cortexpy 0.46.1

The python sister project to CortexJDK

Overview of Cortexpy_
=====================

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.. list-table::
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* - 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/v0.46.1.svg
:alt: Commits since latest release
:target: https://github.com/winni2k/cortexpy/compare/v0.46.1...master

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:alt: PyPI Wheel
:target: https://pypi.python.org/pypi/cortexpy

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:alt: Supported versions
:target: https://pypi.python.org/pypi/cortexpy

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:alt: Supported implementations
:target: https://pypi.python.org/pypi/cortexpy

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:target: https://cortexpy.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status


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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 :doc:`Apache License version 2.0</license>`. 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