Boundary Review Prompts

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Reference"]
  page["Boundary Review Prompts"]
  capstone["Capstone evidence"]

  family --> program --> section --> page
  page -.applies in.-> capstone

flowchart LR
  orient["Orient on the page map"] --> read["Read the main claim and examples"]
  read --> inspect["Inspect the related code, proof, or capstone surface"]
  inspect --> verify["Run or review the verification path"]
  verify --> apply["Apply the idea back to the module and capstone"]

Use this page when a Snakemake review needs sharper keep, change, or reject questions tied to workflow boundaries.

Workflow versus policy

• Does this change alter workflow meaning or only execution policy?
• Would a dry-run reveal the important part of the behavior honestly?
• Has a profile started carrying semantic meaning it should not own?

Discovery versus folklore

• Does dynamic discovery leave a durable artifact that another reviewer can inspect?
• Which rule or artifact actually settles the discovered set?
• Would the workflow still be reviewable if logs were missing?

Publish and repository boundaries

• Is the published contract smaller and clearer than the whole repository?
• Which layer should own this behavior: Snakefile, rules, modules, scripts, package code, or profiles?
• What ambiguity would make you reject the current boundary as too blurry to trust?

Authority prompts

• Which surface is actually allowed to settle this trust question?
• Is this claim being supported by workflow contracts, durable artifacts, or only logs and memory?
• Would the repository still be reviewable if runtime output disappeared?