Categorical Score Calibrations#589

Merged

bencap merged 24 commits intorelease-2025.6.0from

feature/bencap/538/categorical-calibrations

Jan 14, 2026

Commits on Dec 18, 2025

feat: centralized model rebuilding for more maintainable Pydantic circular dependencies
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feat: rebuilt Pydantic models up front for availability within entire module
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feat: add flexible model loader for Pydantic models from JSON body or multipart form data
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feat: Introduce Score Calibration Functional Classification
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feat: remove deprecated functional_ranges_deprecated_json column from ScoreCalibration model
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feat: add variants_for_functional_classification function to filter variants by score range
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feat: add support for class based score ranges
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feat: update standardize_dataframe to accept custom standard columns and adjust related tests
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fix: update inclusive bound checks to allow None values in FunctionalClassificationBase
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refactor: remove default values for inclusive bounds in ScoreCalibrationFunctionalClassification
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feat: add validation and standardization for calibration classes dataframe
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feat: allow creation and modification of class based calibrations
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refactor: replace ValueError with ValidationError for calibration class validation
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feat: add error handling for validation of class files in score calibration creation and modification
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feat: add file presence/absence checks in calibration creation and modification routes
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feat: allow class-based calibration definitions from hgvs_nt and hgvs_pro
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fixup
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feat: don't allow class-based calibrations during score set creatoin
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fix: only check resource existence for index columns
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fix: improperly renamed functional_ranges property in alembic downgrade
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fix: correct index column reference in validation function
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refactor: update calibrated variant effects script for new classification format
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Commits on Dec 30, 2025

fix: use functional classification enum in place of old style strings
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Commits on Jan 14, 2026

fix: remove duplicate score calibration urn idx in migration
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