fixed imports, bump version patch

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2019, Kyle Dunovan, Timothy Verstynen, Catalina Vich, Jonathan Rubin
+Copyright (c) 2019, Kyle Dunovan, Matthew Clapp, Timothy Verstynen, Jonathan Rubin, Catalina Vich
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,4 +1,4 @@
-# bgNetwork
+# CBGT
 
 This repository contains code for implementing the spiking cortico-basal ganglia-thalamus (CBGT) network and drift-diffusion model (DDM) fits described in the manuscript [**Reward-driven changes in striatal pathway competition shape evidence evaluation in decision-making**](https://www.biorxiv.org/content/10.1101/418756v2.abstract). 
 
@@ -20,35 +20,32 @@ The code requires several dependencies to be installed (see below for instructio
 ```sh
 # create a new conda environment with python 3.6
 # and hit 'y' to verify the install 
-conda create -n py36 python=3.6 anaconda
+conda create -n cbgt_env python=3.6 anaconda ipykernel
 
-# activate 'py36' environment
-source activate py36
+# activate 'cbgt_env' environment
+source activate cbgt_env
 
 # use conda (not pip) to install pymc
 conda install pymc=2.3.6 --no-deps
 
 # install hddm and kabuki
 pip install --upgrade kabuki hddm
 
-# Alternative Install: (not recommended) 
-# conda install -c pymc hddm
-
 # finally install numpy version 1.11.3
 # (avoids hddm incompatibility with later numpy)
 pip install numpy==1.11.3
-```
-
-* After installing everything, run the line below to open up Jupyter in your browser, then drag/drop the demo notebook (`CBGT_PLOSCompBio2019_Demo.ipynb`) into the Jupyter browser window (see [**this tutorial**](https://medium.com/codingthesmartway-com-blog/getting-started-with-jupyter-notebook-for-python-4e7082bd5d46) if you're new to Jupyter)
 
-```sh
-# make sure you've activated the py36 env first
-jupyter notebook
+# install cbgt package
+pip install -U cbgt --no-cache-dir
 ```
 
+* After installing everything, run `jupyter notebook` in your terminal to start Jupyter in your browser 
+* Drag/drop the demo notebook (`CBGT_PLOSCompBio2019_Demo.ipynb`) into the Jupyter browser window
+
 
 
-#### HDDM Resources:
+#### Miscellaneous:
 
-- For those interested in working more with HDDM, see the [**methods paper here**](https://www.frontiersin.org/articles/10.3389/fninf.2013.00014/full) as well as the introductory [**demo**](http://ski.clps.brown.edu/hddm_docs/tutorial_python.html) and [**how-to**](http://ski.clps.brown.edu/hddm_docs/howto.html) sections
+* HDDM resources: ([**methods paper**](https://www.frontiersin.org/articles/10.3389/fninf.2013.00014/full), [**demo**](http://ski.clps.brown.edu/hddm_docs/tutorial_python.html), [**how-to**](http://ski.clps.brown.edu/hddm_docs/howto.html))
+* Jupyter Notebook [**tutorial**](https://medium.com/codingthesmartway-com-blog/getting-started-with-jupyter-notebook-for-python-4e7082bd5d46)