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Feat/duckdb classification - #51
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What changed in this PR
Adds DuckDB support for relationship classification and graph use, integrating an optional dependency extra with the existing database configuration and ORM models.
Changes:
- Adds a DuckDB-compatible predicate enum while preserving native enums elsewhere.
- Adds disposable DuckDB test fixtures and integration coverage for classification, constraints, and idempotency.
- Documents DuckDB installation and updates dependencies.
| File | Description |
|---|---|
uv.lock |
Locks DuckDB dependencies and updates optional extras. |
tests/test_relationship_classification_duckdb.py |
Tests classification results, enum constraints, and repeat execution. |
tests/conftest.py |
Adds a disposable DuckDB fixture and shares database setup logic. |
src/omop_graph/extensions/omop_alchemy.py |
Uses a constrained VARCHAR-backed predicate enum on DuckDB. |
src/omop_graph/config.py |
Adds a DuckDB test database configuration field. |
README.md |
Documents installation with the DuckDB extra. |
pyproject.toml |
Adds the DuckDB extra and includes it in development dependencies. |
docs/usage/installation.md |
Adds DuckDB installation instructions for pip and uv. |
Review effort: Balanced
nicoloesch
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Nov 7, 2026
Pulls in DuckDB classification support (#51). Resolved the conflict in extensions/omop_alchemy.py by keeping this branch's CDMExtensionTableBase inheritance while adopting main's DuckDB-safe _predicate_kind_enum(), parameterized on schema instead of hardcoding Role.PRIMARY. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
Adds duckdb graph support
Checklist
breaking,feature,fix,dependencies, orchore)uv run pytest -q)uv run ruff check .)