Hetio

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This version upgrades the Travis CI environment to fix a Pandoc bug that resulted in a malformated long_description in `setup.py`. As a result, the [v0.2.2 PyPI page](https://pypi.org/project/hetio/0.2.2/) is really ugly.

Added py2neo 3 support by veleritas . See 4 6 8.

Change default queue sizes in neo4j importing for speed improvement. See 5. Thanks veleritas.

Add `n_nodes` and `n_nodes` attributes that store the total number of nodes and edges in the graph.

This version has a malformated description on PyPI, hence users are recommend to use v0.2.3 instead.

This release provides some bugfixes as well as many new features. Development for this release occurred during work on [Project Rephetio](https://doi.org/10.15363/thinklab.4). This is the first release that has been uploaded to PyPI.

New modules
- The new `neo4j` module provides support for exporting a `hetio.graph` into Neo4j. The module also supports creating DWPC Cypher queries from a metagraph. See https://doi.org/10.15363/thinklab.d112 for more information on our adoption of Neo4j.
- The new `permute` module provides hetnet permutation functionality. For an example use, see https://doi.org/10.15363/thinklab.d178.
- The new `stats` module produces user-friendly TSVs and visualizations with hetnet summary stats.

Enhancements
- MetaGraphs now have a `metapath_from_abbrev` method which takes a metapath abbreviation str and returns the corresponding metapath object.
- The `hetio.readwrite` module now supports reading metagraphs and graphs from a (compressed) URL.
- Pretty formatting of (meta)edges and (meta)paths using the `get_unicode_str` method.
- Support for Graph Modeling Language (GML) was removed to do the poor documentation and esoterism of this format.
- Improved `abbreviation` module.

[](https://doi.org/10.5281/zenodo.31763)

This is the first release of `hetio` for hetnets in Python.

Currently, the following features are supported:
- creating a hetnet consisting of a metagraph (types) and a graph (nodes and edges)
- metanode and metaedge abbreviations
- node and edge properties using the `data` attribute
- node and edge masking
- writing and reading hetnets
- summary statistics
- summary visualizations
- metapath extraction from the metagraph
- graph traversal to extract paths
- feature computation, specifically DWPCs

The following features are not currently supported:
- node or edge deletion
- network permutation (edge swaps)

Documentation is lacking, but see these examples of [network creation](https://github.com/dhimmel/integrate/blob/bab40969df989d3446bacc97a5532cf3d3cab4b5/integrate.ipynb) and [feature extraction](https://github.com/dhimmel/learn/blob/eabff6bdbe777cb21ad731a7b788720eb1d622f8/learn.ipynb).