Merge pull request #210 from GillesPy2/develop

Release 1.2.1

README.md

@@ -1,11 +1,11 @@
 <p align="left">
-<img src=".graphics/gillespy2-logo.png">
+<img src="https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/gillespy2-logo.png">
 </p>
 
 GillesPy2 is a Python package for stochastic simulation of biochemical systems.  It offers an object-oriented approach for creating mathematical models of biological systems, as well as a variety of methods for performing time simulation of those models.  The methods include the [Gillespie direct method (SSA)](https://en.wikipedia.org/wiki/Gillespie_algorithm), several variant stochastic simulation methods including [tau-leaping](https://en.wikipedia.org/wiki/Tau-leaping), and numerical integration of ODEs.  The solvers support a variety of user environments, with optimized code for C++, [Cython](https://cython.org), and [NumPy](https://numpy.org).  GillesPy2 also supports [SBML](https://en.wikipedia.org/wiki/SBML).
 
 <table><tr><td><b>
-<img width="20%" align="right" src=".graphics/stochss-logo.svg">
+<img width="20%" align="right" src="https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/stochss-logo.png">
 <a href="https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform">PLEASE REGISTER AS A USER</a>, so that we can prove GillesPy2 has many users when we seek funding to support development. GillesPy2 is part of the <a href="http://www.stochss.org">StochSS</a> project.
 </td></tr></table>
 
@@ -119,7 +119,7 @@ results.plot()
 ```
 
 <p align="center">
-<img width="500px" src=".graphics/dimerization-example-plot.png">
+<img width="500px" src="https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/dimerization-example-plot.png">
 </p>
 
 Alternatively, the results object inherits python-builtin `UserDict` for single trajectories, and `UserList` for multiple trajectories.  Results can be plotted easily using any plotting library such as matplot lib as shown below:
@@ -134,7 +134,7 @@ for index in range(0, 10):
 With a few additional Python Matplotlib commands to create figure labels and such, we end up with a plot like this:
 
 <p align="center">
-<img width="500px" src=".graphics/dimerization-example-matplotlib.png">
+<img width="500px" src="https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/dimerization-example-matplotlib.png">
 </p>
 
 
@@ -176,7 +176,7 @@ New developments happen primarily in the [`develop`](https://github.com/GillesPy
 
 | Master Branch   | Develop Branch | Coverage |
 |:---------------:|:--------------:|:--------:|
-| [![Build Status](https://travis-ci.org/GillesPy2/GillesPy2.svg?branch=master)](https://travis-ci.org/GillesPy2/GillesPy2) | [![Build Status](https://travis-ci.org/GillesPy2/GillesPy2.svg?branch=develop)](https://travis-ci.org/GillesPy2/GillesPy2) | ![Coverage](.graphics/coverage.svg) |
+| [![Build Status](https://travis-ci.org/GillesPy2/GillesPy2.svg?branch=master)](https://travis-ci.org/GillesPy2/GillesPy2) | [![Build Status](https://travis-ci.org/GillesPy2/GillesPy2.svg?branch=develop)](https://travis-ci.org/GillesPy2/GillesPy2) | ![Coverage](https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/coverage.png) |
 
 
 
@@ -198,22 +198,22 @@ Finally, we are grateful for institutional resources made available by the [UNC
 
 <div align="center">
   <a href="https://www.nigms.nih.gov">
-    <img width="100" height="100" src=".graphics/US-NIH-NIGMS-Logo.svg">
+    <img width="100" height="100" src="https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/US-NIH-NIGMS-Logo.png">
   </a>
   &nbsp;&nbsp;
   <a href="https://www.unca.edu">
-    <img height="102" src=".graphics/UNCASEAL_blue.png">
+    <img height="102" src="https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/UNCASEAL_blue.png">
   </a>
   &nbsp;&nbsp;
   <a href="https://www.ucsb.edu">
-    <img height="108" src=".graphics/ucsb-seal-navy.jpg">
+    <img height="108" src="https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/ucsb-seal-navy.jpg">
   </a>
   &nbsp;&nbsp;
   <a href="https://www.it.uu.se">
-    <img height="115" src=".graphics/uppsala-universitet-logo-svg-vector.svg">
+    <img height="115" src="https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/uppsala-universitet-logo-svg-vector.png">
   </a>
   &nbsp;&nbsp;
   <a href="https://www.caltech.edu">
-    <img width="100" height="100" src=".graphics/caltech-round.svg">
+    <img width="115" src="https://raw.githubusercontent.com/GillesPy2/GillesPy2/develop/.graphics/caltech-round.png">
   </a>
 </div>

gillespy2/__version__.py

@@ -5,7 +5,7 @@
 # @website https://github.com/GillesPy2/GillesPy2
 # =============================================================================
 
-__version__      = '1.2'
+__version__      = '1.2.1'
 __title__        = 'GillesPy2'
 __description__  = 'Python interface for Gillespie-style biochemical simulations'
 __url__          = 'https://github.com/GillesPy2/GillesPy2'