medcat-trainer/v3.6.1

What's Changed

• paper(medcat): MedCAT 2 paper related scripts and documentation by @mart-r in #526
• chore(medcat-trainer): test improvements & coverage report in CI by @tomolopolis in #529
• fix(medcat-trainer): Fix Try Model bug after medcat V2 by @alhendrickson in #531
• chore(medcat-trainer): Harden MCT plugin scaffold with trust docs and URL/signal guards. by @tomolopolis in #530
• fix(medcat-trainer): Fix Concepts tab for CDBs with no heirarchy by @alhendrickson in #532
• test(medcat-trainer): Fix the Concept view test broken in PR 532 by @alhendrickson in #534
• fix(medcat-trainer): Fix Spaces in model pack names breaking CDB import by @alhendrickson in #533
• fix(medcat-trainer): Handle where SOLR contains collections aren't from trainer by @alhendrickson in #536
• docs(medcat-service): Fix link formatting and add v2 model pack section by @alhendrickson in #535
• Fix/medcat trainer/error handling fetch entities by @tomolopolis in #537
• chore(medcat): Change log WARN to DEBUG for tokenizer internals path by @alhendrickson in #541
• feat(medcat-trainer): Set token expiry for OIDC sessions by @jocelyneholdbrook in #543

Full Changelog: medcat-trainer/v3.6.0...medcat-trainer/v3.6.1

medcat/v2.8.2

This patch release fixes a regression in supervised training (#527) compare to v2.7.

Full Changelog: medcat/v2.8.1...medcat/v2.8.2

medcat-trainer/v3.6.0

What's Changed

• Mc trainer fix cui UI by @vladd-bit in #423
• fix(medcat-trainer): Fix Username emails missing when using oauth users by @alhendrickson in #429
• feat(medcat-trainer-client): Support OIDC in medcat trainer client by @alhendrickson in #428
• fix(medcattrainer) - solve irrelevant annotations document submit error by @silverfoxdoc in #430
• fix(medcattrainer) - solve JSON CUI filter export error by @silverfoxdoc in #431
• build: Dependabot config to keep updates separated by @alhendrickson in #434
• build(medcat-trainer): bump the npm-deps group in /medcat-trainer/webapp/frontend with 195 updates by @dependabot[bot] in #495
• build: Disable dependabot updates by @alhendrickson in #498
• fix(medcat-trainer): CU-869danbhd: UI Fixes on project admin by @tomolopolis in #500
• fix(medcat-trainer): CU-869dcmyex: ProjectAdmin concept db import fix by @tomolopolis in #502
• fix(medcat-trainer): CU-869808bru: project list fixes, filtering, sorting by @tomolopolis in #501
• test(medcat-trainer): expand backend and frontend unit test coverage by @tomolopolis in #510
• test(medcat-trainer): Add simple example dataset for use for UAT testing by @alhendrickson in #519
• feat(medcat-trainer): trainer-ee-scaffolding by @tomolopolis in #524

New Contributors

• @silverfoxdoc made their first contribution in #430

Full Changelog: medcat-den/v0.5.4...medcat-trainer/3.6.0

medcat/v2.8.1

This patch release addresses the spacy and click issue in a better way (see #518).

Full Changelog: medcat/v2.8.0...medcat/v2.8.1

medcat/v2.7.2

This patch release addresses spacy issue better (see #518 )

Full Changelog: medcat/v2.7.1...medcat/v2.7.2

medcat/v2.8.0

🩺 MedCAT v2.8 Release Notes

This release focuses on training and inference performance improvements, MetaCAT robustness, and several fixes around packaging and dependency handling.

🚀 New Features & Performance Improvements

• Supervised Training Overhaul – Improved the internal supervised training flow to avoid running the pipeline twice during training.
  This significantly reduces unnecessary processing and improves training efficiency, particularly for trainable linker implementations.
• Inference Speed Improvements – Added several optimisations across the MedCAT inference pipeline to reduce overhead and improve runtime performance.
• MetaCAT & Linking Optimisations – Reduced avoidable allocations and improved hot-path lookups in MetaCAT and linking workflows, leading to lower overhead during annotation and training.
• Core Pipeline Optimisations – Additional low-level optimisations to internal allocation and lookup paths improve overall pipeline efficiency.

🐛 Bug Fixes

• MetaCAT Training Stability – Fixed issues where unmapped entity tokens could cause crashes during MetaCAT training.
• Supervised Training Order Fix – Corrected an order-of-operations issue during supervised training that could lead to inconsistent behaviour in some workflows.
• Embedding Linker Packaging Cleanup – Removed the obsolete embedding linker optional extra from the core package configuration following the linker’s move to a standalone plugin package.
• Dependency / Lockfile Fixes – Fixed lockfile and packaging issues related to dependency resolution.

🧰 Other Improvements

• Documentation Updates
  • Added MedCAT Tutorials to the public documentation page
  • Expanded test coverage around supervised training and name count handling
• Release Packaging Improvements – Excluded unnecessary test resources from release artifacts to reduce package size and improve release cleanliness.
• Stability & Dependency Reliability – This release also resolves issues caused by upstream dependency changes (notably around click / typer interactions affecting spaCy environments).

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This release continues the focus on performance, training robustness, and deployment reliability, while further stabilising the MedCAT v2 training and inference stack.

What's Changed

• fix(metacat): handle unmapped entity tokens and training crashes by @bgriffen in #399
• perf: fix low-hanging performance issues in MetaCAT and linking by @bgriffen in #400
• perf(medcat-v2): optimize hot path allocations and lookups by @bgriffen in #401
• fix(medcat): CU-869cub2m7 Remove embedding linker optional extra from pyproject.toml @mart-r in #405
• bug(medcat): CU-869cunfx7 Fix supervised training order of operations issue by @mart-r in #408
• feat(medcat): CU-869cw9zmj Improve inference speed by @mart-r in #410
• docs(medcat): Add Medcat Tutorials into public documentation page by @alhendrickson in #417
• tests(medcat): CU-869d8wft4 Add tests to name count during supervised training by @mart-r in #435
• feat(medcat):CU-869cy3xa0 Improve training by @mart-r in #414
• feat(medcat): CU-869d9n2rg Avoid running pipe twice for supervised training by @mart-r in #467
• build(medcat and medcat-den): CU-869ddh1jv Avoid test resources in releases by @mart-r in #503
• fix(medcat): CU-869ddh1jv: Fix lock file issue. by @mart-r in #505

New Contributors

• @bgriffen made their first contribution in #399

Full Changelog: medcat/v2.7.0...medcat/v2.8.0

medcat/v2.7.1 patch release

This patch release is mainly to fix installation issues caused by spacy. See #505 for details.

Full Changelog: medcat/v2.7.0...medcat/v2.7.1

MedCAT-den v0.5.4

What's Changed

• feat(medcat-den): Make credentials optional for remote dens by @alhendrickson in #418

Full Changelog: medcat-den/v0.5.3...medcat-den/v0.5.4

MedCAT v2.7.0

🩺 MedCAT v2.7 Release Notes

This release focuses on usability improvements, pipeline observability, and several bug fixes across MedCAT components, including fixes for RelCAT and MetaCAT behaviour.

🚀 New Features & Enhancements

• Pipeline Timing / Speed Metrics – Added options to report the time spent in different pipeline stages, including:
  • Tokenisation
  • NER
  • Entity linking
  • Individual addon components
    This helps users understand performance bottlenecks in their MedCAT pipelines.
• Shorthand DeID Imports – Added a simplified import path for the DeID model:

  from medcat.deid import DeIdModel

  This replaces the longer internal import path previously required.

• Australian Model Bundle Support – Added explicit support for AU model bundles, enabling easier building and distribution of Australian clinical models.

🐛 Bug Fixes

• RelCAT Usability Fix – Fixed a typo that prevented RelCAT (relation extraction) from functioning correctly.
• MetaCAT Shuffle Fix – Corrected an issue where shuffling could still occur even when shuffle was disabled.
• RelCAT Typing Fix – Resolved typing issues affecting RelCAT components.
• Supervised Training Improvements – Improved the way supervised training synchronises entities in documents with expected dataset annotations.
  This simplifies batched training workflows for some linker implementations (e.g. embedding linker) and prevents edge cases where batched annotations could remain unprocessed.

🧰 Other Improvements

• Documentation Migration – MedCAT documentation has been migrated to MkDocs, improving maintainability and navigation.
• Tutorial & Script Automation – Fixed issues with the script used to automatically update tutorial and script versions.

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This release improves pipeline transparency, training robustness, and component usability, while continuing to stabilise the MedCAT v2 ecosystem.

What's Changed

• issue(medcat): CU-869c5kge0 Fix the script for automated bumps of tutorials / scripts. by @mart-r in #343
• feature(medcat): CU-869c7cxh7 Add shorthand import for deid by @mart-r in #346
• issue(medcat): CU-869c87tt9 Fix typo in relcat. by @mart-r in #349
• docs(medcat): Switch Medcat to Mkdocs by @alhendrickson in #361
• feat(medcat):CU-869cgny1k Add pipe speed options by @mart-r in #369
• feat(medcat): CU-869ccxgj7 Add AU model bundle support by @mart-r in #371
• feat(medcat): CU-869cgny1k Add pipe tokenizer speed by @mart-r in #370
• Pushing bug fix for shuffle by @shubham-s-agarwal in #381
• bug(medcat): CU-869cqnmtk Fix RelCAT typing issue by @mart-r in #388
• bug(medcat): CU-869ckx6dr Allow for better supervised training by @mart-r in #374

New Contributors

• @github-actions[bot] made their first contribution in #342

Full Changelog: MedCAT/v2.6.0...medcat/v2.7.0

MedCAT v1.16.12 patch release

This patch release addresses a few minor issues:

• Fix setuptools for MedCAT (#331)
• Fix issue with missing pkg_resources (#336)
• Fix data shuffle issue in MetaCAT test/train split (#381)

Full Changelog: medcat/v1.16.8...medcat/v1.16.12