fix: normalize supporting study provenance - #111
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…tations # Conflicts: # docs/agent.md # docs/cli.md # docs/configuration/advanced-example.md # docs/configuration/table.md # src/tablassert/lib.py
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Moves supporting-study output to Biolink 4.4.4 Study metadata, removes synthesized
#identities and row names, and preserves provenance with scopedrow:<N>results.Supporting-study provenance
Study.iduses the publication CURIE or config stem;Study.nameuses the worksheet/source filename.study_*fields are emitted onStudy; legacy aliases remain accepted.StudyResult.idisrow:<N>with no generated name. Contentless unpublished studies are omitted.Biolink 4.4.4
effect_sizeas numeric and significance qualifiers as bare enum tokens.openpyxltest dependency and updatesuv.lock.Documentation
Updated README, CLI/configuration docs, tutorials, examples, agent prompts, tests, and
CHANGELOG.md.Testing
uv run pytest tests/ -q --no-header -p no:cacheprovider→ 1023 passed, 38 skippeduv run pre-commit run --all-files→ passeduv run pre-commit run --all-files --hook-stage pre-push→ passed, including Pyright and Clippyuv lock --check→ passedcargo fmt --manifest-path rust/Cargo.toml --check→ passedcargo testremains blocked locally by a stale Nix linker-wrapper path; no Rust files changed.