Hypabase

by hypabase

327 downloads

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GitHub

About

Hypergraph database for AI agents. Store n-ary relationships (edges connecting 2+ nodes), track provenance (source and confidence), and query paths — all backed by local

Details

Author: hypabase
Downloads: 327
Categories: Other, Database, Knowledge Base

- Hyperedges connecting 2+ nodes in a single relationship
- Provenance tracking: every edge carries source and confidence
- SQLite persistence to a local file automatically
- O(1) vertex‑set lookup for exact node sets
- Namespace isolation via .database("name") within a single file
- MCP server with 14 tools and 2 resources for AI agents
- CLI for initialisation, nodes, edges, and queries

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below
Plugin Name Hypabase

Command (node, npx, python, etc.) hypabase-mcp
Environment
- HYPABASE_DB_PATH hypabase.db
Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

From the repository

Install via uv add hypabase (or uv add hypabase[mcp] for the MCP server, uv add hypabase[cli] for CLI). Use the Python API to create a Hypabase("file.db") instance, then call .edge(), .edges(), .paths(), .node(), .nodes(), .sources(), etc. Run the MCP server with hypabase mcp. CLI commands include hypabase init, hypabase node, hypabase edge, hypabase query, and hypabase stats.

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "hypabase": {
            "command": "hypabase-mcp",
            "env": {
                "HYPABASE_DB_PATH": "hypabase.db"
            }
        }
    }
}

Command

"hypabase-mcp"

Env

{
    "HYPABASE_DB_PATH": "hypabase.db"
}

Hypabase

A Python hypergraph library with provenance and SQLite persistence.

Install

uv add hypabase

Quick example

```python
from hypabase import Hypabase

hb = Hypabase("my.db")

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Details

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Setting up with Highlight

From the repository

Claude Desktop / Cursor

Command

Env

Hypabase

Install

Quick example

Install

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