hetio 0.2.2

Hetnets in Python

Hetnets in Python
=================

`|Latest DOI| <https://zenodo.org/badge/latestdoi/14475/dhimmel/hetio>`_
`|GitHub issues| <https://github.com/dhimmel/hetio/issues>`_ `|Build
Status| <https://travis-ci.org/dhimmel/hetio>`_

Background
----------

**Hetnets**: Hetnets, also
`called <https://doi.org/10.15363/thinklab.d104>`_ *heterogeneous
information networks*, are graphs with multiple node and edge types.
Hetnets are both multipartite and multirelational. They provide a
scalable, intuitive, and frictionless structure for data integration.

**Purpose**: This package provides data structures for hetnets and
algorithms for `edge prediction <http://het.io/hnep/>`_. It only
supports hetnets, which is its primary advantage compared to other
network software. Node/edge attributes and edge directionality are
supported.

**Impetus**: Development originated with a
`study <https://doi.org/10.1371/journal.pcbi.1004259>`_ to predict
disease-associated genes and continues with a successive
`study <https://doi.org/10.15363/thinklab.4>`_ to repurpose drugs.

**Caution**: Documentation is currently lacking, testing coverage is
poor, and the API is unstable. Contributions are welcome. Please use
`GitHub Issues <https://github.com/dhimmel/hetio/issues>`_ for feedback,
questions, or troubleshooting.

Installation
------------

`|PyPI| <https://pypi.python.org/pypi/hetio>`_

Please use Python 3.4 or higher. To install the current PyPI version
(recommended), run:

::

pip install hetio

For the latest GitHub version, run:

::

pip install git+https://github.com/dhimmel/hetio.git#egg=hetio

For development, clone or download-and-extract the repository. Then run
``pip install -e .`` from the repository's root directory. The ``-e``
flag specifies
`editable <https://pythonhosted.org/setuptools/setuptools.html#development-mode>`_
mode, so updating the source updates your installation.

Once installed, tests can be executed by running ``py.test test/`` from
the repository's root directory.

Design
------

A Graph object stores a heterogeneous network and relies on the
following classes:

1. Graph
2. MetaGraph
3. Edge
4. MetaEdge

.. |Latest DOI| image:: https://zenodo.org/badge/14475/dhimmel/hetio.svg
.. |GitHub
issues| image:: https://img.shields.io/github/issues/dhimmel/hetio.svg
.. |Build
Status| image:: https://travis-ci.org/dhimmel/hetio.svg?branch=master
.. |PyPI| image:: https://img.shields.io/pypi/v/hetio.svg