v1.14.0

The main change in this release is the hard removal of python 3.8 support (#498).
But the release comes with some other minor changes as well. See the full list below.

What's Changed since v1.13.2

• CU-8695q21f6: Replace rosalind links with S3 ones in docs by @mart-r in #489
• CU-8695m5q4x: Fix issues detecting 1-token concepts by @mart-r in #485
• CU-8695knfbg Add name edits to regression suite by @mart-r in #486
• CU-869574kvp update snomed preprocessing naming by @mart-r in #469
• CU-8695vu71q: Make report identical run to run in identical cases by @mart-r in #492
• CU-86967nnra Drop python 3.8 support (EoL) by @mart-r in #498
• CU-86964zm4d fix preprocessing by @mart-r in #496
• CU-8695hghww backwards compatibility workflow by @mart-r in #478
• CU-8696m1mch: Remove versioning utility since all its parts were deprecated by @mart-r in #500
• v1.14.0 release PR by @mart-r in #506

Full Changelog: v1.13.2...v1.14.0

v1.13.2

This release is mainly focused on fixing DeID models. This fix was supposed tom out in 1.13.1 but were accidentally omitted.

What's Changed

• CU-869671bn4: Update requirements to fix workflow issue due to mypy by @mart-r in #497
• CU-8696n7w95: Remove commented code to fix DeID (oversight in PR 490) by @mart-r in #502

Full Changelog: v1.13.1...v1.13.2

v1.13.1

This PR is mostly designed to address a few issues related to MetaCAT (see #495).
But a few other changes were also pulled from the master class to fix previous issues and/or make sure the patch release is stable.

What's Changed

• CU-8695jwnjk: Fix description of an argument for --help to work in CLI by @mart-r in #484
• Pushing bug fix for metacat by @shubham-s-agarwal in #487
• CU-8695uhe5n: Update docs dependency pins by @mart-r in #491
• CU-8695pvhfe fix usage monitoring for multiprocessing by @mart-r in #488
• CU-8695ucw9b deid transformers fix by @mart-r in #490
• CU-869637yfx: Pin spacy dependency to lower than 3.8 by @mart-r in #494
• MetaCAT fixes and upgrades by @shubham-s-agarwal in #495

Full Changelog: v1.13.0...v1.13.1

v1.12.2

This PR is mostly designed to address a few issues related to MetaCAT (see #495).
But a few other changes were also pulled from the master class to fix previous issues and/or make sure the patch release is stable.

What's Changed

• CU-869588fdc: Bin blis to 1.0.0 by @mart-r in #471
• Fixing bug for metacat by @shubham-s-agarwal in #474
• Use the loaded model hash for usage monitor instead of recalculating it by @mart-r in #477
• CU8695gyxrt CDB Merge Typo by @adam-sutton-1992 in #479
• Pushing bug fix for metacat by @shubham-s-agarwal in #487
• CU-8695uhe5n: Update docs dependency pins by @mart-r in #491
• CU-8695ucw9b deid transformers fix by @mart-r in #490
• CU-869637yfx: Pin spacy dependency to lower than 3.8 by @mart-r in #494
• MetaCAT fixes and upgrades by @shubham-s-agarwal in #495

Full Changelog: v1.12.1...v1.12.2

v1.13.0

Release for 1.13 release.

What's Changed

• CU-86951923u: Add option for simplified hash along with a few tests by @mart-r in #461
• CU-8694vbw6y k-fold stats Standard Deviation by @mart-r in #459
• CU-8694wh3d5 track usage by @mart-r in #458
• Deid logging update by @shubham-s-agarwal in #466
• CU-8694vv985 transitive deps by @mart-r in #463
• CU-869588fdc: Bin blis to 1.0.0 by @mart-r in #471
• Changes to documentation for metacat by @shubham-s-agarwal in #472
• Fixing bug for metacat by @shubham-s-agarwal in #474
• CU-86956duhb: Add method to backport a model pack from 1.12 to previous version by @mart-r in #465
• CU-8694cd9t2: Allow merging config into model pack config before init by @mart-r in #462
• CU-8694fwyje: Update all configs with pre-load parts documented by @mart-r in #473
• Use the loaded model hash for usage monitor instead of recalculating it by @mart-r in #477
• CU8695gyxrt CDB Merge Typo by @adam-sutton-1992 in #479
• CU-86956du3q revisit regression by @mart-r in #470
• CU-8695hydt9: Fix various typos by @mart-r in #480
• CU-8695j1be2: Remove deprecated method on CDB by @mart-r in #481
• v1.13.0 release PR by @mart-r in #482

Full Changelog: v1.12.1...v1.13.0

v1.10.3

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: v1.10.2...v1.10.3

v1.12.1

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.

What's Changed

• #471 CU-869588fdc: Bin blis to 1.0.0

Full Changelog: v1.12.0...v1.12.1

v1.11.1

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: v1.11.0...v1.11.1

v1.12.0

NOTE:
There's a few deprecated methods being removed in this version. Refer to #454.

What's Changed

• Relation extraction by @vladd-bit in #173
• CU-8694fae3r: Avoid publishing PyPI release when doing GH pre-releases by @mart-r in #424
• Merging changes from master to metacat_bert branch by @shubham-s-agarwal in #431
• Adding Bert-style model for MetaCAT by @shubham-s-agarwal in #419
• CU-8694hukwm: Document the materialising of generator when multiproce… by @mart-r in #433
• CU-8694fk90t (almost) only primitive config by @mart-r in #425
• CU-8694gza88 Create codeql.yml by @mart-r in #434
• CU-8694mbn03: Remove the web app by @mart-r in #441
• CU-8694n48uw better deprecation by @mart-r in #443
• CU-8694pey4u: extract cdb load to cls method by @tomolopolis in #446
• CU-8694pey4u: missing extra config if passed in by @tomolopolis in #448
• CU-8694py1jr fix old config load with reg json by @mart-r in #449
• CU-8694vcvz7: Trust remote code when loading transfomers NER dataset by @mart-r in #453
• CU-8694gzbn3 k fold metrics by @mart-r in #432
• CU-8693n892x environment/dependency snapshots by @mart-r in #438
• CU-8694p8y0k deprecation GHA check by @mart-r in #445
• CU-8694u3yd2 cleanup name removal by @mart-r in #450
• CU-8694vte2g 1.12 depr removal by @mart-r in #454

Full Changelog: v1.11.0...v1.12.0

v1.11.0

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 #408
• CU-86947ja9y dill old weights by @mart-r in #411
• CU-86949yar7: Add logged warning for when multiprocessing fails due to being out of memory by @mart-r in #415
• CU-86949zjg9 mp progress by @mart-r in #416
• CU-86948uv4g docstring signature consistency by @mart-r in #413
• CU-86948uv4g docstring signature consistency by @mart-r in #417
• Small addition to contribution guidelines by @mart-r in #420
• CU-8694cbcpu: Allow specifying an AU Snomed when preprocessing by @mart-r in #421
• CU-8694dpy1c: Return empty generator upon empty stream by @mart-r in #423
• Relation extraction by @vladd-bit in #173
• CU-8694fae3r: Avoid publishing PyPI release when doing GH pre-releases by @mart-r in #424
• v1.11.0 PR by @mart-r in #426

New Contributors

• @vladd-bit made their first contribution in #173

Full Changelog: v1.10.2...v1.11.0