2.4.3

Added

• Missing documentation for the pronto.Entity.relationships property.

Fixed

• RDX/XML parser crashing on files containing a relationship and a term with the same ID (#138).

2.4.2

Added

• Support for chardet version 4.0 (in addition to older 3.0).

Fixed

• Serialization of Ontology failing with non-empty idspaces.
• Typo in OWL2 URL in README.md (#130).

2.4.1

Changed

• pronto.pv.PropertyValue is now an abstract class.
• pronto.parsers.RdfXmlParser now ignores synonym Xrefs not in
  the right format.

Fixed

• pronto.Entity.definition documentation now lists return type as
  pronto.definition.Definition as expected.
• CURIE compaction in RDF/XML not being handled consistently, causing
  some crashes on ontologies using aliased relationships.
• pronto.utils.typechecked.disabled is now reentrant and should
  not be disabled in multithreaded contexts anymore.

Removed

• Implicit injection of lxml instead of xml.etree, which caused
  issues with RdfXmlParser.

2.4.0

Added

• Deprecation warnings for the retrieval of relationships via
  indexing, to be deprecated in v3.

Changed

• Replaced Travis-CI with GitHub Actions to handle continuous integration.
• Bumped fastobo dependency to v0.10.0.

Removed

• Retrieval of terms via their alternate IDs (introduced in v2.3.0,
  caused multiple issues (#120,
  #126).

2.3.2

Added

• Support for path-like objects when creating an Ontology
  (#108).

Fixed

• Avoid decoding file-like objects if they are already UTF-8
  encoded when creating an Ontology
  (#110).

2.3.1

Fixed

• pronto.entity package not being included in source distribution.

2.3.0

Added

• Retrieval of entities via their alternate IDs on the source Ontology.
• Direct edition of entity relationships via the Relationships view.
• __all__ attribute to all modules of the data model.
• RelationshipSet container like TermSet with shortcut attributes and
  proxying of actual Relationship instances.
• Relationship.subproperties and Relationship.superproperties methods
  to add, remove, clear and iterate over the subproperties and superproperties
  of a Relationship instance.
• Ontology.synonym_types method to count (via SizedIterator) and iterate
  over the synonym types of an ontology and all of its imports.
• Ontology.get_synonym_type method to retrieve a single synonym type by ID
  from an ontology or one of its imports.

Changed

• Management of sub-properties / super-properties is now consistent with
  the management of subclasses / superclasses.
• consider, disjoint_from, disjoint_over, equivalent_to, replaced_by
transitive_over and union_of properties of Relationship now return
  a RelationshipSet.

Fixed

• Outdated documentation in Term.subclasses describing the performances of
  the previous algorithm.
• Possible AttributeError with the setter of the Entity.synonyms property.
• Issue with synonym types declared in imported ontologies not being usable
  with synonyms of the actual ontology.
• Various type annotations not updated since version 2.2.2.

2.2.4

Changed

• Make Entity.annotations return a mutable set and add a setter.

Fixed

• Term.relationship erroneously updating the Ontology._lineage cache.
• Unneeded code in pronto.serializers._fastobo handling is_a clauses.

2.2.3

Changed

• Replaced frozendict with immutabledict (#90).
• Bumped fastobo dependency to v0.9.0 to support inline comments.
• Parsers will now process their imports in parallel using a thread pool.

Fixed

• Argument type checking in view layer is now disabled during the parsing
  phase to reduce overhead.

2.2.2

Added

• Extraction of basic relationships from RDF/XML documents.

Fixed

• Erroneous type annotations on Term.subclasses and Term.superclasses.
• Bug with Term.equivalent_to setter crashing with a NameError.
• Bug with Entity.synonyms setter not extracting synonym data.