Skip to content

AGENTS.md

Latest commit

 

History

History
27 lines (21 loc) · 1.3 KB

AGENTS.md

File metadata and controls

27 lines (21 loc) · 1.3 KB
Raw

Repository instructions for Codex

  • Preserve the separation between src/ (package), tests/ (developer checks), examples/demo/ (reviewer-facing smoke test), and paper/ (manuscript reproduction).
  • Do not commit raw or controlled data.
  • Run ruff format, ruff check, and pytest before committing Python changes.
  • Keep figure calculations in scripts and export figure-facing source tables.

Cell Reports Methods major revision

For work on CRM_R1 or revision Priorities 1-5, first read:

  1. paper/revision/CRM_R1/ANALYSIS_PLAN.md
  2. paper/revision/CRM_R1/config/priority1_protocol.json
  3. The priority-specific protocol under paper/revision/CRM_R1/config/
  4. paper/revision/CRM_R1/AGENTS.md
  5. paper/scripts/README.md
  6. paper/FIGURE_MAP.csv

Do not calculate the Priority 1 held-out 72 h endpoint while the protocol status is DRAFT_NOT_FROZEN. Status FROZEN is still insufficient until paper/revision/CRM_R1/scripts/17_check_priority1_freeze.py passes against the immutable external freeze manifest.

For Priorities 3 and 4, preserve the frozen Priority 2 claim census and randomized review IDs. Never expose audit status, method membership, stability, or context-review outputs in a grading or rater packet. PubMed abstracts and raw XML are private working artifacts and must not be committed.