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

medcat-service/v1.3.0

What's Changed

• fix(medcat-service): Metrics API not registering when demo is enabled by @alhendrickson in #348
• chore(medcat-service): CU-869ckmu2r bump medcat to 2.6.0 by @mart-r in #372
• build(medcat-service): CU-869ckmuga automate medcat dependency bumps by @mart-r in #373

New Contributors

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

Full Changelog: medcat-service/v1.2.0...medcat-service/v1.3.0

MedCAT-den v0.5.3

This is a MedCAT den patch release, mostly focusing on model card adaption for legacy / fake models (#352).

What's Changed

• build(medcat-den): CU-869c7zhpv Avoid using newly introduced rules for ruff by @mart-r in #347
• issue(medcat-den): CU-869c96xwg Improve model card adaption by @mart-r in #352

Full Changelog: medcat-den/v0.5.2...medcat-den/v0.5.3

medcat-trainer/v3.5.1

What's Changed

• issue(medcat): CU-869c5kge0 Fix the script for automated bumps of tutorials / scripts. by @mart-r in #343
• chore(medcat-scripts): bump medcat to ~=v2.6.0 by @github-actions[bot] in #342
• build: bump the actions-deps group with 2 updates by @dependabot[bot] in #344
• feat(medcat-trainer): Remove callback URL fragments after successful login. by @jocelyneholdbrook in #340
• feature(medcat): CU-869c7cxh7 Add shorthand import for deid by @mart-r in #346
• feat(medcat-trainer): Determine whether user is admin based on Keycloak group by @jocelyneholdbrook in #345

New Contributors

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

Full Changelog: MedCAT/v2.6.0...medcat-trainer/v3.5.1