Setup Medsci

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:

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

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.

Setup Diagnostic Checklist

Verbatim list of every check setup-medsci runs, with the exact command, the parse rule, and the documentation link to print on failure.

Required Components

Optional Components

Version Comparison Rule

For required-version checks (R1-R4), parse the major.minor version from stdout, compare against minimum. If parse fails, mark ❌ and report the parse failure verbatim.

Examples of parsing:

• Python 3.11.9 → 3.11, compare to 3.11 → pass
• Python 3.10.13 → 3.10, compare to 3.11 → fail
• R scripting front-end version 4.3.1 (2023-06-16) → 4.3, compare to 4.0 → pass
• v20.11.1 → 20.11, compare to 20.0 → pass
• git version 2.42.0 → 2.42, compare to 2.30 → pass

Summary Rules

After running all checks:

• All required ✅: print "Your environment is ready. Try Demo 1 with cd ~/medsci-skills/demo/01_wisconsin_bc && claude '/orchestrate --e2e'."
• One or more required ❌: print "Setup incomplete. Address the ❌ rows above using the linked docs, then re-run /setup-medsci."
• All required ✅, optional MCP all ❌: print "Core environment ready. Optional MCP servers (Zotero / Google Drive / PubMed) are not configured — see docs/setup/mcp-setup.md for richer integration."

What This Skill Does NOT Check

To keep the diagnostic fast and read-only, these are explicitly out of scope:

• Python package installs (matplotlib, pandas, scikit-learn, etc.) — checked by individual analysis skills when invoked
• R package installs (metafor, survey, etc.) — checked by analyze-stats and meta-analysis when invoked
• Disk space — irrelevant for skill execution
• Anthropic API quota / rate limits — visible only at runtime
• Claude Code skill installation — validate_skills.sh covers this
• Zotero library content / collection structure — lit-sync and verify-refs cover this