bump version #; add paper ref.

Author: artgoldberg

codemeta.json

@@ -33,7 +33,7 @@
     "codeRepository": "https://github.com/KarrLab/de_sim",
     "contIntegration": "https://circleci.com/gh/KarrLab/de_sim",
     "issueTracker": "https://github.com/KarrLab/de_sim/issues",
-    "version": "0.0.7",
+    "version": "0.0.8",
     "developmentStatus": "active",
     "datePublished": "2020-07-28",
     "dateCreated": "2019-01-20",

de_sim/_version.py

@@ -1 +1 @@
-__version__ = '0.0.7'
+__version__ = '0.0.8'

de_sim/examples/jupyter_examples/1. DE-Sim tutorial.ipynb

@@ -26,7 +26,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Requirement already satisfied: de_sim in /usr/local/lib/python3.7/site-packages (0.0.7)\n",
+      "Requirement already satisfied: de_sim in /usr/local/lib/python3.7/site-packages (0.0.8)\n",
       "Requirement already satisfied: configobj in /usr/local/lib/python3.7/site-packages (from de_sim) (5.0.6)\n",
       "Requirement already satisfied: pympler in /usr/local/lib/python3.7/site-packages (from de_sim) (0.8)\n",
       "Requirement already satisfied: wc-utils[git]>=0.0.16 in /root/.wc/wc_sandbox/packages/wc_utils (from de_sim) (0.0.21)\n",

de_sim/examples/jupyter_examples/2. DE-Sim advanced, simultaneous events.ipynb

@@ -26,7 +26,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Requirement already satisfied: de_sim in /usr/local/lib/python3.7/site-packages (0.0.7)\n",
+      "Requirement already satisfied: de_sim in /usr/local/lib/python3.7/site-packages (0.0.8)\n",
       "Requirement already satisfied: logging2 in /usr/local/lib/python3.7/site-packages (from de_sim) (0.1.2)\n",
       "Requirement already satisfied: matplotlib in /usr/local/lib/python3.7/site-packages (from de_sim) (3.1.2)\n",
       "Requirement already satisfied: configobj in /usr/local/lib/python3.7/site-packages (from de_sim) (5.0.6)\n",

de_sim/examples/jupyter_examples/3. An epidemic model using DE-Sim.ipynb

@@ -50,7 +50,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Requirement already satisfied: de_sim in /usr/local/lib/python3.7/site-packages (0.0.7)\n",
+      "Requirement already satisfied: de_sim in /usr/local/lib/python3.7/site-packages (0.0.8)\n",
       "Requirement already satisfied: wc-utils[git]>=0.0.16 in /root/.wc/wc_sandbox/packages/wc_utils (from de_sim) (0.0.21)\n",
       "Requirement already satisfied: progressbar2>=3.39 in /usr/local/lib/python3.7/site-packages (from de_sim) (3.47.0)\n",
       "Requirement already satisfied: pympler in /usr/local/lib/python3.7/site-packages (from de_sim) (0.8)\n",

joss_paper/paper.bib

@@ -322,5 +322,34 @@ @misc{muller2011running
   year={2011}
 }
 
-
-
+@Article{Hunter:2007,
+  Author    = {Hunter, J. D.},
+  Title     = {Matplotlib: A 2D graphics environment},
+  Journal   = {Computing in Science \& Engineering},
+  Volume    = {9},
+  Number    = {3},
+  Pages     = {90--95},
+  abstract  = {Matplotlib is a 2D graphics package used for Python for
+  application development, interactive scripting, and publication-quality
+  image generation across user interfaces and operating systems.},
+  publisher = {IEEE COMPUTER SOC},
+  doi       = {10.1109/MCSE.2007.55},
+  year      = 2007
+}
+
+@techreport{hagberg2008exploring,
+  title={Exploring network structure, dynamics, and function using NetworkX},
+  author={Hagberg, Aric and Swart, Pieter and S Chult, Daniel},
+  year={2008},
+  institution={Los Alamos National Lab.(LANL), Los Alamos, NM (United States)}
+}
+
+@article{malengier2018odes,
+  title={ODES: a high level interface to ODE and DAE solvers},
+  author={Malengier, Benny and Ki{\v{s}}on, Pavol and Tocknell, James and Abert, Claas and Bruckner, Florian and Bisotti, Marc-Antonio},
+  journal={Journal of Open Source Software},
+  volume={3},
+  number={22},
+  pages={165},
+  year={2018}
+}

joss_paper/paper.md

@@ -282,7 +282,7 @@ DE-Sim is freely and openly available under the MIT license at the locations bel
 
 DE-Sim requires [Python](https://www.python.org/) 3.7 or higher and [pip](https://pip.pypa.io/).
 
-This article discusses version 0.0.7 of DE-Sim.
+This article discusses version 0.0.8 of DE-Sim.
 
 # Acknowledgements