Guides

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Guides"]
  page["Guides"]
  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"]

Read the first diagram as a timing map: the guides shelf is for a named pressure, not for wandering the whole course-book. Read the second diagram as the guide loop: choose one lane, use one page, then leave with one smaller next move.

Use this shelf when you need route choice, proof sizing, or capstone entry help rather than one module chapter.

Choose one lane

If you need...	Start here	Then use
the shortest honest entry	Start Here	Course Guide
the full support-page map	Course Guide	Learning Contract
a route shaped by urgency	Pressure Routes	Proof Ladder
module promises and exit bars	Module Promise Map	Module Checkpoints
workflow split decisions	Topic Boundaries	Boundary Review Prompts
capstone entry	Capstone Guide	Capstone Map

Use the shelf by job

Job	Best page
understand the module arc and support-page roles	Course Guide
see the sequence justified	Module Dependency Map
rehearse the module-to-proof loop	Practice Map
hold the stable review bar steady	Review Checklist
sharpen a keep, change, or reject boundary call	Boundary Review Prompts
keep workflow-versus-policy scope explicit	Topic Boundaries
route a claim to executable evidence	Proof Matrix
choose the smallest honest proof route	Proof Ladder
confirm the local environment before public commands	Platform Setup

Cross into the capstone deliberately

If you need...	Best page
the capstone's role in the course	Capstone
the module-to-repository route	Capstone Map
a bounded first pass through the repository	Capstone Walkthrough
file responsibilities inside the repository	Capstone File Guide
ownership boundaries across workflow, policy, and publish surfaces	Capstone Architecture Guide
the shortest proof route for a concrete claim	Capstone Proof Guide
steward-level workflow review	Capstone Review Worksheet
safe evolution	Capstone Extension Guide

Good stopping point

Stop when you can name the single next page you need and the question it is supposed to answer. If you are still opening whole shelves, go back to the table above and choose a smaller lane.

Shelf vocabulary

Use this section when the support shelf starts sounding more abstract than the course intends. The goal is not to define Snakemake again. The goal is to keep a small set of course-level terms stable so you can move between guides, modules, and capstone routes without changing what the words mean.

Terms that matter on this shelf

Term	Meaning here	Why it matters
reading route	a short reading path for one concrete question	keeps you from opening five pages when one page would do
pressure	the situation shaping what you can realistically read right now	keeps the guides tied to real use instead of generic study advice
proof route	the smallest command, artifact, or file that can honestly test a claim	keeps evidence proportional to the question
workflow contract	the file, path, or publish promise the workflow is making	reminds you the course is about explicit agreements, not ambient behavior
policy boundary	the line between workflow meaning and operational choices such as profiles or retries	helps you keep execution context from masquerading as semantics
publish boundary	the smaller downstream-facing surface another person is allowed to trust	separates results that help the repository run from outputs meant to travel
capstone entry	the first bounded route into the executable repository	prevents the capstone from becoming first-contact reading
bounded review	an inspection pass with a clear stopping point	stops review from turning into aimless browsing

Guide names in plain language

Page	What it is for
Start Here	safest first route into the program
Course Guide	overview of when to use guides, modules, reference pages, or capstone routes
Learning Contract	the bar the course sets for explanation, proof, and honest progress
Module Promise Map	translation of module titles into concrete outcomes
Module Checkpoints	readiness review before you move on
Platform Setup	tooling and version checks before you trust local proof routes
Pressure Routes	shortest honest route when urgency is shaping the reading order
Proof Ladder	how to choose a smaller or larger proof route without guessing
Proof Matrix	where a specific claim is first corroborated

Reading rule

If a guide name still feels vague after you read the tables above, do not open three more guides. Name the job first, pick the one page that owns that job, and stop when you have one clear next move.