build(medcat-plugins): bump the pip-deps group in /medcat-plugins/medcat-gliner with 3 updates

[dependabot]

Updates the requirements on medcat, setuptools and setuptools-scm to permit the latest version.
Updates medcat to 2.7.0

Release notes

Sourced from medcat's releases.

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.

---

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

... (truncated)

Commits

• 7c12cae bug(medcat): CU-869ckx6dr Allow for better supervised training (#374)
• b43c22e bug(medcat): CU-869cqnmtk Fix RelCAT typing issue (#388)
• 2fabac9 CU-869cqb94m: Bump urllib major version to 2. (#384)
• 981e2d8 Pushing bug fix for shuffle (#381)
• 57b9586 feat(medcat): CU-869cgny1k Add pipe tokenizer speed (#370)
• 614af59 feat(medcat): CU-869ccxgj7 Add AU model bundle support (#371)
• a2106b0 CU-869ckmuga: Add automation for medcat-service version bumps (#373)
• 5f3abb6 chore(medcat-service): bump medcat to 2.6.0 (#372)
• 79f00cf feat(medcat):CU-869cgny1k Add pipe speed options (#369)
• e35d9dc fix(medcat-trainer): Fix opentelemetry tracing running with wsgi command (#366)
• Additional commits viewable in compare view

Updates setuptools to 82.0.1

Changelog

Sourced from setuptools's changelog.

v82.0.1

Bugfixes

• Fix the loading of launcher manifest.xml file. (#5047)
• Replaced deprecated json.__version__ with fixture in tests. (#5186)

Improved Documentation

• Add advice about how to improve predictability when installing sdists. (#5168)

Misc

• #4941, #5157, #5169, #5175

v82.0.0

Deprecations and Removals

• pkg_resources has been removed from Setuptools. Most common uses of pkg_resources have been superseded by the importlib.resources <https://docs.python.org/3/library/importlib.resources.html>_ and importlib.metadata <https://docs.python.org/3/library/importlib.metadata.html>_ projects. Projects and environments relying on pkg_resources for namespace packages or other behavior should depend on older versions of setuptools. (#3085)

v81.0.0

Deprecations and Removals

• Removed support for the --dry-run parameter to setup.py. This one feature by its nature threads through lots of core and ancillary functionality, adding complexity and friction. Removal of this parameter will help decouple the compiler functionality from distutils and thus the eventual full integration of distutils. These changes do affect some class and function signatures, so any derivative functionality may require some compatibility shims to support their expected interface. Please report any issues to the Setuptools project for investigation. (#4872)

v80.10.2

Bugfixes

• Update vendored dependencies. (#5159)

Misc

... (truncated)

Commits

• 5a13876 Bump version: 82.0.0 → 82.0.1
• 51ab8f1 Avoid using (deprecated) 'json.version' in tests (#5194)
• f9c37b2 Docs/CI: Fix intersphinx references (#5195)
• 8173db2 Docs: Fix intersphinx references
• 09bafbc Fix past tense on newsfragment
• 461ea56 Add news fragment
• c4ffe53 Avoid using (deprecated) 'json.version' in tests
• 749258b Cleanup pkg_resources dependencies and configuration (#5175)
• 2019c16 Parse ext-module.define-macros from pyproject.toml as list of tuples (#5169)
• b809c86 Sync setuptools schema with validate-pyproject (#5157)
• Additional commits viewable in compare view

Updates setuptools-scm to 10.0.5

Release notes

Sourced from setuptools-scm's releases.

setuptools-scm v10.0.5

Fixed

• Allow dump_version() deprecation warning to be silenced by passing scm_version=None. (#1286)
• Remove [tool.uv.sources] from setuptools-scm/pyproject.toml to fix sdist builds outside the workspace — the workspace root already declares the source mapping for development. (#1330)

Commits

• e2ba34f Merge pull request #1328 from pypa/release/main
• d34d072 Prepare release: setuptools-scm v10.0.5
• 7c62809 Merge pull request #1332 from RonnyPfannschmidt/fix/1330-remove-workspace-sou...
• f600a29 fix: remove workspace source override from setuptools-scm member (fixes #1330)
• f76244e Merge pull request #1327 from RonnyPfannschmidt/update-classifiers-python-3.14
• 8c23c5b Merge pull request #1286 from effigies/scm_version_sentinel
• 629842a build: update trove classifiers and add Python 3.14 support
• 6a1fc3b Merge pull request #1318 from pypa/release/main
• a63b13a Prepare release: setuptools-scm v10.0.4, vcs-versioning v1.1.0
• 59275f7 Merge pull request #1325 from RonnyPfannschmidt/issue-1302-setuptools-build-b...
• Additional commits viewable in compare view

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[tomolopolis]

Task linked: CU-869c5kge0 Fix automated bump PRs script
Task linked: CU-869c7cxh7 Create shortcut for DeID model imports
Task linked: CU-869c87tt9 Fix typo in relcat
Task linked: CU-869cgny1k Add pipeline option for pipeline speed investigations

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