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linkml/linkml-reference-validator: v0.2.0rc1

Authors: Chris Mungall; Dragon-AI Agent; Reasat; Harry Caufield; Claude;

linkml/linkml-reference-validator: v0.2.0rc1

Abstract

Summary This is the first 0.2.0 release candidate. The main change in this RC is configurable preservation of literal square-bracket text in supporting-text validation via literal_bracket_patterns. Highlights add literal_bracket_patterns to ReferenceValidationConfig keep default behavior unchanged when no patterns are configured allow downstream projects to preserve bracketed source text such as [IL-6], [2Fe-2S], [i(12p)], and similar corpus-specific notation document the new configuration option and add validator/config/model coverage Why this is an RC Bracket handling is corpus-specific. The feature is ready for downstream testing, but projects should treat this RC as a configuration-tuning period before 0.2.0 final. Edge Cases Found During In-Situ Testing We tested this RC candidate in an isolated dismech worktree using its real just validate-references-all workflow and a local path override to this exact validator commit. Findings: the worktree setup successfully exercised the local linkml-reference-validator checkout in situ a full dismech reference-validation sweep completed with only 3 remaining errors total one class of desired cases includes literal scientific brackets such as [IL-6] one class of problematic cases includes editorial notes that also contain identifiers or digits, for example [sic, correct designation is R501X] Implication: broad rules like \d can be too permissive for some corpora even more conservative rules can still preserve editorial notes if those notes contain variant names or other alphanumeric identifiers downstreams should choose project-specific patterns carefully and validate them against real corpora before adopting them broadly Suggested Downstream Rollout pin exactly 0.2.0rc1 or an explicit prerelease range for testing start with conservative literal_bracket_patterns run the validator against real project data in an isolated worktree or branch before promoting to wider use Validation just test local build from tag produced linkml_reference_validator-0.2.0rc1.tar.gz and linkml_reference_validator-0.2.0rc1-py3-none-any.whl in-situ dismech run via just validate-references-all Notes for Downstreams No configuration change is required unless a project wants to preserve literal bracketed text. If no literal_bracket_patterns are configured, behavior remains backward compatible.

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