC "The directory containing the zlib include files."
-              )
-    endif()
-    set(USE_ZLIB ON)
-    add_definitions( -DUSE_ZLIB )
-  list(APPEND SWIG_EXTRA_ARGS -DUSE_ZLIB)
-
-    # make sure that we have a valid zip library
-    check_library_exists("${LIBZ_LIBRARY}" "gzopen" "" LIBZ_FOUND_SYMBOL)
-    if(NOT LIBZ_FOUND_SYMBOL)
-        # this is odd, but on windows this check always fails! must be a
-        # bug in the current cmake version so for now only issue this
-        # warning on linux
-        if(UNIX)
-            message(WARNING
-"The chosen zlib library does not appear to be valid because it is
-missing certain required symbols. Please check that ${LIBZ_LIBRARY} is
-the correct zlib library. For details about the error, please see
-${LIBSBML_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log")
-        endif()
-    endif()
-
-    if(NOT EXISTS "${LIBZ_INCLUDE_DIR}/zlib.h")
-        message(FATAL_ERROR
-"The include directory specified for zlib does not appear to be
-valid. It should contain the file zlib.h, but it does not.")
-    endif()
-
-endif(WITH_ZLIB)
-
-
-###############################################################################
-#
-# Find the C# compiler to use and set name for resulting library
-#
-
-if(WITH_CSHARP)
-    FILE(TO_CMAKE_PATH "$ENV{WINDIR}" windir)
-    find_program(CSHARP_COMPILER
-        NAMES gmcs csc mcs
-        PATHS
-            ${windir}/Microsoft.NET/Framework/v2.0.50727/
-            ${windir}/Microsoft.NET/Framework/v3.0/
-            /usr/bin
-            /usr/local/bin
-        DOC "The file name of the C# compiler for the libsbmlcs assembly."
-        )
-    find_program(CSHARP_EXAMPLE_COMPILER
-        NAMES gmcs csc mcs
-        PATHS
-            ${windir}/Microsoft.NET/Framework/v4.0.30319/
-            ${windir}/Microsoft.NET/Framework/v3.5/
-            ${windir}/Microsoft.NET/Framework/v3.0/
-            ${windir}/Microsoft.NET/Framework/v2.0.50727/
-            /usr/bin
-            /usr/local/bin
-        DOC "The file name of the C# compiler to be used for the examples."
-        )
-    if(UNIX)
-    else()
-        if(CMAKE_SIZEOF_VOID_P EQUAL 4)
-            # mark libsbml library as x86
-            set(CSHARP_EXTRA_ARGS -platform:x86 )
-        elseif(CMAKE_SIZEOF_VOID_P EQUAL 8)
-            # mark libsbml library as x64
-            set(CSHARP_EXTRA_ARGS -platform:x64 )
-        endif()
-    endif()
-
-endif(WITH_CSHARP)
-
-
-###############################################################################
-#
-# Enable support for testing ... can be invoked by running ctest
-# or make test
-#
-
-if(WITH_CHECK)
-
-    # we do use tests, that require 2.8.4
-    cmake_minimum_required(VERSION 2.8.4)
-
-    # set test timeout to 3000 as the normal time limit is not sufficient
-    # for the comp tests
-    SET(DART_TESTING_TIMEOUT "3000" CACHE STRING "" FORCE)
-
-    enable_testing()
-
-    find_library(LIBCHECK_LIBRARY
-        NAMES check libcheck
-        PATHS /usr/lib /usr/local/lib ${LIBSBML_DEPENDENCY_DIR}/lib
-        DOC "The file name of the libcheck library."
-    )
-
-    find_path(LIBCHECK_INCLUDE_DIR
-        NAMES check.h
-        PATHS /usr/include /usr/local/include  ${LIBSBML_DEPENDENCY_DIR}/include
-        DOC "The directory containing the libcheck include files."
-              )
-
-    if(NOT EXISTS "${LIBCHECK_INCLUDE_DIR}/check.h")
-        message(FATAL_ERROR
-"The include directory specified for the 'check' library appears to be
-invalid. It should contain the file check.h, but it does not.")
-    endif()
-
-    if(${CMAKE_GENERATOR} MATCHES "Visual Studio 6" OR ${CMAKE_GENERATOR} MATCHES "Visual Studio 7")
-        message(WARNING "Libcheck is not compatible with Visual Studio 2003 (or earlier versions).")
-    endif()
-
-  if (UNIX)
-      # setup valgrind
-      set(CMAKE_MEMORYCHECK_COMMAND valgrind)
-      set(CMAKE_MEMORYCHECK_COMMAND_OPTIONS
-         "--error-exitcode=1 --trace-children=yes --leak-check=full --show-reachable=yes --leak-resolution=high --track-origins=yes --error-limit=no ")
-
-      set(MEMCHECK_COMMAND
-         "${CMAKE_MEMORYCHECK_COMMAND} ${CMAKE_MEMORYCHECK_COMMAND_OPTIONS}")
-      separate_arguments(MEMCHECK_COMMAND)
-
-      # check that check compiles/links - needs cmake 3+
-
-      if(${CMAKE_VERSION} VERSION_GREATER 3.0.0)
-        set(CHECK_CHECK_CODE
-        "
-        #include <check.h>
-        
-        START_TEST (sanity_check)
-        {
-            fail_unless(5 == 5, \"this should succeed\");
-            fail_unless(6 == 5, \"this should fail\");
-        }
-        END_TEST
-        
-        int 
-        main(void)
-        {
-            Suite *s1 = suite_create(\"Core\");
-            TCase *tc1_1 = tcase_create(\"Core\");
-            SRunner *sr = srunner_create(s1);
-            int nf;
-        
-            suite_add_tcase(s1, tc1_1);
-            tcase_add_test(tc1_1, sanity_check);
-        
-            srunner_run_all(sr, CK_ENV);
-            nf = srunner_ntests_failed(sr);
-            srunner_free(sr);
-            ;
-            return nf == 0 ? 0 : 1;
-        }
-        " 
-        )
-
-        set(CMAKE_REQUIRED_LIBRARIES_CACHE ${CMAKE_REQUIRED_LIBRARIES})
-        unset(CHECK_CHECK_TEST CACHE)
-        unset(CHECK_CHECK_TEST2 CACHE)
-
-        set(CHECK_CHECK_TEST)
-        set(CMAKE_REQUIRED_LIBRARIES "-lcheck -lm ${EXTRA_LIBS}")
-        CHECK_C_SOURCE_COMPILES("${CHECK_CHECK_CODE}" CHECK_CHECK_TEST)
-
-        if (NOT CHECK_CHECK_TEST)
-            set(CHECK_CHECK_TEST2)
-            set(CMAKE_REQUIRED_LIBRARIES "-lcheck -lm -pthread -lrt -lsubunit ${EXTRA_LIBS}")
-            CHECK_C_SOURCE_COMPILES("${CHECK_CHECK_CODE}" CHECK_CHECK_TEST2)
-            
-            if (CHECK_CHECK_TEST2)
-                set(CHECK_TMP_LIBS "-pthread -lrt -lsubunit ${EXTRA_LIBS}")
-                string(STRIP "${CHECK_TMP_LIBS}" CHECK_TMP_LIBS)
-                set(EXTRA_LIBS "${CHECK_TMP_LIBS}" CACHE STRING
-                "List of additional libraries to link against.  Separate multiple
-                names using semicolons." FORCE)                
-                unset(CHECK_TMP_LIBS)
-                message(STATUS "Check requires the following EXTRA_LIBS : ${EXTRA_LIBS}")
-            else ()
-                message(WARNING
-"Check cannot compile tests, please specify the correct EXTRA_LIBS for your operating system.")            
-            endif (CHECK_CHECK_TEST2)
-            unset(CHECK_CHECK_TEST2 CACHE)
-
-        endif (NOT CHECK_CHECK_TEST)
-
-        unset(CHECK_CHECK_TEST CACHE)
-        set(CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_FLAGS_CACHE})
-
-      endif(${CMAKE_VERSION} VERSION_GREATER 3.0.0)
-
-  endif(UNIX)
-
-    include(CTest)
-
-endif(WITH_CHECK)
-
-
-###############################################################################
-#
-# Need some variables set up, such as the name for the libSBML
-# library and the Path and file separator characters. The
-# MISC_PREFIX variable will cause libsbml bindings, examples and
-# documentation to be installed in PREFIX/${MISC_PREFIX}.
-#
-
-set( MISC_PREFIX )
-if(UNIX OR CYGWIN)
-    set(PATH_SEP "/")
-    set(FILE_SEP ":")
-    set( MISC_PREFIX "${CMAKE_INSTALL_DATADIR}/libsbml/" )
-    set(LIBSBML_LIBRARY sbml)
-else()
-    set( MISC_PREFIX ".\\" )
-    set(PATH_SEP "\\")
-    set(FILE_SEP ";")
-    if(MINGW)
-        set(LIBSBML_LIBRARY sbml)
-    else()
-        set(LIBSBML_LIBRARY libsbml)
-    endif()
-endif()
-
-# On some Linux  (64bit) systems (64bit) the libraries should be installed into lib64 rather
-# than lib. It will default to 'lib' but can be overwritten.
-
-set(CMAKE_INSTALL_LIBDIR lib CACHE PATH "Full path to the library output directory")
-mark_as_advanced(CMAKE_INSTALL_LIBDIR)
-
-###############################################################################
-#
-# Set up remaining variables, add option for universal binaries
-#
-
-set(USING_INTEL)
-if (WIN32 AND CMAKE_C_COMPILER AND ${CMAKE_C_COMPILER} MATCHES ".*icl.*$")
-  message(STATUS "Detected Intel Compiler")
-  set(USING_INTEL TRUE)
-endif ()
-
-
-set(BUILD_DEFINITIONS)
-if(UNIX)
-    if(APPLE)
-        # on osx starting with xcode 4.3 the system root is in
-        # the app bundle, however cmake (up to 2.8.8) does not seem
-        # to update the path, so lets try it here
-        if (CMAKE_OSX_SYSROOT AND NOT EXISTS ${CMAKE_OSX_SYSROOT})
-          if (EXISTS "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/${CMAKE_OSX_SYSROOT}")
-            set(CMAKE_OSX_SYSROOT "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/${CMAKE_OSX_SYSROOT}" CACHE STRING "The SDK root to be used" FORCE)
-          endif()
-        endif()
-        add_definitions(-DMACOSX)
-        set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DMACOSX")
-
-        # Since we are encountering errors with the use of libc++ on OSX
-        # this option allows to override which stdlib to use
-        if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-          option(CLANG_USE_STDLIB "Use libstdc++ rather than libc++" OFF)
-          if (CLANG_USE_STDLIB)
-            SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++" )
-          endif()
-        endif()
-
-        # On OSX it is common to build universal binaries to support multiple
-        # processor architectures. The default behavior is not to build
-        # multiple architectures, as most users might not need that.
-        option(ENABLE_UNIVERSAL
-          "Create 'universal' binaries on Mac OS X. (Not available on
-other operating systems.)" OFF)
-
-        set(CMAKE_OSX_ARCHITECTURES "${CMAKE_OSX_ARCHITECTURES}" CACHE STRING
-           "A semicolon-separated list of architectures for which libSBML should be built.")
-        if(ENABLE_UNIVERSAL)
-
-            # if universal binaries are requested and none defined so far
-            # overwrite them with all three common architectures. If the user
-            # specified their own list of architectures do not touch!
-            if(CMAKE_OSX_ARCHITECTURES STREQUAL "")
-
-                STRING(REGEX REPLACE "^.*MacOSX([0-9]*\\.[0-9]*)\\.sdk$" "\\1"
-                       OSX_SDK_VERSION "${CMAKE_OSX_SYSROOT}")
-
-                if(OSX_SDK_VERSION  VERSION_EQUAL "10.7" OR
-                   OSX_SDK_VERSION  VERSION_GREATER "10.7" OR
-                   OSX_SDK_VERSION  VERSION_EQUAL "10.8" OR
-                   OSX_SDK_VERSION  VERSION_GREATER "10.8")
-
-                   # OSX Lion no longer supports ppc architecture
-                   set(CMAKE_OSX_ARCHITECTURES "i386;x86_64" CACHE STRING
-                      "A semicolon-separated list of architectures for which libSBML should be built." FORCE)
-
-                elseif(OSX_SDK_VERSION AND OSX_SDK_VERSION  VERSION_LESS "10.7" )
-
-                   set(CMAKE_OSX_ARCHITECTURES "i386;ppc;x86_64" CACHE STRING
-                       "A semicolon-separated list of architectures for which libSBML should be built." FORCE)
-
-                else()
-
-                   set(CMAKE_OSX_ARCHITECTURES "i386;x86_64" CACHE STRING
-                       "A semicolon-separated list of architectures for which libSBML should be built." FORCE)
-
-                endif()
-            endif()
-        endif(ENABLE_UNIVERSAL)
-    else(APPLE)
-        add_definitions(-DLINUX)
-
-        if(NOT CYGWIN)
-            # on cygwin all code is position independent so -fPIC is not needed
-            set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-strict-aliasing -fPIC")
-            set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fno-strict-aliasing -fPIC")
-        endif()
-
-        set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DLINUX")
-    endif(APPLE)
-
-    if(WITH_CHECK)
-        if(CMAKE_VERSION VERSION_GREATER "3.0.0")
-            # https://cmake.org/cmake/help/v3.0/module/CheckCXXSourceCompiles.html
-            # CMAKE_REQUIRED_FLAGS = string of compile command line flags
-            # CMAKE_REQUIRED_DEFINITIONS = list of macros to define (-DFOO=bar)
-            # CMAKE_REQUIRED_INCLUDES = list of include directories
-            # CMAKE_REQUIRED_LIBRARIES = list of libraries to link
-            
-            # <code>       - source code to try to compile, must define 'main'
-            # <var>        - variable to store whether the source code compiled
-            # <fail-regex> - fail if test output matches this regex
-
-            # set(CMAKE_REQUIRED_LIBRARIES "${EXTRA_LIBS}")
-            # CHECK_CXX_SOURCE_COMPILES(<code> <var> [FAIL_REGEX <fail-regex>])
-
-            # set(CMAKE_REQUIRED_LIBRARIES "-lrt -lpthread -lsubunit")
-            # CHECK_CXX_SOURCE_COMPILES(<code> <var> [FAIL_REGEX <fail-regex>])
-
-            # set(CMAKE_REQUIRED_LIBRARIES "-lrt -lpthread")
-            # CHECK_CXX_SOURCE_COMPILES(<code> <var> [FAIL_REGEX <fail-regex>])
-        endif(CMAKE_VERSION VERSION_GREATER "3.0.0")
-        # plan A now extinct
-        #add_subdirectory(dev/utilities/linux-check-libs)
-        #target_link_libraries(${LIBSBML_LIBRARY} ${LIBSBML_LIBS} ${EXTRA_LIBS})
-    endif(WITH_CHECK)
-
-    
-    # not needing these defines, and they do cause warnings
-    # add_definitions( -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\")
-    # set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\"")
-
-else(UNIX)
-    # not needing these defines, and they do cause warnings
-    # add_definitions(-DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"  -DPACKAGE_NAME=\"${PROJECT_NAME}\")
-    add_definitions(-DWIN32 -DLIBSBML_EXPORTS -DLIBLAX_EXPORTS)
-    set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DWIN32 -DLIBSBML_EXPORTS -DLIBLAX_EXPORTS")
-    if(MSVC OR USING_INTEL)
-        add_definitions(-D_CRT_SECURE_NO_WARNINGS -D_CRT_NONSTDC_NO_DEPRECATE)
-        set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -D_CRT_SECURE_NO_WARNINGS")
-        option(WITH_STATIC_RUNTIME "Compile using the static MSVC Runtime." OFF)
-        if(WITH_STATIC_RUNTIME)
-            foreach(flag_var
-                CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
-                CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
-                CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
-                CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
-
-                if(${flag_var} MATCHES "/MD")
-                    string(REGEX REPLACE "/MD" "/MT" ${flag_var} "${${flag_var}}")
-                endif(${flag_var} MATCHES "/MD")
-
-            endforeach(flag_var)
-        add_definitions( -D_MT)
-        endif(WITH_STATIC_RUNTIME)
-
-        # on VS enable multiprocessor build
-        SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /MP")
-
-        # Provide an easy way to use Visual Leak Detector (https://vld.codeplex.com)
-    option(LIBSBML_USE_VLD "When running debug builds with MSVC use Visual Leak Detector." OFF)
-    mark_as_advanced(LIBSBML_USE_VLD)
-    if (LIBSBML_USE_VLD)
-          find_path(VLD_INCLUDE_DIR
-            NAMES vld.h
-            PATHS ${LIBSBML_DEPENDENCY_DIR}/include
-            "$ENV{PROGRAMFILES}/Visual Leak Detector/include"
-            "$ENV{ProgramW6432}/Visual Leak Detector/include"
-            DOC "Directory containing VLD files."
-          )
-          if (NOT VLD_INCLUDE_DIR)
-            message(WARNING "VLD is not found on your system, please ensure you installed it correctly.")
-      else()
-        include_directories(${VLD_INCLUDE_DIR})
-      endif()
-
-      add_definitions( -DLIBSBML_USE_VLD)
-
-    endif (LIBSBML_USE_VLD)
-
-    # CMake no longer creates PDB files for static libraries after 2.8.11
-    # so we store debug information in the object files instead
-    if (${CMAKE_VERSION} VERSION_GREATER "2.8.11")
-            foreach(flag_var
-                CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
-                CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO
-                CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
-                CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
-
-                if(${flag_var} MATCHES "/Zi")
-            STRING(REPLACE "/Zi"  "/Z7" "${flag_var}" "${${flag_var}}")
-                endif(${flag_var} MATCHES "/Zi")
-
-            endforeach(flag_var)
-        # add /bigobj to allow debug builds to work with swig and packages
-        ADD_DEFINITIONS(/bigobj)
-        SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /bigobj")
-        SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} /bigobj")
-    endif()
-
-        file(GLOB WIN32_BINARIES ${LIBSBML_DEPENDENCY_DIR}/bin/*.dll)
-        INSTALL(FILES ${WIN32_BINARIES} DESTINATION bin)
-        file(GLOB WIN32_DEPENDENCIES ${LIBSBML_DEPENDENCY_DIR}/lib/*.lib)
-        install(FILES ${WIN32_DEPENDENCIES} DESTINATION lib)
-        if(WITH_LIBXML)
-      if (EXTRA_LIBS STREQUAL "")
-        # populate EXTRA_LIBS variable
-              find_library(LIBICONV_LIBRARY
-                NAMES libiconv.lib iconv.lib iconv
-                PATHS /usr/lib /usr/local/lib
-                      ${CMAKE_OSX_SYSROOT}/usr/lib
-                      ${LIBSBML_DEPENDENCY_DIR}/lib
-                DOC "The file name of the libiconv library."
-              )
-
-        set(ADDITIONAL_LIBS)
-        if (EXISTS ${LIBICONV_LIBRARY})
-        set(ADDITIONAL_LIBS "${ADDITIONAL_LIBS}${LIBICONV_LIBRARY};")
-        endif()
-        if (EXISTS ${LIBZ_LIBRARY})
-        set(ADDITIONAL_LIBS "${ADDITIONAL_LIBS}${LIBZ_LIBRARY};")
-        endif()
-        set(EXTRA_LIBS "WS2_32.lib;${ADDITIONAL_LIBS}" CACHE STRING "List of additional libraries to link against." FORCE)
-      endif()
-    endif()
-    elseif(CYGWIN)
-        add_definitions(-DCYGWIN)
-        set(BUILD_DEFINITIONS "${BUILD_DEFINITIONS} -DCYGWIN")
-    elseif(MINGW)
-        if(WITH_LIBXML)
-            # this is necessary to build with libxml2 on mingw
-            add_definitions(-DLIBXML_STATIC)
-        endif(WITH_LIBXML)
-    endif(MSVC OR USING_INTEL)
-
-endif(UNIX)
-
-
-###############################################################################
-#
-# Disable in-source build
-#
-
-if("${LIBSBML_ROOT_SOURCE_DIR}" STREQUAL "${LIBSBML_ROOT_BINARY_DIR}" )
-    message(FATAL_ERROR "In-source builds of libSBML are disabled.
-Please create a separate build directory.")
-endif()
-
-
-###############################################################################
-#
-# Add check that only one XML library was selection
-#
-
-set(LIBRARY_COUNT 0)
-if(WITH_EXPAT)
-    math(EXPR LIBRARY_COUNT "${LIBRARY_COUNT} + 1")
-endif()
-if(WITH_LIBXML)
-    math(EXPR LIBRARY_COUNT "${LIBRARY_COUNT} + 1")
-endif()
-if(WITH_XERCES)
-    math(EXPR LIBRARY_COUNT "${LIBRARY_COUNT} + 1")
-endif()
-
-if(LIBRARY_COUNT GREATER 1)
-    message(FATAL_ERROR
-"Only one XML library should be chosen. Please select only one of the
-following options: WITH_LIBXML, WITH_EXPAT or WITH_XERCES.")
-endif()
-
-
-###############################################################################
-#
-# Add check that at least one XML library was selection
-#
-
-if(LIBRARY_COUNT EQUAL 0)
-    message(FATAL_ERROR
-"A XML library must be selected. Please select one of the following
-options: WITH_LIBXML, WITH_EXPAT or WITH_XERCES.")
-endif()
-
-###############################################################################
-#
-# Include options for all libSBML packages
-#
-set(LIBSBML_PACKAGE_INCLUDES)
-set(LIBSBML_PACKAGE_SUMMARY)
-file(GLOB PACKAGE_OPTIONS "*package.cmake")
-foreach(package ${PACKAGE_OPTIONS})
-    include(${package})
-endforeach()
-
-if (LIBSBML_PACKAGE_INCLUDES)
-  list(REMOVE_DUPLICATES LIBSBML_PACKAGE_INCLUDES)
-endif()
-
-###############################################################################
-#
-# Build the actual libSBML library
-#
-
-add_subdirectory(src)
-
-
-###############################################################################
-#
-# Build examples if specified
-#
-
-if(WITH_EXAMPLES)
-
-    # code that builds the examples
-    add_subdirectory(examples)
-
-endif(WITH_EXAMPLES)
-
-
-if(WITH_DOXYGEN)
-    add_subdirectory(docs)
-endif()
-
-
-###############################################################################
-#
-# Install documentation
-#
-
-set(DOCUMENTATION_FILES
-        COPYING.txt
-        FUNDING.txt
-        LICENSE.txt
-        NEWS.txt
-        OLD_NEWS.txt
-        README.txt
-        VERSION.txt
-)
-
-install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})
-
-###############################################################################
-#
-# Write libsbml.pc
-#
-
-set (PRIVATE_LIBS "-lstdc++ -lm")
-if (WITH_ZLIB)
-set (PRIVATE_LIBS "${LIBZ_LIBRARY} ${PRIVATE_LIBS}")
-endif()
-if (WITH_BZIP2)
-set (PRIVATE_LIBS "${LIBBZ_LIBRARY} ${PRIVATE_LIBS}")
-endif()
-if (WITH_LIBXML)
-set (PRIVATE_LIBS "${LIBXML_LIBRARY} ${PRIVATE_LIBS}")
-endif()
-if (WITH_EXPAT)
-set (PRIVATE_LIBS "${LIBEXPAT_LIBRARY} ${PRIVATE_LIBS}")
-endif()
-if (WITH_XERCES)
-set (PRIVATE_LIBS "${XERCES_LIBRARY} ${PRIVATE_LIBS}")
-endif()
-
-file(WRITE  "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Name: ${PACKAGE_NAME}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Description: A library for reading/writing/manipulating SBML\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "URL: http://sbml.org/Software/libSBML\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Version: ${PACKAGE_VERSION}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "prefix=${CMAKE_INSTALL_PREFIX}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "libdir=${CMAKE_INSTALL_FULL_LIBDIR}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "includedir=${CMAKE_INSTALL_FULL_INCLUDEDIR}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Libs: -L\${libdir} -lsbml\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Libs.private:        ${PRIVATE_LIBS}\n")
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Cflags: -I\${includedir}\n")
-if (WITH_XERCES)
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Conflicts: xerces-c = 2.6.0\n")
-endif()
-
-if (WITH_LIBXML)
-file(APPEND "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc" "Requires.private: libxml-2.0 >= 2.6.22\n")
-endif()
-
-if (UNIX)
-install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libsbml.pc"
-        DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-endif()
-
-###############################################################################
-#
-# Print Summary
-#
-if (NOT HOSTNAME)
- site_name(HOSTNAME)
-endif()
-
-message(STATUS "
-----------------------------------------------------------------------
-libSBML version ${PACKAGE_VERSION}
-----------------------------------------------------------------------
-
-   More information and the latest version are available online at
-   http://sbml.org/Software/libSBML
-
-   Please report problems using the issue tracker at
-   http://sbml.org/Software/libsbml/issue-tracker
-
-   To contact the developers directly, email lib...@go...
-
-   Configured on host '${HOSTNAME}'
-     host type                       = ${CMAKE_SYSTEM_NAME}
-     host operating system           = ${CMAKE_SYSTEM_NAME} ${CMAKE_SYSTEM_VERSION}
-     host CPU architecture           = ${CMAKE_SYSTEM_PROCESSOR}
-
-   General build flags:
-     CC                              = ${CMAKE_C_COMPILER}
-     CXX                             = ${CMAKE_CXX_COMPILER}
-     CPPFLAGS                        = ${BUILD_DEFINITIONS}
-     CFLAGS                          = ${CMAKE_C_FLAGS}
-     CXXFLAGS                        = ${CMAKE_CXX_FLAGS}
-     LDFLAGS                         = ${CMAKE_EXE_LINKER_FLAGS}
-
-   XML parser library configuration:
-     XML library                     = ${LIBSBML_XML_LIBRARY}
-     CPPFLAGS for XML                = -I${LIBSBML_XML_LIBRARY_INCLUDE}
-     LIBS for XML                    = ${LIBSBML_XML_LIBRARY_LIBS}
-
-   Other libSBML configuration settings:
-     Installation $prefix            = ${CMAKE_INSTALL_PREFIX}")
-
-if(UNIX)
-    if(APPLE)
-        message(STATUS "     Value of $DYLD_LIBRARY_PATH     = $ENV{DYLD_LIBRARY_PATH}")
-    else()
-        message(STATUS "     Value of $LD_LIBRARY_PATH       = $ENV{LD_LIBRARY_PATH}")
-    endif()
-endif()
-
-if(WITH_SWIG)
-    message(STATUS "     Using SWIG                      = ${SWIG_EXECUTABLE} (Version ${SWIG_VERSION})")
-
-    if (SWIG_FOUND AND SWIG_VERSION VERSION_LESS "2.0.4")
-      message(WARNING "   You are using SWIG version ${SWIG_VERSION}. We strongly recommend at least version 2.0.4.")
-    endif()
-
-endif()
-
-
-if(WITH_CSHARP)
-    message(STATUS "     Using C#                        = ${CSHARP_COMPILER}")
-endif()
-
-if(WITH_JAVA)
-    message(STATUS "     Using Java                      = ${Java_JAVA_EXECUTABLE}")
-endif()
-
-if(WITH_JAVASCRIPT)
-    message(STATUS "     Using Node.js                   = ${NODE_GYP_EXECUTABLE}")
-endif()
-
-if(WITH_PYTHON)
-    message(STATUS "     Using Python                    = ${PYTHON_EXECUTABLE}")
-endif()
-
-if(WITH_PERL)
-    message(STATUS "     Using Perl                      = ${PERL_EXECUTABLE}")
-endif()
-
-if(WITH_RUBY)
-    message(STATUS "     Using Ruby                      = ${RUBY_EXECUTABLE}")
-endif()
-
-if(WITH_OCTAVE)
-    message(STATUS "     Using Octave                    = ${MKOCTFILE_EXECUTABLE}")
-endif()
-
-if(WITH_MATLAB)
-    message(STATUS "     Using Matlab                    = ${MATLAB_ROOT_PATH}")
-endif()
-
-if(WITH_R)
-    message(STATUS "     Using R                         = ${R_INTERPRETER}")
-endif()
-
-if(WITH_PHP)
-    message(STATUS "     Using PHP                       = yes")
-endif()
-
-if(WITH_CHECK)
-    message(STATUS "     Using libcheck                  = ${LIBCHECK_LIBRARY}")
-endif()
-
-if(WITH_CPP_NAMESPACE)
-    message(STATUS "     Using C++ namespace ('libsbml') = yes")
-else()
-    message(STATUS "     Using C++ namespace ('libsbml') = no")
-endif()
-
-if(APPLE)
-    if(CMAKE_OSX_ARCHITECTURES STREQUAL "")
-        message(STATUS "     Building 'universal' binaries   = no (using native arch)")
-    else()
-        list(REMOVE_DUPLICATES CMAKE_OSX_ARCHITECTURES)
-        list(REMOVE_ITEM CMAKE_OSX_ARCHITECTURES "")
-        list(SORT CMAKE_OSX_ARCHITECTURES)
-        list(LENGTH CMAKE_OSX_ARCHITECTURES NUM_ARCHS)
-        if(NUMARCHS EQUAL 1)
-            message(STATUS "     Building 'universal' binaries   = no (using ${CMAKE_OSX_ARCHITECTURES})")
-        else()
-            message(STATUS "     Building 'universal' binaries   = yes (using ${CMAKE_OSX_ARCHITECTURES})")
-        endif()
-    endif()
-endif()
-
-message(STATUS "")
-if(WITH_EXAMPLES)
-  message(STATUS "     Build examples                  = yes")
-else()
-  message(STATUS "     Build examples                  = no")
-endif()
-
-message(STATUS "")
-
-if(PYTHON_USE_API2_WARNINGS)
-  message(STATUS "")
-  message(STATUS "     Using Python API2 warnings      = yes")
-endif(PYTHON_USE_API2_WARNINGS)
-
-if (LIBSBML_PACKAGE_SUMMARY)
-  message(STATUS "")
-  message(STATUS "   Support for SBML Level 3 Packages: ")
-  foreach(summary ${LIBSBML_PACKAGE_SUMMARY})
-    message(STATUS "     ${summary}")
-  endforeach()
-endif(LIBSBML_PACKAGE_SUMMARY)
-
-message(STATUS "
-")
-message(STATUS "Other potentially important settings:")
-if(WITH_ZLIB)
-    message(STATUS "  Compression support is enabled for .zip and .gz files")
-else()
-    message(STATUS "
-Warning: reading/writing compressed SBML in .zip or .gz format in
-this copy of libSBML is not supported or has been disabled.
-If this was not your intention, please check the WITH_ZLIB
-option.")
-endif()
-
-if(WITH_BZIP2)
-    message(STATUS "  Compression support is enabled for .bz2 files")
-else()
-    message(STATUS "
-Warning: reading/writing compressed SBML in .bz2 format in
-this copy of libSBML is not supported or has been disabled.
-If this was not your intention, please check the WITH_BZIP2
-option.")
-endif()
-
-message(STATUS "
-----------------------------------------------------------------------")
-
-
-## Add uninstall target
-## as available from http://www.cmake.org/Wiki/RecipeAddUninstallTarget
-CONFIGURE_FILE(
-  "${CMAKE_CURRENT_SOURCE_DIR}/cmake_uninstall.cmake.in"
-  "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
-  IMMEDIATE @ONLY)
-ADD_CUSTOM_TARGET(uninstall
-  "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake")
-
-if (EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/dev/utilities/sboTree/updateSBO.cmake")
-# add update_sbo target
-ADD_CUSTOM_TARGET(update_sbo
-  "${CMAKE_COMMAND}"
-      -DSRC_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
-      -DPYTHON_EXECUTABLE="${PYTHON_EXECUTABLE}"
-      -P "${CMAKE_CURRENT_SOURCE_DIR}/dev/utilities/sboTree/updateSBO.cmake")
-endif()
-## To compile a test program simply comment out the lines below ...
-#
-#OPTION(WITH_TEST_PROGRAM " COMPILE SMALL TEST PROGRAM " ON)
-#
-#if(WITH_TEST_PROGRAM)
-#
-#include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-#
-#add_executable(libsbml_test test.cpp)
-#target_link_libraries(libsbml_test ${LIBSBML_LIBRARY}-static)
-#
-#endif()
-#

Deleted: trunk/libsbml/COPYING.html
===================================================================
--- trunk/libsbml/COPYING.html	2021-10-23 00:01:15 UTC (rev 26317)
+++ trunk/libsbml/COPYING.html	2022-07-13 16:54:48 UTC (rev 26318)
@@ -1,618 +0,0 @@
-<html>
-<body>
-
-<table width="325">
-  <tr>
-    <td width="325">
-<font size="-1">
-<center>
-<h2 align=center>GNU LESSER GENERAL PUBLIC LICENSE</h2>
-<h3 align=center>Version 2.1, February 1999</h3>
-</center>
-
-<p>
-Copyright (C) 1991, 1999 Free Software Foundation, Inc.
-51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-<p>
-Everyone is permitted to copy and distribute verbatim copies
-of this license document, but changing it is not allowed.
-
-<p>
-[This is the first released version of the Lesser GPL.  It also counts
-as the successor of the GNU Library Public License, version 2, hence
-the version number 2.1.]
-
-<p>
-<center>Preamble</center>
-
-<p>
-  The licenses for most software are designed to take away your
-freedom to share and change it.  By contrast, the GNU General Public
-Licenses are intended to guarantee your freedom to share and change
-free software--to make sure the software is free for all its users.
-
-<p>
-  This license, the Lesser General Public License, applies to some
-specially designated software packages--typically libraries--of the
-Free Software Foundation and other authors who decide to use it.  You
-can use it too, but we suggest you first think carefully about whether
-this license or the ordinary General Public License is the better
-strategy to use in any particular case, based on the explanations
-below.
-
-<p>
-  When we speak of fre...
 
[truncated message content]