# Jr2804 Prompts MCP Cytoscnpy

> CytoScnPy MCP Server

- Skill: `tomevault-io/jr2804-prompts-mcp-cytoscnpy` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add tomevault-io/jr2804-prompts-mcp-cytoscnpy`
- Raw SKILL.md: https://api.skillmd.com/api/skills/tomevault-io/jr2804-prompts-mcp-cytoscnpy/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- Author: tomevault-io (https://skillmd.com/u/tomevault-io)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/tomevault-io/jr2804-prompts-mcp-cytoscnpy

---


# CytoScnPy MCP Server

Enable AI assistants (Claude, Cursor, Copilot) to use CytoScnPy code metrics tools via MCP.

> **Requires:** Standalone CLI binary (`cytoscnpy-cli`). The Python package does not support `mcp-server`.

## Quick Setup

### Claude Desktop

Add to `claude_desktop_config.json`:

```json
{
  "mcpServers": {
    "cytoscnpy": {
      "command": "cytoscnpy",
      "args": ["mcp-server"]
    }
  }
}
```

### VS Code + Copilot

The VS Code extension automatically registers the MCP server. Just ask Copilot:

```
"Run a security scan on this file"
```

No extra config needed when extension is installed.

### Cursor

Same config as Claude Desktop — add to Cursor's MCP settings.

## Available Tools

When connected, CytoScnPy exposes code analysis tools to the AI assistant:

- **Security scan** — Detect secrets, keys, tokens
- **Danger scan** — Detect dangerous code patterns
- **Quality scan** — Code quality metrics (complexity, maintainability)
- **Clone detection** — Find duplicate code
- **Raw metrics** — LOC, SLOC, comments, blanks

## VS Code Extension Settings

| Setting | Default | Description |
|---------|---------|-------------|
| `cytoscnpy.analysisMode` | `workspace` | `workspace` (accurate) or `file` (fast) |
| `cytoscnpy.enableSecretsScan` | `false` | Scan for keys/tokens |
| `cytoscnpy.enableDangerScan` | `false` | Dangerous code patterns |
| `cytoscnpy.enableQualityScan` | `false` | Code quality metrics |
| `cytoscnpy.enableCloneScan` | `false` | Clone detection |
| `cytoscnpy.confidenceThreshold` | `0` | Min confidence (0-100) |
| `cytoscnpy.excludeFolders` | `[]` | Folders to exclude |
| `cytoscnpy.includeFolders` | `[]` | Folders to force-include |
| `cytoscnpy.maxComplexity` | `10` | Max Cyclomatic Complexity |
| `cytoscnpy.minMaintainabilityIndex` | `40` | Min Maintainability Index |
| `cytoscnpy.maxNesting` | `3` | Max nesting depth |
| `cytoscnpy.maxArguments` | `5` | Max function arguments |
| `cytoscnpy.maxLines` | `50` | Max function lines |

## CI/CD Output Formats

CytoScnPy supports JSON, GitLab, SARIF, and GitHub Annotations for CI/CD integration.

## Reference

See `references/integrations.md` for full details.

---
> Source: [jr2804/prompts](https://github.com/jr2804/prompts) — distributed by [TomeVault](https://tomevault.io).
<!-- tomevault:4.0:skill_md:2026-06-16 -->