2.2.1

Fixed

• Extraction of subclasses/superclasses hierarchy from nested imports.
• Serialization of OBO frames not being done in order.
• Parsing issue with anti_symmetric clauses in OBO typedefs.
• Xrefs not being extracted when declared as axioms in RDF/XML documents.
• ResourceWarning when creating Ontology from file-handles not mapping
  to a filesystem location.

2.2.0

Added

• threads parameter to Ontology constructor to control the number of
  threads used by parsers supporting multithreading (OBO and OBO JSON at
  the moment).
• Deprecation warnings for suspected uses of the is_a pseudo-relationship
  since subclasses/superclasses is now to be handled by the owner Ontology.
• Support for subclass/superclass edition directly from the objects returned
  by Term.subclasses() and Term.superclasses(). (#84)

Changed

• Updated fastobo to v0.8, which reduce memory footprint of identifiers,
  and improves the parser speed.
• Improved OBO parser performance using threading plus zero-copy validation
  of identifiers on Xref instantiation.
• Improved performance in debug mode by having the typechecker only extract
  the wrapped function signature once.

Fixed

• OBO parser crashing on files containing idspace clauses in their headers.
• Reference management issue with binary operations of TermSet.

Removed

• nanoset depency, which was not useful anymore in Python 3.8 and caused
  issues with multithreading when processing OBO frames in parallel.

2.1.0

Added

• Synonym.xrefs now has a setter. (#70)
• pickle support for Ontology. (#66)
• RdfXmlParser support for owl:inverseOf and rdfs:subPropertyOf.

Changed

• Synonym.xrefs now returns a mutable set that can be used to add
  Xref to the synonym directly.

Fixed

• SynonymType.type setter does not consider all synonym types as
  undeclared anymore. (#71)
• RdfXmlParser crashing on synonym types definition without a label
  like in Uberon. (#67)
• FastoboSerializer crashing when encountering a relationship with
  at least one replaced_by clause.

2.0.1

Fixed

• Internal handling of ontology data forcing an Ontology to outlive all
  of the Terms created from it.
• Term.id property missing a return type annotation.
• Term.equivalent_to not returning a TermSet but a set of strings.

Changed

• Refactored implementation of SubclassesIterator and
  SuperclassesIterator to make both use the interal subclassing cache.
• Make Term.is_leaf use internal subclassing cache to make it run in
  constant time.

2.0.0

Added

• TermSet.subclasses and TermSet.superclasses methods to query all
  the subclasses / superclasses of all Term.
• TermSet class to the top-level pronto module.
• Dynamic management of subclassing cache for the Ontology class.
• Setters for Term.consider, Term.union_of and Term.intersection_of.

Removed

• cache keyword argument for the Ontology.

Fixed

• SuperclassesIterator.to_set being named to_self because of a typo.
• Several bugs affecting the fastobo-backed serializer.

1.2.0

Added

• Parameter with_self to disable reflexivity of Term.subclasses and
  Term.superclasses iterators.
• TermSet class which stores a set of terms efficiently while providing
  some useful shortcuts to access the underlying data.

Changed

• Moved code of Term.subclasses and Term.superclasses to a dedicated
  iterator class in the pronto.logic submodule.
• Dropped contexter requirement.

Fixed

• Fix a typo in Synonym.type setter leading to a potential bug when
  the given type is None.
• Fix miscellaneous bugs found with mypy.
• fastobo serializer crashing on namespace clauses because of a type
  issue.
• fastobo parsers using data version clauses as format version clauses.

1.1.5

Changed

• Bumped fastobo to v0.7.0, switching parser implementation to use
  multi-threading in order to speedup the parser process.

1.1.4

Added

• Explicit support for Python 3.8.
• Support for Windows-style line endings
  (#53)

1.1.3

Fixed

• Handling of some clauses in FastoboParser.
• OboSerializer occasionaly missing lines between term and typedef frames.

Added

• Missing docstrings to some Entity properties.

1.1.2

Fixed

• RdfXMLParser crashing on entities with rdf:label elements
  without literal content.