CU-2e77a31 improve print stats #366
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tomolopolis
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Dec 4, 2023
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Is this largely a straight copy / paste from cat._print_stats into stats?
Does this still produce the same results as the working_with_cogstack w & w/o the change.
Good to merge in if so. Also I noticed CogStack/working_with_cogstack#7 is pretty much rready to go. Should that be merged first?
It should be. For the test that I added, I ran the method with the previous code and used the output from that in the test.
Anthony had a question about that. Didn't fully understand what he was referring to, though. |
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I ran some tests with a bunch of models (SNOMED, UMLS, as well as HPO). Some details of this can be seen in here: |
mart-r
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Jan 8, 2024
* 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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This is my first attempt at improving the
CAT._print_statsmethod.It moves the stats gathering / printing code to a separate module.
It also separates the long method into multiple shorter ones to improve maintainability.
On top of that, I added a small test for it as well.
PS:
There may very well be issues with the PR, so feedback is more than welcome.