v2.0.0

2.0.0 - 2024-06-04

Features

• (De)serialization has been greatly improved, simplified, made correct, and given a slightly more compact serialized representation.
  This does mean there are some small changes in (de)serialization behaviour since the previous release.
• Curation process has been significantly improved and simplified for the end user, including introducing the AutoCurator concept to aid in this. This will enable us to build out better documentation and an interactive tool in future releases, which are currently in draft. Overally, this will greatly simplify upgrading ontology versions, adding curations for a new ontology etc.
• Datamodel has been substantially revised in a backwards incompatible manner to clear up confusing concepts, fix longstanding issues etc.
• New Zero shot NER model with GLiNER

Deprecations and Removals

• Remove deprecated GildaUtils.replace_dashes. This was superceded by GildaUtils.split_on_dashes_or_space and was already deprecated pending removal.
• Remove deprecated SpacyToKazuObjectMapper, as this was renamed to KazuToSpacyObjectMapper, and the old name already deprecated pending removal.
• Remove deprecated create_phrasematchers_using_curations method of OntologyMatcher. This was renamed to create_phrasematchers and was already deprecated pending removal.
• Rename Document.json to to_json, and remove optional arguments.
  The previous name was inconsistent with naming on other classes, as the function signature were parallel to to_json methods.
  The argument drop_unmapped_ents had functionality that was duplicated with DropUnmappedEntityFilter within the CleanupStep,
  and it made sense to add the drop_terms behaviour to a new LinkingCandidateRemovalCleanupAction to collect this behaviour together
  and significantly simplify the Document serialization code.
• Rename ParserActions.from_json and GlobalParserActions.from_json to from_dict.
  The previous names were misleading, as the function signature were parallel to the from_dict methods on other classes, not to their from_json methods.
• Renamed SynonymDatabase.add to SynonymDatabase.add_parser, for consistency with MetadataDatabase.add_parser.