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Add trainer callbacks for Transformer NER #377

Merged
merged 2 commits into from
Dec 5, 2023
Merged

Add trainer callbacks for Transformer NER #377

merged 2 commits into from
Dec 5, 2023

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baixiac
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@baixiac baixiac commented Dec 4, 2023

This PR enables the client side to collect metrics during the training on the Transformers NER model.

@tomolopolis
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Task linked: CU-86938vf30 Enable client-side to collect metrics during Transformers NER training

mart-r
mart-r approved these changes Dec 5, 2023
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The PR looks good to me.

Do we want to have some part of the tutorials to cover this use case as well?
Currently I don't think there's anything that uses TransformersNER explicitly in the tutorials?
In any case, not a necessity but rather food for thoughts.

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baixiac commented Dec 5, 2023

Good point. Given the sole use case ATM is the De-ID, that could be added to the upcoming tutorial when the model has a GA release.

@baixiac baixiac merged commit 7fddac0 into master Dec 5, 2023
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@baixiac baixiac deleted the CU-86938vf30 branch December 5, 2023 17:36
mart-r added a commit that referenced this pull request Jan 8, 2024
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@tomolopolis @adam-sutton-1992 @baixiac @jenniferjiangkells
v1.10.0 (#388)
4e618aa 
* Bump urllib3 from 1.26.5 to 1.26.17 in /webapp/webapp

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]>

* Cu 8692wbcq5 docs builds (#359)

* 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

* Bump urllib3 from 1.26.17 to 1.26.18 in /webapp/webapp

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]>

* CU-8692uznvd: Allow empty-dict config.linking.filters.cuis and convert 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 separate config on save (#350)

* 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

* CU-2cdpd4t: Unify default addl_info in different methdos. (#363)

* Bump django from 3.2.20 to 3.2.23 in /webapp/webapp

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]>

* Changing cdb.add_concept to a protected method

* Re-added deprecated method  with deprecated flag and addtional comments

* 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

* CU-86931prq4: Update GHA versions (checkout and setup-python) to v4 (#368)

* Cu 1yn0v9e duplicate multiprocessing methods (#364)

* 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

* 869377m3u: Add comment regarding demo link load times to README (#376)

* intermediate changes of merge_cdb and testing function

* Added README.md documentation for CPU only installations (#365)

* 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 no preferred name (#367)

* 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

* Add trainer callbacks for Transformer NER (#377)

CU-86938vf30 add trainer callbacks for Transformer NER

* changes to merge_cdb and adding unit tests for method

* fixing lint issues

* fixing flake8 linting

* bug fixes, additional tests, and more documentation

* moved set up of cdbs to be merged to tests.helper

* moved merge_cdb to utils and created test_cdb_utils

* removed class wrapper in cdb utils and fixed class set up in tests

* changed test object setup to class setup

* removed erroneous new line

* CU-2e77a31 improve print stats (#366)

* 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

* Load stopwords in Defaults before spacy model

* CU-8693az82g Remove cdb tests side effects (#380)

* 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

* Added tests

* CU-8693bpq82 fallback spacy model (#384)

* 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

* Remove tests of internals where possible

* Add test for skipping of stopwords

* Avoid supporting only English for stopwords

* Remove debug output

* Make sure stopwords language getter works for file-path spacy models

* CU-8693cv3w0 Fix fallback spacy model existance on pip installs (#386)

* 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 get spacy model version (#381)

* 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

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: tomolopolis <[email protected]>
Co-authored-by: adam-sutton-1992 <[email protected]>
Co-authored-by: adam-sutton-1992 <[email protected]>
Co-authored-by: Xi Bai <[email protected]>
Co-authored-by: jenniferajiang <[email protected]>
Co-authored-by: Jennifer Jiang <[email protected]>
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@baixiac @tomolopolis @mart-r