Progressive learning guides from beginner to expert
Quick Reference: Getting Started | Figures and Analysis | Testing and Reproducibility | Extending and Automation
The guides/ directory contains skill-level specific usage guides that progressively teach users how to use the Research Project Template, from basic document creation to expert-level customization.
Boundary with ../usage/: guides/ = task-driven walkthroughs organized by skill level ("teach me how"); usage/ = format/style reference consulted while actively authoring ("look up the syntax"). New docs that teach a workflow go here; new docs that catalog options or markup go in usage/.
| File | Purpose | Skill Level |
|---|---|---|
startup-and-setup.md |
Install + validation procedure, copy-pasteable for humans and agents | Beginner |
getting-started.md |
Basic usage guide (Levels 1-3) | Beginner |
figures-and-analysis.md |
Figures and analysis guide (Levels 4-6) | Intermediate |
testing-and-reproducibility.md |
Testing and reproducibility guide (Levels 7-9) | Advanced |
extending-and-automation.md |
Extending and automation guide (Levels 10-12) | Expert |
new-project-setup.md |
New project checklist (pitfalls and venv) | All levels |
new-project-one-shot-prompt.md |
Copy-paste LLM prompt (positive controls: template_code_project + template) | All levels |
methods-orchestration.md |
Methods-to-pipeline contracts, artifacts, evidence, validation commands | Advanced |
codegraph-local.md |
Optional local CodeGraph indexing for agent code navigation, with scope guards | Advanced |
leann-local.md |
Optional local LEANN semantic retrieval for agent navigation, with generated-index guards | Advanced |
llm-integration-guide.md |
AI-assisted research with Ollama (LLM review, translation) | Expert |
publishing-guide.md |
Publishing workflow (DOI, Zenodo, arXiv, citations) | Expert |
publication-runbook.md |
Front-door release runbook for standalone public GitHub mirrors, Zenodo DOI minting, new-version releases, status blocks, and archival handoff | Advanced |
secure-research-guide.md |
PDF watermarking, provenance, and integrity | Expert |
zenodo-doi-strategy.md |
Concept vs version DOI strategy for repeat Zenodo releases | Expert |
manuscript-semantics.md |
Canonical manuscript syntax & semantics — Pandoc citations [@key], cross-refs [@eq:/@fig:/@sec:], {{TOKEN}} substitution, preamble. Read before authoring any manuscript. |
All levels |
fork-an-exemplar.md |
Fork-readiness walkthrough for canonical exemplars | All levels |
literature-workflow-guide.md |
Literature discovery → export → synthesis (Ollama-assisted) | Expert |
- Getting Started - Write your first document (Levels 1-3)
- Figures and Analysis - Add figures and automation (Levels 4-6)
- Testing and Reproducibility - Test-driven development and reproducibility (Levels 7-9)
- Extending and Automation - Extending and automation (Levels 10-12)
→ Start with Getting Started
→ Read Figures and Analysis
→ Study Testing and Reproducibility
→ Master Extending and Automation
new-project-setup.md— step-by-step checklist before first pipeline runnew-project-one-shot-prompt.md— one-shot scaffold prompt for AI-assisted projectsmethods-orchestration.md— keep methods prose, pipeline contracts, artifacts, and evidence alignedcodegraph-local.md— optional local code graph indexing for source navigation and impact checksleann-local.md— optional local semantic retrieval for source navigation and impact checks../core/how-to-use.md- usage guide (navigation hub)../usage/- Usage examples and patterns../reference/common-workflows.md- Step-by-step recipes../reference/quick-start-cheatsheet.md- Quick reference
../documentation-index.md- documentation index../README.md- Documentation hub overview