Metadata-Version: 1.2
Name: cortexpy
Version: 0.46.2
Summary: The python sister project to CortexJDK
Home-page: https://github.com/winni2k/cortexpy
Author: Warren W. Kretzschmar, Kiran V Garimella
Author-email: winni@warrenwk.com, kiran.garimella@gmail.com
License: Apache-2.0
Download-URL: https://github.com/winni2k/cortexpy/archive/0.46.2.tar.gz
Description: Overview of Cortexpy_
        =====================
        
        .. start-badges
        
        .. list-table::
            :stub-columns: 1
        
            * - tests
              - | |travis|
                | |coveralls| |codecov|
            * - package
              - | |version| |wheel| |supported-versions|
                | |supported-implementations| |commits-since|
            * - docs
              - | |readthedocs|
        
        .. |travis| image:: https://travis-ci.org/winni2k/cortexpy.svg?branch=master
            :alt: Travis-CI Build Status
            :target: https://travis-ci.org/winni2k/cortexpy
        
        .. |coveralls| image:: https://coveralls.io/repos/winni2k/cortexpy/badge.svg?branch=master&service=github
            :alt: Coverage Status
            :target: https://coveralls.io/r/winni2k/cortexpy
        
        .. |codecov| image:: https://codecov.io/github/winni2k/cortexpy/coverage.svg?branch=master
            :alt: Coverage Status
            :target: https://codecov.io/github/winni2k/cortexpy
        
        .. |version| image:: https://img.shields.io/pypi/v/cortexpy.svg
            :alt: PyPI Package latest release
            :target: https://pypi.python.org/pypi/cortexpy
        
        .. |commits-since| image:: https://img.shields.io/github/commits-since/winni2k/cortexpy/v0.46.2.svg
            :alt: Commits since latest release
            :target: https://github.com/winni2k/cortexpy/compare/v0.46.2...master
        
        .. |wheel| image:: https://img.shields.io/pypi/wheel/cortexpy.svg
            :alt: PyPI Wheel
            :target: https://pypi.python.org/pypi/cortexpy
        
        .. |supported-versions| image:: https://img.shields.io/pypi/pyversions/cortexpy.svg
            :alt: Supported versions
            :target: https://pypi.python.org/pypi/cortexpy
        
        .. |supported-implementations| image:: https://img.shields.io/pypi/implementation/cortexpy.svg
            :alt: Supported implementations
            :target: https://pypi.python.org/pypi/cortexpy
        
        .. |readthedocs| image:: https://readthedocs.org/projects/cortexpy/badge/?version=latest
           :target: https://cortexpy.readthedocs.io/en/latest/?badge=latest
           :alt: Documentation Status
        
        
        .. end-badges
        
        Cortexpy is a Python package for sequence analysis using linked and colored De Bruijn graphs such as
        the ones created by Cortex_ and Mccortex_.
        This project aims to mirror many of the features contained in
        `CortexJDK <https://github.com/mcveanlab/CortexJDK>`_.
        
        .. _cortexpy: https://github.com/winni2k/cortexpy
        
        Cortexpy also comes with a command-line tool for basic inspection and manipulation of Cortex graphs with and without links.
        
        .. _Cortex: https://github.com/iqbal-lab/cortex
        .. _Mccortex: https://github.com/mcveanlab/mccortex
        
        Audience
        --------
        
        The audience of cortexpy is researchers working with colored De Bruijn graphs and link information in Cortex_ and Mccortex_ format.
        
        
        Free software
        -------------
        
        Cortexpy is free software; you can redistribute it and/or modify it under the
        terms of the Apache License version 2.0.  Contributions are welcome. Please join us on `GitHub <https://github.com/winni2k/cortexpy>`_.
        
        
        Installation
        ------------
        
        ::
        
            pip install cortexpy
        
        
        Documentation
        -------------
        
        For more information, please see cortexpy documentation_.
        
        .. _documentation: https://cortexpy.readthedocs.io/en/latest/index.html
        
        Bugs
        ----
        
        Please raise a github issue for any bugs.
        
        Development
        -----------
        
        1. Install `conda <https://docs.conda.io/en/latest/miniconda.html>`_.
        2. Download development and testing tools::
        
            conda env create -f environment.yml -n my-dev-environment
        
        3. Activate development environment::
        
            conda activate my-dev-environment
        
        All remaining commands in the development section need to be run in an activated
        conda dev environment.
        
        
        
        Tests
        ~~~~~
        
        ::
        
            make test
        
        Deploy new cortexpy version to pypi
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Requires access credentials for pypi.
        
        ::
        
            make deploy
        
        Building the docs
        ~~~~~~~~~~~~~~~~~
        
        The documentation is automatically built by read-the-docs on push to master.
        To build the documentation manually::
        
            # install sphinx dependencies
            pip install docs/requirements.txt
        
            make docs
        
        Update the dev environment
        ~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        This section is experimental because it does not work on travis-CI yet.
        
        ::
        
            # Create a new env from the high-level requirements file
            conda env create -f environment.yml -n another-dev-env
        
            # activate the new environment
            conda activate another-dev-env
        
            # save new env to environment.lock.yml
            make lock
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: Implementation :: CPython
Requires-Python: >=3.6
