updated documentation

Author: bgoli

CONTRIBUTORS

@@ -1,27 +1,30 @@
-StochPy Stochastic modeling in Python
-=====================================
+# StochPy Stochastic modeling in Python
 
-Copyright (c) 2011-2016, Timo R. Maarleveld, Brett G. Olivier, and Frank J. Bruggeman
+
+Copyright (c) 2011-2021, Timo R. Maarleveld, Brett G. Olivier, and Frank J. Bruggeman
 All rights reserved.
 
 StochPy is distributed under a BSD style licence.
 
 File releases: http://sourceforge.net/projects/stochpy
 Source code: https://github.com/SystemsBioinformatics/stochpy
 
-Author information
-------------------
+## Author information
 
 Timo R. Maarleveld, Brett G. Olivier and Frank J. Bruggeman
 Centrum Wiskunde en Informatica, Amsterdam, Netherlands
-VU University, Amsterdam, Netherlands
+Vrije Universiteit Amsterdam, Amsterdam, Netherlands
+
+## Major code contributors to the StochPy codebase
+
+- Brett G. Olivier (@bgoli)
+- Catharina Meyer
 
-Contributors to StochPy code
-----------------------------
+## GitHub contributions (per release):
 
- - Brett G. Olivier, 
- - Catharina Meyer
+### Release 2.4
+Thanks for the contributions @zesloth, @enricozb and @developerfab
 
 Please let us know if you feel you should be included in this list.
 
-Last updated: 2016-09-29
+Last updated: 2021-04-30

README.md

@@ -23,9 +23,9 @@ The following software is required before installing StochPy (see user guide for
 - [libxml2](http://xmlsoft.org) (optional)
 - [mpmath](http://mpmath.org) (optional)
 
-Install the StochPy dependencies with PIP using the following command (in your StochPy Python environment):
+Install the StochPy dependencies with PIP using the following command (in your StochPy Python virtual environment):
 ```bash
-pip install numpy scipy matplotlib python-libsbml mpmath lxml
+pip install numpy scipy matplotlib python-libsbml mpmath lxml jedi==0.17.2 ipython
 ```
 
 #### Linux/MAC OS/Cygwin

setup.py

@@ -39,21 +39,26 @@
     url = "http://stochpy.sourceforge.net",
     download_url = "http://stochpy.sourceforge.net/download.html",
     license = " BSD License ",
-    keywords = " Bioinformatics, Computational Systems Biology, Bioinformatics, Modeling, Simulation, Stochastic Simulation Algorithms, Stochastic", 
+    keywords = " Bioinformatics, Computational Systems Biology, Bioinformatics, Modeling, Simulation, Stochastic Simulation Algorithms, Stochastic",
     zip_safe = False,
     requires = ['NumPy'],
     platforms = ["Windows", "Linux","Mac OS-X"],#, "Solaris", "", "Unix"],
     classifiers = [
-    'Development Status :: 4 - Beta',
+    'Development Status :: 5 - Production/Stable',
+    'Development Status :: 6 - Mature',
     'Environment :: Console',
     'Intended Audience :: End Users/Desktop',
     'Intended Audience :: Science/Research',
     'License :: OSI Approved :: BSD License',
     'Natural Language :: English',
-    'Operating System :: OS Independent',    
+    'Operating System :: OS Independent',
     'Programming Language :: Python :: 2.6',
     'Programming Language :: Python :: 2.7',
     'Programming Language :: Python :: 3.4',
+    'Programming Language :: Python :: 3.6',
+    'Programming Language :: Python :: 3.7',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
     'Topic :: Scientific/Engineering :: Bio-Informatics',
     'Topic :: Scientific/Engineering :: Simulations'],
     packages = mypackages,

stochpy/modules/Analysis.py

@@ -7,7 +7,7 @@
 
 Written by TR Maarleveld, Amsterdam, The Netherlands
 E-mail: [email protected]
-Last Change: August 05, 2015
+
 """
 
 from __future__ import division, print_function, absolute_import