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Fix crashes and mismatches in PhylorefWrapper and PhylogenyWrapper on edge-case input - #196

Merged

gaurav merged 17 commits into

masterfrom

fix-wrapper-edge-cases

Nov 10, 2026

Merged

Fix crashes and mismatches in PhylorefWrapper and PhylogenyWrapper on edge-case input#196
gaurav merged 17 commits into
masterfrom
fix-wrapper-edge-cases

Commits on Oct 14, 2026
- Let setSpecifierType make a specifier external on a phyloref with no lists
  
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- Match expectedPhyloreferenceNamed exactly when it is a single name
  
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- Report a draft when a phyloref's last status entry records no status
  
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  d6e8a73
- Name the node of a single-node phylogeny
  
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- Apply a phylogeny's default nomenclatural code to its nodes' taxonomic units
  
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- Default TaxonomicUnitWrapper to owlterms.UNKNOWN_CODE
  
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- Add PR #196 to the changelog
  
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- Don't match an unlabelled phyloref to nodes with no expected name
  
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- Show the single-name form in the expectedPhyloreferenceNamed substring test
  
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- Report a phyloref's last recorded status, skipping entries that record none
  
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- Read a pso:holdsStatusInTime that is a single entry rather than a list
  
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- Don't add an empty specifier list in setSpecifierType
  
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- Name every parsed Newick node in one place
  
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- Fill in a phylogeny's default nomenclatural code on its nodes' taxonomic units
  
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  e7d207f
- Describe PR #196's review fixes in the changelog
  
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  c8d6c51
- Note where setStatus and getCurrentStatus disagree about statusless entries
  
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  b62d77a
Commits on Nov 9, 2026
- Merge master into fix-wrapper-edge-cases
  
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  e577d4e

Commits

Commits on Oct 14, 2026

Commits on Nov 9, 2026