Merge pull request #798 from sys-bio/develop

Release 2.1.0

.gitignore

@@ -57,3 +57,7 @@ install-release
 build-debug
 build-release
 install-debug
+roadrunner-install-rel
+
+# temp.
+sundials

README.md

@@ -1,17 +1,54 @@
 # libRoadRunner
 [![GitHub version](https://badge.fury.io/gh/sys-bio%2Froadrunner.svg)](http://badge.fury.io/gh/sys-bio%2Froadrunner)
-[![Build Status](https://dev.azure.com/TheRoadrunnerProject/roadrunner/_apis/build/status/sys-bio.roadrunner?branchName=develop-new-buildsystem)](https://dev.azure.com/TheRoadrunnerProject/roadrunner/_build/latest?definitionId=8&branchName=develop-new-buildsystem)
+[![Build Status](https://dev.azure.com/TheRoadrunnerProject/roadrunner/_apis/build/status/sys-bio.roadrunner?branchName=develop)](https://dev.azure.com/TheRoadrunnerProject/roadrunner/_build/latest?definitionId=8&branchName=develop)
 
-#[Documentation](http://sys-bio.github.io/roadrunner/)
+<table style="width:100%">
+  <tr>
+    <td><img alt="Read the Docs" src="https://img.shields.io/readthedocs/roadrunner"></td>
+    <td><a href="https://badge.fury.io/gh/sys-bio%2Froadrunner"><img src="https://badge.fury.io/gh/sys-bio%2Froadrunner.svg" alt="GitHub version" height="18"></a></td>
+  </tr>
+</table> 
 
-Copyright 2013-2018
+ <table style="width:100%">
+  <tr>
+    <td><img alt="Licence", src="https://img.shields.io/badge/License-Apache%202.0-yellowgreen"</td>
+    <td><img alt="PyPI - Downloads", src="https://img.shields.io/pypi/dm/roadrunner"></td>
+    <td><img alt="Funding", src="https://img.shields.io/badge/Funding-NIH%20(GM123032)-blue"></td>
+    <td><a href="https://badge.fury.io/py/tellurium"><img src="https://badge.fury.io/py/roadrunner.svg" alt="PyPI version" height="18"></a> </td>
+   </tr>
+</table> 
 
-E. T. Somogyi <sup>1</sup>, J. K. Medley <sup>3</sup>, M. T. Karlsson <sup>2</sup>, M. Swat <sup>1</sup>, M. Galdzicki <sup>3</sup>, K. Choi <sup>3</sup>, W. Copeland <sup>3</sup> and H. M. Sauro <sup>3</sup>
+# Summary
+
+libroadrunner is a C/C++ library that supports simulation of SBML based models. It uses LLVM to generate extremely high performace code and is the fastest SBML based simulator currently avaialable. Its main purpose is for use as a resuable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical. 
+
+We provide C/C++, Python and Julia bindings.
+
+# Installation
+Python front end (stable):
+
+`pip install libroadrunner`
+
+Binaries:
+
+Head over to the [Releases](https://github.com/sys-bio/roadrunner/releases) page to download binaries. 
+
+Experimental front end: 
+
+`pip install libroadrunner-experimental`
+
+# [Click here to get Documentation](http://sys-bio.github.io/roadrunner/)
+
+Copyright 2013-2021
+
+E. T. Somogyi <sup>1</sup>, J. K. Medley <sup>3</sup>, M. T. Karlsson <sup>2</sup>, M. Swat <sup>1</sup>, M. Galdzicki <sup>3</sup>, K. Choi <sup>3</sup>, W. Copeland <sup>3</sup>, L. Smith <sup>3</sup>, C. Welsh <sup>3</sup> and H. M. Sauro <sup>3</sup>
 
 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
 
+The current (2021) developers are Lucian Smith and Ciaran Welsh.
+
 ## Introduction
 
 libRoadRunner is a high-performance and portable simulation engine for systems and synthetic biology.
@@ -46,6 +83,25 @@ Python APIs have comprehensive documentation. On Windows, OS X, and Linux binary
 downloaded from http://sourceforge.net/projects/libroadrunner/files and can be installed 
 ready for use.
 
+## Docker images
+Currently we have a manylinux2014 "base" and "build" docker images. The 
+base provides the environment you need to be able to build roadrunner 
+yourself on manylinux2014 (centos 7). The "build" image, in constrast
+is an image where roadrunner has already been built on top of the "base" 
+image. 
+
+To get the base image: 
+
+`docker pull ciaranwelsh/roadrunner-manylinux2014-base:latest`
+
+and the build image:
+
+`docker pull ciaranwelsh/roadrunner-manylinux2014-build:latest`
+
+Docker build scripts can be found under the `docker` directory from the roadrunner
+root directory. 
+
+We can also build roadrunner in alternative docker environments (ubuntu etc.) on request. 
 
 ## Acknowledgements
 

autotest/CMakeLists.txt

@@ -35,4 +35,5 @@ if(BUILD_PYTHON)
     COMMAND ${PYTHON_EXECUTABLE} run.py
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/python-unit-tests)
   set_tests_properties(PythonUnitTests PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/lib/site-packages:$PYTHONPATH")
+
 endif()