CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

v2.5.8 - 2024-09-14

Fixed

• Extraction of implicit string annotation in RDF/XML files (#231).
• RDF/XML parser crash on oboInOwl:SynonymTypeProperty when missing a scope (#230).

Changed

• Migrate documentation to PyData theme.

v2.5.7 - 2024-04-24

Fixed

• Handling of RDF datatypes in RDF/XML parser (#223, by @chrishmorris).

v2.5.6 - 2024-02-21

Added

• Explicit support for Python 3.12.

Fixed

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

v2.5.5 - 2023-08-17

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).

v2.5.4 - 2023-04-10

Fixed

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

Changed

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

v2.5.3 - 2023-01-11

Fixed

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

v2.5.2 - 2022-12-07

Added

• Explicit support for Python 3.11.

Changed

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

v2.5.1 - 2022-10-12

Fixed

• EntitySet.ids iterating on its elements instead of copying the internal identifiers.
• RDF/XML parser failing on unknown datatypes (#187).

Changed

• Disable typechecking when collecting entities in to_set methods.

v2.5.0 - 2022-07-12

Changed

• Bumped fastobo dependecy to v0.12.1

Removed

• Support for Python 3.6.

v2.4.7 - 2022-06-28

Fixed

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

v2.4.6 - 2022-06-18

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).

v2.4.5 - 2022-04-21

Fixed

• Serialization of metadata tag relationships by fastobo (#164).

v2.4.4 - 2022-01-24

Added

• OwlFunctionalSerializer to dump an Ontology to OWL Functional-style syntax.

Changed

• Bumped fastobo dependency to v0.11.1.
• Make FastoboParser raise a SyntaxWarning when encoutering creation dates that are not datetime.datetime.

v2.4.3 - 2021-08-02

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).

v2.4.2 - 2021-05-26

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).

v2.4.1 - 2021-02-19

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.

v2.4.0 - 2021-02-18

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).

v2.3.2 - 2020-12-17

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).

v2.3.1 - 2020-09-21

Fixed

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

v2.3.0 - 2020-09-21 - YANKED

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 v2.2.2.

v2.2.4 - 2020-09-11

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.

v2.2.3 - 2020-07-31

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.

v2.2.2 - 2020-07-18

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.

v2.2.1 - 2020-06-17

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.

v2.2.0 - 2020-06-17

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.

v2.1.0 - 2020-03-23

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.

v2.0.1 - 2020-02-19

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.

v2.0.0 - 2020-02-14

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.

v1.2.0 - 2020-02-10

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.

v1.1.5 - 2020-01-25

Changed

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

v1.1.4 - 2020-01-21

Added

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

v1.1.3 - 2019-11-10

Fixed

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

Added

• Missing docstrings to some Entity properties.

v1.1.2 - 2019-10-30

Fixed

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

v1.1.1 - 2019-10-29

Fixed

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

v1.1.0 - 2019-10-24

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.

v1.0.0 - 2019-10-11

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.

v1.0.0-alpha.3 - 2019-10-10

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.

v1.0.0-alpha.2 - 2019-10-03

Added

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

Fixed

• Type hints of RelationshipData.synonyms attribute.

v1.0.0-alpha.1 - 2019-10-02

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.