academic-open-source-helper

Skills for helping academic researchers take a research repository from closed to fully open source. Compatible with Claude Code, Gemini CLI, OpenAI Codex, GitHub Copilot, and any agent supporting the Agent Skills open standard.

Skills

Skill	Description
secrets-scan	Safety gate — scans working tree and git history for secrets and PII
assess-readiness	Scorecard across safety, legal, citation, reproducibility, and documentation
citation-check	DOI verification, CITATION.cff validation/generation, codemeta.json
readme-gen	Drafts a research-tuned README with academic sections
open-source-plan	Synthesizes findings into a phased, decision-surfacing migration checklist

Recommended workflow

1. secrets-scan [path] — always first; gate everything on this result
2. assess-readiness [path] — full picture of what needs work
3. citation-check [path] — verify and generate citation metadata
4. readme-gen [path] — draft the README
5. open-source-plan [path] — generate the full migration checklist

Installation

Claude Code — as a plugin (namespaced)

git clone https://github.com/VERSO-UVM/academic-open-source-helper ~/.claude/plugins/academic-open-source-helper

Register in ~/.claude/settings.json:

{
  "plugins": ["~/.claude/plugins/academic-open-source-helper"]
}

Skills are available as /academic-open-source-helper:secrets-scan, etc.

Claude Code — as personal skills (unnamespaced)

# Copy individual skills
cp -r skills/secrets-scan ~/.claude/skills/
cp -r skills/assess-readiness ~/.claude/skills/
# etc.

# Or symlink the whole directory
ln -s $(pwd)/skills/* ~/.claude/skills/

Skills are available as /secrets-scan, etc.

Gemini CLI

git clone https://github.com/VERSO-UVM/academic-open-source-helper ~/.gemini/extensions/academic-open-source-helper

The gemini-extension.json manifest and GEMINI.md context file are included.

OpenAI Codex

git clone https://github.com/VERSO-UVM/academic-open-source-helper

Point Codex to the skills/ directory, or copy AGENTS.md to your project root for context. Individual skill directories follow the Agent Skills standard and are read directly.

Other agents (Goose, OpenHands, Roo Code, Junie, Amp, etc.)

Any agent supporting the Agent Skills standard can load skills from the skills/ directory directly. Clone the repo and configure your agent to read from skills/.

GitHub Copilot

Copilot reads .github/copilot-instructions.md for project context. Copy that file to your research repository to give Copilot the full skill descriptions and recommended workflow. For full skills support, use a Copilot-compatible agent.

Philosophy

Issues-first, researcher-as-author. This plugin never silently makes changes to the scholarly record. CRITICAL findings (secrets, PII, dead DOIs) are reported with exact remediation steps — the researcher acts, not the tool. Generated files (CITATION.cff, README drafts) are clearly marked as drafts for human review.

Project context

Built by VERSO / ORCA at the University of Vermont. Part of a broader effort to make research software open-sourcing repeatable and teachable. See project_spec.md for the full architecture including a planned MCP server layer.

Standards

Skills follow established research-software standards: CITATION.cff, codemeta, FAIR principles, OSI licenses, and Zenodo for DOI minting. The plugin format follows the Agent Skills open standard.