feat: assert every node has an id and every edge has subject, predicate, and object in final graph QC - #107
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Cut 13.0.0 and bump the package version in pyproject.toml, uv.lock, and CITATION.cff. Major: three breaking changes since 12.1.0. The inlined supporting study now carries current Biolink Study metadata with disjoint ids and names and no `#` composition; biolink-model 4.4.4 types the statistical edge slots, so `effect_size` ships as a real JSON number and `statistical_significance_qualifier` rides the edge as a bare enum token (both 99099a1); and an unpaired `effect_size`/`effect_type` half is now DROPPED with an `UnpairedEffectAnnotationWarning` instead of failing the section, retiring the `annotation-effect-size-without-type` / `annotation-effect-type-without-size` codes (#105). Also ships the two final-graph QC assertion sets (#106, #107), the resolve_batch single-materialization win (#110), and the agent's task pre-rendering, planning-off, improve-round cap, and build memoization (#113). The legacy TableConfigs importer (#105) is deliberately absent from the changelog: it landed and was removed (58787f4) inside this window, so it never appeared in a released version and is a net no-op for users. main was red at 7140c37; fixed here so the release is cuttable. Both failures are #112 fixtures/expectations written against biolink-model 4.4.3 and merged after the 4.4.4 bump landed: - The vendored DAKP configs listed `AffinityMeasurement` in `avoid:`, a class 4.4.4 renamed to `ProteinLigandAssayResult`. DAKP generates `avoid` as the sorted complement of each side's prioritize tuple, so the old name is a 4.4.3 generation artifact rather than an intentional deviation; rewritten in place and recorded in the fixture README. - test_copysign_transformation_in_pipeline asserted `effect_size == "-0.85"`, the pre-4.4.4 `{:.4g}` string form. It is a real JSON number now. Deliberate Biolink departures are untouched: p-value columns keep their controlled scientific notation despite the model typing them `float`, and `approval_ids` remains a curated pending pass-through. docs/cli.md's validate-kgx section still printed `biolink-model 4.4.3` and claimed `effect_size`/`effect_type` were pending; rewritten around the fields that are actually pending today (`approval_ids` plus the KGX denormalized carryovers), noting the pair graduated when 4.4.4 shipped #1774. Testing: - uv run pytest -q -> 1047 passed, 15 skipped (94% coverage) - uv run ruff check . && uv run ruff format --check . && uv run pyright -> clean / 0 errors Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01HZQ8rLfhvtyErcq9S4Ao6b
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The
--qcstage-7 study pass now asserts the core KGX join slots outright: every node must carry a non-emptyid, and every edge must carry non-emptysubject,predicate, andobject— completing the required-slot ladder begun by #106'sunnamed-nodes.Study assertions (
src/tablassert/study.py)unidentified-nodes: a node record whoseidkey is missing,null, or strips to empty fails the study. Since the id is exactly what's absent, examples key on the node'sname(or<no name>), making the offender identifiable from the stderr summary.incomplete-edges: an edge record missing any of the three core slots — missing key,null, or strips-to-empty — fails, counted per slot (e.g.predicate (2)), matching thewhitespace-valuesexample format.namealready asserted by feat: assert no unnamed nodes and no null or empty values in final graph QC #106'sunnamed-nodes; that check is untouched. A record with neither id nor name deliberately fires both assertions (pinned by test).Design
strip_nulls(rust/src/json.rs) deletes a null slot outright rather than emitting it, so on pipeline output a hit means the slot was null upstream and the record shipped broken — exactly the condition these assertions exist to catch loudly.Docs
docs/cli.md(--qcrow), thebuild_kgdocstring insrc/tablassert/cli.py(rendered by--help), andCHANGELOG.md(Unreleased).Testing
uv run --no-sync pytest -q --no-cov→1056 passed, 15 skippeduv run --no-sync pytest tests/test_study.py --no-cov -q→28 passeduv run --no-sync ruff check+ruff format --check→ clean;uv run --no-sync pyrighton changed files →0 errors