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

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.