pronto

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.

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.

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.

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.

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.

Changed

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

Added

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

Fixed

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

Added

• Missing docstrings to some Entity properties.

Fixed

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

Fixed

• pronto.serializers module not being embedded in Wheel distribution.

Added

• Entity.add_synonym method to create a new synonym and add it to an entity.
• @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.
• chardet result is now used even when prediction confidence is under 100%
  to detect encoding of the handle passed to Ontology.

Fixed

• SynonymType comparison implementation.
• Synonym.type getter crashing on type not being None.
• RdfXMLParser crashing on synonymtypedefs without scope specifiers.

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.

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.

Added

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

Fixed

• Type hints of RelationshipData.synonyms attribute.

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.

• Fix bug with property annotation on restriction classes

• Fix multi-line summary making PyPI deny the package
• Fix sdist format to release a zip file

• Add support for descriptions with xrefs given by Axioms in OwlXML ontologies
• Drop support of OwlXMLTargetParser
• Remove debug code
• Improve docstrins and documentation

• Relicense to MIT
• Add Description class inheriting from string to hold xrefs
• Use pkg_resources to get the version of the module
• Remove import safeguards in __init__.py : import pronto will fail
  if some of the dependencies are missing
• Add repr method to Ontology
• Add test and dev extras
• Improve docstrings

• Allow creating an Ontology directly from a stream
• Allow data-based parser discovery using a 1KiB data block
• Improve README
• Drop CI support for Python 2.6