v0.5.3

What's Changed

• Test TermId hashing, add editor config and linter config by @ielis in #74

Full Changelog: v0.5.2...v0.5.3

v0.5.2

What's Changed

• Expose OntologyStore resource path and enable resource cleanup by @ielis in #71
• Experimental support for MAxO and Mondo by @ielis in #72

Full Changelog: v0.5.1...v0.5.2

v0.5.1

A patch release with no breaking changes and several bug fixes.

What's Changed

• Support providing custom stream to the logger by @ielis in #65
• Update the way we test the library by @ielis in #66
• Use default ssl context when fetching from https by @ielis in #67
• Update urls after the repo move by @ielis in #68
• Prevent storing ontology file at path with None in name by @ielis in #69

Full Changelog: v0.5.0...v0.5.1

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

v0.4.3

Bugfix for IndexedOntologyGraph.is_leaf.

What's Changed

• Fix bug in IndexedOntologyGraph.is_leaf. by @ielis in #58

Full Changelog: v0.4.2...v0.4.3

v0.4.2

Speed up the boolean queries on indexed ontology graph by working in the term index space.

Note, v0.4.1 was yanked due to release error.

What's Changed

• Speed up the boolean ontology graph queries by @ielis in #55

Full Changelog: v0.4.0...v0.4.2

v0.4.0

Add IndexedOntologyGraph to speed up HPO graph operations by working in the term ID index space.

What's Changed

• Enhance the documentation by @ielis in #48
• Implement edge distance on OntologyGraph by @ielis in #51
• Implement hierarchical distance term id sorting by @ielis in #52
• Add IndexedOntologyGraph by @ielis in #53

Full Changelog: v0.3.1...v0.4.0

v0.3.1post1

Patch with improved documentation and tests. No changes to the production code.

v0.3.1

What's Changed

• Add convenience method for getting term name by @ielis in #43
• Improve documentation by @ielis in #45

Full Changelog: 0.3.0...v0.3.1

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