#158)

* feat(medcat-trainer): improve client api, not importing empty projects

---------

Co-authored-by: Tom Searle <[email protected]>

* - Add tests to increase coverage in medcat-trainer frontend
- Add job in CI and QA workflows to test frontend

* Fix indentation

* Update medcat-trainer_ci.yml

* Fix line endings

* properly fix line endings mismatch

* Create ConceptDatabase.spec.ts

* remove erroneously added test files

* re-add end of file return

* readd new line at end of file

* properly fix line endings mismatch

Create ConceptDatabase.spec.ts

Fix indentation

remove erroneously added test files

readd new line at end of file

* CU-869admfwg: Disable push to dockerhub in QA workflow for testing

* CU-869admfwg: Remove workflow dispatch from QA workflow now that testing is complete

* CU-869ajt55f: Initial dev setup with feature flag

* CU-869ajt55f: Map Keycloak Roles to Django User

* CU-869ajt55f: Add env var expansion to optionally include Traefik labels and gateway auth network

* CU-869ajt55f: Tidy up configuration and fix logout

* CU-869ajt55f: Disable OIDC auth by default

* CU-869ajt55f: Revert unintended changes

* CU-869ajt55f: Addressing code review feedback

* CU-869ajt55f: Fix broken test

* CU-869ary4dq: Add code to check for updates

* CU-869ary4dq: Add option to change log level with environmental variables

* CU-869ary4dq: Use option to change log level with environmental variables

* CU-869ary4dq: Remove debug print output

* CU-869ary4dq: Add separate log level for YANKED releases

* CU-869ary4dq: Add tests for update checker

* CU-869ary4dq: Move cache to subfolder

* CU-869ary4dq: Check the value of version check enabling environmental value

* CU-869ary4dq: Unify environmental value getting

* CU-869ary4dq: Add section regarding version and update checks to README

* Update config for pydantic models - use v2-specific attribute

* Add tests to make sure importing configs procudes no errors

* Add more info to exception raised upon state clear

* Add some more information to an error

* Fix import reload during tests - run the import in a subprocess

…otebooks (#173)

#174)

* CU-869an5f00: Update backend registration tests - use mocking

* CU-869an5f00: Add new optional API for den to fine tune models

* CU-869an5f00: Add eval API

* CU-869an5f00: Add option to disallow local fine-tune and/or push of fine-tuned models

* CU-869an5f00: Allow a DenWrapper to have a den config alongside it

* CU-869an5f00: Disallow local fine tune with remote dens if/when applicable

* CU-869an5f00: Separate local and remote exceptions

* CU-869an5f00: Add a few tests for disallowing push

* CU-869an5f00: Add another simple test

* CU-869an5f00: Add wrapper for training to control disallowing supervised training

* CU-869an5f00: Add a few simple tests for disallowing local training with a remote den

* CU-869an5f00: Add new environmental variables to README

* CU-869an5f00: Add a small note in code regarding defaults

* CU-869an5f00: Propagate new options to get_default_den

* CU-869an5f00: Add small comment regarding pushing base models

* CU-869an5f00: Add more info to failure to load a registered den type

* CU-869an5f00: Fix mocked den for python 3.12.

That is, needed to make sure it is explicitly specced for the protocol for the instanceof check to pass

Bumps the actions-deps group with 2 updates: [github/codeql-action](https://github.com/github/codeql-action) and [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv).


Updates `github/codeql-action` from 3 to 4
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](github/codeql-action@v3...v4)

Updates `astral-sh/setup-uv` from 6 to 7
- [Release notes](https://github.com/astral-sh/setup-uv/releases)
- [Commits](astral-sh/setup-uv@v6...v7)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-version: '4'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-deps
- dependency-name: astral-sh/setup-uv
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-deps
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Add classifier for 3.13 support

* Make workflow run on 3.13

* Update UV lock file with 3.13

* Specify different scipy dependencies depending on python version

* Update uv.lock

* Typing fix for modern bert RelCAT

* Typing fix for regression utils

* CU-869atpd59: Avoid problematic transformers version

* initial commit for embedding linker

* update to embedding logic and additional configutations

* handling no link candidates along with fixes

* added testing and fixes from testing

* mypy fixes

* fixed linting (hopefully)

* added thresholds for short and long contexts

* fixed mypy issues

* Added filter before disambig, and various tests

* handling cases with 1 candidate that's filtered out

* added max length logic and finals suggested changes

* changes to config documentation and filter before disambig

…175)