documentation update, licence and copyright updates, minimum python update

Author: bgoli

CONTRIBUTORS

@@ -1,7 +1,7 @@
 # StochPy Stochastic modeling in Python
 
 
-Copyright (c) 2011-2021, Timo R. Maarleveld, Brett G. Olivier, and Frank J. Bruggeman
+Copyright (c) 2011-2025, Timo R. Maarleveld, Brett G. Olivier, and Frank J. Bruggeman
 All rights reserved.
 
 StochPy is distributed under a BSD style licence.
@@ -22,9 +22,12 @@ Vrije Universiteit Amsterdam, Amsterdam, Netherlands
 
 ## GitHub contributions (per release):
 
+### Release 2.5
+Thanks for the contributions and updates @V-DeVito, @zesloth
+
 ### 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: 2021-04-30
+Last updated: 2025-06-18

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2021, Systems Biology Lab, Vrije Universiteit Amsterdam
+Copyright (c) 2025, Systems Biology Lab, Vrije Universiteit Amsterdam
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -16,8 +16,8 @@ Documentation can be found in the user guide (see Documentation directory or in
 
 The following software is required before installing StochPy (see user guide for more details):
 
-- Python 2.6+ or Python 3.4+
-- [NumPy 1.x+](http://www.numpy.org)
+- Python 3.9+ and Python 2.6+ (obsolete)
+- [NumPy 1.21+](http://www.numpy.org)
 - [SciPy](https://scipy.org)
 - [Matplotlib](https://matplotlib.org) (optional)
 - [libsbml](http://sbml.org/Software/libSBML) (optional)
@@ -26,16 +26,16 @@ The following software is required before installing StochPy (see user guide for
 
 Install StochPy and dependencies with PIP using the following command (in your StochPy Python virtual environment):
 ```bash
-pip install scipy matplotlib python-libsbml jedi==0.17.2 ipython stochpy
+pip install numpy scipy matplotlib python-libsbml ipython stochpy
 ```
 
 If you are using Anaconda, create a custom conda environment for StochPy, for example:
 ```bash
-conda create -n "stochpy39" -c sbmlteam python=3.9 pip scipy matplotlib sympy ipython
+conda create -n "stochpy10" python=3.10 pip numpy scipy matplotlib sympy ipython
 ```
 activate your new environment, install StochPy (only required once per environment) and start ipython.
 ```bash
-conda activate stochpy39
+conda activate stochpy10
 pip install stochpy
 ipython
 
@@ -45,7 +45,7 @@ ipython
 
 In the directory where you downloaded/cloned the StochPy source, for example, the git main branch:
 ```bash
-sudo python setup.py install
+pip install .
 ```
 
 ### Windows
@@ -59,6 +59,8 @@ You can run `ipython` and import `stochpy`:
 ```py
 import stochpy
 smod = stochpy.SSA()
+# Run the demo
+stochpy.Demo()
 ```
 
 ### Basic Simulation with the Direct method
@@ -193,14 +195,15 @@ Centrum Wiskunde en Informatica, Amsterdam, Netherlands
 VU University, Amsterdam, Netherlands
 
 > e-mail: tmd200@users.sourceforge.net
+> e-mail: b.g.olivier@vu.nl
 
 ## Publication
 
 StochPy: A Comprehensive, User-Friendly Tool for Simulating Stochastic Biological Processes
 http://dx.doi.org/10.1371/journal.pone.0079345
 
 ## Licence
-Copyright (c) 2011-2021, Timo R. Maarleveld, Brett G. Olivier, and Frank J. Bruggeman
+Copyright (c) 2011-2025, Timo R. Maarleveld, Brett G. Olivier, and Frank J. Bruggeman
 Vrije Universiteit Amsterdam. All rights reserved.
 
 StochPy is open source software distributed under the BSD 3-Clause License see LICENSE file for more details.

pyproject.toml

@@ -14,7 +14,7 @@ maintainers = [
     {name = "Brett G. Olivier", email = "b.g.olivier@vu.nl"},
 ]
 license = {text = "BSD License"}
-requires-python = ">=3.7"
+requires-python = ">=3.9"
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Development Status :: 6 - Mature",
@@ -38,7 +38,7 @@ dependencies = [
 ]
 
 [project.urls]
-"Homepage" = "http://stochpy.sourceforge.net"
+"Homepage" = "https://github.com/SystemsBioinformatics/stochpy"
 "Download" = "https://github.com/SystemsBioinformatics/stochpy"
 "Bug Tracker" = "https://github.com/SystemsBioinformatics/stochpy/issues"
 

stochpy/__init__.py

@@ -2,7 +2,7 @@
 """
 StochPy - Stochastic modeling in Python (http://stochpy.sourceforge.net)
 
-Copyright (C) 2010-2015 T.R Maarlveld, B.G. Olivier, F.J. Bruggeman all rights reserved.
+Copyright (C) 2010-2025 T.R Maarlveld, B.G. Olivier, F.J. Bruggeman all rights reserved.
 
 Timo R. Maarleveld (tmd200@users.sourceforge.net)
 Centrum Wiskunde & Informatica, Amsterdam, Netherlands
@@ -277,7 +277,7 @@ def SaveInteractiveSession(filename='interactiveSession.py',path=output_dir):
 #######################################################################
 #  StochPy: Stochastic modeling in Python                             #
 #  http://stochpy.sourceforge.net                                     #
-#  Copyright(C) T.R Maarleveld, B.G. Olivier, F.J Bruggeman 2010-2015 #
+#  Copyright(C) T.R Maarleveld, B.G. Olivier, F.J Bruggeman 2010-2025 #
 #  DOI: 10.1371/journal.pone.0079345                                  #
 #  Email: tmd200@users.sourceforge.net                                #
 #  VU University, Amsterdam, Netherlands                              #