Cu 8693u6b4u tests continue on fail #400
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Task linked: CU-8693u6b4u GHA continues on test failure |
mart-r
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mart-r
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* Cu 8693u6b4u tests continue on fail (#400) * CU-8693u6b4u: Make sure failed/errored tests fail the main workflow * CU-8693u6b4u: Attempt to fix deid multiprocessing, at least for GHA * CU-8693u6b4u: Fix small docstring issue * CU-8693v3tt6 SOMED opcs refset selection (#402) * CU-8693v3tt6: Update refset ID for OPCS4 mappings in newer SNOMED releases * CU-8693v3tt6: Add method to get direct refset mappings * CU-8693v3tt6: Add tests to direct refset mappings method * CU-8693v3tt6: Fix OPCS4 refset ID selection logic * CU-8693v3tt6: Add test for OPCS4 refset ID selection * CU-8693v6epd: Move typing imports away from pydantic (#403) * CU-8693qx9yp Deid chunking - hugging face pipeline approach (#405) * Pushing chunking update * Update transformers_ner.py * Pushing update to config Added NER config in cat load function * Update cat.py * Updating chunking overlap * CU-8693qx9yp: Add warning for deid multiprocessing with (potentially) non-functioning chunking window * CU-8693qx9yp: Fix linting issue --------- Co-authored-by: mart-r <[email protected]> --------- Co-authored-by: Shubham Agarwal <[email protected]>
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I added
continue-on-error: trueto the main workflow tests step for testing purposes, but looks like I've not removed it before merging.So now, tests will be marked "passed" regardless of whether or not they fail in GHA.
This PR removed that from the tests in the main workflow.
However, that still remains issues with the deid pipline which fails in multiprocessing.
So I've devised a way to (hopefully) force the installation of cpu-only torch for the deid tests.
Because this now means that without change the deid multiprocessing tests fail, I've also tackled that.
What this PR does is, for the deid multiprocessing test case, set the number of threads to 1 on
torch.PS: The test runs fine without that locally. But stalls on Actions. So I don't really fully know what's the issue.