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MCP server for MNE-Python documentation, source code, GitHub issues, and forum.","maintainers":[{"name":"weiyongxu","email":"subtlelord@gmail.com"}],"readme":"# MNE Docs MCP Server\r\n\r\n> ## ⚠️ Deprecated — this project moved to Python\r\n>\r\n> **`mne-docs-mcp` is archived. It is superseded by [`mne-docs`](https://github.com/weiyongxu/mne-docs), a zero-dependency Python CLI.**\r\n>\r\n> ```bash\r\n> pip install mne-docs\r\n> ```\r\n>\r\n> **Why:** an AI assistant with a shell and local files can grep and read MNE's\r\n> source better than any tool schema can rank for it. The MCP server's 15 tools,\r\n> symbol ranking, and caching turned out to be scaffolding around one good idea —\r\n> *put the user's version of MNE on disk and read it*. That idea is now a single\r\n> command, with no server, no Node runtime, and no GitHub token.\r\n>\r\n> **v1.0.50 is the final release.** It exists to fix one real bug before the lights\r\n> go out: every code and docs search in v1.0.10–v1.0.49 silently returned **zero\r\n> results**, because the GitHub code-search query carried an unsupported `ref:`\r\n> qualifier. If you are staying on this package, upgrade to v1.0.50. Otherwise,\r\n> please move to [`mne-docs`](https://github.com/weiyongxu/mne-docs).\r\n\r\n## What You Get\r\n\r\n- 15 read-only MCP tools for docs/code/issues/forum/error lookup\r\n- HTTP transport (`/mcp`) and stdio transport\r\n- Python AST-based symbol parsing (no extra Python packages required)\r\n- Built-in caching and GitHub rate-limit aware behavior\r\n- Multi-package support across the MNE ecosystem for most code/docs tools\r\n\r\n## Requirements\r\n\r\n- Node.js `>=20`\r\n- Python 3 (`python` on Windows, `python3` on Linux/macOS)\r\n- GitHub token (`MNE_GITHUB_TOKEN`) with access to public repositories\r\n\r\n## Quick Start (Local HTTP)\r\n\r\n```bash\r\ngit clone https://github.com/weiyongxu/mne-docs-mcp.git\r\ncd mne-docs-mcp\r\nnpm install\r\nnpm run build\r\n```\r\n\r\nSet token:\r\n\r\n```bash\r\n# Linux/macOS\r\nexport MNE_GITHUB_TOKEN=ghp_your_token_here\r\n\r\n# Windows PowerShell\r\n$env:MNE_GITHUB_TOKEN=\"ghp_your_token_here\"\r\n```\r\n\r\nStart server:\r\n\r\n```bash\r\nnpm start\r\n```\r\n\r\nDefault endpoint: `http://127.0.0.1:8000/mcp`  \r\nHealth check: `http://127.0.0.1:8000/health`  \r\nMetrics: `http://127.0.0.1:8000/metrics`\r\n\r\n## MCP Client Integration\r\n\r\n### Stdio Mode (Claude Desktop / Kiro / Claude Code)\r\n\r\nUse `dist/index.js` and set `MNE_TRANSPORT=stdio`:\r\n\r\n```json\r\n{\r\n  \"mcpServers\": {\r\n    \"mne-docs\": {\r\n      \"command\": \"node\",\r\n      \"args\": [\"/path/to/mne-docs-mcp/dist/index.js\"],\r\n      \"env\": {\r\n        \"MNE_GITHUB_TOKEN\": \"ghp_your_token_here\",\r\n        \"MNE_TRANSPORT\": \"stdio\"\r\n      }\r\n    }\r\n  }\r\n}\r\n```\r\n\r\n### Remote HTTP Mode\r\n\r\n```json\r\n{\r\n  \"mcpServers\": {\r\n    \"mne-docs\": {\r\n      \"type\": \"http\",\r\n      \"url\": \"https://your-server.com/mcp\"\r\n    }\r\n  }\r\n}\r\n```\r\n\r\n## Docker\r\n\r\n```bash\r\ndocker run -p 8000:8000 \\\r\n  -e MNE_GITHUB_TOKEN=ghp_your_token_here \\\r\n  ghcr.io/weiyongxu/mne-docs-mcp:latest\r\n```\r\n\r\nOr use the included `docker-compose.yml`:\r\n\r\n```bash\r\n# Linux/macOS\r\nexport MNE_GITHUB_TOKEN=ghp_your_token_here\r\n\r\n# Windows PowerShell\r\n$env:MNE_GITHUB_TOKEN=\"ghp_your_token_here\"\r\n\r\ndocker compose pull\r\ndocker compose up -d\r\n```\r\n\r\nThe compose file only requires `MNE_GITHUB_TOKEN`. Other settings use image defaults.\r\n\r\n## Tool List\r\n\r\n- `list_mne_versions`\r\n- `get_mne_file`\r\n- `get_mne_doc`\r\n- `find_mne_symbol`\r\n- `search_mne_docs`\r\n- `search_mne_issues`\r\n- `get_mne_issue`\r\n- `get_mne_issue_comments`\r\n- `search_mne_forum`\r\n- `get_mne_forum_topic`\r\n- `get_symbol_references`\r\n- `get_related_symbols`\r\n- `get_mne_changelog`\r\n- `get_mne_example`\r\n- `lookup_mne_error`\r\n\r\n## Package Support\r\n\r\nSupported packages:\r\n\r\n- `mne-python` (default)\r\n- `mne-bids-pipeline`\r\n- `mne-bids`\r\n- `mne-connectivity`\r\n- `mne-nirs`\r\n- `mne-rsa`\r\n- `mne-icalabel`\r\n- `mne-realtime`\r\n- `mne-lsl`\r\n- `mne-gui-addons`\r\n\r\n`package` parameter is supported by code/docs/issues/changelog/example/symbol tools.  \r\nForum tools (`search_mne_forum`, `get_mne_forum_topic`) and `lookup_mne_error` do not take a `package` parameter.\r\n\r\n## Configuration\r\n\r\nKey environment variables:\r\n\r\n| Variable | Default | Notes |\r\n|---|---|---|\r\n| `MNE_GITHUB_TOKEN` | — | Required |\r\n| `MNE_TRANSPORT` | `http` | `http` or `stdio` |\r\n| `MNE_HOST` | `127.0.0.1` | Use `0.0.0.0` in containers |\r\n| `MNE_PORT` | `8000` | HTTP mode port |\r\n| `MNE_ALLOWED_ORIGINS` | `*` | CORS/Origin allowlist |\r\n| `MNE_DEFAULT_PACKAGE` | `mne-python` | Default package |\r\n| `MNE_PYTHON_PATH` | `python` (Win) / `python3` (Unix) | Parser executable |\r\n| `MNE_LOG_LEVEL` | `info` | `debug`, `info`, `warn`, `error` |\r\n| `MNE_LOG_JSON` | `false` | Structured logs |\r\n\r\nSee [.env.example](.env.example) for a minimal local template.\r\n\r\n## Testing and Diagnostics\r\n\r\nFull tool test run:\r\n\r\n```bash\r\nnode scripts/run-tests.mjs\r\n```\r\n\r\nCurated 25-example smoke test:\r\n\r\n```bash\r\nnode scripts/run-example-tests.mjs\r\n```\r\n\r\nAgainst another endpoint:\r\n\r\n```bash\r\nMNE_MCP_BASE=https://your-server.com/mcp node scripts/run-tests.mjs\r\nMNE_MCP_BASE=https://your-server.com/mcp node scripts/run-example-tests.mjs\r\n```\r\n\r\nAdd timeout guard:\r\n\r\n```bash\r\nMNE_TOOL_TIMEOUT_MS=20000 node scripts/run-tests.mjs\r\n```\r\n\r\nStable benchmark mode (for slow/stuck investigation):\r\n\r\n```bash\r\nnode scripts/run-tests.mjs --benchmark-stable --warm-pass --stable-runs 3\r\n```\r\n\r\n## Development\r\n\r\n```bash\r\nnpm run dev\r\nnpm run typecheck\r\nnpm run lint\r\nnpm test\r\nnpm run build\r\n```\r\n\r\n## Release\r\n\r\n```bash\r\nnpm run release:patch   # or :minor / :major\r\n```\r\n\r\nThe release script:\r\n\r\n1. Bumps version (`package.json`)\r\n2. Updates `server.json`\r\n3. Stages `package.json`, `package-lock.json`, `server.json`\r\n4. Commits (`Release vX.Y.Z`)\r\n5. Tags (`vX.Y.Z`)\r\n6. Pushes commit and tag\r\n\r\nTag push triggers `release.yml`, which publishes:\r\n\r\n- GHCR Docker image\r\n- npm package\r\n- MCP Registry entry\r\n- GitHub Release\r\n\r\n## Troubleshooting\r\n\r\n- `401` / `Bad credentials`: verify `MNE_GITHUB_TOKEN`\r\n- slow code-search tools: use benchmark mode and check `/metrics`\r\n- parser failures: verify Python path (`MNE_PYTHON_PATH`)\r\n- endpoint check: `/health` should return `status=healthy`\r\n\r\n## License\r\n\r\nMIT\r\n","readmeFilename":"README.md"}