medcat/v2.2.0rc1

Pre-release (release candidate) for v2.2.0.

This minor release brings several bug fixes, new features, and maintenance improvements across MedCAT v2.

🚀 New Features

• Ontology Mapping Enhancements – Added support for mapping to additional ontologies, enabling better interoperability with external systems. (#147, #160)
• Parallel Entity Saving – Introduced new method to save entities when multiprocessing. (#144)
• Nested Entities Support – Improved handling and display of nested entities in annotations. (#159)
• PyPI Callback – Added automatic version checks and callback functionality. (#166)
• Embedding Linker – Added a new linker using MLM-based embeddings for more flexible linking. (#65)
• Bulk CUI Removal – Added a convenient method to remove multiple CUIs at once from the CDB. (#175)
• CDB Utilities – Added new utilities for CDB merging and navigation using parent-to-child (pt2ch) relations. (#176)

🐛 Bug Fixes

• Tokenizer Dash Handling – Fixed an issue in the regex tokenizer that included dashes along with words. (#138)
• MetaCAT Behaviour – Ported MetaCAT fixes from v1 to address incorrect context window handling and related issues. (#162 ; see #148 and #155)
• CUI Original Name Resolution – Added CUIInfo['original_names'] in converted legacy models. (#177)

🧰 Other Improvements

• Type Hints & Refactoring – Added missing type hints to various utility methods. (#146)
• Configuration Cleanup – Updated to the new Pydantic config format to remove warnings. (#169)
• Python Version Support – Dropped Python 3.9 support and added support for Python 3.13. (#172, #167)
• Testing and CI – Hotfix for component tests and added a nightly workflow to check library stability. (#125, #171)
• Documentation – Fixed links to demo and example models in documentation. (#164, #180)

What's Changed

• Medcat v2 components test hotfix by @mart-r in #125
• Bug(medcat): CU-869ag0tqj Fix regex tokenizer dashes by @mart-r in #138
• CU-869ahw0mw: Add argument to control data flow when saving results. by @mart-r in #144
• Refactor(medcat):CU-869ak0v7n Add type hints to util methods by @mart-r in #146
• feat(medcat): CU-869aknekf Add mapping to ontologies by @mart-r in #147
• fix for config.general.show_nested_entities by @pisong314 in #159
• feat(medcat): CU-869apb8ju Better ontology mapping by @mart-r in #160
• Bug(medcat)CU-869aprnhg: Port meta cat fixes from v1 by @mart-r in #162
• docs(medcat): CU-869ar9dcf Fix demo and example model links by @mart-r in #164
• feat(medcat): CU-869ary4dq Add PyPI callback by @mart-r in #166
• Bug(medcat): Move to new config for pydantic by @mart-r in #169
• CU-869aupp8v: Remove python 3.9 support by @mart-r in #172
• build(medcat): CU-869atpd59 Add python 3.13 support to MedCAT by @mart-r in #167
• Embedding Linker using MLM based embeddings by @adam-sutton-1992 in #65
• feat (MedCAT): CU-869auz1ck Add a bulk CUI removal method for the CDB by @mart-r in #175
• medact(feat): cdb utils for merging and navigation using pt2ch relations by @tomolopolis in #176
• bug(medcat): CU-869avau57 Fix cui to original names by @mart-r in #177
• build(medcat): CU-869aujr7h Add nightly workflow to check library stability by @mart-r in #171
• docs(medcat): CU-869avu9pv Fix docs by @mart-r in #180

New Contributors

• @pisong314 made their first contribution in #159
• @adam-sutton-1992 made their first contribution in #65

Full Changelog: medcat/v2.1.0...medcat/v2.2.0rc1