0.3.0

v0.3.0 introduces one breaking change (below), adds the user guide and API reference, and a few more enhancements.

Breaking change

The methods for getting ancestors, descendants, parents, and children of a term provide iterators and not iterables, despite the typing annotation. This may lead to a subtle bug if the iterator was used, e.g. within a nested loop:

hpo: MinimalOntology = ...

parents = hpo.graph.get_parents('HP:0001250')
for _ in range(5):
  for parent in parents:
    print(parent)

The loop above would, in fact, print only during the first iteration of the outer loop, and the iterator would be "consumed" for the remaining 4 iterations.

The v0.3.0 version merely corrects the typing annotation, the traversal methods continue to return iterators.

What's Changed

• Setup the documentation in #36
• Add type checks to terms, and ontology in #37
• Require numpy~=1.23.0 to support creating object arrays from iterables by @ldingemans in #35
• Validate input parameters, improve documentation in #38
• Add TermIdSorting in #39
• Fix OntologyGraph type annotations - breaking change in #41

New Contributors

• @ldingemans made their first contribution in #35

Full Changelog: v0.2.0...0.3.0

v0.2.0

Breaking changes

• remove Ratio and SimpleRatio from hpotk.annotations

Minor (non-breaking) changes

• we can test if an ontology node is a leaf on OntologyGraph by @ielis in #27
• Improve IC calculation and graph traversals by @ielis in #28
• Add methods for testing ancestor/descendant relationships to OntologyGraph by @ielis in #29
• Graph methods can work with Identified by @ielis in #30
• Implement observation status for annotations by @ielis in #31
• Graph traversal methods fail if the query node does not exist in the graph by @ielis in #32
• We cache the hash of the TermId by default to increase performance of hash-dependent operations by @ielis in #33

Full Changelog: v0.1.5...v0.2.0

v0.1.5

The highlights of v0.1.5:

• faster HPO loading from obographs JSON file (was 40s, now 3s)
• faster graph traversal, e.g. for finding ancestors or descendants of a term
• new functionality for calculating information content of ontology terms
• improvement of the test coverage, enhancement of the package metadata

What's Changed

• Shorten ontology loading, calculate IC of terms, optimize graph traversal, expose common model elements by @ielis in #22
• Update classifiers to indicate the supported Python versions by @ielis in #24
• Accept Identified and TermIds in RuleValidator by @ielis in #25

Full Changelog: v0.1.4...v0.1.5

v0.1.4

The highlights of the v0.1.4 release include:

• the Term now includes synonyms and cross-references to external vocabularies and data sources
• the HPO annoatation parser can handle both the older and the updated HPO annotation file format

What's Changed

• Export validate module. by @ielis in #18
• Add synonyms and cross-references to Term by @ielis in #20
• Add support for the novel HPO annotation format by @ielis in #20

Full Changelog: v0.1.3...v0.1.4

v0.1.3.post0

Hotfix to export hpotk.validate module.

v0.1.3

What's Changed

• Add support for working with HPO annotations by @ielis in #16

Full Changelog: v0.1.2...v0.1.3

v0.1.2

What's Changed

• Support Python 3.6 by @ielis in #14

Full Changelog: v0.1.1...v0.1.2

v0.1.1

What's Changed

• Remove networkx by @ielis in #8
• Support validation rules by @ielis in #9
• Parse ontology version. by @ielis in #10
• Fix conda issues by @ielis in #11
• Improve the documentation by @ielis in #12

Full Changelog: v0.1.0...v0.1.1