Glossary

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Performance Observability Incident Response"]
  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 09 stable.

The goal is practical incident and performance clarity: when the same terms keep the same meaning, review gets faster and less argumentative.

Terms

Term	Meaning in this module
cost class	A named source of workflow time such as planning, scheduler overhead, storage drag, or tool runtime.
planning cost	Time spent discovering inputs, expanding targets, resolving wildcards, and building the DAG before jobs really run.
scheduler overhead	Time spent launching, tracking, and finalizing jobs rather than performing the scientific or analytic work itself.
storage drag	Delay caused by staging, scratch promotion, shared filesystem latency, or slow visibility of files.
tool runtime	The time spent inside the script, wrapper, or external tool that performs the real step-local work.
evidence surface	A specific artifact or command output used to answer one review question, such as a log, benchmark, summary, or provenance file.
rule-local evidence	Evidence tied to one rule or target, usually logs or benchmark files for a specific job family.
workflow-state evidence	Evidence about the workflow as a whole, such as dry-run output, summaries, or rerun-cause listings.
provenance	The configuration, profile, environment, and runtime identity that explain what produced a given published result.
incident ladder	A fixed sequence for moving from symptom to evidence to classification before editing the workflow.
incident class	The current boundary where the problem appears to live: workflow semantics, operating context, storage behavior, or tool behavior.
noisy evidence	Evidence that exists but does not help answer the actual review question because it is too broad, too vague, or too verbose.
semantic drift	A change that alters workflow meaning, file-contract truth, or published meaning while being framed as something smaller.
honest tuning	A performance improvement that keeps workflow semantics, declared dependencies, and review evidence intact.
runbook	A short operational route that tells maintainers what to run first, what to inspect next, and when to escalate.
escalation trigger	A condition that says the issue has crossed a boundary and should move from local debugging into profile review, publish review, or design review.

How to use these terms

If a performance or incident discussion starts getting vague, ask which term has become unclear:

• are we talking about planning cost or tool runtime?
• do we need workflow-state evidence or rule-local evidence?
• is this still honest tuning, or has it crossed into semantic drift?
• is the next move a local repair or an escalation trigger?

Those questions usually expose the real disagreement quickly.