v0.5.0

Breaking changes

There is one breaking change.

Enhance Term.definition attribute

v0.5.0 enhances the definition of the ontology term with cross-references.

Previous state

Previously, the hpotk.model.Term included a definition attribute which was a simple str:

import hpotk

hpo: hpotk.Ontology = ...  # Get `Ontology` from somewhere
term = hpo.get_term('HP:0001166')
assert term.definition == 'Abnormally long and slender fingers ("spider fingers").'

New state

The v0.5.0 release encapsulates the definition into a hpotk.model.Definition object that includes the definition string along with the cross-references:

term = hpo.get_term('HP:0001166')

# New code
definition = term.definition
assert definition.definition == 'Abnormally long and slender fingers ("spider fingers").'
assert definition.xrefs == ('HPO:probinson',)

How to migrate

All usages of term.definition must be updated to term.definition.definition.

What's Changed

• Setup benchmarking of graph traversals by @ielis in #60
• Add definition cross-references by @ielis in #63
• Add OntologyStore API by @ielis in #62

Full Changelog: v0.4.3...v0.5.0