test: real-world config corpus and production-pattern runtime tests - #112
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Vendor 14 sanitized production configs from MultiomicsNext (.tablassert mokg-v12/refconfigs), DAKP (tables/), and TableConfigs (FLAKASSIST/MBKG/ MOKG) under tests/fixtures/realworld, plus two legacy negative fixtures (QI-era keys, pre-rig graph layout). tests/test_realworld_configs.py validates the vendored corpus with the same recipe as test_docs_examples.py, asserts the negative fixtures are rejected with the expected legacy-key errors, pins production-observed semantics (DAKP override/split_by/nullable qualifier, unpaired effect_size drop, YAML anchor provenance, multi-section expansion, full RIG), and adds an env-gated sweep (TABLASSERT_CONFIG_CORPUS) that validates ~480 live production configs in place. One known-legacy failure (TableConfigs MOKG MIN1.yaml duplicate qualifier) is pinned strict-both-ways. tests/test_production_patterns.py adds pipeline/e2e coverage, shaped after named production configs, for features that previously had only model/op-level tests: enum-ranged qualifier literals bypassing resolution, explode-before-prefix op order, provenance.override URL rehoming in emitted KGX, reindex across all six comparisons plus default-ne, regex capture-group backrefs and qualifier-level regex, avoid/prioritize deciding ambiguous resolution, fill forward/zero, copysign transformation, suffix, nullable+prioritize+avoid qualifier combo, partial-node template merge, and row_slice at e2e level.
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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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Summary
Upgrades the test suite with production-driven coverage, mined from the real-world config corpora (MultiomicsNext
.tablassert, DAKPtables/, TableConfigs FLAKASSIST/MBKG/MOKG):tests/test_realworld_configs.py(22 tests) — a vendored corpus of 14 sanitized production configs undertests/fixtures/realworld/(everylocal:rewritten to a placeholder; provenance in the fixture README), validated with the same recipe astest_docs_examples.py. Includes deliberate-negative legacy fixtures (QI-erasyntax/status/contributorskeys, pre-riggraph layout) and targeted semantic assertions: DAKPprovenance.overridewith per-inforesupstream_source_record_urls,split_by: "|"annotations, nullabledisease_context_qualifier, unpairedeffect_sizedrop, YAML-anchor provenance sharing, multi-section expansion, and a fully populated RIG graph config. An env-gated sweep (TABLASSERT_CONFIG_CORPUS) validates ~480 live production configs in place; the one known-legacy failure (TableConfigsMOKG/MIN1.yaml, duplicate qualifier after template merge, superseded by its own v12 conversion) is pinned strict-both-ways inKNOWN_CORPUS_FAILURES.tests/test_production_patterns.py(18 items) — pipeline/e2e tests against a real inline Rust fullmap for features production configs use that previously had only model/op-level coverage: enum-ranged qualifier literals bypassing resolution, explode-before-prefix op order,provenance.overrideURL rehoming in emitted KGX,reindexacross all six comparisons plus default-ne, regex${1}backrefs and qualifier-level regex,avoid/prioritizedeciding ambiguous resolution,fillforward/zero,copysigntransformation,suffix, the nullable+prioritize+avoid qualifier combo, partial-node template merge, androw_sliceat e2e level. Each test names the production config it is shaped after.Findings surfaced while mining the corpora (no action taken): all 56 TableConfigs QI configs and both
GRAPH/*.yamlare legacy-incompatible with the 12.x schema;row_sliceis 0-based-offset; CURIE value literals need a fullmap synonym row to resolve; qualifier slot attachment is edge-class-dependent.Test plan
uv run pytest -q— 975 passed, 38 skippedTABLASSERT_CONFIG_CORPUS— all pass except the pinned known-legacy MIN1.yamluv run ruff check ./ruff format --check ./uv run pyright— clean