Metadata-Version: 2.1
Name: pyssa
Version: 0.9.1
Summary: Python package for stochastic simulations
Home-page: https://github.com/Heuro-labs/pyssa
Author: Dileep Kishore, Srikiran Chandrasekaran
Author-email: k.dileep1994@gmail.com
License: Apache Software License 2.0
Description: # pyssa : Python package for stochastic simulations
        
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        ## Introduction
        
        `pyssa` is a Python package for stochastic simulations. It offers a simple API to define models, perform stochastic simulations with them and visualize the results in a convenient manner.
        
        Currently under active development in the `develop` branch.
        
        ## Install
        
        Install with `pip`:
        
        ```bash
        $ pip install pyssa
        ```
        
        
        ## Documentation
        
          - General: <https://pyssa.readthedocs.io>.
        
        
        ## Usage
        
        A short summary follows, but a more detailed tutorial can be found at <https://pyssa.readthedocs.io/en/latest/tutorial.html>
        
        ```python
        from pyssa.simulation import Simulation
        V_r = np.array([[1, 0], [0, 1], [0, 0]])  # Reactant matrix
        V_p = np.array([[0, 0], [1, 0], [0, 1]])  # Product matrix
        X0 = np.array([100, 0, 0])  # Initial state
        k = np.array([1.0, 1.0])  # Rate constants
        sim = Simulation(V_r, V_p, X0, k)  # Declare the simulation object
        # Run the simulation
        sim.simulate(max_t=150, max_iter=1000, chem_flag=True, n_rep=10)
        ```
        
        ### Change simulation algorithm
        
        You can change the algorithm used to perform the simulation by changing the `algorithm` parameter
        
        ```python
        sim.simulate(max_t=150, max_iter=1000, chem_flag=True, n_rep=10, algorithm="tau_adaptive")
        ```
        
        ### Run simulations in parallel
        You can run the simulations on multiple cores by specifying the `n_procs` parameter
        
        ```python
        sim.simulate(max_t=150, max_iter=1000, chem_flag=True, n_rep=10, n_procs=4)
        ```
        
        ### Plot simulation results
        
        ```python
        sim.plot()
        ```
        
        ![Plot of species A, B and C](https://raw.githubusercontent.com/Heuro-labs/pyssa/master/docs/images/plot_basic.png)
        
        ### Accessing simulation results
        
        ```python
        results = sim.results
        ```
        
        You can also access the final states of all the simulation runs by
        
        ```python
        final_times, final_states = results.final
        ```
        
        ## License
        
        Copyright (c) 2018-2020, Dileep Kishore, Srikiran Chandrasekaran. Released under: Apache Software License 2.0
        
        ## Credits
        
        - [Cython](https://cython.org/)
        - [pytest](https://docs.pytest.org)
        - [Cookiecutter](https://github.com/audreyr/cookiecutter)
        - [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage)
        - [black](https://github.com/ambv/black)
        
        
        
Keywords: pyssa stochastic gillepsie simulation
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
