fix: remove duplicate retrieval-source identifiers - #115
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Cut 14.0.0 and bump the package version in pyproject.toml, uv.lock, and CITATION.cff. Major: one breaking change since 13.0.0. Generated edges no longer duplicate each nested `sources` entry's provenance identifier into `sources[].id`; `resource_id` is now the sole identifier on a retrieval-source entry (#115). The pinned Biolink model still requires the inherited `Entity.id` on `RetrievalSource`, so the validator supplies it to an in-memory compatibility copy only, and neither the decoded record nor the written NDJSON carries it. Also ships the explicit retrieval-`sources` template with `{edge_id}` record-URL interpolation (#116) and the negative-log p-value un-logging fix (#114). Changelog: - The Unreleased section was missing #116 entirely; added it under `Added`, and gave the two existing entries their PR links plus a reader migration note for the `sources[].id` removal. Docs: - `docs/configuration/table.md`'s automatic-coercion section documented neither half of #114: added a `Negative-log P value` row to the recognition table and a bullet covering the un-logging (`p = 10 ** -x` on rename and on banding), the complete-token requirement, the deliberate pass on unmarked `log10` spellings, raw-beats-alias selection, and the Float64 underflow floor. Every documented spelling was checked against `is_neglog10_column` and `pvalue_target`. - `docs/cli.md`'s validate-kgx section explained the pending-field count but not the mirror case #115 introduced; added the `RetrievalSource` compatibility alias, including that it stops being applied once a model release drops the requirement. - Removed the five em-dashes #115 and #116 reintroduced into the two doc pages, restoring the docs-wide convention set in abb042a. Known gap, deliberately not fixed here: `PVALUE_TOKEN_PATTERN` anchors on `\b`, which does not fire after an underscore, so `raw_pvalue` / `adj_pvalue` / `fdr_pvalue` / `negative_log10_pvalue` are not recognized as p-value columns at all, even though the same names with a separated token (`gene_p_value`) and the bare-P forms (`raw_p`) are. It predates this window and changing recognition would shift behavior for existing configs, so it wants its own PR. Testing: - uv run pytest -q -> 1078 passed, 15 skipped (94% coverage) - uv run ruff check . && uv run ruff format --check . && uv run pyright -> clean / 0 errors - uv lock --check -> up to date - uv run mkdocs build --strict -> clean Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01RRefj7KvacA9PGQYMCt6wy
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Generated
sourcesentries now retainresource_idas their sole provenance identifier; the duplicate nestedidis removed without changing legitimate study/result IDs. Validation remains compatible with the pinned Biolink model by adding the inherited alias only to an in-memory validation copy, and the migration is documented.Fixes
resource_id,resource_role, and provenance URL/upstream fields withoutsources[].id.id.CHANGELOG.md.Testing
uv run pytest tests/test_biolink.py tests/test_lib.py -k 'retrieval_sources or source_record_urls or compile_graph_emits_ndjson or build_pipeline_e2e_smoke or resource_id_only' -q→ 5 passeduv run pytest tests/test_lib.py tests/test_biolink.py tests/test_rig.py tests/test_cover_lib.py tests/test_e2e_smoke.py -q→ 287 passed; 1 pre-existing QC-extra failure (scikit-learn/sentence-transformersunavailable)uv run ruff check src/tablassert/lib.py src/tablassert/biolink.py tests/test_lib.py tests/test_biolink.py tests/test_rig.py tests/test_cover_lib.py→ passeduv run pyright src/tablassert/lib.py src/tablassert/biolink.py→ 0 errors