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@dogversioning dogversioning released this 21 Aug 17:45
· 25 commits to main since this release
v3.0.0
b8c3f5f
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Learn about vigilant mode.

Breaking changes

  • Actions/builders APIs now primarily work from StudyConfig and StudyManifest objects
  • Minimum python is now 3.11
  • Changed _code_system in tables to just _system
  • Replace core__medicationrequest with core__medication, removed previous version
  • Removed core__study_period, offloaded study definitions to downstream studies

Deprecation warning

  • core__observation is now considered deprecated - use a specific observation profile table, if one exists. Once we have more profile coverage, core__observation will be removed.

Major changes

  • Added a generic way to log to a study's transaction table
  • Allow studies to specify their own unique schema (intended for independent data sets, like code systems)
  • Allow studies to specify their own CLI args with --option

Minor changes/bugfixes

  • Several new generic templates & jinja syntax helpers
  • Added StudyManifest, StudyConfig, BaseTableBuilder, and CountsBuilder to the package-level API
  • Use cumulus-fhir-support for reading ndjson
  • Fixed Athena's ability to export "decimal" types
  • Updated CLI to use terms like database and schema in the context of a specific database's nomenclature
  • Added $expand to the UMLS VSAC API, and paginate results
  • clean CLI arg now removes views
  • generate-sql now masks S3 paths in output

Full Changelog: v2.3.0...v3.0.0

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