pronto

Fixed

• Handling of RDF datatypes in RDF/XML parser ([#223](https://github.com/althonos/pronto/pull/223], by @chrishmorris).

Added

• Explicit support for Python 3.12.

Fixed

• Synonym types not being properly extracted by RDF/XML parser (#218).

Fixed

• replaced_by and consider attributes not being extracted from RDF/XML documents on missing RDF datatype (#209).
• Hard requirement on multiprocessing.pool preventing the package to work single-threaded on more restrictive environments (#208).

Fixed

• Entity.synonyms setter not accepting frozenset arguments as expected (#207).

Changed

• Bump supported networkx version to v3.0 (#206).

Fixed

• Crash in LineageIterator.to_set when starting from an empty set of entities.

Added

• Explicit support for Python 3.11.

Changed

• Bumped fastobo dependency to v0.12.2.
• Bumped chardet dependency to v5.0.

Changed

• Bumped fastobo dependecy to v0.12.1

Removed

• Support for Python 3.6.

Fixed

• Serialization of is_class_level properties with fastobo-based serializers (#178).
• Parsing of SynonymTypeProperty elements in RDF/XML without a label attribute (#176).

Added

• Setters for the holds_over_chain and equivalent_to_chain properties of Relationship objects.

Fixed

• Serialization of holds_over_chain properties with fastobo-based serializers (#175).

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).

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).

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.

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).

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).

Fixed

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

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.

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.

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.

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.

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.