pronto

Fixed

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

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

• 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.

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.