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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

Added

  • @roundrepr now adds a minimal docstring to the generated __repr__ method.
  • Ontology caches subclassing relationships to greatly improve performance of Term.subclasses.

Changed

  • Entity subclasses now store their id directly to improve performance.
  • Term.subclasses and Term.superclasses use collections.deque instead of queue.Queue as a LIFO structure since thread-safety is not needed.

1.0.0 - 2019-10-11

Fixed

  • Issues with typedef serialization in FastoboSerializer.
  • Ontology.create_term and Ontology.create_relationship not raising ValueError when given an identifier already in the knowledge graph.
  • Signature of BaseSerializer.dump to remove encoding argument.
  • Missing __slots__ in Entity in non-typechecking runtime.

Changed

  • Bumped fastobo requirement to v0.6.0.

1.0.0-alpha.3 - 2019-10-10

Added

  • Extraction of oboInOwl:consider annotation in RdfXMLParser.
  • Extraction of oboInOwl:savedBy annotation in RdfXMLParser.
  • Extraction of subsetdef and synonymtypedef as annotation properties in RdfXMLParser.
  • Support for doap:Version instead of owl:VersionIri for specification of ontology data version.
  • Proper comparison of PropertyValue classes, based on the lexicographic order of their serialization.
  • Ontology.dump and Ontology.dumps methods to serialize an ontology in obo or obojson format.

Fixed

  • Metadata not storing optional description of ID spaces if any.
  • Wrong type hints in RelationshipData.equivalent_to_chain.

Changed

  • Added type checking to some more property setters.
  • Avoid using networkx in Term.subclasses.
  • fastobo-derived parsers will not create a new entity if one exists in the graph of dependencies already.
  • Exposed pronto.warnings and the complete warnings hierarchy.

1.0.0-alpha.2 - 2019-10-03

Added

  • Support for extraction of relationships from OWL/XML files to OwlXMLParser.

Fixed

  • Type hints of RelationshipData.synonyms attribute.

1.0.0-alpha.1 - 2019-10-02

Changed

  • Dropped support for Python earlier than 3.6.
  • Brand new data model that follow the OBO 1.4 object model.
  • Partial OWL XML parser implementation using the OBO 1.4 semantics.
  • New OBO parser implementation based on fastobo.
  • Imports are properly separated from the top-level ontology.
  • Ontology.__getitem__ can also access entities from imports.
  • Term, Relationship, Xref, SynonymType compare only based on their ID.
  • Subset, Definition compare only based on their textual value.

Added

  • Support for OBO JSON parser based on fastobo.
  • Provisional mypy type hints.
  • Type checking for most properties in __debug__ mode.
  • Proper repr implementation that should roundtrip most of the time.
  • Detection of file format and encoding based on buffer content.

Removed

  • OBO and JSON serialization support (for now).
  • Term.rchildren and Term.rparents and stop making direction assumptions on relationships.