Metadata-Version: 1.1
Name: stocal
Version: 1.0.2
Summary: simple rule-based stochastic simulation
Home-page: https://github.com/harfel/
Author: Harold Fellermann
Author-email: harold.fellermann@newcastle.ac.uk
License: MIT
Description-Content-Type: UNKNOWN
Description: # stocal
        
        A python framework for regular and rule-based stochastic simulations.
        
        
        ## What is Stocal?
        
        Stocal is a framework for stochastic simulation of continuous
        time Markov processes (also known as [Gillespie simulations](https://en.wikipedia.org/wiki/Gillespie_algorithm)). 
        
        Features of stocal:
        * support for reactions of any order
        * support for unique and periodic (deterministic) events
        * support for rules that generate novel reactions on the fly
        * support for complex chemical states
        
        Stocal works with python version 2.7 as well as version 3.5.
        
        
        ### Basic Usage
        
        Running a simple stochastic simulation is straight forward:
        ```python
        import stocal
        
        # Define a stochastic process
        process = stocal.Process([
        	stocal.MassAction({'A': 2}, {'A2': 1}, 1.0),
        	stocal.MassAction({'A2': 1}, {'A': 2}, 10.0),
        	stocal.Event({}, {'A': 100}, 0.0, frequency=10.0),
        ])
        
        # Sample a stochastic trajectory of the process
        initial_state = {}
        trajectory = process.trajectory(initial_state, tmax=100) :
        	print trajectory.time, trajectory.state['A2']
        ```
        
        
        ### API / Tutorial
        
        A tutorial on how to use stocal can be found [here](https://github.com/harfel/stocal/wiki).
        Various usage examples are provided in stocal/examples.
        The package API is thoroughly documented and can be accessed through
        pydoc. The behavior of stocal is specified via tests. The test suite
        can be run with `python setup.py test`.
        
        
        ### Installation
        
        The latest stable release of stocal is available from the python package index:
        ```shell
        pip install stocal
        ```
        The development version can be obtained from github using the following commands:
        ```shell
        git clone https://github.com/harfel/stocal.git
        cd stocal
        git checkout develop
        sudo python setup.py install
        ```
        
        
        ## Issue Reporting and Contributing
        
        Please post any issues that might occur with stocal on the
        <a href="https://github.com/harfel/stocal/issues">github issue
        tracker</a>.
        If you are interested in contributing to stocal, pull requests
        and any other inquiries will be dealt with as soon as possible.
        
        
        ## License
        
        Stocal is distributed under the MIT Software license.
        (c) 2018 Harold Fellermann
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.5
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
