overgraph 0.2.0

An absurdly fast embedded graph database for Python. Sub-microsecond reads, pure Rust core.

OverGraph

An absurdly fast embedded graph database.
Pure Rust. Sub-microsecond reads. Native connectors for Node.js and Python.
Built for AI agent memory, knowledge graphs, and analytics.

overgraph.io

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OverGraph is a graph database that runs inside your process. No server, no network calls, no Docker containers. You open a directory, and you have a full graph database with temporal edges, weighted relationships, and sub-microsecond lookups.

I built it because I wanted a graph database that was genuinely fast. Not "fast for a database," but fast enough that you forget it's there. Node lookups in 200 nanoseconds. Neighbor traversals in 2 microseconds. Batch writes at 600K+ nodes per second. And I wanted it to work everywhere I work: Rust, Node.js, and Python, all backed by the same engine.

It's written entirely in Rust and it ships native connectors for Node.js (napi-rs) and Python (PyO3) so you can use it from whatever you're building in.

Built for

• AI agent memory. Store conversations, tool outputs, entity relationships. Decay scoring ages out stale context automatically.
• Knowledge graphs. Domain ontologies with shortest path queries, degree analysis, and structure exploration.
• Recommendation engines. Collaborative filtering through graph traversal. PPR from seed items, top-K by weight.
• RAG pipelines. Graph-augmented retrieval. Export adjacency for GNN input, PageRank for context ranking.
• Social and network analysis. Degree centrality, shortest paths, and connectivity checks. The building blocks of network science.
• Fraud detection. Spot suspicious structures through connectivity patterns and graph algorithms.

What makes it different

• Truly embedded. No separate process. No socket. Your database is a folder on disk. Copy it, move it, back it up with cp -r.
• Rich graph primitives. Weighted nodes and edges, temporal validity windows, exponential decay scoring, automatic retention policies. Model relationships that evolve over time, and let the graph clean up what's no longer relevant.
• Fast where it matters. Node lookups in ~200ns. Neighbor traversal in ~2μs. Batch writes at 600K+ nodes/sec. The storage engine is a log-structured merge tree with mmap'd immutable segments, so reads never block writes.
• Three languages, one engine. Rust core with native bindings for Node.js (napi-rs) and Python (PyO3). Not a wrapper around a REST API. Actual FFI into the same Rust engine, with <3x overhead on most operations.
• No query language. Just functions. upsert_node, neighbors, find_nodes. If you can call a function, you can use OverGraph.

Performance

All numbers from a real benchmark suite running on the Rust core (group-commit durability mode, small profile: 10K nodes / 50K edges). Full methodology and reproducibility guide in docs/04-quality/Benchmark-Methodology.md.

Operation	Latency	Throughput
get_node	0.2 μs	5.5M ops/s
upsert_node	2.2 μs	807K ops/s
neighbors (1-hop)	2.1 μs	541K ops/s
batch_upsert_nodes (100)	236 μs	625K nodes/s
top_k_neighbors	17.5 μs	81K ops/s
personalized_pagerank	254 μs	4.3K ops/s

Node.js and Python connectors add roughly 1.5-3x overhead depending on the operation. Batch operations are nearly 1:1 because they amortize the FFI boundary cost. Full cross-language comparison in the launch benchmark pack.

Install

Prebuilt binaries are available for macOS (ARM + Intel), Linux (x64), and Windows (x64). No Rust toolchain required.

Rust

cargo add overgraph

Node.js

npm install overgraph

Python

pip install overgraph

Quick start

Rust

use overgraph::{DatabaseEngine, DbOptions, Direction, PropValue};
use std::collections::BTreeMap;
use std::path::Path;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let mut db = DatabaseEngine::open(Path::new("./my-graph"), &DbOptions::default())?;

    // Create some nodes
    let mut props = BTreeMap::new();
    props.insert("name".into(), PropValue::String("Alice".into()));
    props.insert("role".into(), PropValue::String("engineer".into()));
    let alice = db.upsert_node(1, "user:alice", props, 1.0)?;

    let mut props = BTreeMap::new();
    props.insert("status".into(), PropValue::String("active".into()));
    let project = db.upsert_node(2, "project:overgraph", props, 0.9)?;

    // Connect them
    let _edge = db.upsert_edge(alice, project, 10, Default::default(), 1.0, None, None)?;

    // Traverse
    let neighbors = db.neighbors(alice, Direction::Outgoing, Some(&[10]), 50, None, None)?;
    println!("Alice is connected to {} nodes", neighbors.len());

    db.close()?;
    Ok(())
}

Node.js

import { OverGraph } from 'overgraph';

const db = await OverGraph.openAsync('./my-graph');

// Create nodes
const [alice, project] = await db.batchUpsertNodesAsync([
  { typeId: 1, key: 'user:alice', props: { name: 'Alice', role: 'engineer' }, weight: 1.0 },
  { typeId: 2, key: 'project:overgraph', props: { status: 'active' }, weight: 0.9 },
]);

// Connect them
await db.upsertEdgeAsync(alice, project, 10, { role: 'creator' }, 1.0);

// Traverse
const neighbors = await db.neighborsAsync(alice, 'outgoing', [10], 50);
console.log(`Alice is connected to ${neighbors.length} nodes`);

await db.closeAsync();

Python

from overgraph import OverGraph

with OverGraph.open("./my-graph") as db:
    # Create nodes
    alice = db.upsert_node(1, "user:alice",
        props={"name": "Alice", "role": "engineer"}, weight=1.0)
    project = db.upsert_node(2, "project:overgraph",
        props={"status": "active"}, weight=0.9)

    # Connect them
    db.upsert_edge(alice, project, 10, props={"role": "creator"}, weight=1.0)

    # Traverse
    neighbors = db.neighbors(alice, "outgoing", type_filter=[10], limit=50)
    print(f"Alice is connected to {len(neighbors)} nodes")

Or async:

from overgraph import AsyncOverGraph

async with await AsyncOverGraph.open("./my-graph") as db:
    alice = await db.upsert_node(1, "user:alice", props={"name": "Alice"})
    neighbors = await db.neighbors(alice, "outgoing")

Features

Core graph operations

• Upsert semantics. Nodes are keyed by (type_id, key). Upsert the same key twice and you get an update, not a duplicate. Edges can optionally enforce uniqueness on (from, to, type_id).
• Batch operations. batch_upsert_nodes and batch_upsert_edges amortize WAL and memtable overhead. There's also a packed binary format for maximum throughput.
• Atomic graph patch. graph_patch lets you upsert nodes, upsert edges, delete nodes, delete edges, and invalidate edges in a single atomic operation.

Temporal edges

• Validity windows. Edges have optional valid_from and valid_to timestamps. Query at any point in time with the at_epoch parameter and only see edges that were valid at that moment.
• Edge invalidation. Mark an edge as no longer valid without deleting it. The history is preserved.
• Decay scoring. Pass a decay_lambda to neighbor queries and edge weights are automatically scaled by exp(-lambda * age_hours). Recent connections matter more.

Queries and traversal

• Neighbors and bounded traversal. neighbors() handles 1-hop expansion; traverse() covers deterministic breadth-first traversal across arbitrary depth windows with optional edge-type filtering, emission-only node-type filtering, and traversal-specific pagination.
• Depth slices without special-case APIs. Exact depth-2 traversals are expressed as traverse(..., min_depth=2, max_depth=2, ...), so the old 2-hop use cases stay available without a separate public method family.
• Top-K neighbors. Get the K highest-scoring neighbors by weight, recency, or decay-adjusted score.
• Personalized PageRank. Run PPR from seed nodes to find the most relevant nodes in the graph. Useful for context retrieval in RAG pipelines.
• Subgraph extraction. Pull out a connected subgraph up to N hops deep. Good for building local context windows.
• Shortest path. BFS (unweighted) or bidirectional Dijkstra (weighted). is_connected for fast reachability checks. all_shortest_paths when there are ties.
• Connected components. connected_components() returns a global WCC labelling (union-find, near-linear). component_of(node) returns the members of a single node's component via BFS. Both support edge-type, node-type, and temporal filters.
• Degree counts. Count edges, sum weights, and compute averages without materializing neighbor lists. Batch degrees for bulk analysis.
• Property search. Find nodes by type_id + property equality. Hash-indexed for O(1) lookup.
• Time-range queries. Find nodes created or updated within a time window. Sorted timestamp index for efficient range scans.

Pagination

ID-keyed collection APIs use keyset pagination with limit and after. traverse() uses limit plus a traversal cursor keyed by (depth, node_id). No offset-based pagination. Traversal cursors assume the same query arguments and a stable logical graph state; strict snapshot isolation across intervening writes is not promised.

Retention and pruning

• Manual prune. Drop nodes older than X, below weight Y, or matching type Z. Incident edges cascade automatically.
• Named prune policies. Register policies like "short_term_memory" that run automatically during compaction. Nodes matching any policy are invisible to reads immediately (lazy expiration) and cleaned up during the next compaction pass.

Storage engine

• Write-ahead log. Every mutation hits the WAL before the memtable. Crash recovery replays the WAL on startup.
• Configurable durability. Immediate mode fsyncs every write for maximum safety. GroupCommit mode (default) batches fsyncs on a 10ms timer for ~20x better write throughput with at most one timer interval of data at risk.
• Background compaction. Segments are merged automatically when thresholds are met. Compaction runs on a background thread and never blocks reads or writes. Uses metadata sidecars for fast filtered merging without full record decoding.
• mmap'd reads. Immutable segments are memory-mapped. The OS page cache handles caching. Reads never block writes.
• Portable databases. Each database is a self-contained directory. cp -r ./my-db /backup/my-db and you're done.

How it works

OverGraph uses a log-structured storage engine purpose-built from scratch in pure Rust. Unlike generic LSM key-value stores, every segment is a fully indexed graph structure. Adjacency lists, label indexes, and temporal indexes are all materialized at flush time, not just at compaction. Reads are near-optimal the moment data hits disk, while writes stay append-only and fast.

Write path: Mutations are appended to a write-ahead log and applied to an in-memory memtable. When the memtable reaches its threshold, it's frozen and flushed to disk as an immutable segment in the background. Writes continue unblocked against a fresh memtable. Each segment ships with pre-built adjacency indexes (inbound and outbound), so neighbor lookups are direct index hits, never key-range scans.

Read path: Queries check the memtable first (freshest data), then merge results across immutable segments using the per-segment indexes. Because every segment carries its own adjacency index, a neighbor query is a handful of index lookups, not a scan across sorted keys. Pagination uses early termination to avoid unnecessary work.

Compaction: A background thread merges older segments together, applying tombstones, prune policies, and deduplication. The compaction path uses metadata sidecars to plan merges and raw-copies winning records without full deserialization, then rebuilds unified indexes from metadata. Fewer segments after compaction means fewer index lookups per query, but even before compaction, reads are fast because every segment is self-indexed.

On-disk layout:

my-graph/
  manifest.current    # atomic checkpoint (JSON)
  data.wal            # append-only write-ahead log
  segments/
    seg_0001/
      nodes.dat       # node records
      edges.dat       # edge records
      adj_out.idx     # outgoing adjacency index
      adj_in.idx      # incoming adjacency index
      key_index.dat   # (type_id, key) -> node_id
      type_index.dat  # type_id -> [id...]
      tombstones.dat  # deleted IDs
    seg_0002/
      ...

For a deeper dive, see the architecture overview.

API reference

• Rust: Run cargo doc --open to browse the full rustdoc. All public types and methods are documented.
• Node.js: See the TypeScript declarations for the complete API surface. Every method has a sync and async variant.
• Python: See the type stubs for the complete API surface. Both sync (OverGraph) and async (AsyncOverGraph) classes are available.

Running the benchmarks

# Rust
scripts/bench/run-rust.sh --profile small --warmup 20 --iters 80

# Node.js
scripts/bench/run-node.sh --profile small --warmup 20 --iters 80

# Python
scripts/bench/run-python.sh --profile small --warmup 20 --iters 80

Benchmark methodology, FAQ, and reproducibility instructions are in docs/04-quality/.

Building from source

# Rust core
cargo build --release
cargo test

# Node.js connector
cd overgraph-node
npm install
npm run build
npm test

# Python connector
cd overgraph-python
pip install maturin
maturin develop
pytest

Contributing

See CONTRIBUTING.md for build instructions, coding conventions, and how to submit a pull request.

License

Licensed under either of

• MIT License
• Apache License, Version 2.0

at your option.