dhimmel/hetio v0.2.3: fix PyPI description formatting

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 is really ugly.

dhimmel/hetio v0.2.2: add py2neo 3 support

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.

Neo4j export, Cypher query creation, hetnet stats, and other enhancements

This release provides some bugfixes as well as many new features. Development for this release occurred during work on Project Rephetio. 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.

v0.1.0 initial release

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 and feature extraction.