Medcat

This patch release mostly addresses the blis (dependency) issue.
For some reason, a new version of blis is often automatically installed.
And that new version of blis depends on numpy>=2, which medcat is incompatible with.

It also addresses allowing remote code for Transfomers NER parts (the default previously, but new dependencies require it to be explicitly stated).

What's Changed

- 453 CU-8694vcvz7: Trust remote code when loading transfomers NER dataset
- 471 CU-869588fdc: Bin blis to 1.0.0

**Full Changelog**: https://github.com/CogStack/MedCAT/compare/v1.11.0...v1.11.1

Main change is the addition of RelCAT, i.e the relation extraction addon. It's still in a bit of a WIP status and subject to change, however.

What's Changed
* Bump django from 3.2.24 to 3.2.25 in /webapp/webapp by dependabot in https://github.com/CogStack/MedCAT/pull/408
* CU-86947ja9y dill old weights by mart-r in https://github.com/CogStack/MedCAT/pull/411
* CU-86949yar7: Add logged warning for when multiprocessing fails due to being out of memory by mart-r in https://github.com/CogStack/MedCAT/pull/415
* CU-86949zjg9 mp progress by mart-r in https://github.com/CogStack/MedCAT/pull/416
* CU-86948uv4g docstring signature consistency by mart-r in https://github.com/CogStack/MedCAT/pull/413
* CU-86948uv4g docstring signature consistency by mart-r in https://github.com/CogStack/MedCAT/pull/417
* Small addition to contribution guidelines by mart-r in https://github.com/CogStack/MedCAT/pull/420
* CU-8694cbcpu: Allow specifying an AU Snomed when preprocessing by mart-r in https://github.com/CogStack/MedCAT/pull/421
* CU-8694dpy1c: Return empty generator upon empty stream by mart-r in https://github.com/CogStack/MedCAT/pull/423
* Relation extraction by vladd-bit in https://github.com/CogStack/MedCAT/pull/173
* CU-8694fae3r: Avoid publishing PyPI release when doing GH pre-releases by mart-r in https://github.com/CogStack/MedCAT/pull/424
* v1.11.0 PR by mart-r in https://github.com/CogStack/MedCAT/pull/426

New Contributors
* vladd-bit made their first contribution in https://github.com/CogStack/MedCAT/pull/173

**Full Changelog**: https://github.com/CogStack/MedCAT/compare/v1.10.2...v1.11.0

This patch release mostly addresses the blis (dependency) issue.
For some reason, a new version of blis is often automatically installed.
And that new version of blis depends on numpy>=2, which medcat is incompatible with.

It also addresses allowing remote code for Transfomers NER parts (the default previously, but new dependencies require it to be explicitly stated).

Furthermore, this PR addresses a small issue to do with empty generator returning (internal issue) that does not affect the use of the library in any way.

What's Changed

- 423 CU-8694dpy1c: Return empty generator upon empty
- 453 CU-8694vcvz7: Trust remote code when loading transfomers NER dataset
- 471 CU-869588fdc: Bin blis to 1.0.0

**Full Changelog**: https://github.com/CogStack/MedCAT/compare/v1.10.2...v1.10.3

This patch release mostly addresses another issue with the DeID model(s).

The underlying RoBERTa models have a token limit (512) and because of that later parts of larger documents would fail to de-identify.
This Release (or more specifically, PR 405) fixes that issue by allowing the user to specify the overlapping tokens (and defaults to 5).

What's Changed
* CU-8693v3tt6 SOMED opcs refset selection by mart-r in https://github.com/CogStack/MedCAT/pull/402
* CU-8693v6epd: Move typing imports away from pydantic by mart-r in https://github.com/CogStack/MedCAT/pull/403
* CU-8693qx9yp Deid chunking - hugging face pipeline approach by shubham-s-agarwal in https://github.com/CogStack/MedCAT/pull/405

New Contributors
* shubham-s-agarwal made their first contribution in https://github.com/CogStack/MedCAT/pull/405

**Full Changelog**: https://github.com/CogStack/MedCAT/compare/v1.10.1...v1.10.2

This patch release mostly addresses two things regarding DeID models:
1. DeID models created with older `medcat` versions (prior to `v1.9.3`) would silently fail to deidentify anything [397].
2. DeID model multiprocessing doesn't work in all cases. This release adds a more descriptive exception when this happens as well as a description of two workarounds (either save the model on disk and load back up; or use the cpu-only `torch`)[393 and 400].

The patch release also fixes some of the issues with dependencies [392].

There are a few other smaller changes which you can see below.

What's Changed
* CU-8693cv3w0 Fix fallback spacy model existance on pip installs by mart-r in https://github.com/CogStack/MedCAT/pull/386
* CU-8693b0a61 Add method to get spacy model version by mart-r in https://github.com/CogStack/MedCAT/pull/381
* CU-8693kp0gw: Pin more recent versions for major dependencies; Avoid major bumps where applicable by mart-r in https://github.com/CogStack/MedCAT/pull/392
* add: metacat can predict on spans in arbitrary spangroups by jkgenser in https://github.com/CogStack/MedCAT/pull/391
* CU-8693ruk7p: Bump mypy version in dev-requirements by mart-r in https://github.com/CogStack/MedCAT/pull/396
* Bump django from 3.2.23 to 3.2.24 in /webapp/webapp by dependabot in https://github.com/CogStack/MedCAT/pull/395
* CU-8693t24ed: Add workaround for older DeID models in newer MedCAT by mart-r in https://github.com/CogStack/MedCAT/pull/397
* CU-2hz5ump deid mulitprocessing by mart-r in https://github.com/CogStack/MedCAT/pull/393
* Cu 8693u6b4u tests continue on fail by mart-r in https://github.com/CogStack/MedCAT/pull/400

New Contributors
* jkgenser made their first contribution in https://github.com/CogStack/MedCAT/pull/391

**Full Changelog**: https://github.com/CogStack/MedCAT/compare/v1.10.0...v1.10.1

Main changes to mention:
- Better model-compatibility regarding known `config.linking.filters.cuis` issue
- The default value (an empty dict `{}`) will be converted to an empty `set` in memory
- When saving a model, the config is now saved separately
- We retain backwards compatibility for when the config is saved alongside the CDB (as was the case this far)
- Add a CDB merge method (in `medcat.utils.cdb_utils`)
- We can now safely fall back to `en_core_web_md` spacy model
- If the spacy model isn't provided by the CAT for some reason
- This includes the possibility of automatically downloading the dependency if it doesn't exist
- Many other changes as per below

What's Changed
* Bump urllib3 from 1.26.5 to 1.26.17 in /webapp/webapp by dependabot in https://github.com/CogStack/MedCAT/pull/351
* Cu 8692wbcq5 docs builds by mart-r in https://github.com/CogStack/MedCAT/pull/359
* CU-8692uznvd: Allow empty-dict config.linking.filters.cuis and convert to set in memory by mart-r in https://github.com/CogStack/MedCAT/pull/352
* CU-8692t3fdf separate config on save by mart-r in https://github.com/CogStack/MedCAT/pull/350
* CU-2cdpd4t: Unify default addl_info in different methods. by mart-r in https://github.com/CogStack/MedCAT/pull/363
* CU-86931prq4: GHA runs on node12 by mart-r in https://github.com/CogStack/MedCAT/pull/368
* Cu 1yn0v9e duplicate multiprocessing methods by mart-r in https://github.com/CogStack/MedCAT/pull/364
* CU-2exy49p: Make sure the cdb.add_concept really adds a concept or somehow make it clear by adam-sutton-1992 in https://github.com/CogStack/MedCAT/pull/370
* 869377m3u: Add comment regarding demo link load times to README by mart-r in https://github.com/CogStack/MedCAT/pull/376
* Added README.md documentation for CPU only installations by adam-sutton-1992 in https://github.com/CogStack/MedCAT/pull/365
* Cu 8692zguyq no preferred name by mart-r in https://github.com/CogStack/MedCAT/pull/367
* Add trainer callbacks for Transformer NER by baixiac in https://github.com/CogStack/MedCAT/pull/377
* Bump django from 3.2.20 to 3.2.23 in /webapp/webapp by dependabot in https://github.com/CogStack/MedCAT/pull/369
* Bump urllib3 from 1.26.17 to 1.26.18 in /webapp/webapp by dependabot in https://github.com/CogStack/MedCAT/pull/360
* CU-2e77a31 improve print stats by mart-r in https://github.com/CogStack/MedCAT/pull/366
* CU2e77a5x - Add a CDB merge function by adam-sutton-1992 in https://github.com/CogStack/MedCAT/pull/373
* CU-8693az82g Remove cdb tests side effects by mart-r in https://github.com/CogStack/MedCAT/pull/380
* CU-8693bpq82 fallback spacy model by mart-r in https://github.com/CogStack/MedCAT/pull/384
* Fix stopwords loading bug by jenniferajiang in https://github.com/CogStack/MedCAT/pull/383
* CU-8693cv3w0 Fix fallback spacy model existance on pip installs by mart-r in https://github.com/CogStack/MedCAT/pull/386
* CU-8693b0a61 Add method to get spacy model version by mart-r in https://github.com/CogStack/MedCAT/pull/381

New Contributors
* adam-sutton-1992 made their first contribution in https://github.com/CogStack/MedCAT/pull/370
* jenniferajiang made their first contribution in https://github.com/CogStack/MedCAT/pull/383

**Full Changelog**: https://github.com/CogStack/MedCAT/compare/v1.9.3...v1.10.0