Software Open Access

dhimmel/hetio v0.2.0: Neo4j export, Cypher query creation, hetnet stats, and other enhancements

Daniel Himmelstein

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.

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