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feat!: fold validate-infores into validate-kgx - #218
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SkyeAv
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Oct 15, 2026
Cut 21.0.0 and bump the package version in pyproject.toml, CITATION.cff, and uv.lock. Major: two breaking changes ship since 20.0.0. Derived-path builds emit section source record URLs on the upstream repository supporting sources entry (infores:pubmed-central for PMC sections) instead of the primary graph-infores entry, and the inlined supporting Study is named after the table config file plus its 1-based section index (#220); validate-infores is folded into validate-kgx as the knowledge-source identity half, and the standalone validate-infores command is gone (#218). Also adds no_map on NodeEncoding to pass subject/object CURIEs through verbatim (#219) and normalizes documentation prose to plain ASCII (#217). Changelog: - Versioned the Unreleased section as 21.0.0 - 2026-10-15. - Added the missing #218 (breaking, with migration note), #219, and #217 entries so no merged PR ships unmentioned. Docs: none needed here; the release commit only versions existing prose. Testing: - make check -> ruff clean, pyright 0 errors, pytest 1239 passed + 1 skipped, cargo test ok, cargo clippy --all-targets -- -D warnings clean - uv run mkdocs build --strict -> pass
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tablassert validate-kgxnow also validates knowledge-source identity: every emittedinfores:CURIE is classified against the Translator registry in the same run that checks Biolink structure, and the separatevalidate-inforescommand is gone.Merged command
validate_kgx_command(src/tablassert/cli.py) gains--rig, repeatable--allow-infores,--registry snapshot|refresh|off, and--strict;--nodes/--edges/--limitare shared with the structural half.--strictas the CI gate and--allow-inforesfor locally minted CURIEs.--registry offskips identity entirely, reproducing the old structure-onlyvalidate-kgxbehavior in output and exit code.--prune, the identity half classifies the PRUNED edges file, so the verdict describes the artifact that ships.tablassert validate-infores ...becomestablassert validate-kgx ...with the same flags; scripts invoking the old command name must switch.Docs
docs/cli.md: six -> five subcommands, and the oldvalidate-inforessection becomes the "Checking knowledge-source identity" subsection ofvalidate-kgxwith the new flag rows and the prune note.llms.txt: command list updated to the five surviving commands.Testing
tests/test_cli_validate_kgx.py(18 tests): pins the merged contract: advisory default, strict gate, allowlist,--registry offskipping identity, refresh fetch + cache + garbage/empty-body rejection, missing inputs, RIG scan, prune classifying the pruned file, and help rendering every flag.make check: ruff,ruff format --check,uv run pyright(0 errors),uv run pytest(1213 passed, 1 skipped, the pre-existing corpus-gated skip),cargo test, andcargo clippy --all-targets -- -D warningsall pass.uv run mkdocs build --strict: pass.