Merge branch 'develop' into more_on_distro

Conflicts:
	AUTHORS.txt
	LICENSE.txt
	NEWS.txt
	NOTICE.txt
	README.txt
	VERSION.txt
	plugins/CMakeLists.txt
	plugins/wrappers/Python/CMakeLists.txt
	wrappers/Python/CMakeLists.txt

AUTHORS.txt

@@ -0,0 +1,30 @@
+The orginal C# version of roadRunner was developed as part of the SBW project by
+
+    Herbert M Sauro and Frank Bergmann
+
+The current version of roadRunner, now renamed libRoadRunner, was rewritten and 
+considerably modified and enhanced in C/C++ by
+
+    Andy Somogyi, Totte Karlsson and Herbert M Sauro
+
+The Python interface to the C API was developed by
+
+    Greg Medlock ([email protected]), Totte Karlsson and Herbert M Sauro
+
+The Python SWIG interface to the C++ API was developed by
+
+    Andy Somogyi
+
+The LLVM backend and refactoring of the core was designed and undertaken by
+
+    Andy Somogyi
+
+The C backend was ported to C++ by
+
+    Totte Karlsson
+
+The Plugin Framework was designed and developed by
+
+    Totte Karlsson
+
+For more information visit libroadRunner.org

CMakeLists.txt

@@ -67,10 +67,10 @@ endif()
 option (BUILD_TEST_TOOLS "Build and install test tools" OFF)
 
 # should we use LLVM ?
-option (BUILD_LLVM "Build the LLVM back end" OFF)
+option (BUILD_LLVM "Build the LLVM back end" ON)
 
 # should we build the swig python wrapper?
-option (BUILD_SWIG_PYTHON "build the *EXPERIMENTAL* SWIG generated python wrapper" OFF)
+option (BUILD_PYTHON "build the SWIG generated python wrapper" OFF)
 
 if(BUILD_LLVM AND NOT LLVM_FOUND)
     message(FATAL_ERROR "BUILD_LLVM is enabled, but no LLVM installation was found")
@@ -80,7 +80,7 @@ mark_as_advanced(
     INSTALL_APPS
     INSTALL_CXX_API
     INSTALL_C_API
-    INSTALL_PYTHON
+    INSTALL_C_API_PYTHON
     INSTALL_STATIC_LIB
     )
 
@@ -89,16 +89,16 @@ set(RR_ROADRUNNER_INSTALL_PATH ${CMAKE_INSTALL_PREFIX})
 set(RR_ROADRUNNER_INSTALL_LIB_PATH ${RR_ROADRUNNER_INSTALL_PATH}/lib)
 set(RR_SOURCE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
 
-OPTION (INSTALL_CXX_API          "Generate C++ api"                        ON )
-OPTION (INSTALL_C_API            "Generate C API"                          ON )
-OPTION (INSTALL_PYTHON           "Package Python wrapper"                  ON )
-OPTION (INSTALL_APPS             "Build and install Apps"                  ON )
-OPTION (INSTALL_EXAMPLES         "Build and install Examples"              OFF)
-OPTION (INSTALL_STATIC_LIB       "Install RoadRunner CXX static lib"       OFF)
-OPTION (RR_BUILD_SHARED_CORE     "Build RoadRunner Core Shared library"    OFF)
-OPTION (BUILD_TESTS              "Build the SBML C API test suite"         OFF)
-OPTION (INSTALL_SBML_MODELS      "Install SBML Models"                     ON )
-OPTION (BUILD_PLUGINS            "Build and Install Plugins"               OFF )
+OPTION (INSTALL_CXX_API          "Generate C++ api"                               ON )
+OPTION (INSTALL_C_API            "Generate C API"                                 ON )
+OPTION (INSTALL_C_API_PYTHON     "Package ctypes  Python wrapper for the C API"   ON )
+OPTION (INSTALL_APPS             "Build and install Apps"                         ON )
+OPTION (INSTALL_EXAMPLES         "Build and install Examples"                     OFF)
+OPTION (INSTALL_STATIC_LIB       "Install RoadRunner CXX static lib"              OFF)
+OPTION (RR_BUILD_SHARED_CORE     "Build RoadRunner Core Shared library"           OFF)
+OPTION (BUILD_TESTS              "Build the SBML C API test suite"                OFF)
+OPTION (INSTALL_SBML_MODELS      "Install SBML Models"                            ON )
+OPTION (BUILD_PLUGINS            "Build and Install Plugins"                      OFF)
 
 #Setup so that roadrunner is always built as a dll and linked statically with 'as much as possible'
 set(BUILD_SHARED_LIBS            ON)
@@ -268,7 +268,7 @@ if(INSTALL_CXX_API)
         COMPONENT rr_core)
 endif(INSTALL_CXX_API)
 
-install(FILES Readme.txt License.txt
+install(FILES README.txt LICENSE.txt AUTHORS.txt
         DESTINATION .
         COMPONENT info
         )
@@ -294,10 +294,18 @@ foreach(runtime ${RUNTIMES})
 endforeach()
 endif()
 
-install(    FILES     
-NOTICE.txt
-VERSION.txt
-NEWS.txt
-COPYING.txt
-DESTINATION .)
+install(
+    FILES     
+    NOTICE.txt
+    VERSION.txt
+    NEWS.txt
+    COPYING.txt
+    DESTINATION .
+)
+
 
+if(WIN32)
+    install(
+        FILES win32_bin_README.txt DESTINATION bin/ RENAME README.txt
+    )
+endif(WIN32)

FUNDING.txt

@@ -0,0 +1,3 @@
+
+The development of libRoadRunner was funded through generous support
+of the NIH/NIGMS. Grant Number: GM081070

LICENSE.txt

@@ -0,0 +1,33 @@
+Licensing and Distribution Terms for RoadRunner
+ * Copyright (C) 2012-2013
+ *   University of Washington, Seattle, WA, USA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * In plain english this means:
+ *
+ * You CAN freely download and use this software, in whole or in part, for personal,
+ * company internal, or commercial purposes;
+ *
+ * You CAN use the software in packages or distributions that you create.
+ *
+ * You SHOULD include a copy of the license in any redistribution you may make;
+ *
+ * You are NOT required include the source of software, or of any modifications you may
+ * have made to it, in any redistribution you may assemble that includes it.
+ *
+ * YOU CANNOT:
+ *
+ * redistribute any piece of this software without proper attribution;
+
+

NEWS.txt

@@ -0,0 +1,2 @@
+Dec 10 2013
+    This file was added and Version 1.0.0 is released (TK)

NOTICE.txt

@@ -0,0 +1,97 @@
+   libRoadRunner v 1.0
+   Copyright 2013 Andy Somogyi, Totte Karlsson, Herbert Sauro
+
+
+This product makes use of the following software packages:
+
+libSBML
+    Copyright (C) 2009-2013 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
+    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 and associated examples.)
+    http://sbml.org/Software/libSBML/LibSBML_License
+    California Institute of Technology, Pasadena, CA, USA and others. 
+
+POCO
+    Distributed under the Boost License
+    http://pocoproject.org/license.html
+
+SUNDIALS
+    Copyright (c) 2002, The Regents of the University of California. 
+    Produced at the Lawrence Livermore National Laboratory.
+    Distributed uner BSD License
+    http://computation.llnl.gov/casc/sundials/download/license.html
+
+NLEQ2
+    KONRAD-ZUSE-ZENTRUM FUR INFORMATIONSTECHNIK (ZIB)
+    BERLIN
+
+     Licence
+       You may use or modify this code for your own non commercial
+       purposes for an unlimited time. In any case you should not deliver 
+       this code without a special permission of ZIB. In case you intend 
+       to use the code commercially, we oblige you to sign an according 
+       licence agreement with ZIB.
+
+    http://www.zib.de/en/numerik/software/ant/nleq2.html   
+
+CLAPACK
+    Copyright (c) 1992-2008 The University of Tennessee.  All rights reserved.
+    Distributed under the modified BSD Licesne
+    http://www.netlib.org/lapack/LICENSE.txt
+
+LMFIT Package
+    Copyrighted by Joachim Wuttke
+    Distributed under the FreeBSD License.
+    http://apps.jcns.fz-juelich.de/doku/sc/lmfit
+
+tcc Tiny C Compiler
+    Copyright (c) 2001-2009 Fabrice Bellard
+    Distributed under the GNU Lesser General Public License.
+    http://bellard.org/tcc/
+
+LibStruct
+    Distributed under the BSD license
+    http://sourceforge.net/p/libstruct/wiki/Home/
+
+LLVM
+    Copyright (c) 2003-2013 University of Illinois at Urbana-Champaign.
+    All rights reserved.
+
+    Developed by:
+        LLVM Team
+        University of Illinois at Urbana-Champaign
+        http://llvm.org
+
+    License:
+        The University of Illinois/NCSA Open Source License
+        http://opensource.org/licenses/UoI-NCSA.php
+
+
+libxml2
+    Copyright (C) 1998-2012 Daniel Veillard.  All Rights Reserved.
+    Distributed under the MIT License;
+    http://www.xmlsoft.org/index.html
+
+libiconv
+    Copyright (C) 2007 Free Software Foundation, Inc.
+    GNU GENERAL PUBLIC LICENSE Version 3
+    http://www.gnu.org/software/libiconv/
+
+zlib
+    Copyright (C) 1995-2013 Jean-loup Gailly and Mark Adler
+    Distributed under the zlib License http://opensource.org/licenses/Zlib
+    http://zlib.net/
+
+libbzip2
+    Copyright (C) 1996-2010 Julian R Seward. 
+    Distributed under the BSD-style license
+    http://www.bzip.org/

README.txt

@@ -0,0 +1,77 @@
+libRoadRunner
+Copyright 2013
+
+E. T. Somogyi 1, M. T. Karlsson 2, M. Swat 1, M. Galdzicki 3 and H. M Sauro 3
+
+1 Biocomplexity Institute, Indiana University, Simon Hall MSB1, Bloomington, IN 47405
+2 Dune Scientific, 10522 Lake City Way NE, #302 Seattle WA
+3 Department of Bioengineering, University of Washington, Seattle, WA, 98195
+
+libRoadRunner high performance and portable simulation engine for systems and synthetic biology.
+
+libRoadRunner 1.0 supports the following features:
+
+- Time Dependent Simulation (with optional conservation law reduction) using CVODE
+- Supports SBML Level 2 to 3 but currently excludes algebraic rules and delay differential equations
+- Uses latest libSBML distribution
+- Defaults to LLVM code generation on the backend, resulting is very fast simulation times
+- Optional generation of model C code and linking at run-time
+- Add plugins, distribution comes with Levenberg-Marquardt optimizer plugin
+- Compute steady state
+- Metabolic Control Analysis
+- Frequency Domain Analysis
+- Access to:
+  - Eigenvalues and Eigenvectors
+  - Jacobian, full and reduced
+  - Structural Matrices of the stoichiometry matrix
+
+
+Availability
+
+RoadRunner is licensed for free as an open source programmatic library for use in other 
+applications and as a standalone command line driven application. Its C++ API, C API, and 
+Python APIs have comprehensive documentation. On Windows, OS X, and Linux binary files can be 
+
+downloaded from http://sourceforge.net/projects/libroadrunner/files and can be installed 
+ready for use.
+
+
+Acknowledgements
+
+This work is funded by NIGMS grant: GM081070
+
+Licence
+
+Licensed under the Apache License, Version 2.0 (the License); you may not use this 
+file except in compliance with the License. You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software distributed 
+under the License is distributed on an �AS IS BASIS, WITHOUT WARRANTIES OR CONDITIONS 
+OF ANY KIND, either express or implied. See the License for the specific language 
+governing permissions and limitations under the License.
+
+In plain english this means:
+
+You CAN freely download and use this software, in whole or in part, for personal, 
+company internal, or commercial purposes;
+
+You CAN use the software in packages or distributions that you create.
+
+You SHOULD include a copy of the license in any redistribution you may make;
+
+You are NOT required include the source of software, or of any modifications you may 
+have made to it, in any redistribution you may assemble that includes it.
+
+YOU CANNOT: redistribute any piece of this software without proper attribution;
+
+
+
+
+libRoadRunner logo
+
+  The libroadrunner logo is an adaptation of the image originally posted to Flickr by 
+  El Brujo+ at http://flickr.com/photos/11039104@N08/2954808342. It was reviewed on 
+  9 August 2009 by the FlickreviewR robot and was confirmed to be licensed under the 
+  terms of the cc-by-sa-2.0.

VERSION.txt

@@ -0,0 +1 @@
+1.0.0

models/CMakeLists.txt

@@ -3,6 +3,7 @@ cmake_minimum_required(VERSION 2.8)
 PROJECT(rrModels)
 
 set(models
+README.txt
 bistable.xml
 feedback.xml
 sbml_test_0001.xml