pronto

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

• Make setup.py Python2.6 compatible
• Fix obo export to display synonyms in lexicographic order
• Fix terms not being exported in obo correctly
• Fix error occuring when calling Synonym.obo
• Fix bug causing synonyms not being imported from obo files

• Fix tests being added to source distribution

• Fix owl parser crashing on inline comments in some specific files
• Add decorator to silence warnings in xml target parser code

• Switch to coroutines for Obo parsing
• Add support for Python 3.6
• Fix several bugs
• Embed custom materials in tests

• Fix unpickling of Term not adding back attributes