NEWS

ducksemantics 0.2.1

Kept Monarch array-provenance tests on DuckDB's native list values rather than autoloading the optional json extension, so offline checks remain portable.

Added ducksemantics_monarch_project_pack() for narrow, read-only, connection-local projections of an already attached exact dated Monarch annotation pack. It validates the official pack shape—including Monarch's serialized text negation and node/phenotype/IC tables—and an exact typed provider/release binding, preserves edge/provenance fields and arrays, and exposes explicit normalized-role statuses without downloads, copies, merges, ranking, or causal defaults.
Updated the public package origin to RGenomicsETL/ducksemantics.

Sealed package ownership around ontology graphs, validated HPO observations, typed release-cataloged Monarch relations, snapshot-catalog-bound literature retrieval, and source-grounded semantic/provider protocols.
Added the final relational HPO observation contract. It validates exact, non-empty zero-based half-open source spans and records context, method, provider identity/version, confidence, and explicit accepted status.
Added caller-supplied Monarch gene-phenotype/gene-disease facts with a required typed provider/release catalog. Exact and Date/order as-of queries reject unknown releases; historical gene-disease holdouts are provenance-preserving anti-join audits.
Literature retrieval now consumes RClinVarbitration's caller-owned append-only source-order projection: cataloged integer cutoffs select the latest article event, discard latest deletion events, and join exact same-version sections before returning source spans. ducksemantics neither imports nor stores literature relations.
Removed ducksemantics benchmark APIs (owned by VariantStoryBench), generic cache APIs, and S7 wrappers for relations, connections, matrices, batches, queries, indexes, and clustering specifications. Embedding and reranking now use ordinary data frames, matrices, and scalar arguments.