minor README changes (#168)

* minor changes in README
* adding minimum version requirement for bokeh: bokeh>=1.4.0

README.md

@@ -1,19 +1,21 @@
-# BioCRNpyler: Compiling Chemical Reaction Networks from Parts in Diverse Contexts
-## Python framework and library that compiles SBML models from simple specifications
+# BioCRNPyler — Biomolecular Chemical Reaction Network Compiler
+## Python toolbox to create CRN models in SBML for biomolecular mechanisms
 
 [![Build Status](https://travis-ci.com/BuildACell/BioCRNPyler.svg?branch=master)](https://travis-ci.com/BuildACell/BioCRNPyler)
 [![codecov](https://codecov.io/gh/BuildACell/BioCRNPyler/branch/master/graph/badge.svg)](https://codecov.io/gh/BuildACell/BioCRNPyler)
 [![PyPI version](https://badge.fury.io/py/biocrnpyler.svg)](https://badge.fury.io/py/biocrnpyler)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/BuildACell/BioCRNPyler/master?filepath=%2Fexamples%2F)
 
-BioCRNPyler is a Python package for the creation, manipulation,
+BioCRNPyler (pronounced Bio-Compiler) is a Python package for the creation, manipulation,
 and study of the structure, dynamics, and functions
 of complex biochemical networks.
 
-- **Website:** http://buildacell.io/BioCRNPyler
-- **Mailing list:** TBA
+- **Website:** https://github.com/BuildACell/BioCRNPyler
+- **Mailing list:** [SBTools Google Group](https://groups.google.com/g/sbtools/) Email: [email protected]
 - **Source:** https://github.com/BuildACell/BioCRNPyler
 - **Bug reports:** https://github.com/BuildACell/BioCRNPyler/issues
+- **Documentation** [biocrnpyler.readthedocs.io](https://readthedocs.org/projects/biocrnpyler/)
+- **Slack** Join the #biocrnpyler channel on SBTools slack: Ask on the public SBTools Google group to be added or send a message to one of the maintainers. 
 
 # Example 1: Building Simple CRNs by Hand
 
@@ -95,18 +97,21 @@ Install with all optional dependencies::
     $ pip install biocrnpyler[all]
 
 Further details about the installation process can be found in the [BioCRNPyler wiki](https://github.com/BuildACell/BioCRNPyler/wiki#installation).
+
 # Bugs
+
 Please report any bugs that you find [here](https://github.com/BuildACell/BioCRNPyler/issues).
 Or, even better, fork the repository on [GitHub](https://github.com/BuildACell/BioCRNPyler),
 and create a pull request (PR). We welcome all changes, big or small, and we
 will help you make the PR if you are new to `git` (just ask on the issue and/or
-see `docs/CONTRIBUTING.md`).
+see [contribution guidelines](https://github.com/BuildACell/BioCRNPyler/blob/master/docs/CONTRIBUTING.md)).
 
 # Versions
 
 BioCRNpyler versions:
 
 * 1.0.0 (latest stable release): To install run `pip install biocrnpyler` 
+* 0.9.0 (beta release): To install run `pip install biocrnpyler==0.9.0`
 * 0.2.1 (alpha release): To install run `pip install biocrnpyler==0.2.1`
 
 # License

examples/1. Building CRNs Directly.ipynb

@@ -91,7 +91,7 @@
       "]\n",
       "\n",
       "CRN.pretty_print(...) is a function that prints a more customizable version of the CRN, but doesn't show the proper string representation of species.\n",
-      "Species (4) = {0. m1[A(attribute)], 1. m1[B], 2. m2[B], 3. D}\n",
+      "Species (4) = {0. m1[A(attribute)] init_conc = 0, 1. m1[B] init_conc = 0, 2. m2[B] init_conc = 0, 3. D init_conc = 0}\n",
       "\n",
       "Reactions (2) = [\n",
       "0. m1[A(attribute)] --> 2m1[B]\n",
@@ -412,9 +412,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}

setup.cfg

@@ -1,2 +1,4 @@
+[metadata]
+long_description_content_type = text/markdown
 [aliases]
 test=pytest

setup.py

@@ -29,7 +29,7 @@
             "numpy",
             "matplotlib",
             "networkx",
-            "bokeh",
+            "bokeh>=1.4.0",
             "fa2"
             ],
         },