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fix: normalize supporting study provenance - #111

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SkyeAv merged 2 commits into
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remove-yaml-auto-annotations
Aug 24, 2026
Merged

fix: normalize supporting study provenance#111
SkyeAv merged 2 commits into
mainfrom
remove-yaml-auto-annotations

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@SkyeAv

@SkyeAv SkyeAv commented Aug 24, 2026

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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 scoped row:<N> results.

Supporting-study provenance

  • Identity: Study.id uses the publication CURIE or config stem; Study.name uses the worksheet/source filename.
  • Metadata: Canonical study_* fields are emitted on Study; legacy aliases remain accepted.
  • Results: StudyResult.id is row:<N> with no generated name. Contentless unpublished studies are omitted.
  • Compatibility: Duplicate study-size aliases are dropped to prevent provenance leakage.

Biolink 4.4.4

  • Derives field ownership and enums from the installed model.
  • Emits effect_size as numeric and significance qualifiers as bare enum tokens.
  • Adds explicit openpyxl test dependency and updates uv.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:cacheprovider1023 passed, 38 skipped
  • uv run pre-commit run --all-files → passed
  • uv run pre-commit run --all-files --hook-stage pre-push → passed, including Pyright and Clippy
  • uv lock --check → passed
  • cargo fmt --manifest-path rust/Cargo.toml --check → passed

cargo test remains blocked locally by a stale Nix linker-wrapper path; no Rust files changed.

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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
@SkyeAv
SkyeAv merged commit 99099a1 into main Aug 24, 2026
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@SkyeAv
SkyeAv deleted the remove-yaml-auto-annotations branch August 24, 2026 17:10
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