pirl-unc / mhcgnomes

90%

main: 89%

LAST BUILD ON BRANCH fix-mhcseqs-parse-failures

branch: fix-mhcseqs-parse-failures

CHANGE BRANCH

x

Reset

Sync Branches

• fix-mhcseqs-parse-failures
• 3.18.0-mhcseqs-wishlist
• add-agents-md
• add-intermediate-clade-nodes
• add-mkdocs-gh-pages
• add-species-and-gene-aliases
• add-species-fix-genes
• add-unknown-species-batch
• archosaur-gene-expansion
• batch-add-species-v3-23
• batch-species-and-genes
• batch-species-intermediate-taxa
• combined-v3.12.0
• curate-more-mhcseqs-obvious-cases
• docs-links-and-references
• docs-pages-release-artifacts
• docs-reorg-v3.14.1
• fill-clade-gaps-numbered-loci
• finish-todo-list
• fix-class2-pairing-non-human
• fix-gene-class-misannotations
• fix-mhc-roman-numeral-and-dot-aliases
• fix-mhcseqs-residual-patterns
• fix-missing-allele-ontology
• fix-parsing-bugs-v3.30.0
• fix-remaining-gene-gaps
• fix-remaining-genes
• fix-remaining-parser-leaks
• fix-species-strict-v3.9.1
• fix-sticky-species-parsing
• fix-tree-gaps-v3.12.1
• immutable-data-objects
• ingest-mhcseqs-genes
• main
• mhcseqs-gap-compat
• more-species-and-aliases
• normalize-allele-field-widths
• novel-prefix-4x4-standard
• ontology-audit-fixes
• ontology-cleanup
• ontology-provenance-dedup
• paper-scraping-tools
• parse-mouse-mhc-class2-variants
• plan-nonmammal-mhc-expansion
• preserve-wip-app-and-tasks
• release-on-tag-trusted-publishing
• saha-dft2-alleles
• species-latin-name-identity
• taxonomy-cleanup-v3.13.0
• todo-cleanup-and-chicken
• v2.0
• v2.0.2
• v2.0.3
• v2.0.4
• v2.0.5
• v2.0.6
• v2.0.7
• v2.0.8
• v2.0.9
• v3.0.0
• v3.0.1
• v3.0.2
• v3.1.0
• v3.1.1
• v3.14.0-species-genes
• v3.2.0
• v3.3.0
• v3.4.0

Build # 23144667940

Build Type

Pull #36

github

Committed by iskandr

Commit Message

Reconcile registry status with runtime, document provenance gaps

Fix finding #1 from code review: Sica, Anca, and Ansa registry entries
said partial_capture_only but are already in runtime. Update:
- Sica: capture_status → runtime_ready (has DAA/DAB in species.yaml)
- Anca/Ansa: ontology_status → runtime_added_species_only,
  capture_status → runtime_ready (species-only placeholders)
- Clarify that blockers apply to expanding these entries, not to their
  existing runtime presence.

Add provenance and curation gap items to TODO from code review
findings #2 and #3 (machine-readable provenance, gene alias
provenance, CI checks for source documentation).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Pull Request Pull Request #36: Expand nonmammal MHC ontology and fix mhcseqs parse failures

Coverage Stats

2970 of 3299 relevant lines covered (90.03%)

0.9 hits per line