Medcat

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

What's Changed
* CU-8692wgmkm: Remove py2neo dependency and the code that used it by mart-r in https://github.com/CogStack/MedCAT/pull/356
* CU-8692wcmp7: update transformers to the latest version by tomolopolis in https://github.com/CogStack/MedCAT/pull/355
* v1.19.3 by tomolopolis in https://github.com/CogStack/MedCAT/pull/357


**Full Changelog**: https://github.com/CogStack/MedCAT/compare/v1.9.2...v1.9.3

What's Changed
* CU-8692kpchc Fix for Rosalind link not working by mart-r in https://github.com/CogStack/MedCAT/pull/342
* Fix issue 340 (snomed preprocessing) by mart-r in https://github.com/CogStack/MedCAT/pull/343
* CU-8692kn0yv Fix issue with fake dict in identifier based config by mart-r in https://github.com/CogStack/MedCAT/pull/341
* CU-8692mevx8 Fix issue with filters not taking effect in train_supervised method by mart-r in https://github.com/CogStack/MedCAT/pull/345
* CU-8692wb8gf: 'tokenizers>=0.12.0', 0.13.1 doesn't seem to build by tomolopolis in https://github.com/CogStack/MedCAT/pull/353
* v1.19.2 Patch Fix by tomolopolis in https://github.com/CogStack/MedCAT/pull/354


**Full Changelog**: https://github.com/CogStack/MedCAT/compare/v1.9.1...v1.9.2

Patch release to fix some issues.

This fixes an issue with configs not working as dicts (the `.get` method would not work if the attribute didn't exist). Issue introduced in v1.4.0.
It also fixes an issue with filters not working properly in `CAT.train_supervised`. Issue introduced in 1.6.0.
And some other smaller changes.


What's Changed
* CU-8692kpchc Fix for Rosalind link not working by mart-r in https://github.com/CogStack/MedCAT/pull/342
* Fix issue 340 (snomed preprocessing) by mart-r in https://github.com/CogStack/MedCAT/pull/343
* CU-8692kn0yv Fix issue with fake dict in identifier based config by mart-r in https://github.com/CogStack/MedCAT/pull/341
* CU-8692mevx8 Fix issue with filters not taking effect in train_supervised method by mart-r in https://github.com/CogStack/MedCAT/pull/345


**Full Changelog**: https://github.com/CogStack/MedCAT/compare/v1.9.0...v1.9.1