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Changelog

metasalmon 0.0.6

  • Added read_github_csv_dir() to read all CSV files from a GitHub directory into a named list, similar to using dir() with lapply() for local files.
  • Supports pattern matching, version pinning, and passes options to read_csv() for all files.
  • Added comprehensive test coverage for the new function.

metasalmon 0.0.5

metasalmon 0.0.4

  • Added ms_setup_github() to guide one-time PAT setup (git check, browser token creation, git credential storage) and verify access to the private Qualark data repository.
  • Added qualark_raw_url() and read_qualark_csv() to build stable raw GitHub URLs and read Qualark CSVs using the stored PAT (with SSO-aware error messages and retry logic).
  • New tests cover URL construction, blob/raw URL normalization, and an opt-in Qualark fetch when a token is configured.

metasalmon 0.0.3

  • Added find_terms() function for searching candidate terms across external vocabularies (OLS, NVS, BioPortal).
  • find_terms() now ranks results deterministically using I-ADOPT role hints from inst/extdata/iadopt-terminologies.csv (preferred vocabularies boosted; ties stable).
  • suggest_semantics() now returns best-effort suggestions (stored in attr(,'semantic_suggestions')) instead of a placeholder message.
  • Added I-ADOPT component fields (property_iri, entity_iri, constraint_iri, method_iri) to dictionary schema and package creation/reading.
  • Enhanced validation: measurement columns now require I-ADOPT components (term_iri, property_iri, entity_iri, unit_iri).
  • Updated table metadata: renamed entity_type/entity_iri to observation_unit/observation_unit_iri for clarity.
  • Added httr package dependency for vocabulary search functionality.
  • Dictionary validation now normalizes optional semantic columns and returns the normalized dictionary.
  • Vignettes now show end-to-end semantic enrichment (I-ADOPT-aware suggestions) and how to align with smn-gpt.

metasalmon 0.0.2

  • Unified semantic fields to term_iri + term_type and reserved concept_scheme_iri for code lists only.
  • Updated GPT collaboration guidance, schemas, and pkgdown outputs to match the new fields.
  • Refreshed vignettes, tests, and reference docs; bumped package version.

metasalmon 0.0.1

  • Initial development snapshot.