Glossary

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Publishing Downstream Contracts"]
  page["Glossary"]
  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"]

This glossary keeps the language of Module 06 stable. The goal is practical clarity: publish review gets much easier when the same terms keep the same meaning.

Terms

Term	Meaning in this module
internal state	Workflow-owned outputs that help execution, debugging, or intermediate reasoning but are not the downstream contract.
public contract	The smaller set of published artifacts that downstream users are allowed to trust and depend on.
publish boundary	The directory and artifact set that define the downstream-facing contract, such as publish/v1/.
versioned boundary	A publish surface whose version communicates compatibility expectations over time.
compatible change	A change that preserves existing downstream expectations within the current publish version.
contract change	A change to paths, meanings, or required fields that alters the published promise and may require a new version.
manifest	The inventory of published artifacts, ideally including paths and digests.
checksum	A digest used to confirm file identity, detect corruption, or spot silent replacement.
bundle integrity	The degree to which a publish bundle can prove completeness and identity coherently.
provenance	Evidence about the software and execution context that produced the published outputs.
machine-readable artifact	A structured output designed for programmatic downstream use, such as summary.json or summary.tsv.
human-readable artifact	An output designed to help a person interpret the run, such as report/index.html.
file API	A document that explains what published artifacts exist, what they mean, and how stable they are.
publish drift	Any change that weakens or alters the downstream contract, whether through paths, semantics, or artifact-role confusion.
downstream trust	The confidence that another person or tool can use the published bundle without reverse engineering the workflow internals.

How to use these terms

If a publish review starts to feel vague, ask which term has become unclear:

• is the boundary internal or public?
• is the change compatible or contract-breaking?
• is this artifact for machines, humans, integrity, or provenance?

That question usually reveals the real problem quickly.