setup-medsci

name	setup-medsci
description	Diagnostic checklist for the MedSci Skills runtime. Verifies Python, R, Node, Claude Code, Git, Zotero, and configured MCP servers, and prints a pass/fail table with links to the right setup doc for any missing component. Read-only — does not install anything.
triggers	setup, install, environment, diagnostic, check setup, why doesn't this work, missing python, missing R, MCP not connected, 환경 설정, 설치 점검
tools	Bash, Read
model	inherit

Setup-MedSci Skill

You are helping a medical researcher verify that their environment is correctly configured to run MedSci Skills. You do not install anything — you only diagnose what's present, what's missing, and where to find the setup doc for any missing component. This skill is intentionally read-only so that a doctor can run it safely without worrying about breaking their system.

Communication Rules

• Communicate with the user in their preferred language (Korean or English).
• The diagnostic table itself is in English so it can be pasted into GitHub issues for support.
• All recommended remediation links point to docs/setup/ markdown guides in the medsci-skills repo.

Workflow

Phase 1: Detect OS

Run:

uname -s

• Darwin → macOS path → recommend docs/setup/mac.md
• Linux → Linux path (uses similar tooling to Mac) → recommend docs/setup/mac.md
• MINGW*, MSYS*, CYGWIN*, or detection failure on Windows → recommend docs/setup/windows.md

Phase 2: Run Diagnostic Commands

For each tool, run the command and capture both the version output and the exit code:

Tool	Command	Required version
Python	python3 --version (Mac/Linux) or python --version (Windows)	3.11 or higher
R	Rscript --version (writes to stderr)	4.0 or higher
Node.js	node --version	v20 or higher
Git	git --version	2.30 or higher
Claude Code CLI	claude --version	any
MCP servers	claude mcp list	at least one of: zotero, gdrive, pubmed, filesystem

Use command -v <tool> first to detect presence without running it (avoids triggering long initialization).

Phase 3: Emit Checklist Table

Print a single Markdown table to stdout in this exact format:

## MedSci Skills Setup Diagnostic

OS detected: <macOS | Linux | Windows>
Date: <YYYY-MM-DD>

| Component | Status | Detected | Required | Action |
|---|:---:|---|---|---|
| Python 3.11+ | ✅ / ❌ | 3.11.9 | 3.11+ | OK / See docs/setup/mac.md Step 2 |
| R 4.x | ✅ / ❌ | 4.3.1 | 4.0+ | OK / See docs/setup/mac.md Step 3 |
| Node.js 20+ | ✅ / ❌ | v20.11.1 | v20+ | OK / See docs/setup/mac.md Step 4 |
| Git | ✅ / ❌ | 2.42.0 | 2.30+ | OK / See docs/setup/<os>.md Step 5 |
| Claude Code CLI | ✅ / ❌ | 1.5.x | any | OK / See docs/setup/<os>.md Step 6 |
| MCP: zotero | ✅ / ❌ / ⚠️ | Connected | optional | OK / See docs/setup/mcp-setup.md |
| MCP: gdrive | ✅ / ❌ / ⚠️ | Connected | optional | OK / See docs/setup/mcp-setup.md |
| MCP: filesystem | ✅ / ❌ | Connected | recommended | OK / See docs/setup/mcp-setup.md |

Summary: <X required components passed, Y missing>
Next step: <one-sentence action>

Status legend:

• ✅ Present and meets minimum version
• ❌ Missing or below minimum version
• ⚠️ Present but optional and not connected

Phase 4: Suggest Remediation

If everything ✅: "Your environment is ready. Try Demo 1 with cd ~/medsci-skills/demo/01_wisconsin_bc && claude '/orchestrate --e2e'."

If anything ❌ in required rows: print the corresponding doc link. Do not offer to install — direct the user to follow the doc step. The doc tells them exactly what to copy-paste.

If only optional MCP rows are ❌: explain that MedSci Skills work without MCP servers but lit-sync, verify-refs, and write-paper are smoother with Zotero MCP. Offer the docs/setup/mcp-setup.md link.

Reference Files

• references/setup-checklist.md — verbatim list of every check this skill runs and the corresponding documentation link

Output Contract

Artifact	Filename	Format
Diagnostic report	stdout (Markdown table)	Markdown
Optional log	~/.medsci-skills/diagnostic-YYYY-MM-DD.md	Markdown

If the user asks for a copyable report (e.g., for a GitHub issue), write the diagnostic to the optional log path and tell them where it is.

What This Skill Does NOT Do

• Does not install anything. No brew install, winget install, pip install, Rscript -e 'install.packages(...)', or any other state-changing command. Read-only diagnostics only.
• Does not modify ~/.claude.json or any MCP configuration. It only reads claude mcp list output.
• Does not check skill versions or skill content. That is the job of validate_skills.sh and manage-project status.
• Does not auto-fix anything. If a tool is missing, the user must go to the setup doc and follow the steps themselves. This is intentional — auto-installers for system Python and R are a support nightmare for non-developer users.

Anti-Hallucination

• Never fabricate version numbers. Always run the actual command and report the exact stdout. If the command fails, report the failure verbatim — do not guess what version is "probably" installed.
• Never invent doc paths. The five setup docs are: docs/setup/README.md, docs/setup/mac.md, docs/setup/windows.md, docs/setup/mcp-setup.md, docs/setup/common-issues.md. Do not link to a doc that does not exist in the repo.
• Never claim an MCP server works without verifying via claude mcp list. A configured-but-disconnected server is ⚠️, not ✅.
• If command -v reports a tool present but the version flag fails, mark the row ❌ and report the failure command — the install is broken, not just outdated.