v1.10.1 PR #399
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v1.10.1 PR #399
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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] <[email protected]>
…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] <[email protected]>
…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] <[email protected]>
* CU-1yn0v9e: Rename and deprecate one of the multiprocessing methods; Add docstring. Trying to be more explicit regarding usage and differences between different methods * CU-1yn0v9e: Rename and deprecate the multiprocessing_pipe method; Add docstring. Trying to be more explicit regarding usage and differences between different methods * CU-1yn0v9e: Fix typo in docstring; more consistent naming
CU-2exy49p: Make sure the cdb.add_concept really adds a concept or somehow make it clear
* changed README.md to reflect installation options. * added setup script to demonstrate how wrapper could look for CPU installations * removed setup.sh as unnessescary for cpu only builds * Initial commit for merge_cdb method * Added indentation to make merge_cdb a class method * fixed syntax issues * more lint fixes * more lint fixes * bug fixes of merge_cdb * removed print statements * Added commentary on disk space usage of pytorch-gpu * removed merge_cdb from branch --------- Co-authored-by: adam-sutton-1992 <[email protected]>
* CU-8692zguyq: Slight simplification of minimum-name-length logic * CU-8692zguyq: Add some tests for prepare_name preprocessor * CU-8692zguyq: Add warning if no preferred name was added along a new CUI * CU-8692zguyq: Add additional warning messages when adding/training a new CUI with no preferred name * CU-8692zguyq: Make no preferred name warnings only run if name status is preferred * CU-8692zguyq: Add tests for no-preferred name warnings * CU-8692zguyq: Add Vocab.make_unigram_table to CAT tests * CU-8692zguyq: Move to built in asserting for logging instead of patching the method * CU-8692zguyq: Add workaround for assertNoLogs on python 3.8 and 3.9
CU-86938vf30 add trainer callbacks for Transformer NER
…ango-3.2.23 Bump django from 3.2.20 to 3.2.23 in /webapp/webapp
…llib3-1.26.18 Bump urllib3 from 1.26.17 to 1.26.18 in /webapp/webapp
* Add base class for CAT * Add CDB base class * Some whitespace fixes for base modules * CU-2e77a31: Move print stats to their own module and class * CU-2e77a31: Fix issues introduced by moving print stats * CU-2e77a31: Rename print_stats to get_stats and add option to avoid printed output * CU-2e77a31: Add test for print_stats * CU-2e77a31: Remove unused import * CU-2e77a31: Add new package to setup.py * CU-2e77a31: Fix a bunch of typing issues * CU-2e77a31: Revert CAT and CDB abstraction
CU2e77a5x - Add a CDB merge function Given two CDBs, a new CDB will be created combining the entries from both CDBs.
* 8693az82g: Add method to CDBMaker to reset the CDB * 8693az82g: Add test in CDB tests to ensure a new CDB is used for each test * 8693az82g: Reset CDB in CDB tests before each test to avoid side effects
* CU-8693bpq82: Add fallback spacy model along with test * CU-8693bpq82: Remove debug output * CU-8693bpq82: Add exception info to warning upon spacy model load failure and fallback
Implement my recommended changes
Fix stopwords loading bug
* CU-8693cv3w0: Add method to ensure spacy model and use it when falling back to default model * CU-8693cv3w0: Add logged output when installing/downloading spacy model
* CU-8693b0a61: Add method to find spacy folder in model pack along with some tests * CU-8693b0a61: Add test for spacy folder finding (full path) * CU-8693b0a61: Add method for finding spacy model in model pack along with tests * CU-8693b0a61: Add method for finding current spacy version * CU-8693b0a61: Add method for getting spacy model version installed * CU-8693b0a61: Fix getting spacy model folder return path * CU-8693b0a61: Add method to get name and meta of spacy model based on model pack * CU-8693b0a61: Add missing fake spacy model meta * CU-8693b0a61: Add missing docstrings * CU-8693b0a61: Change name of method for clarity * CU-8693b0a61: Add method to get spacy model name and version from model pack path * CU-8693b0a61: Fix a few typing issues * CU-8693b0a61: Add a missing docstring * CU-8693b0a61: Match folder name of fake spacy model to its name * CU-8693b0a61: Make the final method return true name of spacy model instead of folder name * Add additional output to method for getting spacy model version - the compatible spacy versions * CU-8693b0a61: Add method for querying whether the spacy version is compatible with a range * CU-8693b0a61: Add better abstraction for spacy version mocking in tests * CU-8693b0a61: Add some more abstraction for fake model pack in tests * CU-8693b0a61: Add method for checking whethera model pack has a spacy model compatible with installed spacy version * CU-8693b0a61: Improve abstraction within tests * CU-8693b0a61: Add method to check which of two versions is older * CU-8693b0a61: Fix fake spacy model versioning * CU-8693b0a61: Add method for determining whether a model pack has semi-compatible spacy model * CU-8693b0a61: Add missing word in docstring. * CU-8693b0a61: Change some method to protected ones
…major bumps where applicable (#392) * CU-8693kp0gw: Pin more recent versions for major dependencies; Avoid major bumps where applicable * CU-8693kp0gw: Bump default spacy model version (3.4.0 -> 3.6.0) * CU-8693kp0gw: Bump fakse test-spacy model version compatibility range * CU-8693kp0gw: Fix spacy compatibility tests for new fake model * CU-8693kp0gw: Undo what I thought was a typo fix (moved back from 'movar~virus' to 'movar~viruse')
* add: ability to predict on other spangroups * add: pr comments and better error * fix: typo * fix: linting
* CU-8693ruk7p: Bump mypy version (along with extensions) in dev-requirements * CU-8693ruk7p: Pin max major version for mypy
* Bump django from 3.2.23 to 3.2.24 in /webapp/webapp Bumps [django](https://github.com/django/django) from 3.2.23 to 3.2.24. - [Commits](django/django@3.2.23...3.2.24) --- updated-dependencies: - dependency-name: django dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * CU-8693ruk7p: Bump mypy version in dev-requirements (#396) (#398) * CU-8693ruk7p: Bump mypy version (along with extensions) in dev-requirements * CU-8693ruk7p: Pin max major version for mypy --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Mart Ratas <[email protected]>
* CU-2hz5ump: Separate the text replacement in deid * CU-2hz5ump: Fix some indentation on multiprocessing methods in CAT * CU-2hz5ump: Add method to deid multithreaded * CU-2hz5ump: Add tests for deid multiprocessing * CU-2hz5ump: Fix return type for multiprocessing deid method * CU-2hz5ump: Remove unused import * CU-2hz5ump: Fix typing issue within deid multi texts method * CU-2hz5ump: Add removal parts to deid tests * CU-2hz5ump: Add error handling with message to deid multiprocessing issues * CU-2hz5ump: Unpin mypy for dev requirements * CU-2hz5ump: Fix mypy unpin typo * CU-2hz5ump: Force later version of mypy * CU-2hz5ump: Force mypy extensions to newer version * CU-2hz5ump: Add 20 minute timeout to main workflow * CU-2hz5ump: Add 20 minute timeout to main workflow (build) * CU-2hz5ump: Add 19 minute timeout to tests step of main workflow * CU-2hz5ump: Move to a 17 minute timeout to tests step of main workflow * CU-2hz5ump: Add a 10 minute timeout for multiprocessing DeID tests * Revert "CU-2hz5ump: Add a 10 minute timeout for multiprocessing DeID tests" This reverts commit 5e22334. * CU-2hz5ump: Add a 3 minute timeout (through a decorator) to multiprocessing DeID tests * CU-2hz5ump: Remove overly strict DeID test * CU-2hz5ump: Add condition for number of results for multiprocessing DeID test
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Prepare for patch release.