{
  "name": "@seqyuan/annodex",
  "version": "0.1.137",
  "description": "AI-native bioinformatics workspace by Annoroad",
  "license": "MIT",
  "bin": {
    "annodex": "bin/annodex.js",
    "annodex-memory-mcp": "bin/annodex-memory-mcp.js",
    "annodex-notebook-mcp": "bin/annodex-notebook-mcp.js",
    "annodex-im-gateway": "bin/annodex-im-gateway.js"
  },
  "files": [
    "bin",
    "bin/annodex-memory-mcp.js",
    "bin/annodex-notebook-mcp.js",
    "bin/annodex-im-gateway.js",
    ".next",
    "!.next/cache",
    "!.next/dev",
    "!.next/types",
    "!.next/**/*.js.map",
    "!.next/trace",
    "!.next/trace-build",
    "lib/app-settings.js",
    "lib/macos-codex-security.js",
    "lib/default-SOUL.md",
    "lib/default-HARNESS.md",
    "lib/im-media.js",
    "lib/im-cancel.js",
    "public",
    "next.config.ts",
    "server",
    "package.json"
  ],
  "scripts": {
    "dev": "PORT=30121 NODE_ENV=development node server/annodex-next-server.mjs",
    "build": "next build --webpack",
    "start": "next start -p 30121",
    "lint": "eslint .",
    "test:compat": "node --test tests/compat-proxy.test.mjs",
    "test:notebook": "node --test tests/notebook-core.test.mjs",
    "pack:check": "node scripts/check-npm-pack.mjs",
    "prepublishOnly": "node scripts/check-npm-pack.mjs",
    "release": "npm version patch --no-git-tag-version && npm run build && npm run pack:check && npm publish --access public"
  },
  "dependencies": {
    "@openai/codex": "^0.118.0",
    "bcryptjs": "^3.0.3",
    "next": "16.2.1",
    "react": "^19.2.4",
    "react-dom": "^19.2.4",
    "ws": "^8.18.0"
  },
  "overrides": {
    "@types/react": "^19.2.17",
    "@types/react-dom": "^19.2.3"
  },
  "devDependencies": {
    "@codemirror/autocomplete": "^6.20.2",
    "@codemirror/commands": "^6.10.3",
    "@codemirror/lang-css": "^6.3.1",
    "@codemirror/lang-go": "^6.0.1",
    "@codemirror/lang-html": "^6.4.11",
    "@codemirror/lang-java": "^6.0.2",
    "@codemirror/lang-javascript": "^6.2.5",
    "@codemirror/lang-json": "^6.0.2",
    "@codemirror/lang-markdown": "^6.5.0",
    "@codemirror/lang-python": "^6.2.1",
    "@codemirror/lang-rust": "^6.0.2",
    "@codemirror/lang-sql": "^6.10.0",
    "@codemirror/lang-xml": "^6.1.0",
    "@codemirror/search": "^6.7.0",
    "@codemirror/state": "^6.6.0",
    "@codemirror/theme-one-dark": "^6.1.3",
    "@codemirror/view": "^6.43.0",
    "@tailwindcss/postcss": "^4.2.2",
    "@types/bcryptjs": "^2.4.6",
    "@types/mdx": "^2.0.14",
    "@types/node": "^25",
    "@types/react": "^19.2.17",
    "@types/react-dom": "^19.2.3",
    "@types/react-syntax-highlighter": "^15.5.13",
    "@types/ws": "^8.18.1",
    "codemirror": "^6.0.2",
    "docx-preview": "^0.3.7",
    "eslint": "^9",
    "eslint-config-next": "16.2.1",
    "fumadocs-core": "^16.10.7",
    "fumadocs-mdx": "^15.0.8",
    "fumadocs-ui": "^16.10.7",
    "jszip": "^3.10.1",
    "lucide-react": "^1.17.0",
    "mermaid": "^11.15.0",
    "pdfjs-dist": "^5.7.284",
    "postcss": "^8",
    "react-markdown": "^10.1.0",
    "react-syntax-highlighter": "^16.1.1",
    "remark-gfm": "^4.0.1",
    "smol-toml": "^1.6.1",
    "tailwindcss": "^4.2.2",
    "typescript": "5.9.3",
    "xlsx": "^0.18.5"
  }
}