From 6c9ac7ebb4bcb762750d1c051ce1a06b28a91994 Mon Sep 17 00:00:00 2001 From: Andy Somogyi Date: Tue, 10 Dec 2013 20:35:58 -0500 Subject: [PATCH 1/6] bumped version info to 1.0.0, ran tests --- ...MSVC__Release_develop_2013-12-10_20-25.xml | 1072 +++++++++++++++++ source/rrVersionInfo.cpp | 2 +- 2 files changed, 1073 insertions(+), 1 deletion(-) create mode 100644 reports/win_i386/c_tests_MSVC__Release_develop_2013-12-10_20-25.xml 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 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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"; From f3d821e619077e3ad0293fb3d7ff151d7b5d86e1 Mon Sep 17 00:00:00 2001 From: Andy Somogyi Date: Wed, 11 Dec 2013 01:25:56 -0500 Subject: [PATCH 2/6] added Herbert's docs, updated dir names to new standard --- Authors.txt => AUTHORS.txt | 16 +- CMakeLists.txt | 48 +- FUNDING.txt | 3 + Funding.txt | 1 - License.txt => LICENSE.txt | 0 News.txt => NEWS.txt | 0 Notice.txt => NOTICE.txt | 18 +- Readme.txt => README.txt | 144 ++- Version.txt => VERSION.txt | 0 models/CMakeLists.txt | 1 + models/README.txt | 78 ++ plugins/CMakeLists.txt | 68 +- plugins/README.txt | 14 + ...lang__Release_develop_2013-12-11_01-13.xml | 1074 +++++++++++++++++ testing/CMakeLists.txt | 41 +- third_party/CMakeLists.txt | 5 +- wrappers/CMakeLists.txt | 8 +- wrappers/{SWIGPython => Python}/.gitignore | 0 wrappers/Python/CMakeLists.txt | 52 +- .../{SWIGPython => Python}/FindSWIG.cmake | 0 wrappers/Python/Readme.txt | 3 - wrappers/{SWIGPython => Python}/doc/Makefile | 0 .../doc/accessing_model.rst | 0 .../doc/api_reference.rst | 0 wrappers/{SWIGPython => Python}/doc/conf.py | 0 wrappers/{SWIGPython => Python}/doc/index.rst | 0 .../doc/installing_rr.rst | 0 .../doc/introduction.rst | 0 .../doc/looking_at_results.rst | 0 wrappers/{SWIGPython => Python}/doc/make.bat | 0 .../{SWIGPython => Python}/doc/metabolic.rst | 0 .../cls_ConservedMoietyConverter.rst | 0 .../mod_roadrunner/cls_ExecutableModel.rst | 0 .../doc/mod_roadrunner/cls_RoadRunner.rst | 0 .../mod_roadrunner/cls_SelectionRecord.rst | 0 .../mod_roadrunner/cls_SimulateOptions.rst | 0 .../doc/mod_roadrunner/mod_roadrunner.rst | 0 .../doc/read_write_functions.rst | 0 .../{SWIGPython => Python}/doc/rr_basics.rst | 0 .../doc/running_simulation.rst | 0 .../doc/selecting_values.rst | 0 .../{SWIGPython => Python}/doc/stability.rst | 0 .../doc/starting_py_and_rr.rst | 0 .../doc/steady_state.rst | 0 .../doc/stoichiometric.rst | 0 .../doc/timecourse_simulation.rst | 0 .../doc/using_roadrunner.rst | 0 .../doc/utility_functions.rst | 0 .../{SWIGPython => Python}/doc/what_is_rr.rst | 0 .../doc/what_is_sbml.rst | 0 .../{SWIGPython => Python}/include/numpy.i | 0 .../{SWIGPython => Python}/include/rr_numpy.i | 0 .../include/rr_stdint.i | 0 .../install_roadrunner.py | 0 wrappers/{SWIGPython => Python}/mkswigdocs.py | 0 .../{SWIGPython => Python}/numpy_notes.txt | 0 .../roadrunner/CMakeLists.txt | 2 +- .../roadrunner/__init__.py | 0 .../roadrunner/roadrunner.i | 0 .../roadrunner/rr_docstrings.i | 0 .../Python/roadrunner/testing/__init__.py | 16 + .../roadrunner/testing/__main__.py | 0 .../roadrunner/testing/feedback.xml | 0 .../testing/results_roadRunnerTest_1.txt | 0 .../roadrunner/testing/test_1.xml | 0 .../roadrunner/testing/tester.py | 0 .../roadrunner/testing/testfiles.py | 0 wrappers/SWIGPython/CMakeLists.txt | 34 - .../SWIGPython/roadrunner/testing/README.txt | 0 .../SWIGPython/roadrunner/testing/__init__.py | 2 - wrappers/c_api_python/CMakeLists.txt | 19 + .../Examples/CMakeLists.txt | 10 +- .../Examples/getStoichMatrix.py | 0 .../Examples/plotData.py | 0 .../Examples/rrPluginDocumentationDemo.py | 0 .../Examples/rrPluginParameterDemo.py | 0 .../Examples/simulateSelectionList.py | 0 .../Examples/threeLineSimulation.py | 0 wrappers/c_api_python/README.txt | 10 + .../Testing/CMakeLists.txt | 10 +- .../Testing/results_roadRunnerTest_1.txt | 0 .../Testing/rrDebug.py | 0 .../Testing/rrRunTests.py | 0 .../Testing/rrTestCompiler.py | 0 .../Testing/rrTester.py | 0 wrappers/{Python => c_api_python}/rrPython.py | 0 86 files changed, 1447 insertions(+), 230 deletions(-) rename Authors.txt => AUTHORS.txt (65%) create mode 100644 FUNDING.txt delete mode 100644 Funding.txt rename License.txt => LICENSE.txt (100%) rename News.txt => NEWS.txt (100%) rename Notice.txt => NOTICE.txt (81%) rename Readme.txt => README.txt (66%) rename Version.txt => VERSION.txt (100%) create mode 100644 models/README.txt create mode 100644 plugins/README.txt create mode 100644 reports/macosx_amd64/c_tests_Clang__Release_develop_2013-12-11_01-13.xml rename wrappers/{SWIGPython => Python}/.gitignore (100%) rename wrappers/{SWIGPython => Python}/FindSWIG.cmake (100%) delete mode 100644 wrappers/Python/Readme.txt rename wrappers/{SWIGPython => Python}/doc/Makefile (100%) rename wrappers/{SWIGPython => Python}/doc/accessing_model.rst (100%) rename wrappers/{SWIGPython => Python}/doc/api_reference.rst (100%) rename wrappers/{SWIGPython => Python}/doc/conf.py (100%) rename wrappers/{SWIGPython => Python}/doc/index.rst (100%) rename wrappers/{SWIGPython => Python}/doc/installing_rr.rst (100%) rename wrappers/{SWIGPython => Python}/doc/introduction.rst (100%) rename wrappers/{SWIGPython => Python}/doc/looking_at_results.rst (100%) rename wrappers/{SWIGPython => Python}/doc/make.bat (100%) rename wrappers/{SWIGPython => Python}/doc/metabolic.rst (100%) rename wrappers/{SWIGPython => Python}/doc/mod_roadrunner/cls_ConservedMoietyConverter.rst (100%) rename wrappers/{SWIGPython => Python}/doc/mod_roadrunner/cls_ExecutableModel.rst (100%) rename wrappers/{SWIGPython => Python}/doc/mod_roadrunner/cls_RoadRunner.rst (100%) rename wrappers/{SWIGPython => Python}/doc/mod_roadrunner/cls_SelectionRecord.rst (100%) rename wrappers/{SWIGPython => Python}/doc/mod_roadrunner/cls_SimulateOptions.rst (100%) rename wrappers/{SWIGPython => Python}/doc/mod_roadrunner/mod_roadrunner.rst (100%) rename wrappers/{SWIGPython => Python}/doc/read_write_functions.rst (100%) rename wrappers/{SWIGPython => Python}/doc/rr_basics.rst (100%) rename wrappers/{SWIGPython => Python}/doc/running_simulation.rst (100%) rename wrappers/{SWIGPython => Python}/doc/selecting_values.rst (100%) rename wrappers/{SWIGPython => Python}/doc/stability.rst (100%) rename wrappers/{SWIGPython => Python}/doc/starting_py_and_rr.rst (100%) rename wrappers/{SWIGPython => Python}/doc/steady_state.rst (100%) rename wrappers/{SWIGPython => Python}/doc/stoichiometric.rst (100%) rename wrappers/{SWIGPython => Python}/doc/timecourse_simulation.rst (100%) rename wrappers/{SWIGPython => Python}/doc/using_roadrunner.rst (100%) rename wrappers/{SWIGPython => Python}/doc/utility_functions.rst (100%) rename wrappers/{SWIGPython => Python}/doc/what_is_rr.rst (100%) rename wrappers/{SWIGPython => Python}/doc/what_is_sbml.rst (100%) rename wrappers/{SWIGPython => Python}/include/numpy.i (100%) rename wrappers/{SWIGPython => Python}/include/rr_numpy.i (100%) rename wrappers/{SWIGPython => Python}/include/rr_stdint.i (100%) rename wrappers/{SWIGPython => Python}/install_roadrunner.py (100%) rename wrappers/{SWIGPython => Python}/mkswigdocs.py (100%) rename wrappers/{SWIGPython => Python}/numpy_notes.txt (100%) rename wrappers/{SWIGPython => Python}/roadrunner/CMakeLists.txt (97%) rename wrappers/{SWIGPython => Python}/roadrunner/__init__.py (100%) rename wrappers/{SWIGPython => Python}/roadrunner/roadrunner.i (100%) rename wrappers/{SWIGPython => Python}/roadrunner/rr_docstrings.i (100%) create mode 100644 wrappers/Python/roadrunner/testing/__init__.py rename wrappers/{SWIGPython => Python}/roadrunner/testing/__main__.py (100%) rename wrappers/{SWIGPython => Python}/roadrunner/testing/feedback.xml (100%) rename wrappers/{SWIGPython => Python}/roadrunner/testing/results_roadRunnerTest_1.txt (100%) rename wrappers/{SWIGPython => Python}/roadrunner/testing/test_1.xml (100%) rename wrappers/{SWIGPython => Python}/roadrunner/testing/tester.py (100%) rename wrappers/{SWIGPython => Python}/roadrunner/testing/testfiles.py (100%) delete mode 100644 wrappers/SWIGPython/CMakeLists.txt delete mode 100644 wrappers/SWIGPython/roadrunner/testing/README.txt delete mode 100644 wrappers/SWIGPython/roadrunner/testing/__init__.py create mode 100644 wrappers/c_api_python/CMakeLists.txt rename wrappers/{Python => c_api_python}/Examples/CMakeLists.txt (59%) rename wrappers/{Python => c_api_python}/Examples/getStoichMatrix.py (100%) rename wrappers/{Python => c_api_python}/Examples/plotData.py (100%) rename wrappers/{Python => c_api_python}/Examples/rrPluginDocumentationDemo.py (100%) rename wrappers/{Python => c_api_python}/Examples/rrPluginParameterDemo.py (100%) rename wrappers/{Python => c_api_python}/Examples/simulateSelectionList.py (100%) rename wrappers/{Python => c_api_python}/Examples/threeLineSimulation.py (100%) create mode 100644 wrappers/c_api_python/README.txt rename wrappers/{Python => c_api_python}/Testing/CMakeLists.txt (77%) rename wrappers/{Python => c_api_python}/Testing/results_roadRunnerTest_1.txt (100%) rename wrappers/{Python => c_api_python}/Testing/rrDebug.py (100%) rename wrappers/{Python => c_api_python}/Testing/rrRunTests.py (100%) rename wrappers/{Python => c_api_python}/Testing/rrTestCompiler.py (100%) rename wrappers/{Python => c_api_python}/Testing/rrTester.py (100%) rename wrappers/{Python => c_api_python}/rrPython.py (100%) diff --git a/Authors.txt b/AUTHORS.txt similarity index 65% rename from Authors.txt rename to AUTHORS.txt index 00bc4f6d69..23b9a891e0 100644 --- a/Authors.txt +++ b/AUTHORS.txt @@ -1,30 +1,30 @@ The orginal C# version of roadRunner was developed as part of the SBW project by - Herbert M Sauro and Frank Bergmann + 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 + Andy Somogyi, Totte Karlsson and Herbert M Sauro The Python interface to the C API was developed by -Totte Karlsson and Herbert M Sauro + Greg Medlock (gmedlo@uw.edu), Totte Karlsson and Herbert M Sauro The Python SWIG interface to the C++ API was developed by -Andy Somogyi + Andy Somogyi The LLVM backend and refactoring of the core was designed and undertaken by -Andy Somogyi + Andy Somogyi -The C backend was developed by +The C backend was ported to C++ by -Totte Karlsson + Totte Karlsson The Plugin Framework was designed and developed by -Totte Karlsson + Totte Karlsson For more information visit libroadRunner.org diff --git a/CMakeLists.txt b/CMakeLists.txt index 8d5a0dea5b..64d850d65e 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/ + ) +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/Funding.txt b/Funding.txt deleted file mode 100644 index 09a4ae5c0d..0000000000 --- a/Funding.txt +++ /dev/null @@ -1 +0,0 @@ -The roadRunner project is funded by the NIH/NIGMS (GM081070). diff --git a/License.txt b/LICENSE.txt similarity index 100% rename from License.txt rename to LICENSE.txt diff --git a/News.txt b/NEWS.txt similarity index 100% rename from News.txt rename to NEWS.txt diff --git a/Notice.txt b/NOTICE.txt similarity index 81% rename from Notice.txt rename to NOTICE.txt index 7a3c37a15a..d6333f671b 100644 --- a/Notice.txt +++ b/NOTICE.txt @@ -2,7 +2,7 @@ Copyright 2013 Andy Somogyi, Totte Karlsson, Herbert Sauro -This product make use of the following software packages: +This product makes use of the following software packages: libSBML Copyright (C) 2009-2013 jointly by the following organizations: @@ -12,8 +12,11 @@ libSBML 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 Î÷Î÷ 2004-2008 by European Media Laboratories Research gGmbH, Heidelberg, Germany (for the "SBML Layout" code and associated examples.) + 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. @@ -33,11 +36,10 @@ NLEQ2 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. + 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 diff --git a/Readme.txt b/README.txt similarity index 66% rename from Readme.txt rename to README.txt index 2a321a7714..174b16fb99 100644 --- a/Readme.txt +++ b/README.txt @@ -1,67 +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. +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 similarity index 100% rename from Version.txt rename to VERSION.txt diff --git a/models/CMakeLists.txt b/models/CMakeLists.txt index 68c40f0611..dcc1e68368 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 test_1.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/plugins/CMakeLists.txt b/plugins/CMakeLists.txt index e8acb4bc66..2fb8b7795f 100644 --- a/plugins/CMakeLists.txt +++ b/plugins/CMakeLists.txt @@ -1,32 +1,36 @@ -cmake_minimum_required(VERSION 2.8) -project(rr_plugins) - -if(${BUILD_PLUGINS} STREQUAL ON) - -include_directories( - ../wrappers/C -) - -OPTION (RRP_BUILD_ADD_NOISE_PLUGIN "Build add noise plugin" ON) -OPTION (RRP_BUILD_LEVENBERG_MARQUARDT_PLUGIN "Build Levenberg-Marquardt plugin" ON) -OPTION (RRP_BUILD_EXAMPLES "Build Plugin Examples" OFF) - -add_subdirectory(source) - -if(${RRP_BUILD_ADD_NOISE_PLUGIN} STREQUAL ON) -add_subdirectory(add_noise) -endif() - -if(${RRP_BUILD_LEVENBERG_MARQUARDT_PLUGIN} STREQUAL ON) -add_subdirectory(lmfit) -endif() - -if(${RRP_BUILD_EXAMPLES} STREQUAL ON) -add_subdirectory(examples) -endif() - - -endif() - -add_subdirectory(wrappers) - +cmake_minimum_required(VERSION 2.8) +project(rr_plugins) + +if(${BUILD_PLUGINS} STREQUAL ON) + +include_directories( + ../wrappers/C +) + +OPTION (RRP_BUILD_ADD_NOISE_PLUGIN "Build add noise plugin" ON) +OPTION (RRP_BUILD_LEVENBERG_MARQUARDT_PLUGIN "Build Levenberg-Marquardt plugin" ON) +OPTION (RRP_BUILD_EXAMPLES "Build Plugin Examples" OFF) + +add_subdirectory(source) + +if(${RRP_BUILD_ADD_NOISE_PLUGIN} STREQUAL ON) +add_subdirectory(add_noise) +endif() + +if(${RRP_BUILD_LEVENBERG_MARQUARDT_PLUGIN} STREQUAL ON) +add_subdirectory(lmfit) +endif() + +if(${RRP_BUILD_EXAMPLES} STREQUAL ON) +add_subdirectory(examples) +endif() + + +endif() + +add_subdirectory(wrappers) + +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/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/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 ${tests} + DESTINATION testing COMPONENT testing +) + diff --git a/third_party/CMakeLists.txt b/third_party/CMakeLists.txt index daf41e1926..2b05e81967 100644 --- a/third_party/CMakeLists.txt +++ b/third_party/CMakeLists.txt @@ -150,10 +150,13 @@ add_subdirectory(sundials) add_subdirectory(nleq) add_subdirectory(rr-libstruct) add_subdirectory(unit_test) -add_subdirectory(compilers) add_subdirectory(poco) add_subdirectory(rr_support) +if(WIN32) + add_subdirectory(compilers) +endif(WIN32) + #==== SYSTEM FILES (COMPILER SPECIFICS) ================================================= if(${BORLAND}) set(CG_RUNTIMES cc32110MT.dll) diff --git a/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 56ad050342..d06b3aa4ce 100644 --- a/wrappers/Python/CMakeLists.txt +++ b/wrappers/Python/CMakeLists.txt @@ -1,18 +1,34 @@ -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 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) \ No newline at end of file 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.py similarity index 100% rename from wrappers/SWIGPython/install_roadrunner.py rename to wrappers/Python/install_roadrunner.py 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 From 51b5de5a2f7abe84122c3832210ad287ef85984b Mon Sep 17 00:00:00 2001 From: Andy Somogyi Date: Wed, 11 Dec 2013 01:36:15 -0500 Subject: [PATCH 3/6] install win32 python module install script --- wrappers/Python/CMakeLists.txt | 8 +++++++- .../{install_roadrunner.py => install_roadrunner_win.py} | 8 ++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) rename wrappers/Python/{install_roadrunner.py => install_roadrunner_win.py} (84%) diff --git a/wrappers/Python/CMakeLists.txt b/wrappers/Python/CMakeLists.txt index d06b3aa4ce..c364b859e5 100644 --- a/wrappers/Python/CMakeLists.txt +++ b/wrappers/Python/CMakeLists.txt @@ -31,4 +31,10 @@ 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 +ENDIF(SWIG_FOUND) + +if(WIN32) + install(FILES install_roadrunner_win.py + DESTINATION . + ) +endif(WIN32) diff --git a/wrappers/Python/install_roadrunner.py b/wrappers/Python/install_roadrunner_win.py similarity index 84% rename from wrappers/Python/install_roadrunner.py rename to wrappers/Python/install_roadrunner_win.py index dacd6a9f5c..6a33af0488 100644 --- a/wrappers/Python/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 From 8073df309bc50f9788482022c48055ef8053d9bb Mon Sep 17 00:00:00 2001 From: Andy Somogyi Date: Wed, 11 Dec 2013 01:55:21 -0500 Subject: [PATCH 4/6] added doc file --- win32_bin_README.txt | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 win32_bin_README.txt 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 + + From 8cd401ecbd6ac51bec724620d4e111ff3f212ed3 Mon Sep 17 00:00:00 2001 From: Andy Somogyi Date: Wed, 11 Dec 2013 01:56:54 -0500 Subject: [PATCH 5/6] added doc file --- testing/README.txt | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 testing/README.txt 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 From cad6fa7bb25e447331778394d555894286a7913f Mon Sep 17 00:00:00 2001 From: Andy Somogyi Date: Wed, 11 Dec 2013 02:12:44 -0500 Subject: [PATCH 6/6] tweak for MSVC build, ran win32 tests --- CMakeLists.txt | 2 +- plugins/wrappers/Python/CMakeLists.txt | 2 +- ...MSVC__Release_develop_2013-12-11_02-11.xml | 1072 +++++++++++++++++ 3 files changed, 1074 insertions(+), 2 deletions(-) create mode 100644 reports/win_i386/c_tests_MSVC__Release_develop_2013-12-11_02-11.xml diff --git a/CMakeLists.txt b/CMakeLists.txt index 64d850d65e..8ae0ff32f8 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -306,6 +306,6 @@ install( if(WIN32) install( - FILES win32_bin_README.txt DESTINATION bin/ + FILES win32_bin_README.txt DESTINATION bin/ RENAME README.txt ) endif(WIN32) diff --git a/plugins/wrappers/Python/CMakeLists.txt b/plugins/wrappers/Python/CMakeLists.txt index 2897a3eb57..32895a9728 100644 --- a/plugins/wrappers/Python/CMakeLists.txt +++ b/plugins/wrappers/Python/CMakeLists.txt @@ -12,7 +12,7 @@ endif() install( FILES rrPlugins.py - DESTINATION python + DESTINATION c_api_python COMPONENT plugins_api ) 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 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +