Computational · Paper · 2026

A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication

Zenodo

Catalog Row1
Citation KeyFriedman2026TemplateApproachReproducibleGenerative001
Paper FolderAvailable
DOI10.5281/zenodo.19139090

Overview

Extracted from the local paper documentation when available.

The reproducibility crisis in computational research is fundamentally structural: research artifacts are scattered across disconnected tools—LaTeX editors, Jupyter notebooks, ad-hoc shell scripts—with no enforced mechanism to keep code, data, and manuscript synchronized. template/ applies the principle of Infrastructure as Code to the research lifecycle, making the manuscript, test suite, and provenance chain version-controlled, deterministically buildable, and independently verifiable. It is built on a Two-Layer Architecture that separates 12 reusable infrastructure subpackages (~150 Python modules, validated by ~3,083 tests) from self-contained project workspaces, connected by an eight-stage build pipeline progressing from environment sanitization through test execution (with a Zero-Mock testing policy enforcing 90% project-level and 60% infrastructure-level coverage via real filesyste

reproducible researchinfrastructure as codebuild pipelineZero-Mock testingsteganographic watermarkingAI-agent documentationModel Context Protocolcryptographic provenanceliterate programmingopen science

Use Notes

Concise findings and methods pulled from README/SKILL documentation.

Findings / Concepts
  • Introduces a Two-Layer Architecture separating reusable infrastructure (~150 modules, ~3,083 tests) from self-contained project workspaces
  • Defines an eight-stage build pipeline from environment sanitization through LLM-assisted review
  • Enforces a Zero-Mock testing policy (90% project / 60% infrastructure coverage) using real filesystem operations
  • Implements SHA-256 cryptographic hashing with steganographic watermarking for provenance
  • Introduces Documentation Duality (README.md + AGENTS.md) and SKILL.md aligned with Model Context Protocol
Methods / Techniques
  • Two-Layer Architecture: infrastructure subpackages vs. project workspaces
  • Eight-stage build pipeline: sanitization → tests → analysis → Pandoc/XeLaTeX → SHA-256 → steganographic watermarking → PDF validation → LLM review
  • Zero-Mock testing policy enforcing real filesystem and subprocess operations
  • Documentation Duality standard with MCP-aligned SKILL.md files
  • Comparative feature analysis against Snakemake, Nextflow, CWL, Quarto, Jupyter Book, R Markdown, Overleaf, DVC, OpenAI Prism

Citation

Plain-text citation for quick reuse.

Friedman, Daniel Ari. 2026. A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication. Zenodo.

Primary source Documentation BibTeX