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* CU-8692kpchc Add the 403 exception to vocab downloader * CU-8692kpchc Add the new vocab download link
To `_refset_df2dict ` method in Snomed preprocessing
More specifically the get method which was not able to return default values for non-existant keys (#341)
…ised method (#345) * CU-8692mevx8 Fix issue with filters not taking effect in train_supervised method * CU-8692mevx8 Fix filter retention in train_supervised method
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.5 to 1.26.17. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](urllib3/urllib3@1.26.5...1.26.17) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
…s, as we can't use 0.14 due to de-id transformers dep reliance
CU-8692wb8gf: 'tokenizers>=0.12.0', # 0.13.1 doesn't seem to build
* CU-8692wgmkm: Remove py2neo dependency and the code that used it * CU-8692wgmkm: Remove medcat.neo package from setup.py
* CU-8692wgmkm: Remove py2neo dependency and the code that used it * CU-8692wgmkm: Remove medcat.neo package from setup.py
CU-8692wcmp7: update transformers to the latest version
…llib3-1.26.17 Bump urllib3 from 1.26.5 to 1.26.17 in /webapp/webapp
* CU-8692wbcq5: Pin max version of numpy * CU-8692wbcq5: Pin max version of numpy in setup.py * CU-8692wbcq5: Bump python version for readthedocs workflow * CU-8692wbcq5: Pin all requirement versions in docs requirements * CU-8692wbcq5: Move docs requirements before setuptools * CU-8692wbcq5: Fix typo in docs requirements * CU-8692wbcq5: Remove some less relevant stuff from docs requirements * CU-8692wbcq5: Add back sphinx-based requirements to docs requirements * CU-8692wbcq5: Move back to python 3.9 on docs build workflow * CU-8692wbcq5: Bump sphinx-autoapi version * CU-8692wbcq5: Bump sphinx version * CU-8692wbcq5: Bump python version back to 3.10 for future-proofing * CU-8692wbcq5: Undo pinning numpy to max version in setup.py * CU-8692wbcq5: Remove docs-build specific dependencies in setup.py
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.17 to 1.26.18. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](urllib3/urllib3@1.26.17...1.26.18) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
…t to set in memory (#352) * CU-8692uznvd: Allow empty-dict config.linking.filters.cuis and convert to set in memory * CU-8692uznvd: Move the empty-set detection and conversion from validator to init * CU-8692uznvd: Remove unused import
* CU-8692t3fdf Move saving config outside of the cdb.dat; Add test to make sure the config does not get saved with the CDB; patch a few existing tests * CU-8692t3fdf Use class methods on class instead of instance in a few tests * CU-8692t3fdf Fix typing issue * CU-8692t3fdf Add additional tests for 2 configs and zero configs when loading model pack * CU-8692t3fdf: Make sure CDB is linked to the correct config; Treat incorrect configs as dirty CDBs and force a recalc of the hash
Bumps [django](https://github.com/django/django) from 3.2.20 to 3.2.23. - [Commits](django/django@3.2.20...3.2.23) --- updated-dependencies: - dependency-name: django dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
* CU-8694n493m: Add deprecation and removal versions to deprecation decorator * CU-8694n493m: Deprecation version to existing deprecated methods. Made the removal version 2 minor versions from the minor version in which the method was deprecated, or the next minor version if the method had been deprecated for longer. * CU-8694n4ff0: Raise exception upon deprecated method call at test time * CU-8694n4ff0: Fix usage of deprecated methods call during test time
…or model pack loading
CU-8694pey4u: extract cdb load to cls method
CU-8694pey4u: missing extra config if passed in
…with-reg-json CU-8694py1jr fix old config load with reg json
…453) * CU-8694vcvz7: Trust remote code when loading transfomers NER dataset * CU-8694vcvz7: Add support for older datasets without the remote code trusing kwarg
* CU-8694gzbud: Add context manager that is able to snapshot CDB state * CU-8694gzbud: Add tests to snapshotting CDB state * CU-8694gzbud: Refactor tests for CDB state snapshotting * CU-8694gzbud: Remove use of deprecated method in CDB utils and use non-deprecated one instead * CU-8694gzbud: Add tests for training and CDB state capturing * CU-8694gzbud: Small refactor in tests * CU-8694gzbud: Add option to save state on disk * CU-8694gzbud: Add debug logging output when saving state on disk * CU-8694gzbud: Remove unused import * CU-8694gzbud: Add tests for disk-based state save * CU-8694gzbud: Move CDB state code to its own module * CU-8694gzbud: Remove unused import * CU-8694gzbud: Add doc strings to methods * CU-8694gzbx4: Small optimisation for stats * CU-8694gzbx4: Add MCTExport related module * CU-8694gzbx4: Add MCTExport related tests * CU-8694gzbx4: Add code for k-fold statistics * CU-8694gzbx4: Add tests for k-fold statistics * CU-8694gzbx4: Add test-MCT export with fake concepts * CU-8694gzbx4: Fix a doc string * CU-8694gzbx4: Fix types in MCT export module * CU-8694gzbx4: Fix types in k-fold module * CU-8694gzbx4: Remove accidentally committed test class * CU-8694gzbn3: Add missing test helper file * CU-8694gzbn3: Remove whitespace change from otherwise uncahnged file * CU-8694gzbn3: Allow 5 minutes longer for tests * CU-8694gzbn3: Move to python 3.8-compatible typed dict * CU-8694gzbn3: Add more time for tests in worklow (now 30 minutes) * CU-8694gzbn3: Add more time for tests in worklow (now 45 minutes) * CU-8694gzbn3: Update test-pypi timeout to 45 minutes * CU-8694gzbn3: Remove timeout from unit tests in main workflow * CU-8694gzbn3: Make tests stop upon first failure * CU-8694gzbn3: Fix test stop upon first failure (arg/option order) * CU-8694gzbn3: Remove debug code and old comments * CU-8694gzbn3: Remove all timeouts from main workflow * CU-8694gzbn3: Remove more old / useless comments in tests * CU-8694gzbn3: Add debug output when running k-fold tests to see where it may be stalling * CU-8694gzbn3: Add debug output when ANY tests to see where it may be stalling * CU-8694gzbn3: Remove explicit debug output from k-fold test cases * CU-8694gzbn3: Remove timeouts from DEID tests in case they're the ones creating issues * GHA/test fixes (#437) * Revert "CU-8694gzbn3: Remove timeouts from DEID tests in case they're the ones creating issues" This reverts commit faaf7fb. * Revert "CU-8694gzbn3: Remove explicit debug output from k-fold test cases" This reverts commit 9b02925. * Revert "CU-8694gzbn3: Add debug output when ANY tests to see where it may be stalling" This reverts commit 12c519a. * Revert "CU-8694gzbn3: Add debug output when running k-fold tests to see where it may be stalling" This reverts commit 03531da. * Revert "CU-8694gzbn3: Remove all timeouts from main workflow" This reverts commit e6debce. * Revert "CU-8694gzbn3: Fix test stop upon first failure (arg/option order)" This reverts commit 666c013. * Revert "CU-8694gzbn3: Make tests stop upon first failure" This reverts commit 94bce56. * Revert "CU-8694gzbn3: Remove timeout from unit tests in main workflow" This reverts commit 3618b9c. * CU-8694gzbn3: Improve state copy code in CDB state tests * CU-8694gzbn3: Fix a CDB state test issue * CU-8694gzbn3: Split all tests into 2 halves * CU-8694gzbn3: Remove legacy / archived / unused tests * CU-8694gzbn3: Add doc strings for FoldCreator init * CU-8694gzbn3: Move to a split-type enum * CU-8694gzbn3: Add documentation to split-type enum * CU-8694gzbn3: Create separate fold creators for different types of splitting strategies * CU-8694gzbn3: Resort document order in test time nullification process * CU-8694gzbn3: Add option to count number of annotations in doc for MCT export * CU-8694gzbn3: Add weighted documents based split option along with relevant tests * CU-8694gzbn3: Update default fold creation split type to weighted documents * CU-8694gzbn3: Add test to ensure weighted documents split creates a reasonable number of annotations per split
* CU-8693n892x: Save environment/dependency snapshot upon model pack creation * CU-8693n892x: Fix typing for env snapshot module * CU-8693n892x: Add test for env file existance in .zip * CU-8693n892x: Add doc strings * CU-8693n892x: Centralise env snapshot file name * CU-8693n892x: Add env snapshot file to exceptions in serialisation tests * CU-8693n892x: Only list direct dependencies * CU-8693n892x: Add test that verifies all direct dependencies are listed in environment * CU-8693n892x: Move requirements to separate file and use that for environment snapshot * CU-8693n892x: Remove unused constants * CU-8693n892x: Allow URL based dependencies when using direct dependencies * CU-8693n892x: Distribute install_requires.txt alongside the package; use correct path in distributed version
* CU-8694p8y0k: Add check for deprecations (code) * CU-8694p8y0k: Add workflow check for deprecations * CU-8694p8y0k: Fix (hopefully) workflow check for deprecations * CU-8694p8y0k: Add option to remove version prefix when checking deprecation * CU-8694p8y0k: Update deprecation checks with more detail (i.e current/next version). * CU-8694p8y0k: Only run deprecation checking step when merging master into production
* CU-8694u3yd2: Add logged warning for when using full-unlink * CU-8694u3yd2: Make CDB.remove_names simply expect an iterable of names * CU-8694u3yd2: Improve CDB.remove_names doc string * CU-8694u3yd2: Explicitly pass the keys to CDB.remove_names in CAT.unlink_concept_name * CU-8694u3yd2: Add note regarding state (and order) dependent tests to some CDB maker tests * CU-8694u3yd2: Rename/make protected CDB.remove_names method * CU-8694u3yd2: Create deprecated CDB.remove_names method
* CU-8694vte2g: Remove CDB.add_concept method * CU-8694vte2g: Remove unused import (deprecated decorator) * CU-8694vte2g: Remove CAT.get_spacy_nlp method * CU-8694vte2g: Remove CAT.train_supervised method * CU-8694vte2g: Remove CAT multiprocessing methods * CU-8694vte2g: Remove MetaCAT.train method * CU-8694vte2g: Remove medcat.utils.ner.helper.deid_text method * CU-8694vte2g: Remove use of deprecated method * CU-8694vte2g: Add back removed deprecation import
* Split tests in production workflow to avoid Ouf Of Memory (137) (#456) --------- Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: zethson <lukas.heumos@posteo.net> Co-authored-by: tomolopolis <tsearle88@gmail.com> Co-authored-by: Xi Bai <82581439+baixiac@users.noreply.github.com> Co-authored-by: Anthony Shek <55877857+antsh3k@users.noreply.github.com> Co-authored-by: antsh3k <antshek@hotmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Zeljko <w.kraljevic@gmail.com> Co-authored-by: Sander Tan <s.c.tan-3@umcutrecht.nl> Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net> Co-authored-by: James Brandreth <james.brandreth@gmail.com> Co-authored-by: Xi Bai <baixiac@gmail.com> Co-authored-by: adam-sutton-1992 <adam.sutton@kcl.ac.uk> Co-authored-by: adam-sutton-1992 <60137864+adam-sutton-1992@users.noreply.github.com> Co-authored-by: jenniferajiang <jennigato95@gmail.com> Co-authored-by: Jennifer Jiang <37081323+jenniferajiang@users.noreply.github.com> Co-authored-by: Shubham Agarwal <66172189+shubham-s-agarwal@users.noreply.github.com> Co-authored-by: Vlad Dinu <62345326+vladd-bit@users.noreply.github.com>
…461) * CU-86951923u: Add option for simplified hash along with a few tests * CU-86951923u: Make sure simplified hashing test compares regular to simplified timings * CU-86951923u: Hopefully fix hashing test with simplified hash after saving * CU-86951923u: Call patched methods when performing fake save during tests for python 3.8 support * CU-86951923u: Fix fake save during tests for python 3.11 support
* CU-8694vbw6y: Update k-fold metrics to allow including standard deviation in results * CU-8694vbw6y: Add tests for new parts of k-fold metrics (e.g standard deviation) * CU-8694vbw6y: Fix typing issues k-fold metrics and standard deviation
* CU-8694wh3d5: Add config for usage monitor * CU-8694wh3d5: Add buffered Usage Monitor along with relevant tests * CU-8694wh3d5: Add Usage Monitor to CAT.__call__ * CU-8694wh3d5: Add tests for usage monitoring to CAT tests * CU-8694wh3d5: Add tests for usage monitor to make sure the input length is correctly monitored * CU-8694wh3d5: Disable usage monitor by default * CU-8694wh3d5: Enable usage monitor during test time * CU-8694wh3d5: Use correct entities when using nested entities * CU-8694wh3d5: Allow 'auto' for usage monitor enable status in config Add relevant documentation to log_folder that it's not used on 'auto' * CU-8694wh3d5: Update config documentation to include environmental variables * CU-8694wh3d5: Add automatic usage monitoring * CU-8694wh3d5: Add relevant tests to automatic usage monitoring * CU-8694wh3d5: Rename usage monitoring environmental variables to be more desciptive
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