Code

CU-8694gzbn3 k fold metrics#432

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mart-r merged 55 commits intomasterCogStack/MedCAT:masterfrom CU-8694gzbn3-k-fold-metricsCogStack/MedCAT:CU-8694gzbn3-k-fold-metricsCopy head branch name to clipboardJun 19, 2024

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Commits

Commits on May 8, 2024

• CU-8694gzbud: Add context manager that is able to snapshot CDB state

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• CU-8694gzbud: Add tests to snapshotting CDB state

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• CU-8694gzbud: Refactor tests for CDB state snapshotting

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• CU-8694gzbud: Remove use of deprecated method in CDB utils and use non-deprecated one instead

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• CU-8694gzbud: Add tests for training and CDB state capturing

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• CU-8694gzbud: Small refactor in tests

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• CU-8694gzbud: Add option to save state on disk

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• CU-8694gzbud: Add debug logging output when saving state on disk

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• CU-8694gzbud: Remove unused import

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Commits on May 9, 2024

• CU-8694gzbud: Add tests for disk-based state save

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• CU-8694gzbud: Move CDB state code to its own module

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• CU-8694gzbud: Remove unused import

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• CU-8694gzbud: Add doc strings to methods

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• CU-8694gzbx4: Small optimisation for stats

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Commits on May 10, 2024

• CU-8694gzbx4: Add MCTExport related module

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• CU-8694gzbx4: Add MCTExport related tests

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• CU-8694gzbx4: Add code for k-fold statistics

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• CU-8694gzbx4: Add tests for k-fold statistics

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• CU-8694gzbx4: Add test-MCT export with fake concepts

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• CU-8694gzbx4: Fix a doc string

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• CU-8694gzbx4: Fix types in MCT export module

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• CU-8694gzbx4: Fix types in k-fold module

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• CU-8694gzbx4: Remove accidentally committed test class

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Commits on May 11, 2024

• CU-8694gzbn3: Add missing test helper file

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• CU-8694gzbn3: Remove whitespace change from otherwise uncahnged file

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• CU-8694gzbn3: Allow 5 minutes longer for tests

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• CU-8694gzbn3: Move to python 3.8-compatible typed dict

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Commits on May 12, 2024

• CU-8694gzbn3: Add more time for tests in worklow (now 30 minutes)

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Commits on May 13, 2024

• CU-8694gzbn3: Add more time for tests in worklow (now 45 minutes)

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• CU-8694gzbn3: Update test-pypi timeout to 45 minutes

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• CU-8694gzbn3: Remove timeout from unit tests in main workflow

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• CU-8694gzbn3: Make tests stop upon first failure

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• CU-8694gzbn3: Fix test stop upon first failure (arg/option order)

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• CU-8694gzbn3: Remove debug code and old comments

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• CU-8694gzbn3: Remove all timeouts from main workflow

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Commits on May 14, 2024

• CU-8694gzbn3: Remove more old / useless comments in tests

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• CU-8694gzbn3: Add debug output when running k-fold tests to see where it may be stalling

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• CU-8694gzbn3: Add debug output when ANY tests to see where it may be stalling

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• CU-8694gzbn3: Remove explicit debug output from k-fold test cases

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• CU-8694gzbn3: Remove timeouts from DEID tests in case they're the ones creating issues

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Commits on May 16, 2024

• GHA/test fixes (#437)

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• CU-8694gzbn3: Remove legacy / archived / unused tests

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• Merge branch 'master' into CU-8694gzbn3-k-fold-metrics

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Commits on May 22, 2024

• Merge branch 'master' into CU-8694gzbn3-k-fold-metrics

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• CU-8694gzbn3: Add doc strings for FoldCreator init

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Commits on May 24, 2024

• Merge branch 'master' into CU-8694gzbn3-k-fold-metrics

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• CU-8694gzbn3: Move to a split-type enum

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• CU-8694gzbn3: Add documentation to split-type enum

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• CU-8694gzbn3: Create separate fold creators for different types of splitting strategies

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• CU-8694gzbn3: Resort document order in test time nullification process

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• CU-8694gzbn3: Add option to count number of annotations in doc for MCT export

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• CU-8694gzbn3: Add weighted documents based split option along with relevant tests

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• CU-8694gzbn3: Update default fold creation split type to weighted documents

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• CU-8694gzbn3: Add test to ensure weighted documents split creates a reasonable number of annotations per split

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Commits on Jun 19, 2024

• Merge branch 'master' into CU-8694gzbn3-k-fold-metrics

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