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Pull Request Overview
This PR upgrades the project to MEDS v0.4 and updates all references to legacy fields and schema objects (e.g. subject_id_field, time_field) to use the new DataSchema, SubjectSplitSchema, and CodeMetadataSchema. It also updates configuration examples and dependency versions accordingly.
- Updated imports and field references throughout stages (reshard_to_split, extract_values, bin_numeric_values, etc.) to use the new MEDS v0.4 schema.
- Adjusted examples and configuration in tests and documentation to reflect dependency and API changes.
- Upgraded dependency versions in pyproject.toml for meds and meds_testing_helpers.
Reviewed Changes
Copilot reviewed 14 out of 14 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| src/MEDS_transforms/stages/reshard_to_split/reshard_to_split.py | Replaced legacy field names with new DataSchema/SubjectSplitSchema references and updated sorting keys. |
| src/MEDS_transforms/stages/extract_values/extract_values.py | Updated mandatory types and casting expressions to use DataSchema fields. |
| src/MEDS_transforms/stages/examples.py | Revised example usage to instantiate DatasetMetadataSchema instead of a plain dict. |
| src/MEDS_transforms/stages/bin_numeric_values/bin_numeric_values.py | Changed field references and join column names to their new schema counterparts. |
| src/MEDS_transforms/stages/aggregate_code_metadata/aggregate_code_metadata.py | Switched subject id references to DataSchema.subject_id_name for aggregation consistency. |
| src/MEDS_transforms/stages/add_time_derived_measurements/* | Updated multiple modules to consistently refer to MEDS v0.4 fields for time, subject id, and code. |
| src/MEDS_transforms/mapreduce/stage.py | Adjusted filtering and merge functions to use the new schema definitions. |
| src/MEDS_transforms/configs/dataset.py | Updated dataset metadata handling to use DatasetMetadataSchema and its API. |
| src/MEDS_transforms/compute_modes/match_revise.py | Updated sorting and field references in match-revise functions to use DataSchema. |
| pyproject.toml | Upgraded dependency versions to use meds~=0.4.0 and meds_testing_helpers~=0.3.0. |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #323 +/- ##
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Coverage 100.00% 100.00%
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Files 54 54
Lines 2397 2401 +4
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+ Hits 2397 2401 +4 ☔ View full report in Codecov by Sentry. |
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Closes #322