Metadata-Version: 2.1
Name: phykit
Version: 0.1.0
Summary: UNKNOWN
Home-page: https://github.com/jlsteenwyk/phykit
Author: Jacob L. Steenwyk
Author-email: jlsteenwyk@gmail.com
License: UNKNOWN
Description: <p align="center">
          <a href="https://github.com/jlsteenwyk/phykit">
            <img src="https://raw.githubusercontent.com/JLSteenwyk/PhyKIT/master/docs/_static/img/phykit_logo.png" alt="Logo" width="400">
          </a>
          <p align="center">
            <a href="https://jlsteenwyk.com/PhyKIT/">Docs</a>
            ·
            <a href="https://github.com/jlsteenwyk/phykit/issues">Report Bug</a>
            ·
            <a href="https://github.com/jlsteenwyk/phykit/issues">Request Feature</a>
          </p>
            <p align="center">
                <a href="https://lbesson.mit-license.org/" alt="License">
                    <img src="https://img.shields.io/badge/License-MIT-blue.svg">
                </a>
                <a href="https://pypi.org/project/phykit/" alt="PyPI - Python Version">
                    <img src="https://img.shields.io/pypi/pyversions/phykit">
                </a>
                <a href="https://github.com/JLSteenwyk/PhyKIT/actions" alt="Build">
                    <img src="https://img.shields.io/github/workflow/status/jlsteenwyk/phykit/CI/master">
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                <a href="https://codecov.io/gh/jlsteenwyk/phykit" alt="Coverage">
                  <img src="https://codecov.io/gh/jlsteenwyk/phykit/branch/master/graph/badge.svg?token=0J49I6441V">
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                <a href="https://github.com/jlsteenwyk/phykit/graphs/contributors" alt="Contributors">
                    <img src="https://img.shields.io/github/contributors/jlsteenwyk/phykit">
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                <a href="https://twitter.com/intent/follow?screen_name=jlsteenwyk" alt="Author Twitter">
                    <img src="https://img.shields.io/twitter/follow/jlsteenwyk?style=social&logo=twitter"
                        alt="follow on Twitter">
                </a>
            </p>
        </p>
        
        PhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data.<br /><br />
        If you found PhyKIT useful, please cite *PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data*. bioRxiv. doi: [10.1101/2020.10.27.358143](https://www.biorxiv.org/content/10.1101/2020.10.27.358143v1).
        <br /><br />
        
        ---
        
        This documentation covers downloading and installing PhyKIT. Details about each function as well as tutorials for using PhyKIT are available in the <a href="https://jlsteenwyk.com/PhyKIT/">online documentation</a>.
        
        <br />
        
        **Installation** <br />
        
        **If you are having trouble installing PhyKIT, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) to get help.**
        
        To install using *pip*, we strongly recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:
        ```shell
        # create virtual environment
        python -m venv .venv
        # activate virtual environment
        source .venv/bin/activate
        # install phykit
        pip install phykit
        ```
        
        **Note, the virtual environment must be activated to use phykit.**
        
        After using PhyKIT, you may wish to deactivate your virtual environment and can do so using the following command:
        ```shell
        # deactivate virtual environment
        deactivate
        ```
        
        <br />
        
        Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:
        ```shell
        # download
        git clone https://github.com/JLSteenwyk/PhyKIT.git
        cd PhyKIT/
        # create virtual environment
        python -m venv .venv
        # activate virtual environment
        source .venv/bin/activate
        # install
        make install
        ```
        To deactivate your virtual environment, use the following command:
        ```shell
        # deactivate virtual environment
        deactivate
        ```
        **Note, the virtual environment must be activated to use phykit.**
        
        <br />
        
        To install via anaconda, execute the following command:
        ```shell
        conda install -c jlsteenwyk phykit
        ```
        Visit here for more information:
        https://anaconda.org/JLSteenwyk/phykit
        
        <br />
        
        To test phykit installation, launch the help message
        
        ```shell
        phykit -h
        ```
        
Platform: UNKNOWN
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering
Description-Content-Type: text/markdown
