Merge pull request #88 from dcasasor-purdue/master

Working on the README file

README.md

@@ -1,14 +1,22 @@
 # PharmaPy
 
-PharmaPy is a pythonic library for the analysis of pharmaceutical manufacturing systems.\
+<img align="left" src="./doc/online_docs/images/PharmaPy_logo.jpeg" alt="PharmaPy_logo" height="250">
 
-It allows to simulate the dynamics of standalone, drug substance unit operations in a variety of operating modes (batch, continuous, semibatch). Also, PharmaPy facilitates setting up and simulating pharmaceutical **flowsheets**, i.e., interconnected unit operations in a variety of operation modes, ranging from end-to-end batch, end-to-end continuous, and hybrid operation (combination of batch and/or continuous and semicontinuous unit operations).
+<!-- BEGIN Status badges -->
+![GitHub all releases](https://img.shields.io/github/downloads/CryPTSys/PharmaPy/total)
+[![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.compchemeng.2021.107408-blue)](https://www.sciencedirect.com/science/article/abs/pii/S0098135421001861)
+<!-- END Status badges -->
+
+PharmaPy is a pythonic library for the analysis of pharmaceutical manufacturing systems.
+
+It allows to simulate the dynamics of standalone, drug substance unit operations in a variety of operating modes (batch, continuous, semibatch). Also, PharmaPy facilitates setting up and simulating pharmaceutical **flowsheets**, i.e., interconnected unit operations running in one or more operation modes, offering flexibility to simulate end-to-end batch, end-to-end continuous, and hybrid operation schemes (combination of batch and/or continuous and semicontinuous unit operations).
+
+<br clear="left"/>
 
 ## Getting started
-Read our [link to documentation page] for more information on how to install and use PharmaPy.
+To install PharmaPy, download and unzip the code from the release section, and then follow the instructions on the `install_instructions.txt` file.
+
+Read our [link to documentation page] for more information on how to install and how to use PharmaPy.
+
 
-To install PharmaPy, download and unzip the code from this page, and then follow the instructions on the `install_instructions.txt` file.
 
-<!-- BEGIN Status badges -->
-[![Downloads]]
-<!-- END Status badges -->

doc/online_docs/index.rst

@@ -19,7 +19,12 @@ PharmaPy is an open-source library for the analysis of pharmaceutical manufactur
 
 How to cite us:
 
-* Casas-Orozco D, Laky D, Wang V, Abdi M, Feng X,  Wood E,  Laird C, Reklaitis, G V, Nagy, Z K. *PharmaPy: An object-oriented tool for the development of hybrid pharmaceutical flowsheets.* Computers & Chemical Engineering. 2021;153:107408::
+.. bibliography::
+   :list: bullet
+
+   Casas-Orozco2020
+
+Bibtex entry::
 
         @article{Casas-Orozco2020,
           author = {Casas-Orozco, Daniel and Laky, Daniel and Wang, Vivian and Abdi, Mesfin and Feng, X. and Wood, E. and Laird, Carl and Reklaitis, Gintaras V. and Nagy, Zoltan K.},
@@ -76,17 +81,6 @@ PharmaPy has been made with the collaboration and support from the following ins
    publications
    advanced_usage
 
-..   examples/PFR_Batch_solved
-
-..   installations.rst
-..   general_features.rst
-..   unit_operations.rst
-..   simulation_executive.rst
-..   advanced_features.rst
-..   phases.rst
-..   kinetics.rst
-
-
 Indices and tables
 ==================