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v2.9.6: Output cleanups across convert_ids, europepmc_search, fetch_articles, lookup_mesh

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@cyanheads cyanheads released this 18 Jun 12:49
v2.9.6
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cyanheads Casey Hand
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cyanheads Casey Hand
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Output cleanups across convert_ids, europepmc_search, fetch_articles, lookup_mesh

Five output-quality fixes: cleaner inputs accepted, leaked upstream markup stripped, error hints made actionable, and a non-navigable field value filtered.

Fixed:

  • pubmed_convert_ids: canonicalize bare-digit PMCIDs to PMC+digits so a batch mixing prefixed and bare forms resolves instead of 400-ing; format hint corrected (#73)
  • pubmed_europepmc_search: abstractSnippet stripped of JATS/HTML, entity-decoded, and soft-hyphen-cleaned before truncation (#74)
  • pubmed_fetch_articles: grantList fields decode NCBI's residual double-encoded & (CSR&D, not CSR&D) (#74)
  • pubmed_europepmc_search: silent-rejection error now carries a distinct diagnosis vs. recovery hint instead of byte-identical Error:/Recovery: blocks (#75)
  • pubmed_lookup_mesh: treeNumbers drops @-prefixed SCR mapped-heading pointers, keeping only navigable tree numbers (#76)

Dependency bumps:

  • defuddle ^0.18.1 → ^0.19.0
  • fast-xml-parser ^5.8.0 → ^5.9.2
  • vitest ^4.1.8 → ^4.1.9
  • @vitest/coverage-istanbul ^4.1.8 → ^4.1.9

864 tests pass; bun run devcheck clean.

Assets 3
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