Metadata-Version: 2.1
Name: ecophylo
Version: 0.1.2
Summary: Coalescent-based simulations of eco-evolutionary biodiverity dynamics
Home-page: https://github.com/thegreatlizzyator/ecophylo
Author: Elizabeth Barthelemy
Author-email: elizabeth.barthelemy@univ-grenoble-alpes.fr
License: CeCILL
Description: # EcoPhylo
        
        [![PyPI status](https://img.shields.io/pypi/status/ecophylo.svg)](https://pypi.python.org/pypi/ecophylo/)
        [![PyPI version](https://badge.fury.io/py/ecophylo.svg)](https://badge.fury.io/py/ecophylo)
        [![PyPI license](https://img.shields.io/pypi/l/ecophylo.svg)](https://pypi.python.org/pypi/ecophylo/)
        [![PyPI pyversions](https://img.shields.io/pypi/pyversions/ecophylo.svg)](https://pypi.python.org/pypi/ecophylo/)
        
        *Ecophylo* is dedicated to coalescent-based simulation of eco-evolutionary dynamics. Species assemblages and their shared ancestry can be simulated by jointly taking into account the influence of past demographic fluctuations and extinctions along with how divergent genotypes have introduced new species over time through speciation.
        
        The source for this project is available [here][src].
        
        ----
        
        [src]: https://github.com/thegreatlizzyator/ecophylo
        
        ## Dependencies
        
        This package depend on **python 3.7**.
        
        There are multiple dependencies to other python packages. This will be done when installing ecophylo tool in most cases. 
        
        You can experiment difficulties for installing msprime, check the help [here][msprime]
        
        [msprime]: https://tskit.dev/msprime/docs/stable/installation.html
        
        ## Install (with pip)
        
        To install this package, you can either download the tar.gz file in the *dist* directory of the repository :
        ```shell
        python3 -m pip install <path_to>/ecophylo-<VERSION>.tar.gz
        ``` 
        
        or install from the Python Package index (Pypi) :
        
        ```shell
        python3 -m pip install ecophylo
        ``` 
        
        or install from github (it does not work for private repository):
        
        ```shell
        python3 -m pip install git+https://github.com/thegreatlizzyator/ecophylo/tree/packaging/dist/ecophylo-0.0.5.tar.gz
        ```
        
        ## Usage
        
        You can simulate trees using this package main function in python.
        
        ```python
        import ecophylo
        n = 25 #the number of sampled individuals
        com_size = [[5000,10000,50000]] # the size of the assemblage in the past, the first element is the current assemblage size
        mu = 0.001 # the point mutation rate
        changetime = [[0,700,10000]] # the dates (in generation time) at which the assemblage has changed sizes in the past
        
        tree = ecophylo.simulate(samples = n,
                                 com_size= com_size, 
                                 mu = mu, 
                                 changetime= changetime, seed= 42)
        
        print(tree)
        ```
        
        ## Maintainers
        
        [@thegreatlizzyator](https://github.com/thegreatlizzyator) & [@gowachin](https://github.com/gowachin).
        
        ## Contributing
        
        Feel free to dive in! [Open an issue](https://github.com/thegreatlizzyator/ecophylo/issues/new) or submit PRs.
        
        thegreatlizzyator follows the [Contributor Covenant](http://contributor-covenant.org/version/1/3/0/) Code of Conduct.
        
        ### Contributors
        
        This project exists thanks to all the people who contribute. 
        <a href = "https://github.com/thegreatlizzyator/ecophylo/graphs/contributors">
          <img src = "https://contrib.rocks/image?repo = thegreatlizzyator/ecophylo"/>
        </a>
        
        ## License
        
        [CeCILL-B](LICENSE) © Richard Littauer
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.7
Classifier: License :: CeCILL-B Free Software License Agreement (CECILL-B)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
