medcat/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

medcatrainer/v3.1.0 - medcat upgrade

New header, Small fixes, medcat v2 upgrade

What's Changed

• New header #179
• CU-869awj4r1: medcat-trainer (chore): update dep by @tomolopolis in #183
• CU-869awpaf3: (chore): medcat-trainer: remove cdb_utils, fix vestigia… by @tomolopolis in #188
• medcattrainer (chore): client update release, compose cfgs by @tomolopolis in #190

Full Changelog: medcat-trainer/v3.0.0...medcat-trainer/v3.1.0

MedCAT den v0.3.0

Minor release.

Most notably difference is the addition of additional API to the den.

What's Changed

• docs (medcat-den): Fix homepage and repo links in pyproject.toml by @mart-r in #168
• build(medcat-den): CU-869auqkgc Fix duplicates in TestPyPI publish by @mart-r in #174
• feat(medcat-den): CU-869an5f00 Add remote api by @mart-r in #163
• build: bump the actions-deps group with 2 updates by @dependabot[bot] in #170
• build(medcat-den): Fix duplicate push versions to TestPyPI by @mart-r in #178

Full Changelog: medcat-den/v0.2.1...medcat-den/v0.3.0

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

medcat/v1.16.7

This is a MedCAT v1 patch release.

It mostly addresses 2 MetaCAT issues that now have a fix: #148 and #155 .
One of these issues has been present since MedCAT v1.12 from June of 2024.

⚠️ This is now the only supported version of MedCAT v1. Unfortunately we do not have the resources to backport this change to older versions.

What's Changed

• Update dependabot.yml to update github actions by @alhendrickson in #81
• Medcat v1 release hotfix 4 by @mart-r in #82

Full Changelog: medcat/v1.16.5...medcat/v1.16.7

medcat-trainer/v3.0.0 - medcatv2 support, client fixes, api fixes

medcatrainer/v3.0 - medcatv2 support, client fixes, tests etc.

What's Changed

• chore(medcat-trainer): CU-869a4br6j Create a copy of the v1 medcat-trainer in the v1 folder by @alhendrickson in
• CU-869a4wpek Trainer qa workflow fix by @mart-r in #99
• feat(medcat-trainer): CU-869a5rv2z: Extra fields for MedCATtery by @tomolopolis in #101
• chore(medcat-trainer-v1): CU-869a5wkcx: remove client from v1 code by @tomolopolis in #103
• Fix trainer v1 QA workflow by @mart-r in #107
• chore(medcattrainer): update to latest release by @tomolopolis in #117
• build: bump the actions-deps group with 3 updates by @dependabot[bot] in #130
• feat(medcat-trainer): CU-869adnv5w Add Postgres database support to trainer by @alhendrickson in
• CU-869admfwg: Add basic tests in MedCAT Trainer by @jocelyneholdbrook in #133
• Revert "CU-869admfwg: Add basic tests in MedCAT Trainer" by @jocelyneholdbrook in #134
• build: bump the npm_and_yarn group across 1 directory with 7 updates by @dependabot[bot] in #132
• feat(medcat-trainer): CU-869adnv5w k8s improvements. Health checks, fix load_examples, fix solr logging by @alhendrickson in #131
• CU-869admfwg: Increase test coverage in medcattrainer by @jocelyneholdbrook in #135
• feat(medcat-trainer): CU-869a4br6j Support MedCAT v2 for trainer by @alhendrickson in #68
• Upload Export docs fix by @tomolopolis in #150
• Trainer upload export test by @tomolopolis in #151

New Contributors

• @dependabot[bot] made their first contribution in #94
• @jocelyneholdbrook made their first contribution in #133
• @vladd-bit made their first contribution in #137

Full Changelog: medcat/v1.16.5...medcattrainer/v3.0.0

medcat/v2.1.0

Minor release.

Highlighted features:

• Offline loading of BERT based MetaCATs (#67, #85)
• Allow loading models with config dicts (applied before pipe init) again (#53)
• Simplified access and imports (#112, #119), e.g:
  • CAT.pipe instead of CAT._pipeline
  • from medcat.stats import get_stats instead of from medcat.stats.stats import get_stats
• Improved supervised training flexibility by logging issues (#121)

Important bug fixes

• Stats edge cases for 0 precion and recall (#109)
• Fix issue with model pack removal upon save in some situations (#115)

What's Changed

• Add permissions for MedCAT release by @mart-r in #42
• Remove install bundles before pushing to PyPI by @mart-r in #44
• Allow patch releases for pre-releases by @mart-r in #43
• Update to valid classifiers by @mart-r in #45
• CU-8699twteb: Update docs links to point to up to date page by @mart-r in #48
• Fix license in pyproject.toml by @mart-r in #49
• Improve some logging in MetaCAT when no suitable category is found by @mart-r in #50
• CU-8699upt9a Allow saving output onto disk when multiprocessing by @mart-r in #52
• CU-8699vkmu4: Allow load with merging config(s) by @mart-r in #53
• CU-8699vq0he: Improve addon access from CAT by @mart-r in #55
• CU-8699vnuwf Ignore hidden files when loading model packs by @mart-r in #54
• CU-8699zxxnt: Fix v2 tutorials link to point to correct version by @mart-r in #61
• Adding functionality for offline loading by @shubham-s-agarwal in #67
• Remove unnecessary method from tutorial example by @mart-r in #73
• CU-8698x63kt: Add v2 migration guide by @mart-r in #66
• CU-8699mrvup docs: update urls throughout to point to new cogstack-nlp repo by @alhendrickson in #71
• Update dependabot.yml to update github actions by @alhendrickson in #81
• Avoid v2 release workflow run in case of v1 release by @mart-r in #83
• CU-8699wc4zb Port offline BERT MetaCAT load to v2 by @mart-r in #85
• build: Update dependabot config by @alhendrickson in #91
• build: Update dependabot config. Add commit prefix by @alhendrickson in #93
• CU-869a6w9c7 Fix stats on 0 prec and 0 rec by @mart-r in #109
• CU-869a6v8qd: Fix tutorial links by @mart-r in #108
• Explicitly specify an empty HF cache during testing of offline load by @mart-r in #106
• CU-869a71q73: Rename multi-text method and deprecate old one by @mart-r in #110
• CU-869a2kpv0 Add method for model card load off disk by @mart-r in #111
• build: bump the actions-deps group with 6 updates by @dependabot[bot] in #94
• chore(medcat): CU-869a971xa: Update readme by @tomolopolis in #116
• CU-869a95nu1 Fix spacy model cleanup by @mart-r in #115
• CU-8699qzfdk Improve optional part checks by @mart-r in #113
• CU-869a7mjaa: Add simplified method of getting pipe from CAT object by @mart-r in #112
• chore(medcat): CU-869a98zwq: use old name by @tomolopolis in #118
• CU-869a9mten Improve duplicate name imports by @mart-r in #119
• CU-869a9q6rm: Include MetaCAT model cards in overall model card by @mart-r in #120
• CU-869a9w9v8: Allow a warning instead of a raised exception when doing supervised training by @mart-r in #121
• Medcat conversion model name hotfix by @mart-r in #122

New Contributors

• @shubham-s-agarwal made their first contribution in #67
• @dependabot[bot] made their first contribution in #94

Full Changelog: medcat/v2.0.0...medcat/v2.1.0

medcat/v2.0.0

We’re excited to announce the release of MedCAT v2. This is a major refactor that brings a more modular, flexible, and maintainable foundation for clinical NLP, while staying compatible with existing v1 models.

This release focuses on:

• Refactored structure for lower coupling and greater extensibility
• Modularity via optional install extras (install only what you need)
• Improved flexibility in tokenization, NER, and annotation pipelines
• Backwards compatibility for v1 models, with automatic conversion

✨ What’s New

• Decoupled from spacy → now possible to use lightweight regex tokenizer or other (custom) backends
• Optional extras: install support only for the components you need (spacy, meta-cat, deid, rel-cat, dict-ner)
• Training is now structured around dedicated classes for clearer workflows
• Tutorials and scripts have been rebuilt from the ground up for v2
• Added support for a supervised training web service (experimental, under development)

⚠️ Breaking Changes

• Saving/Loading:
  • Save method has a new name (CAT.save_model_pack)
  • v2 saves models in a new format (but still loads v1 models, with slower load times due to conversion)
• Training:
  • Training APIs now go through separate trainer classes
• Defaults:
  • Default install no longer includes spacy or advanced components (see migration guide for how to enable them)

For a complete list, see: BREAKING_CHANGES.md

📖 Migration Guide

If you’re upgrading from v1, please read the dedicated Migration Guide. It covers:

• Installation instructions
• Changes to saving/loading
• v1 model compatibility notes
• Updated tutorials and example scripts
• FAQ and troubleshooting

🔗 Useful Links

📦 PyPI

📘 Documentation

🧩 Migration Guide

💬 Discussion Forum

🛠️ Repository

Feedback

v2 is a big step forward, and we’d love your input!
Please open a GitHub issue or join the discussion forum for:

• Missing documentation
• Bugs or breaking behaviour
• Feedback on error/log messages
• Suggestions for future improvements

MedCAT v1.16.5

Mostly workflow changes to release #67 .

What's Changed

• Adding functionality for offline loading by @shubham-s-agarwal in #67
• Fix typo in v1 production workflow by @mart-r in #80

Full Changelog: medcat/v1.16.0...medcat/v1.16.5

medcat/v2.0.0b4

There's a fair few fixes in this patch / beta release.
Most notably, some bug fixes for multiprocessing and some quality of life changes for that as well as well as other QoL changes.

What's Changed

• CU-8699twteb: Update docs links to point to up to date page by @mart-r in #48
• CU-8699rvhe9 Refer to PyPI medcat v2 by @mart-r in #46
• CU-8699td0xq: Move to v2 model pack by @mart-r in #47
• Fix license in pyproject.toml by @mart-r in #49
• Improve some logging in MetaCAT when no suitable category is found by @mart-r in #50
• CU-8699upt9a Allow saving output onto disk when multiprocessing by @mart-r in #52
• CU-8699vkmu4: Allow load with merging config(s) by @mart-r in #53
• CU-8699vq0he: Improve addon access from CAT by @mart-r in #55
• CU-8699vnuwf Ignore hidden files when loading model packs by @mart-r in #54

Full Changelog: medcat/v2.0.0b3...medcat/v2.0.0b4