cocoindex-mcp 0.0.1.2

MCP server for querying cocoindex code embeddings database

cocoindex-mcp

Semantic code search for Model Context Protocol clients, powered by cocoindex flows and a Postgres + pgvector backend.

---

At a glance

• 🔍 Semantic search over the embeddings produced by the cocoindex CodeEmbedding flow.
• 🤝 MCP-native stdio server that drops straight into Claude Desktop, Cursor, and other MCP hosts.
• ⚙️ Zero-surprise configuration via a single COCOINDEX_DATABASE_URL environment variable (with .env support).
• 🚀 Packaged for uv – run it instantly with uvx --from yalattas/cocoindex-mcp cocoindex-mcp.

Table of contents

• At a glance
• How it works
• Prerequisites
• Quick start
• Configuration
• Running the server
• Available MCP tools
• Troubleshooting
• Local development
• Contributing
• License

How it works

The server wraps a cocoindex flow that embeds local source files into a Postgres table called code_embeddings. Every query is transformed with the same SentenceTransformer model and matched against the stored vectors using cosine similarity via pgvector. Results are streamed back to the MCP client with file paths, the matched snippet, score, and optional line numbers.

Internally the server is built with:

• mcp.server.fastmcp to expose stdio-based MCP tools.
• cocoindex for defining and running the embedding flow.
• psycopg_pool and pgvector for high-throughput vector queries.
• python-dotenv to honor environment files automatically.

Prerequisites

1. Python ≥ 3.11 (only needed for local installs; uvx ships its own runtime).
2. PostgreSQL with the pgvector extension enabled.
3. A code_embeddings table populated by running the CodeEmbedding cocoindex flow (see src/cocoindex_mcp/search.py).
4. Credentials with read access to the embeddings table.

If you're starting from scratch, run the cocoindex flow once to generate the embeddings. The flow definition lives in this repository and targets the code_embeddings table by default.

Quick start

Run without installing (recommended)

uvx --from yalattas/cocoindex-mcp cocoindex-mcp --help

Pass any CLI options after cocoindex-mcp. Use --env (or a .env file) to supply the Postgres URL when launching via uvx.

Install into an existing environment

uv pip install cocoindex-mcp

or with plain pip:

pip install cocoindex-mcp

Verify the installation:

cocoindex-mcp --version

Configuration

Set the database connection string before starting the server:

export COCOINDEX_DATABASE_URL="postgres://user:password@localhost:5432/cocoindex"

Environment variables are loaded from a .env file automatically:

echo 'COCOINDEX_DATABASE_URL=postgres://user:password@localhost:5432/cocoindex' >> .env

Minimum database requirements

• CREATE EXTENSION IF NOT EXISTS vector;
• A code_embeddings table with columns: filename, code, embedding vector, start, end.
• A compatible cocoindex-generated vector index (cosine similarity).

If the connection fails, the CLI surfaces descriptive errors that include the masked Postgres host/DB to help with debugging.

Running the server

The server communicates over stdio, which is the preferred transport for MCP clients.

Choose the entrypoint that best fits your workflow:

• uvx --from yalattas/cocoindex-mcp cocoindex-mcp
• cocoindex-mcp (console script exposed after installation)
• python -m cocoindex_mcp
• python main.py

All of these entrypoints share the same FastMCP runtime configured in src/cocoindex_mcp/cli.py.

Example Claude Desktop configuration

{
  "mcpServers": {
    "cocoindex": {
      "command": "uvx",
      "args": [
        "--from",
        "yalattas/cocoindex-mcp",
        "cocoindex-mcp"
      ],
      "env": {
        "COCOINDEX_DATABASE_URL": "postgres://user:password@localhost:5432/cocoindex"
      }
    }
  }
}

CLI options

cocoindex-mcp [--log-level LEVEL] [--version]

  --log-level   CRITICAL | ERROR | WARNING | INFO | DEBUG (default: INFO)
  --version     Print the installed version and exit

Use --log-level DEBUG while integrating to see the Postgres readiness checks and tool invocations.

Available MCP tools

Tool	Description	Parameters
cocoindex_search	Perform a semantic search and return filename, snippet, similarity score, and optional line range.	query (str, required) · limit (int, default 10, range 1–50)
cocoindex_info	Inspect the server's metadata, environment requirements, and exposed tools.	None

Errors raised by the underlying database connectivity (missing URL, connection refused, etc.) are surfaced as structured error messages in the tool response.

Troubleshooting

Symptom	Likely cause	Fix
COCOINDEX_DATABASE_URL is not set	Environment variable missing.	Export the variable or add it to .env before launching.
Could not connect to Postgres ...	Credentials, host, or pgvector extension not available.	Confirm the URL, ensure the database is reachable, enable the vector extension.
Empty search results	Embeddings table not populated or query too specific.	Run the cocoindex CodeEmbedding flow; try a broader query or higher limit.

Enable debug logging (--log-level DEBUG) to display stack traces and raw SQL queries if you need deeper insight.

Local development

Clone the repository and install dependencies using uv:

uv sync

Run the server locally:

uv run python -m cocoindex_mcp --no-banner --log-level DEBUG

Useful entrypoints:

• src/cocoindex_mcp/search.py – cocoindex flow and search helpers.
• src/cocoindex_mcp/db.py – connection pooling and diagnostics.
• src/cocoindex_mcp/config.py – FastMCP server wiring and tool definitions.

Publishing to PyPI

PyPI removed password-based uploads in 2023, so you'll need either an API token or a trusted publisher workflow to ship new releases.

Using a PyPI API token (local uploads)

1. Create a token: In your PyPI account, go to Account settings → API tokens and create a token scoped to cocoindex-mcp (or scoped to an entire account if you prefer).
2. Keep it secret: Store the issued value (it starts with pypi-) in a secure credential store or as an environment variable. For a one-off upload you can export it temporarily:

export UV_PUBLISH_TOKEN="pypi-xxxxxxxxxxxxxxxxxxxxxxxxxxxx"

1. Build the distribution:

uv build

1. Publish:

uv publish

uv will automatically pick up UV_PUBLISH_TOKEN. Alternatively, pass it inline with uv publish --token pypi-….

Pro tip: bump the version in pyproject.toml before publishing; PyPI rejects duplicate versions.

Using trusted publishers (CI uploads)

If you're publishing from GitHub Actions, enable trusted publishing instead of storing long-lived secrets:

uv publish --trusted-publishing automatic

This flag only configures the workflow file uv will generate; it does not allow local uploads without a token. For manual publishes you still need UV_PUBLISH_TOKEN as described above.

Follow the PyPI trusted publisher docs to register your repository. Once activated, the workflow OIDC identity replaces tokens entirely during CI runs on GitHub.

Contributing

Issues and pull requests are welcome at yalattas/cocoindex-mcp. If you're proposing a new tool or changing the database schema, please include integration notes and update the README accordingly.

License

This project is licensed under the terms of the MIT License.