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Module Promise Map

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Guides"]
  page["Module Promise Map"]
  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 module title sounds right but still too compressed. A strong module title should tell you what kind of judgment you will leave with, not just which topic bucket the chapter belongs to.

How to read this map

Each row answers four practical questions:

  1. what the module is trying to change in your mental model
  2. what boundary that promise is really about
  3. what you should be able to do afterward
  4. what capstone route first corroborates the lesson

If a module drifts away from that contract, the drift should be visible here.

Module contracts

Module The promise The boundary You should leave able to... First corroboration route
01 File Contracts make Snakemake legible as a file-contract system instead of command folklore rules, targets, rerun causes, publish discipline explain why a job appears in the DAG before any execution happens Capstone Walkthrough
02 Dynamic DAGs show how discovery can change the DAG without becoming magic checkpoints, discovered-set artifacts, wildcard limits, publish integrity point to the artifact that records what discovery found Capstone Walkthrough
03 Production Operations separate workflow meaning from operational policy profiles, retries, staging, clean-room proof, governance explain what may vary across runs without changing workflow semantics Capstone Architecture Guide
04 Scaling Workflows grow the repository without hiding the visible workflow graph includes, modules, file APIs, validation, CI review surfaces decide where a scaling change belongs before splitting files Capstone File Guide
05 Software Boundaries teach the line between workflow orchestration and the software it drives scripts, packages, environments, provenance, runtime contracts explain where rule logic ends and helper software begins Capstone Proof Guide
06 Publishing make publish surfaces explicit downstream contracts instead of convenience folders results/ versus publish/v1/, manifests, reports, provenance explain which outputs a downstream consumer is allowed to trust Capstone Review Worksheet
07 Workflow Architecture teach repository architecture as part of reproducibility and reviewability entrypoints, rule families, file APIs, helper boundaries, repository layers point to the owning layer for a structural workflow change Capstone File Guide
08 Operating Contexts keep executor and profile differences reviewable without semantic drift local, CI, and scheduler policy; retries; storage and staging assumptions explain what changed across contexts and why the workflow promise stayed stable Capstone Architecture Guide
09 Incident Response make workflow incidents diagnosable before edits begin logs, benchmarks, summaries, provenance, triage routes choose the next evidence surface before touching the workflow Capstone Review Worksheet
10 Governance teach stewardship, migration order, and honest tool boundaries review method, migration sequencing, governance rules, handoff decisions improve the repository while preserving trust in current outputs and proof routes Capstone Review Worksheet

What this page prevents

This map exists to prevent four common course failures:

  • a module promises judgment but only delivers syntax
  • a module promises operations but never reaches executable proof
  • a module promises architecture but leaves ownership blurry
  • a module promises stewardship but never turns into review behavior

If you notice one of those failures while reading, come back here and name the missing piece directly.

Best companion pages