diff --git a/AUTHORS.txt b/AUTHORS.txt new file mode 100644 index 0000000000..23b9a891e0 --- /dev/null +++ b/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 (gmedlo@uw.edu), 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 diff --git a/CMakeLists.txt b/CMakeLists.txt index 20efc96f1e..9189d96bf4 100644 --- a/CMakeLists.txt +++ b/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) diff --git a/FUNDING.txt b/FUNDING.txt new file mode 100644 index 0000000000..dd559deeb7 --- /dev/null +++ b/FUNDING.txt @@ -0,0 +1,3 @@ + +The development of libRoadRunner was funded through generous support +of the NIH/NIGMS. Grant Number: GM081070 \ No newline at end of file diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000000..63e3d35956 --- /dev/null +++ b/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; + + diff --git a/NEWS.txt b/NEWS.txt new file mode 100644 index 0000000000..c076cba317 --- /dev/null +++ b/NEWS.txt @@ -0,0 +1,2 @@ +Dec 10 2013 + This file was added and Version 1.0.0 is released (TK) diff --git a/NOTICE.txt b/NOTICE.txt new file mode 100644 index 0000000000..d6333f671b --- /dev/null +++ b/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/ diff --git a/README.txt b/README.txt new file mode 100644 index 0000000000..174b16fb99 --- /dev/null +++ b/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 ÎAS 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. diff --git a/VERSION.txt b/VERSION.txt new file mode 100644 index 0000000000..3eefcb9dd5 --- /dev/null +++ b/VERSION.txt @@ -0,0 +1 @@ +1.0.0 diff --git a/models/CMakeLists.txt b/models/CMakeLists.txt index a5f46d1b84..15ea3fd041 100644 --- a/models/CMakeLists.txt +++ b/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 diff --git a/models/README.txt b/models/README.txt new file mode 100644 index 0000000000..2977a7e65c --- /dev/null +++ b/models/README.txt @@ -0,0 +1,78 @@ +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 ÎAS 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. diff --git a/models/Readme.txt b/models/Readme.txt index f7b12edd24..d06627a97a 100644 --- a/models/Readme.txt +++ b/models/Readme.txt @@ -1,5 +1,78 @@ -This folder contain a few SBML models for demonstration and testing. -You can simulate any of these models by using rr.exe command line client as the simulator, e.g. - rr.exe -msbml_test_1.xml +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 ÎAS 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. diff --git a/plugins/CMakeLists.txt b/plugins/CMakeLists.txt index 2f4e95835c..1a6b5ad928 100644 --- a/plugins/CMakeLists.txt +++ b/plugins/CMakeLists.txt @@ -29,7 +29,7 @@ endif() add_subdirectory(wrappers) -install(FILES Readme.txt -DESTINATION plugins +install( + FILES README.txt + DESTINATION plugins ) - diff --git a/plugins/README.txt b/plugins/README.txt new file mode 100644 index 0000000000..039907c201 --- /dev/null +++ b/plugins/README.txt @@ -0,0 +1,14 @@ + +This directory contains to sample plugins: + +1. rrp_lm.dll + +This supports the Levenberg-Marquardt optimizer for fitting data to models. +See libroadrunner.org for details. + +2. rrp_add_noise.dll + +This plugin can be used to generate Gaussian noise, useful for generating synthetic data sets to test +the rrp_lm.dll. See libroadrunner.org for details. + + diff --git a/plugins/Readme.txt b/plugins/Readme.txt index d34a201dd3..2615d60c90 100644 --- a/plugins/Readme.txt +++ b/plugins/Readme.txt @@ -1,14 +1,14 @@ -PLUGINS -The shared libraries in this folders are RoadRunner plugins. -They are to be loaded with a plugin manager, see http://docs.libroadrunner.org/c++_plugin_api_docs/html/index.html -Brief descriptions -rrp_add_noise - This plugin can be used to add artificial noise to synthetic data. +This directory contains to sample plugins: -rrp_lm - This plugin is used to fit model parameters to 'observed' data. +1. rrp_lm.dll + +This supports the Levenberg-Marquardt optimizer for fitting data to models. +See libroadrunner.org for details. + +2. rrp_add_noise.dll + +This plugin can be used to generate Gaussian noise, useful for generating synthetic data sets to test +the rrp_lm.dll. See libroadrunner.org for details. -See the RoadRunner website on how to load and run these plugins. - diff --git a/reports/macosx_amd64/c_tests_Clang__Release_develop_2013-12-11_01-13.xml b/reports/macosx_amd64/c_tests_Clang__Release_develop_2013-12-11_01-13.xml new file mode 100644 index 0000000000..cb0e155d3a --- /dev/null +++ b/reports/macosx_amd64/c_tests_Clang__Release_develop_2013-12-11_01-13.xml @@ -0,0 +1,1074 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/reports/win_i386/c_tests_MSVC__Release_develop_2013-12-10_20-25.xml b/reports/win_i386/c_tests_MSVC__Release_develop_2013-12-10_20-25.xml new file mode 100644 index 0000000000..98ff3aaa97 --- /dev/null +++ b/reports/win_i386/c_tests_MSVC__Release_develop_2013-12-10_20-25.xml @@ -0,0 +1,1072 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + diff --git a/reports/win_i386/c_tests_MSVC__Release_develop_2013-12-11_02-11.xml b/reports/win_i386/c_tests_MSVC__Release_develop_2013-12-11_02-11.xml new file mode 100644 index 0000000000..54ce1c442a --- /dev/null +++ b/reports/win_i386/c_tests_MSVC__Release_develop_2013-12-11_02-11.xml @@ -0,0 +1,1072 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/source/rrVersionInfo.cpp b/source/rrVersionInfo.cpp index 0c29e75546..1e141907ff 100644 --- a/source/rrVersionInfo.cpp +++ b/source/rrVersionInfo.cpp @@ -1,4 +1,4 @@ #include "rrConstants.h" //--------------------------------------------------------------------------- -const char* RR_VERSION = "0.9.5"; +const char* RR_VERSION = "1.0.0"; diff --git a/testing/CMakeLists.txt b/testing/CMakeLists.txt index b0754ba1e6..61e2027325 100644 --- a/testing/CMakeLists.txt +++ b/testing/CMakeLists.txt @@ -1,20 +1,21 @@ -cmake_minimum_required(VERSION 2.8) -PROJECT(tests) - -set(tests -NOM_Test.dat -LibStructTest.dat -Test_1.dat -Test_1.xml -Test_1.txt -ModelSourceTest.h -ModelSourceTest.c -feedback.xml -) - - -install( -FILES ${tests} -DESTINATION testing COMPONENT testing -) - +cmake_minimum_required(VERSION 2.8) +PROJECT(tests) + +set(tests + README.txt + NOM_Test.dat + LibStructTest.dat + Test_1.dat + Test_1.xml + Test_1.txt + ModelSourceTest.h + ModelSourceTest.c + feedback.xml +) + + +install( + FILES ${tests} + DESTINATION testing COMPONENT testing +) + diff --git a/testing/README.txt b/testing/README.txt new file mode 100644 index 0000000000..2a7410fdde --- /dev/null +++ b/testing/README.txt @@ -0,0 +1,2 @@ + +These files are used to test the roadRunner C++ API. \ No newline at end of file diff --git a/third_party/CMakeLists.txt b/third_party/CMakeLists.txt index daf41e1926..2b05e81967 100644 --- a/third_party/CMakeLists.txt +++ b/third_party/CMakeLists.txt @@ -150,10 +150,13 @@ add_subdirectory(sundials) add_subdirectory(nleq) add_subdirectory(rr-libstruct) add_subdirectory(unit_test) -add_subdirectory(compilers) add_subdirectory(poco) add_subdirectory(rr_support) +if(WIN32) + add_subdirectory(compilers) +endif(WIN32) + #==== SYSTEM FILES (COMPILER SPECIFICS) ================================================= if(${BORLAND}) set(CG_RUNTIMES cc32110MT.dll) diff --git a/win32_bin_README.txt b/win32_bin_README.txt new file mode 100644 index 0000000000..4fd5263042 --- /dev/null +++ b/win32_bin_README.txt @@ -0,0 +1,29 @@ +This directory includes various execiutable and DLL files. The most important ones +are listed here: + +1. iconv.dll, libsbml.dll libxml2.dll, zlib1.dll are all associated with SBML support + +2. rrc_api.dll - This DLL supports the C API + +3. roadrunner.dll - This DLL supports the C++ API + +4. rrplugins_c_api.dll - This DLL supports the C API and the C Plugin API + +5. rr.exe + +RoadRunner Standalone program. The rr.exe executable can be used to test the integrity +of the current build, but also as a fully fledged SBML simulator. Type rr.exe to get help +or go to the liroadrunner.org web site for more details. + +Of unknown function or usage, email somogyie@umail.iu.edu for details: + +run_test_suite.exe +sbml_ts_tester.exe +run_cpp_tests.bat +run_c_tests.sh +run_c_tests.bat +rr-sbml-benchmark.exe +cxx_api_tests.exe +llvm_testing.exe + + diff --git a/wrappers/CMakeLists.txt b/wrappers/CMakeLists.txt index 21cfea8905..3cdacea7e4 100644 --- a/wrappers/CMakeLists.txt +++ b/wrappers/CMakeLists.txt @@ -5,15 +5,15 @@ if(INSTALL_C_API) add_subdirectory("C") endif() -if(INSTALL_PYTHON) -add_subdirectory("Python") +if(INSTALL_C_API_PYTHON) +add_subdirectory("c_api_python") endif() if(INSTALL_DELPHI) add_subdirectory("Delphi") endif() -if(BUILD_SWIG_PYTHON) - add_subdirectory("SWIGPython") +if(BUILD_PYTHON) + add_subdirectory("Python") endif() diff --git a/wrappers/SWIGPython/.gitignore b/wrappers/Python/.gitignore similarity index 100% rename from wrappers/SWIGPython/.gitignore rename to wrappers/Python/.gitignore diff --git a/wrappers/Python/CMakeLists.txt b/wrappers/Python/CMakeLists.txt index 1671b0a417..f59f63e714 100644 --- a/wrappers/Python/CMakeLists.txt +++ b/wrappers/Python/CMakeLists.txt @@ -1,18 +1,40 @@ -CMAKE_MINIMUM_REQUIRED(VERSION 2.6.3 FATAL_ERROR) -PROJECT(rrWrappers) - -if(BUILD_TESTS) -add_subdirectory(Testing) -endif() - -if(INSTALL_EXAMPLES) -add_subdirectory(Examples) -endif() -#=============== INSTALL ===================== -install( - FILES - rrPython.py - DESTINATION c_api_python - COMPONENT testing - ) +include(${CMAKE_CURRENT_SOURCE_DIR}/FindSWIG.cmake) # this is slightly modified FindSWIG.cmake file - had to tune it to work with OSX +FIND_PACKAGE(SWIG REQUIRED) + +INCLUDE(UseSWIG) + +FIND_PACKAGE(PythonLibs) +FIND_PACKAGE(PythonInterp) +FIND_PACKAGE(NumPy) + +MESSAGE ("THIS IS NUMPY_VERSION " ${NUMPY_VERSION}) + +MESSAGE ("THIS IS NUMPY_INCLUDE_DIRS " ${NUMPY_INCLUDE_DIRS}) + +MESSAGE ("THIS IS PYTHON_INCLUDE_PATH " ${PYTHON_INCLUDE_PATH}) + +INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_PATH}) +INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) +INCLUDE_DIRECTORIES(${CMAKE_BINARY_DIR}/include) +INCLUDE_DIRECTORIES(${NUMPY_INCLUDE_DIRS}) +INCLUDE_DIRECTORIES(${RR_SOURCE_PATH}/third_party/rr-libstruct) + + + +SET(PYINTERFACE_SRC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/pyinterface) +SET(CMAKE_SWIG_FLAGS "") + + + +IF(SWIG_FOUND) + add_subdirectory(roadrunner) +ELSE(SWIG_FOUND) + message("could not find SWIG in your system") +ENDIF(SWIG_FOUND) + +if(WIN32) + install(FILES install_roadrunner_win.py + DESTINATION . + ) +endif(WIN32) diff --git a/wrappers/SWIGPython/FindSWIG.cmake b/wrappers/Python/FindSWIG.cmake similarity index 100% rename from wrappers/SWIGPython/FindSWIG.cmake rename to wrappers/Python/FindSWIG.cmake diff --git a/wrappers/Python/Readme.txt b/wrappers/Python/Readme.txt deleted file mode 100644 index 14a805bc29..0000000000 --- a/wrappers/Python/Readme.txt +++ /dev/null @@ -1,3 +0,0 @@ -RoadRunner Python Module - -Greg Medlock (gmedlo@uw.edu) diff --git a/wrappers/SWIGPython/doc/Makefile b/wrappers/Python/doc/Makefile similarity index 100% rename from wrappers/SWIGPython/doc/Makefile rename to wrappers/Python/doc/Makefile diff --git a/wrappers/SWIGPython/doc/accessing_model.rst b/wrappers/Python/doc/accessing_model.rst similarity index 100% rename from wrappers/SWIGPython/doc/accessing_model.rst rename to wrappers/Python/doc/accessing_model.rst diff --git a/wrappers/SWIGPython/doc/api_reference.rst b/wrappers/Python/doc/api_reference.rst similarity index 100% rename from wrappers/SWIGPython/doc/api_reference.rst rename to wrappers/Python/doc/api_reference.rst diff --git a/wrappers/SWIGPython/doc/conf.py b/wrappers/Python/doc/conf.py similarity index 100% rename from wrappers/SWIGPython/doc/conf.py rename to wrappers/Python/doc/conf.py diff --git a/wrappers/SWIGPython/doc/index.rst b/wrappers/Python/doc/index.rst similarity index 100% rename from wrappers/SWIGPython/doc/index.rst rename to wrappers/Python/doc/index.rst diff --git a/wrappers/SWIGPython/doc/installing_rr.rst b/wrappers/Python/doc/installing_rr.rst similarity index 100% rename from wrappers/SWIGPython/doc/installing_rr.rst rename to wrappers/Python/doc/installing_rr.rst diff --git a/wrappers/SWIGPython/doc/introduction.rst b/wrappers/Python/doc/introduction.rst similarity index 100% rename from wrappers/SWIGPython/doc/introduction.rst rename to wrappers/Python/doc/introduction.rst diff --git a/wrappers/SWIGPython/doc/looking_at_results.rst b/wrappers/Python/doc/looking_at_results.rst similarity index 100% rename from wrappers/SWIGPython/doc/looking_at_results.rst rename to wrappers/Python/doc/looking_at_results.rst diff --git a/wrappers/SWIGPython/doc/make.bat b/wrappers/Python/doc/make.bat similarity index 100% rename from wrappers/SWIGPython/doc/make.bat rename to wrappers/Python/doc/make.bat diff --git a/wrappers/SWIGPython/doc/metabolic.rst b/wrappers/Python/doc/metabolic.rst similarity index 100% rename from wrappers/SWIGPython/doc/metabolic.rst rename to wrappers/Python/doc/metabolic.rst diff --git a/wrappers/SWIGPython/doc/mod_roadrunner/cls_ConservedMoietyConverter.rst b/wrappers/Python/doc/mod_roadrunner/cls_ConservedMoietyConverter.rst similarity index 100% rename from wrappers/SWIGPython/doc/mod_roadrunner/cls_ConservedMoietyConverter.rst rename to wrappers/Python/doc/mod_roadrunner/cls_ConservedMoietyConverter.rst diff --git a/wrappers/SWIGPython/doc/mod_roadrunner/cls_ExecutableModel.rst b/wrappers/Python/doc/mod_roadrunner/cls_ExecutableModel.rst similarity index 100% rename from wrappers/SWIGPython/doc/mod_roadrunner/cls_ExecutableModel.rst rename to wrappers/Python/doc/mod_roadrunner/cls_ExecutableModel.rst diff --git a/wrappers/SWIGPython/doc/mod_roadrunner/cls_RoadRunner.rst b/wrappers/Python/doc/mod_roadrunner/cls_RoadRunner.rst similarity index 100% rename from wrappers/SWIGPython/doc/mod_roadrunner/cls_RoadRunner.rst rename to wrappers/Python/doc/mod_roadrunner/cls_RoadRunner.rst diff --git a/wrappers/SWIGPython/doc/mod_roadrunner/cls_SelectionRecord.rst b/wrappers/Python/doc/mod_roadrunner/cls_SelectionRecord.rst similarity index 100% rename from wrappers/SWIGPython/doc/mod_roadrunner/cls_SelectionRecord.rst rename to wrappers/Python/doc/mod_roadrunner/cls_SelectionRecord.rst diff --git a/wrappers/SWIGPython/doc/mod_roadrunner/cls_SimulateOptions.rst b/wrappers/Python/doc/mod_roadrunner/cls_SimulateOptions.rst similarity index 100% rename from wrappers/SWIGPython/doc/mod_roadrunner/cls_SimulateOptions.rst rename to wrappers/Python/doc/mod_roadrunner/cls_SimulateOptions.rst diff --git a/wrappers/SWIGPython/doc/mod_roadrunner/mod_roadrunner.rst b/wrappers/Python/doc/mod_roadrunner/mod_roadrunner.rst similarity index 100% rename from wrappers/SWIGPython/doc/mod_roadrunner/mod_roadrunner.rst rename to wrappers/Python/doc/mod_roadrunner/mod_roadrunner.rst diff --git a/wrappers/SWIGPython/doc/read_write_functions.rst b/wrappers/Python/doc/read_write_functions.rst similarity index 100% rename from wrappers/SWIGPython/doc/read_write_functions.rst rename to wrappers/Python/doc/read_write_functions.rst diff --git a/wrappers/SWIGPython/doc/rr_basics.rst b/wrappers/Python/doc/rr_basics.rst similarity index 100% rename from wrappers/SWIGPython/doc/rr_basics.rst rename to wrappers/Python/doc/rr_basics.rst diff --git a/wrappers/SWIGPython/doc/running_simulation.rst b/wrappers/Python/doc/running_simulation.rst similarity index 100% rename from wrappers/SWIGPython/doc/running_simulation.rst rename to wrappers/Python/doc/running_simulation.rst diff --git a/wrappers/SWIGPython/doc/selecting_values.rst b/wrappers/Python/doc/selecting_values.rst similarity index 100% rename from wrappers/SWIGPython/doc/selecting_values.rst rename to wrappers/Python/doc/selecting_values.rst diff --git a/wrappers/SWIGPython/doc/stability.rst b/wrappers/Python/doc/stability.rst similarity index 100% rename from wrappers/SWIGPython/doc/stability.rst rename to wrappers/Python/doc/stability.rst diff --git a/wrappers/SWIGPython/doc/starting_py_and_rr.rst b/wrappers/Python/doc/starting_py_and_rr.rst similarity index 100% rename from wrappers/SWIGPython/doc/starting_py_and_rr.rst rename to wrappers/Python/doc/starting_py_and_rr.rst diff --git a/wrappers/SWIGPython/doc/steady_state.rst b/wrappers/Python/doc/steady_state.rst similarity index 100% rename from wrappers/SWIGPython/doc/steady_state.rst rename to wrappers/Python/doc/steady_state.rst diff --git a/wrappers/SWIGPython/doc/stoichiometric.rst b/wrappers/Python/doc/stoichiometric.rst similarity index 100% rename from wrappers/SWIGPython/doc/stoichiometric.rst rename to wrappers/Python/doc/stoichiometric.rst diff --git a/wrappers/SWIGPython/doc/timecourse_simulation.rst b/wrappers/Python/doc/timecourse_simulation.rst similarity index 100% rename from wrappers/SWIGPython/doc/timecourse_simulation.rst rename to wrappers/Python/doc/timecourse_simulation.rst diff --git a/wrappers/SWIGPython/doc/using_roadrunner.rst b/wrappers/Python/doc/using_roadrunner.rst similarity index 100% rename from wrappers/SWIGPython/doc/using_roadrunner.rst rename to wrappers/Python/doc/using_roadrunner.rst diff --git a/wrappers/SWIGPython/doc/utility_functions.rst b/wrappers/Python/doc/utility_functions.rst similarity index 100% rename from wrappers/SWIGPython/doc/utility_functions.rst rename to wrappers/Python/doc/utility_functions.rst diff --git a/wrappers/SWIGPython/doc/what_is_rr.rst b/wrappers/Python/doc/what_is_rr.rst similarity index 100% rename from wrappers/SWIGPython/doc/what_is_rr.rst rename to wrappers/Python/doc/what_is_rr.rst diff --git a/wrappers/SWIGPython/doc/what_is_sbml.rst b/wrappers/Python/doc/what_is_sbml.rst similarity index 100% rename from wrappers/SWIGPython/doc/what_is_sbml.rst rename to wrappers/Python/doc/what_is_sbml.rst diff --git a/wrappers/SWIGPython/include/numpy.i b/wrappers/Python/include/numpy.i similarity index 100% rename from wrappers/SWIGPython/include/numpy.i rename to wrappers/Python/include/numpy.i diff --git a/wrappers/SWIGPython/include/rr_numpy.i b/wrappers/Python/include/rr_numpy.i similarity index 100% rename from wrappers/SWIGPython/include/rr_numpy.i rename to wrappers/Python/include/rr_numpy.i diff --git a/wrappers/SWIGPython/include/rr_stdint.i b/wrappers/Python/include/rr_stdint.i similarity index 100% rename from wrappers/SWIGPython/include/rr_stdint.i rename to wrappers/Python/include/rr_stdint.i diff --git a/wrappers/SWIGPython/install_roadrunner.py b/wrappers/Python/install_roadrunner_win.py similarity index 84% rename from wrappers/SWIGPython/install_roadrunner.py rename to wrappers/Python/install_roadrunner_win.py index dacd6a9f5c..6a33af0488 100644 --- a/wrappers/SWIGPython/install_roadrunner.py +++ b/wrappers/Python/install_roadrunner_win.py @@ -1,3 +1,11 @@ +""" +Usage: + python install_roadrunner.py + + This file will install all the relevant roadRunner files + so that roadrunner can be used from Python +""" + import site import shutil import os.path diff --git a/wrappers/SWIGPython/mkswigdocs.py b/wrappers/Python/mkswigdocs.py similarity index 100% rename from wrappers/SWIGPython/mkswigdocs.py rename to wrappers/Python/mkswigdocs.py diff --git a/wrappers/SWIGPython/numpy_notes.txt b/wrappers/Python/numpy_notes.txt similarity index 100% rename from wrappers/SWIGPython/numpy_notes.txt rename to wrappers/Python/numpy_notes.txt diff --git a/wrappers/SWIGPython/roadrunner/CMakeLists.txt b/wrappers/Python/roadrunner/CMakeLists.txt similarity index 97% rename from wrappers/SWIGPython/roadrunner/CMakeLists.txt rename to wrappers/Python/roadrunner/CMakeLists.txt index 8bb907ecec..2a8eca16de 100644 --- a/wrappers/SWIGPython/roadrunner/CMakeLists.txt +++ b/wrappers/Python/roadrunner/CMakeLists.txt @@ -102,7 +102,7 @@ install( DESTINATION ${RR_PACKAGE_DIR} ) -set(python_files_path ${CMAKE_BINARY_DIR}/wrappers/SWIGPython/roadrunner/) +set(python_files_path ${CMAKE_BINARY_DIR}/wrappers/Python/roadrunner/) #THIS IS EXAMPLE OF WORKING COMMAND # ADD_CUSTOM_COMMAND( diff --git a/wrappers/SWIGPython/roadrunner/__init__.py b/wrappers/Python/roadrunner/__init__.py similarity index 100% rename from wrappers/SWIGPython/roadrunner/__init__.py rename to wrappers/Python/roadrunner/__init__.py diff --git a/wrappers/SWIGPython/roadrunner/roadrunner.i b/wrappers/Python/roadrunner/roadrunner.i similarity index 100% rename from wrappers/SWIGPython/roadrunner/roadrunner.i rename to wrappers/Python/roadrunner/roadrunner.i diff --git a/wrappers/SWIGPython/roadrunner/rr_docstrings.i b/wrappers/Python/roadrunner/rr_docstrings.i similarity index 100% rename from wrappers/SWIGPython/roadrunner/rr_docstrings.i rename to wrappers/Python/roadrunner/rr_docstrings.i diff --git a/wrappers/Python/roadrunner/testing/__init__.py b/wrappers/Python/roadrunner/testing/__init__.py new file mode 100644 index 0000000000..54d26ae214 --- /dev/null +++ b/wrappers/Python/roadrunner/testing/__init__.py @@ -0,0 +1,16 @@ +""" +This module has testing function and test data to excecise the roadrunner +python interface. + +This module can also be run direct from the command line as it is +an runnable module as:: + pythom -m "roadrunner.testing" + +This module basically has a single function,:: + runTester() + +This runs the built in unit tests.. +""" + +from tester import * +from testfiles import * diff --git a/wrappers/SWIGPython/roadrunner/testing/__main__.py b/wrappers/Python/roadrunner/testing/__main__.py similarity index 100% rename from wrappers/SWIGPython/roadrunner/testing/__main__.py rename to wrappers/Python/roadrunner/testing/__main__.py diff --git a/wrappers/SWIGPython/roadrunner/testing/feedback.xml b/wrappers/Python/roadrunner/testing/feedback.xml similarity index 100% rename from wrappers/SWIGPython/roadrunner/testing/feedback.xml rename to wrappers/Python/roadrunner/testing/feedback.xml diff --git a/wrappers/SWIGPython/roadrunner/testing/results_roadRunnerTest_1.txt b/wrappers/Python/roadrunner/testing/results_roadRunnerTest_1.txt similarity index 100% rename from wrappers/SWIGPython/roadrunner/testing/results_roadRunnerTest_1.txt rename to wrappers/Python/roadrunner/testing/results_roadRunnerTest_1.txt diff --git a/wrappers/SWIGPython/roadrunner/testing/test_1.xml b/wrappers/Python/roadrunner/testing/test_1.xml similarity index 100% rename from wrappers/SWIGPython/roadrunner/testing/test_1.xml rename to wrappers/Python/roadrunner/testing/test_1.xml diff --git a/wrappers/SWIGPython/roadrunner/testing/tester.py b/wrappers/Python/roadrunner/testing/tester.py similarity index 100% rename from wrappers/SWIGPython/roadrunner/testing/tester.py rename to wrappers/Python/roadrunner/testing/tester.py diff --git a/wrappers/SWIGPython/roadrunner/testing/testfiles.py b/wrappers/Python/roadrunner/testing/testfiles.py similarity index 100% rename from wrappers/SWIGPython/roadrunner/testing/testfiles.py rename to wrappers/Python/roadrunner/testing/testfiles.py diff --git a/wrappers/SWIGPython/CMakeLists.txt b/wrappers/SWIGPython/CMakeLists.txt deleted file mode 100644 index d06b3aa4ce..0000000000 --- a/wrappers/SWIGPython/CMakeLists.txt +++ /dev/null @@ -1,34 +0,0 @@ -include(${CMAKE_CURRENT_SOURCE_DIR}/FindSWIG.cmake) # this is slightly modified FindSWIG.cmake file - had to tune it to work with OSX - -FIND_PACKAGE(SWIG REQUIRED) - -INCLUDE(UseSWIG) - -FIND_PACKAGE(PythonLibs) -FIND_PACKAGE(PythonInterp) -FIND_PACKAGE(NumPy) - -MESSAGE ("THIS IS NUMPY_VERSION " ${NUMPY_VERSION}) - -MESSAGE ("THIS IS NUMPY_INCLUDE_DIRS " ${NUMPY_INCLUDE_DIRS}) - -MESSAGE ("THIS IS PYTHON_INCLUDE_PATH " ${PYTHON_INCLUDE_PATH}) - -INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_PATH}) -INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) -INCLUDE_DIRECTORIES(${CMAKE_BINARY_DIR}/include) -INCLUDE_DIRECTORIES(${NUMPY_INCLUDE_DIRS}) -INCLUDE_DIRECTORIES(${RR_SOURCE_PATH}/third_party/rr-libstruct) - - - -SET(PYINTERFACE_SRC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/pyinterface) -SET(CMAKE_SWIG_FLAGS "") - - - -IF(SWIG_FOUND) - add_subdirectory(roadrunner) -ELSE(SWIG_FOUND) - message("could not find SWIG in your system") -ENDIF(SWIG_FOUND) \ No newline at end of file diff --git a/wrappers/SWIGPython/roadrunner/testing/README.txt b/wrappers/SWIGPython/roadrunner/testing/README.txt deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/wrappers/SWIGPython/roadrunner/testing/__init__.py b/wrappers/SWIGPython/roadrunner/testing/__init__.py deleted file mode 100644 index 2518685536..0000000000 --- a/wrappers/SWIGPython/roadrunner/testing/__init__.py +++ /dev/null @@ -1,2 +0,0 @@ -from tester import * -from testfiles import * diff --git a/wrappers/c_api_python/CMakeLists.txt b/wrappers/c_api_python/CMakeLists.txt new file mode 100644 index 0000000000..8657e7e861 --- /dev/null +++ b/wrappers/c_api_python/CMakeLists.txt @@ -0,0 +1,19 @@ +CMAKE_MINIMUM_REQUIRED(VERSION 2.6.3 FATAL_ERROR) +PROJECT(rrWrappers) + +if(BUILD_TESTS) +add_subdirectory(Testing) +endif() + +if(INSTALL_EXAMPLES) +add_subdirectory(Examples) +endif() + +#=============== INSTALL ===================== +install( + FILES + rrPython.py README.txt + DESTINATION c_api_python + COMPONENT testing + ) + diff --git a/wrappers/Python/Examples/CMakeLists.txt b/wrappers/c_api_python/Examples/CMakeLists.txt similarity index 59% rename from wrappers/Python/Examples/CMakeLists.txt rename to wrappers/c_api_python/Examples/CMakeLists.txt index 297faf1e14..04d766177a 100644 --- a/wrappers/Python/Examples/CMakeLists.txt +++ b/wrappers/c_api_python/Examples/CMakeLists.txt @@ -9,9 +9,9 @@ plotData.py ) install( - FILES - ${examples} - DESTINATION python - COMPONENT Python - ) + FILES + ${examples} + DESTINATION c_api_python + COMPONENT Python + ) diff --git a/wrappers/Python/Examples/getStoichMatrix.py b/wrappers/c_api_python/Examples/getStoichMatrix.py similarity index 100% rename from wrappers/Python/Examples/getStoichMatrix.py rename to wrappers/c_api_python/Examples/getStoichMatrix.py diff --git a/wrappers/Python/Examples/plotData.py b/wrappers/c_api_python/Examples/plotData.py similarity index 100% rename from wrappers/Python/Examples/plotData.py rename to wrappers/c_api_python/Examples/plotData.py diff --git a/wrappers/Python/Examples/rrPluginDocumentationDemo.py b/wrappers/c_api_python/Examples/rrPluginDocumentationDemo.py similarity index 100% rename from wrappers/Python/Examples/rrPluginDocumentationDemo.py rename to wrappers/c_api_python/Examples/rrPluginDocumentationDemo.py diff --git a/wrappers/Python/Examples/rrPluginParameterDemo.py b/wrappers/c_api_python/Examples/rrPluginParameterDemo.py similarity index 100% rename from wrappers/Python/Examples/rrPluginParameterDemo.py rename to wrappers/c_api_python/Examples/rrPluginParameterDemo.py diff --git a/wrappers/Python/Examples/simulateSelectionList.py b/wrappers/c_api_python/Examples/simulateSelectionList.py similarity index 100% rename from wrappers/Python/Examples/simulateSelectionList.py rename to wrappers/c_api_python/Examples/simulateSelectionList.py diff --git a/wrappers/Python/Examples/threeLineSimulation.py b/wrappers/c_api_python/Examples/threeLineSimulation.py similarity index 100% rename from wrappers/Python/Examples/threeLineSimulation.py rename to wrappers/c_api_python/Examples/threeLineSimulation.py diff --git a/wrappers/c_api_python/README.txt b/wrappers/c_api_python/README.txt new file mode 100644 index 0000000000..4104e5de1a --- /dev/null +++ b/wrappers/c_api_python/README.txt @@ -0,0 +1,10 @@ + +The files in this directory are used for a number of purposes: + +rrPython.py is a ctypes binding to the roadRunner C API + +rrPlugins.py is a ctypes binding to the roadRunner Plugin API + +rrRunTests.py and rrTester.py are used to tesdt the C API via Python. + +At this point in time, it is not known how to install these so that they can be used. \ No newline at end of file diff --git a/wrappers/Python/Testing/CMakeLists.txt b/wrappers/c_api_python/Testing/CMakeLists.txt similarity index 77% rename from wrappers/Python/Testing/CMakeLists.txt rename to wrappers/c_api_python/Testing/CMakeLists.txt index 037a01235d..18ec6261f3 100644 --- a/wrappers/Python/Testing/CMakeLists.txt +++ b/wrappers/c_api_python/Testing/CMakeLists.txt @@ -15,11 +15,9 @@ DIRECTORY_PERMISSIONS #=============== INSTALL ===================== install( -FILES -#rrTestCompiler.py -rrRunTests.py -rrTester.py -#rrDebug.py -DESTINATION python COMPONENT testing + FILES + rrRunTests.py + rrTester.py + DESTINATION c_api_python COMPONENT testing ) diff --git a/wrappers/Python/Testing/results_roadRunnerTest_1.txt b/wrappers/c_api_python/Testing/results_roadRunnerTest_1.txt similarity index 100% rename from wrappers/Python/Testing/results_roadRunnerTest_1.txt rename to wrappers/c_api_python/Testing/results_roadRunnerTest_1.txt diff --git a/wrappers/Python/Testing/rrDebug.py b/wrappers/c_api_python/Testing/rrDebug.py similarity index 100% rename from wrappers/Python/Testing/rrDebug.py rename to wrappers/c_api_python/Testing/rrDebug.py diff --git a/wrappers/Python/Testing/rrRunTests.py b/wrappers/c_api_python/Testing/rrRunTests.py similarity index 100% rename from wrappers/Python/Testing/rrRunTests.py rename to wrappers/c_api_python/Testing/rrRunTests.py diff --git a/wrappers/Python/Testing/rrTestCompiler.py b/wrappers/c_api_python/Testing/rrTestCompiler.py similarity index 100% rename from wrappers/Python/Testing/rrTestCompiler.py rename to wrappers/c_api_python/Testing/rrTestCompiler.py diff --git a/wrappers/Python/Testing/rrTester.py b/wrappers/c_api_python/Testing/rrTester.py similarity index 100% rename from wrappers/Python/Testing/rrTester.py rename to wrappers/c_api_python/Testing/rrTester.py diff --git a/wrappers/Python/rrPython.py b/wrappers/c_api_python/rrPython.py similarity index 100% rename from wrappers/Python/rrPython.py rename to wrappers/c_api_python/rrPython.py