npm - mne-docs-mcp - Versions diffs - 1.0.29 → 1.0.31 - Mend

mne-docs-mcp 1.0.29 → 1.0.31

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Files changed (8) hide show

package/README.md +137 -176
package/dist/tools/getMneExample.d.ts.map +1 -1
package/dist/tools/getMneExample.js +16 -2
package/dist/tools/getMneExample.js.map +1 -1
package/dist/tools/searchMneDocs.d.ts.map +1 -1
package/dist/tools/searchMneDocs.js +26 -7
package/dist/tools/searchMneDocs.js.map +1 -1
package/package.json +1 -1

package/README.md CHANGED Viewed

@@ -1,32 +1,55 @@
 # MNE Docs MCP Server
-MCP server providing access to MNE-Python documentation, source code, GitHub issues, and community forum across the MNE ecosystem.
+MCP server for MNE ecosystem docs, source code, issues, and forum content.
-## Quick Start
+## What You Get
+- 15 read-only MCP tools for docs/code/issues/forum/error lookup
+- HTTP transport (`/mcp`) and stdio transport
+- Python AST-based symbol parsing (no extra Python packages required)
+- Built-in caching and GitHub rate-limit aware behavior
+- Multi-package support across the MNE ecosystem for most code/docs tools
+## Requirements
+- Node.js `>=20`
+- Python 3 (`python` on Windows, `python3` on Linux/macOS)
+- GitHub token (`MNE_GITHUB_TOKEN`) with access to public repositories
+## Quick Start (Local HTTP)
 ```bash
-# Clone and install
 git clone https://github.com/weiyongxu/mne-docs-mcp.git
 cd mne-docs-mcp
 npm install
+npm run build
+```
-# Set GitHub token (required)
-export MNE_GITHUB_TOKEN=ghp_your_token_here   # Linux/macOS
-$env:MNE_GITHUB_TOKEN="ghp_your_token_here"   # Windows PowerShell
+Set token:
-# Start server
-npm start
+```bash
+# Linux/macOS
+export MNE_GITHUB_TOKEN=ghp_your_token_here
+# Windows PowerShell
+$env:MNE_GITHUB_TOKEN="ghp_your_token_here"
 ```
-Server runs on `http://127.0.0.1:8000` by default. Verify with `curl http://localhost:8000/health`.
+Start server:
+```bash
+npm start
+```
-> **Prerequisites:** Node.js ≥ 20 and Python 3 (used for AST parsing — no pip packages required).
+Default endpoint: `http://127.0.0.1:8000/mcp`
+Health check: `http://127.0.0.1:8000/health`
+Metrics: `http://127.0.0.1:8000/metrics`
 ## MCP Client Integration
-### Claude Desktop / Kiro / Claude Code
+### Stdio Mode (Claude Desktop / Kiro / Claude Code)
-Add to your MCP config (`claude_desktop_config.json`, `.kiro/settings/mcp.json`, or `~/.claude/settings.json`):
+Use `dist/index.js` and set `MNE_TRANSPORT=stdio`:
 ```json
 {
@@ -43,18 +66,8 @@ Add to your MCP config (`claude_desktop_config.json`, `.kiro/settings/mcp.json`,
 }
 ```
-> **Note:** On Windows, `MNE_PYTHON_PATH` defaults to `python` automatically.
-### Remote HTTP Server
-If you're running the server on a VPS or remote host:
-**Claude Code CLI:**
-```bash
-claude mcp add --transport http mne-docs https://your-server.com/mcp
-```
+### Remote HTTP Mode
-**Config file** (`.mcp.json` or `~/.claude.json`):
 ```json
 {
   "mcpServers": {
@@ -66,199 +79,147 @@ claude mcp add --transport http mne-docs https://your-server.com/mcp
 }
 ```
-### Local HTTP Mode
+## Docker
 ```bash
-MNE_TRANSPORT=http npm start
-# Connect to http://localhost:8000/mcp
+docker run -p 8000:8000 \
+  -e MNE_GITHUB_TOKEN=ghp_your_token_here \
+  ghcr.io/weiyongxu/mne-docs-mcp:latest
 ```
-**HTTP endpoints:**
-| Endpoint | Description |
-|----------|-------------|
-| `POST /mcp` | MCP protocol (JSON-RPC) |
-| `GET /health` | Health check — returns `{"status":"healthy"}` |
-| `GET /metrics` | Runtime metrics (request counts, cache hit rate, GitHub rate limit) |
-### Docker
+Or use the included `docker-compose.yml`:
 ```bash
-docker run -p 8000:8000 -e MNE_GITHUB_TOKEN=ghp_your_token ghcr.io/weiyongxu/mne-docs-mcp:latest
-```
-Multi-arch images available for both `linux/amd64` and `linux/arm64`.
-### Docker Compose
+# Linux/macOS
+export MNE_GITHUB_TOKEN=ghp_your_token_here
-Create a `docker-compose.yml`:
+# Windows PowerShell
+$env:MNE_GITHUB_TOKEN="ghp_your_token_here"
-```yaml
-services:
-  mne-docs-mcp:
-    image: ghcr.io/weiyongxu/mne-docs-mcp:latest
-    container_name: mne-docs-mcp
-    ports:
-      - "8000:8000"
-    environment:
-      - MNE_GITHUB_TOKEN=${MNE_GITHUB_TOKEN:?MNE_GITHUB_TOKEN is required}
-    restart: unless-stopped
+docker compose pull
+docker compose up -d
 ```
-Then run:
+The compose file only requires `MNE_GITHUB_TOKEN`. Other settings use image defaults.
+## Tool List
+- `list_mne_versions`
+- `get_mne_file`
+- `get_mne_doc`
+- `find_mne_symbol`
+- `search_mne_docs`
+- `search_mne_issues`
+- `get_mne_issue`
+- `get_mne_issue_comments`
+- `search_mne_forum`
+- `get_mne_forum_topic`
+- `get_symbol_references`
+- `get_related_symbols`
+- `get_mne_changelog`
+- `get_mne_example`
+- `lookup_mne_error`
+## Package Support
+Supported packages:
+- `mne-python` (default)
+- `mne-bids-pipeline`
+- `mne-bids`
+- `mne-connectivity`
+- `mne-nirs`
+- `mne-rsa`
+- `mne-icalabel`
+- `mne-realtime`
+- `mne-lsl`
+- `mne-gui-addons`
+`package` parameter is supported by code/docs/issues/changelog/example/symbol tools.
+Forum tools (`search_mne_forum`, `get_mne_forum_topic`) and `lookup_mne_error` do not take a `package` parameter.
-```bash
-export MNE_GITHUB_TOKEN=ghp_your_token_here
-docker-compose up -d
-docker-compose logs -f
-```
+## Configuration
-## Tools
-| Tool | Description |
-|------|-------------|
-| `list_mne_versions` | List available MNE releases |
-| `get_mne_file` | Fetch source code |
-| `get_mne_doc` | Get symbol documentation |
-| `find_mne_symbol` | Search for symbols |
-| `search_mne_docs` | Unified code/docs search |
-| `search_mne_issues` | Search GitHub issues |
-| `get_mne_issue` | Get issue details |
-| `get_mne_issue_comments` | Get issue comments |
-| `search_mne_forum` | Search community forum |
-| `get_mne_forum_topic` | Get full forum discussion |
-| `get_symbol_references` | Get callees/callers |
-| `get_related_symbols` | Find related functions |
-| `get_mne_changelog` | Get version changes |
-| `get_mne_example` | Get tutorial code |
-| `lookup_mne_error` | Diagnose MNE errors |
-All tools support a `package` parameter to query across the MNE ecosystem: `mne-python` (default), `mne-bids-pipeline`, `mne-bids`, `mne-connectivity`, `mne-nirs`, `mne-rsa`, `mne-icalabel`, `mne-realtime`, `mne-lsl`, `mne-gui-addons`.
+Key environment variables:
-## Configuration
+| Variable | Default | Notes |
+|---|---|---|
+| `MNE_GITHUB_TOKEN` | — | Required |
+| `MNE_TRANSPORT` | `http` | `http` or `stdio` |
+| `MNE_HOST` | `127.0.0.1` | Use `0.0.0.0` in containers |
+| `MNE_PORT` | `8000` | HTTP mode port |
+| `MNE_ALLOWED_ORIGINS` | `*` | CORS/Origin allowlist |
+| `MNE_DEFAULT_PACKAGE` | `mne-python` | Default package |
+| `MNE_PYTHON_PATH` | `python` (Win) / `python3` (Unix) | Parser executable |
+| `MNE_LOG_LEVEL` | `info` | `debug`, `info`, `warn`, `error` |
+| `MNE_LOG_JSON` | `false` | Structured logs |
-| Variable | Description | Default |
-|----------|-------------|---------|
-| `MNE_GITHUB_TOKEN` | GitHub PAT (**required**) | — |
-| `MNE_PORT` | Server port (HTTP mode) | `8000` |
-| `MNE_HOST` | Bind address (use `0.0.0.0` in Docker) | `127.0.0.1` |
-| `MNE_TRANSPORT` | `http` or `stdio` | `http` |
-| `MNE_ALLOWED_ORIGINS` | Comma-separated origins for CORS (use `*` to allow all) | `*` |
-| `MNE_DEFAULT_PACKAGE` | Default MNE package | `mne-python` |
-| `MNE_PYTHON_PATH` | Python executable path | `python` (Win) / `python3` (Unix) |
-| `MNE_LOG_LEVEL` | `debug` / `info` / `warn` / `error` | `info` |
-| `MNE_LOG_JSON` | Emit logs as JSON (useful for log aggregators) | `false` |
+See [.env.example](.env.example) for a minimal local template.
-See `.env.example` for advanced options: cache TTLs (`MNE_CACHE_TTL_MINUTES`, `MNE_SYMBOL_CACHE_TTL_MINUTES`, `MNE_FILE_CACHE_TTL_MINUTES`), timeouts (`MNE_GITHUB_TIMEOUT`, `MNE_PARSER_TIMEOUT`, `MNE_FORUM_TIMEOUT`), and API base URLs.
+## Testing and Diagnostics
-## Architecture
+Full tool test run:
+```bash
+node scripts/run-tests.mjs
 ```
-┌─────────────────────────────────────────────────────────┐
-│  TypeScript Server (Node.js)                            │
-│  ├─ MCP Tools (McpServer API, SDK v1.18+)               │
-│  │  · Tool annotations (readOnly, idempotent, etc.)     │
-│  │  · Structured output + resource_link content        │
-│  ├─ GitHub Client (rate limiting, caching)              │
-│  └─ Python Parser Bridge ──┐                            │
-└────────────────────────────┼────────────────────────────┘
-                             ▼
-                    ┌─────────────────┐
-                    │  Python Parser │
-                    │  (AST, stdlib)  │
-                    └─────────────────┘
-```
-Built with the official [MCP TypeScript SDK](https://github.com/modelcontextprotocol/typescript-sdk). This server conforms to the [Model Context Protocol specification 2025-06-18](https://modelcontextprotocol.io/specification/2025-06-18) (tool annotations, structured output, resource links, Origin validation, Streamable HTTP).
-## Development
+Against another endpoint:
 ```bash
-npm run dev          # Watch mode
-npm run build        # Compile TypeScript
-npm test             # Run tests
-npm run lint         # ESLint
+MNE_MCP_BASE=https://your-server.com/mcp node scripts/run-tests.mjs
 ```
-## Releasing
-### One-command release
+Add timeout guard:
 ```bash
-npm run release:patch   # 1.0.0 → 1.0.1  (bug fixes)
-npm run release:minor   # 1.0.0 → 1.1.0  (new features)
-npm run release:major   # 1.0.0 → 2.0.0  (breaking changes)
+MNE_TOOL_TIMEOUT_MS=20000 node scripts/run-tests.mjs
 ```
-This script (`scripts/release.js`) does everything locally:
-1. Bumps version in `package.json` and `server.json`
-2. Commits both files
-3. Creates a `v*` git tag
-4. Pushes the commit and tag
-Pushing the tag triggers the release pipeline automatically — no further action needed.
+Stable benchmark mode (for slow/stuck investigation):
-### CI/CD pipeline
+```bash
+node scripts/run-tests.mjs --benchmark-stable --warm-pass --stable-runs 3
+```
-Two GitHub Actions workflows handle all automation:
+## Development
-**`ci.yml`** — runs on every push and pull request:
-- TypeScript type checking + ESLint
-- Full test suite (Vitest)
-- Build verification
-- Docker image build test (no push)
+```bash
+npm run dev
+npm run typecheck
+npm run lint
+npm test
+npm run build
+```
-**`release.yml`** — runs only when a `v*` tag is pushed:
+## Release
-```
-test ──┬── docker (linux/amd64) ──┐
-       │                          ├── docker manifest (semver tags) ──┐
-       │── docker (linux/arm64) ──┘                                   ├── GitHub Release
-       │                                                              │
-       ├── npm publish ── MCP Registry ──────────────────────────────┘
+```bash
+npm run release:patch   # or :minor / :major
 ```
-Published artefacts per release:
+The release script:
-| Platform | Tag / identifier |
-|----------|-----------------|
-| GHCR Docker | `ghcr.io/weiyongxu/mne-docs-mcp:1.x.y`, `:1.x`, `:latest` |
-| npm | `mne-docs-mcp@1.x.y` |
-| MCP Registry | `io.github.weiyongxu/mne-docs@1.x.y` |
-| GitHub Releases | auto-generated changelog |
+1. Bumps version (`package.json`)
+2. Updates `server.json`
+3. Stages `package.json`, `package-lock.json`, `server.json`
+4. Commits (`Release vX.Y.Z`)
+5. Tags (`vX.Y.Z`)
+6. Pushes commit and tag
-### Required repository secrets
+Tag push triggers `release.yml`, which publishes:
-| Secret | Purpose |
-|--------|---------|
-| `NPM_TOKEN` | Publish to npm registry |
-| `GITHUB_TOKEN` | Push Docker to GHCR + create GitHub Release (auto-provided) |
-OIDC is used for MCP Registry authentication (no extra secret needed).
+- GHCR Docker image
+- npm package
+- MCP Registry entry
+- GitHub Release
 ## Troubleshooting
-- **Rate limits:** Ensure `MNE_GITHUB_TOKEN` is set
-- **Parser fails:** Check Python 3 is installed (path auto-detected per platform)
-- **Test setup:** Run `node scripts/run-tests.mjs` to verify (requires the server running on your MCP endpoint)
-  - By default the test runner targets `http://localhost:8000/mcp`
-  - Override with `MNE_MCP_BASE`, e.g.:
-    ```bash
-    # Local server on a non-default port
-    MNE_MCP_BASE=http://localhost:8004/mcp node scripts/run-tests.mjs
-    # Remote HTTP server
-    MNE_MCP_BASE=https://your-server.com/mcp node scripts/run-tests.mjs
-    ```
-## Security
-- GitHub token needs only `public_repo` scope — never commit tokens to version control
-- Python parser uses `ast.parse()` only (no code execution)
-- HTTP mode validates the `Origin` header when `MNE_ALLOWED_ORIGINS` is set (comma-separated list); use `*` to allow all (default)
-- By default the server binds to `127.0.0.1`; set `MNE_HOST=0.0.0.0` only when needed (e.g. in Docker)
-- For production: restrict outbound to `api.github.com` and `mne.discourse.group`, don't expose to public internet
+- `401` / `Bad credentials`: verify `MNE_GITHUB_TOKEN`
+- slow code-search tools: use benchmark mode and check `/metrics`
+- parser failures: verify Python path (`MNE_PYTHON_PATH`)
+- endpoint check: `/health` should return `status=healthy`
 ## License

package/dist/tools/getMneExample.d.ts.map CHANGED Viewed

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package/dist/tools/getMneExample.js CHANGED Viewed

@@ -6,6 +6,18 @@ import { READ_ONLY_TOOL_ANNOTATIONS } from './annotations.js';
 import { stripRst } from '../utils/docstring.js';
 import { resolveVersion, buildSourceUrl } from '../utils/helpers.js';
 const logger = getLogger();
+function getNoExamplesSuggestion(pkg) {
+    if (pkg === 'mne-python') {
+        return 'Try broader search terms like "epochs", "filtering", "ICA", or "source"';
+    }
+    return 'This package may not publish many gallery examples. Use search_mne_docs, then open matching files via get_mne_file (for mne-bids-pipeline, start with mne_bids_pipeline/_config.py).';
+}
+function getFetchFailureSuggestion(pkg) {
+    if (pkg === 'mne-python') {
+        return 'The examples may have moved. Try searching with different terms.';
+    }
+    return 'Examples were found but could not be retrieved. Use search_mne_docs + get_mne_file to inspect package docs/source files directly.';
+}
 const GetMneExampleParamsSchema = z.object({
     query: z.string().trim().min(1, 'Query is required'),
     maxResults: z.number().int().min(1).max(20).optional().default(5),
@@ -36,6 +48,8 @@ export async function getMneExample(params, context) {
     const { query, maxResults, version, summaryOnly, maxCodeLines, package: packageName } = GetMneExampleParamsSchema.parse(params);
     const pkg = packageName || 'mne-python';
     const packageInfo = getPackageInfo(pkg);
+    const noExamplesSuggestion = getNoExamplesSuggestion(pkg);
+    const fetchFailureSuggestion = getFetchFailureSuggestion(pkg);
     const resolvedVersion = await resolveVersion(version, context.github, packageName);
     logger.debug(`Searching examples for: ${query} in ${pkg} (version ${resolvedVersion})`);
     const isGalleryPath = (path) => path.startsWith('examples/') || path.startsWith('tutorials/');
@@ -69,7 +83,7 @@ export async function getMneExample(params, context) {
     if (combinedItems.length === 0) {
         throw new McpError('FILE_NOT_FOUND', `No examples found for query: ${query}`, {
             details: `Package: ${pkg}`,
-            suggestion: 'Try broader search terms like "epochs", "filtering", "ICA", or "source"',
+            suggestion: noExamplesSuggestion,
         });
     }
     const candidates = combinedItems.filter(item => {
@@ -135,7 +149,7 @@ export async function getMneExample(params, context) {
     if (examples.length === 0) {
         throw new McpError('FILE_NOT_FOUND', `Could not fetch any examples for: ${query}`, {
             details: `Package: ${pkg}`,
-            suggestion: 'The examples may have moved. Try searching with different terms.',
+            suggestion: fetchFailureSuggestion,
         });
     }
     return {

package/dist/tools/getMneExample.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/tools/searchMneDocs.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"searchMneDocs.d.ts","sourceRoot":"","sources":["../../src/tools/searchMneDocs.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AACxB,OAAO,EAAE,YAAY,EAAE,WAAW,EAAqC,MAAM,aAAa,CAAC;AAa3F,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;CAWtB,CAAC;~~AA8BF~~,wBAAsB,aAAa,CAC/B,MAAM,EAAE,OAAO,EACf,OAAO,EAAE,WAAW,GACrB,OAAO,CAAC,YAAY,CAAC,~~CA8GvB~~;AAED,OAAO,EAAE,aAAa,IAAI,OAAO,EAAE,CAAC"}
1	+ {"version":3,"file":"searchMneDocs.d.ts","sourceRoot":"","sources":["../../src/tools/searchMneDocs.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AACxB,OAAO,EAAE,YAAY,EAAE,WAAW,EAAqC,MAAM,aAAa,CAAC;AAa3F,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;CAWtB,CAAC;AAyCF,wBAAsB,aAAa,CAC/B,MAAM,EAAE,OAAO,EACf,OAAO,EAAE,WAAW,GACrB,OAAO,CAAC,YAAY,CAAC,CAuHvB;AAED,OAAO,EAAE,aAAa,IAAI,OAAO,EAAE,CAAC"}

package/dist/tools/searchMneDocs.js CHANGED Viewed

@@ -40,11 +40,21 @@ function addUniqueItems(target, incoming) {
         target.push(item);
     }
 }
+function getDocsPathPrefixes(packageName) {
+    if (packageName === 'mne-python') {
+        return ['doc/', 'docs/'];
+    }
+    return ['docs/', 'doc/'];
+}
+function isDocsPath(path, docsPathPrefixes) {
+    return docsPathPrefixes.some(prefix => path.startsWith(prefix));
+}
 export async function searchMneDocs(params, context) {
     const { query, version, maxResultsPerSource = 5, package: packageName } = SearchMneDocsParamsSchema.parse(params);
     const normalizedQuery = query.replace(/\s+/g, ' ').trim();
     const pkg = packageName || 'mne-python';
     const packageInfo = getPackageInfo(pkg);
+    const docsPathPrefixes = getDocsPathPrefixes(pkg);
     const resolvedVersion = await resolveVersion(version, context.github, packageName);
     // Check cache - include package and maxResultsPerSource in key for consistency
     const cacheKey = `${pkg}:${normalizedQuery.toLowerCase()}:${maxResultsPerSource}`;
@@ -67,7 +77,7 @@ export async function searchMneDocs(params, context) {
     try {
         const broadResults = await context.github.searchCode(normalizedQuery, { version: resolvedVersion, perPage: broadPerPage, packageName, textMatches: true });
         for (const item of broadResults.items) {
-            if (item.path.startsWith('doc/')) {
+            if (isDocsPath(item.path, docsPathPrefixes)) {
                 docItems.push(item);
             }
             else if (item.path.startsWith(packageInfo.sourcePath)) {
@@ -97,12 +107,21 @@ export async function searchMneDocs(params, context) {
         }
         if (docItems.length === 0) {
             topUps.push((async () => {
-                try {
-                    const docsResults = await context.github.searchCode(`${normalizedQuery} path:doc/`, { version: resolvedVersion, perPage: maxResultsPerSource, packageName, textMatches: true });
-                    addUniqueItems(docItems, docsResults.items);
-                }
-                catch (error) {
-                    logger.warn('Docs top-up search failed in search_mne_docs', { query: normalizedQuery, package: pkg, error });
+                for (const docsPath of docsPathPrefixes) {
+                    try {
+                        const docsResults = await context.github.searchCode(`${normalizedQuery} path:${docsPath}`, { version: resolvedVersion, perPage: maxResultsPerSource, packageName, textMatches: true });
+                        addUniqueItems(docItems, docsResults.items);
+                        if (docItems.length > 0)
+                            break;
+                    }
+                    catch (error) {
+                        logger.warn('Docs top-up search failed in search_mne_docs', {
+                            query: normalizedQuery,
+                            package: pkg,
+                            docsPath,
+                            error,
+                        });
+                    }
                 }
             })());
         }

package/dist/tools/searchMneDocs.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "mne-docs-mcp",
-  "version": "1.0.29",
+  "version": "1.0.31",
   "mcpName": "io.github.weiyongxu/mne-docs",
   "description": "MCP server providing access to MNE-Python documentation, source code, GitHub issues, and community forum",
   "type": "module",