Issues

• A job file's text is written as single 30-60 KB lines, so a reading agent cannot open it

  Cellular-Semantics/Atlas-reporter#80 · Filter by author cellsemantic opened on Sep 24, 2026

• Manifest schema overfits table content into fixed categories; free text should carry the description

  Cellular-Semantics/Atlas-reporter#79 · Filter by author cellsemantic opened on Sep 23, 2026

• Supplement indexing reads every sheet, then throws the reading away

  Cellular-Semantics/Atlas-reporter#78 · Filter by author cellsemantic opened on Sep 23, 2026
  1

• Supplement ingest ignores the JATS already on disk when a paper has no PMCID

  Cellular-Semantics/Atlas-reporter#77 · Filter by author cellsemantic opened on Sep 23, 2026

• Evidence records carry their own cell-type identity, and a collector is how they are read back

  enhancement
  Cellular-Semantics/Atlas-reporter#75 · Filter by author cellsemantic opened on Sep 23, 2026

• Extract differential expression at setup, into a store a lookup can query

  enhancement
  Cellular-Semantics/Atlas-reporter#70 · Filter by author cellsemantic opened on Sep 10, 2026

• Retrieving a paper: one skill, a real waterfall, and a route on the record

  enhancement
  Cellular-Semantics/Atlas-reporter#69 · Filter by author cellsemantic opened on Sep 9, 2026

• Add author_annotation_cell_type to the CAS+ annotation object

  Cellular-Semantics/Atlas-reporter#68 · Filter by author ubyndr opened on Sep 9, 2026

• Restricting on composition: the vocabulary first, a store only if asked for

  enhancementquestion
  Cellular-Semantics/Atlas-reporter#66 · Filter by author cellsemantic opened on Sep 9, 2026

• CAS+ validation: add a CLI validator and call it from the skills that write cas.json

  enhancement
  Cellular-Semantics/Atlas-reporter#55 · Filter by author cellsemantic opened on Sep 7, 2026
  1

• Port read-source from cxg-author-probe; standard output is an obs parquet

  Cellular-Semantics/Atlas-reporter#54 · Filter by author cellsemantic opened on Sep 7, 2026

• Tidy up: review the four unrequested schema changes from #50

  Cellular-Semantics/Atlas-reporter#53 · Filter by author cellsemantic opened on Sep 7, 2026

• Skill: populate atlas and subatlas paper metadata in CAS+

  Cellular-Semantics/Atlas-reporter#51 · Filter by author cellsemantic opened on Sep 6, 2026

• Ingest to CAS+: improvised extraction, programmatic assembly

  Cellular-Semantics/Atlas-reporter#49 · Filter by author cellsemantic opened on Sep 6, 2026

• Report contract and synthesis spec: structure, marker rules, and no workflow terminology in the text

  enhancement
  Cellular-Semantics/Atlas-reporter#47 · Filter by author cellsemantic opened on Sep 5, 2026

• Evidence record: one shape for every producer, with marker comparison context and model/source separation

  enhancement
  Cellular-Semantics/Atlas-reporter#46 · Filter by author cellsemantic opened on Sep 5, 2026
  1

• Harden schema and quote validation on dev

  Cellular-Semantics/Atlas-reporter#43 · Filter by author cellsemantic opened on Sep 5, 2026
  1

• Subatlas prioritisation at setup (deterministic cutoffs), consistency judged at read + synthesis

  enhancement
  Cellular-Semantics/Atlas-reporter#42 · Filter by author cellsemantic opened on Sep 4, 2026
  1

• Extend supplement indexing: prose vs tabular content, PDF/docx extraction, and a cheap-model content report

  enhancement
  Cellular-Semantics/Atlas-reporter#41 · Filter by author cellsemantic opened on Sep 4, 2026

• Lightweight PDF text extraction: a callable service + skill that writes text to disk

  enhancement
  Cellular-Semantics/Atlas-reporter#40 · Filter by author cellsemantic opened on Sep 4, 2026

• CLAUDE.md tool rule 3 is wrong: get_paper does return CorpusId via fields=externalIds

  documentation
  Cellular-Semantics/Atlas-reporter#38 · Filter by author cellsemantic opened on Aug 27, 2026

• Quote validation pools ASTA and PMC renderings together, so grounding checks are unsound

  Cellular-Semantics/Atlas-reporter#36 · Filter by author cellsemantic opened on Aug 27, 2026

• ASTA indexing band is cached with no invalidation (probed_at is written but never read)

  bugenhancement
  Cellular-Semantics/Atlas-reporter#33 · Filter by author cellsemantic opened on Aug 26, 2026

• Review: three per-paper state stores, and where the ASTA indexing band belongs

  enhancementquestion
  Cellular-Semantics/Atlas-reporter#32 · Filter by author cellsemantic opened on Aug 26, 2026

• Content: rebuild every local snippet index after the #23 embedding fix

  Cellular-Semantics/Atlas-reporter#30 · Filter by author cellsemantic opened on Aug 25, 2026
  1