kglite 0.14.0

Embedded Cypher knowledge graph for Python with a bundled MCP server and describe() schema for LLM agents

KGLite — Knowledge graph for Python, built for LLM agents

KGLite is an embedded, Cypher-queryable knowledge graph for Python, built so you can hand it to an LLM agent. pip install kglite, shape your data as DataFrames, and query it with Cypher — your first graph in seconds. The 18 MB wheel links zero network code and ships a bundled MCP server, a describe() method that emits a system-prompt-shaped schema, and structural validators that compose with Cypher.

kglite is a pure-Rust knowledge graph engine (crates/kglite) packaged for Python via pip install kglite. The interactive shell, Bolt-server, and MCP-server binaries are sibling Rust crates wrapping the same engine. If you want kglite as a Rust library — without the Python wheel in your build — see Use from Rust below.

Interactive shell. pip install kglite also gives you the kglite command — a sqlite3-style REPL: kglite app.kgl opens a Cypher prompt with .import, .dump, .schema, multi-line input, and tab-completion. For a standalone CLI-only install, use pip install kglite-cli or cargo install kglite-cli.

Ecosystem

kglite is the engine. Two companion projects build graphs it serves — each released and versioned on its own cadence:

• kglite — the embedded Cypher knowledge-graph engine (this project): graph + Cypher + fluent API + bundled MCP server.
• codingest — parses codebases into code graphs (14 languages, web-framework route detection). Build with it, query the .kgl here. Requires kglite ≥ 0.14.
• kglite-datasets — fetch-build-cache loaders for public registries (SEC EDGAR, Wikidata, Sodir).

Upgrading from 0.13? The code-graph builder and dataset loaders moved out of the wheel in 0.14 — see the 0.13 → 0.14 migration guide. Pin back anytime with pip install "kglite<0.14".

Use cases

The same agent-facing surface works whether the graph holds legal precedents, a Wikidata slice, a SQL warehouse, a RAG corpus, or a parsed codebase.

• 🏛️ Domain knowledge for agents. Legal precedents + citations, regulatory rules, medical ontologies, manufacturing BOMs, scientific catalogues — anything with structure becomes a queryable graph an MCP-capable agent can reason over. See the legal-graph example for a Norwegian-Supreme-Court walk-through (laws + decisions + citation edges + judge metadata).
• 📊 Business data → queryable graph. Any tabular source — SQL, CSV, Parquet, REST API responses, pandas DataFrames — goes straight in via add_nodes(df, ...) and add_connections(df, ...). Layer a graph on top of your warehouse and the agent reasons over the relationships without you writing a server. → Data Loading guide.
• 🌐 Public datasets. Pre-packaged loaders for SEC EDGAR, Wikidata, and Sodir live in the companion kglite-datasets project — they handle the fetch + build + cache cycle and return a queryable KnowledgeGraph. kglite's mapped and disk storage then query graphs that don't fit in RAM — a billion-edge Wikidata graph on a 16 GB laptop. → See Public datasets below.
• 📚 RAG with structure. Documents, chunks, entities, and the edges between them in one graph. Combine text_score() vector similarity with Cypher traversal — "find court cases semantically similar to my fact pattern, then walk one hop to related precedents" — hybrid retrieval in one query, no second vector DB. Scale to large corpora with an opt-in HNSW index (build_vector_index()). → Semantic Search guide.
• 📂 Codebase analysis. The codingest builder parses 14 languages into Function / Class / Module / Route nodes with web-framework route detection (Flask, FastAPI, Django). Build from any git revision, or merge several into one multi-revision graph for structural diffs (multi-rev builds). kglite serves and queries those graphs. The builder and the code → Claude Desktop workflow live in the codingest project.
• 🤝 A shared graph as an agent contract. One .kgl can be the two-way contract between collaborating agents (e.g. a research agent that batch-rebuilds specs and coding agents that plan and mutate status live). The primitives that make this safe are first-class: ownership layers (define_schema(layer='managed'|'runtime') + add_nodes(managed_reload=True) so a rebuild provably can't clobber agent-owned nodes), role-scoped writes (cypher(..., write_scope=[...]) rejects out-of-scope CREATE/SET), a verbatim instructions slot at the top of describe() (set_instructions(text)), native list properties, JSON-native ingestion (from_records(spec)), and a dependency frontier (CALL ready_set(...)) to find the next actionable work. Keep the graph general — these are small, opt-in building blocks, not a baked-in workflow.
• 🧠 Markdown knowledge bases & agent memory. kglite.okf.build(dir) ingests an Open Knowledge Format bundle — or a Claude memory dir, skills folder, or Obsidian vault — into a graph: frontmatter → node properties, markdown links → typed edges. Then cluster it (CALL leiden), find orphaned or stale notes, and surface dangling references — the query engine OKF itself doesn't ship. → OKF guide.

Why Cypher?

Questions over connected data — which insiders sold this stock, who sits on two boards, what cites this case — are pattern matches. In SQL they become multi-table joins; in Cypher the pattern is the query:

-- Insider sells, most recent first
MATCH (t:InsiderTransaction {direction: 'sale'})-[:BY_INSIDER]->(p:Person)
MATCH (t)-[:IN_COMPANY]->(c:Company)
RETURN p.title, c.title, t.shares, t.price_per_share
ORDER BY t.transaction_date DESC LIMIT 10

Cypher pays off most when the data has real structure and your questions traverse it.

How it compares

	KGLite	LadybugDB (formerly Kuzu)	NetworkX	rustworkx	Neo4j Embedded
Install	pip install kglite	pip install ladybug	pip install networkx	pip install rustworkx	JVM + Java deps
Query language	Cypher (broad coverage)	Cypher	Python API	Python API	Cypher (full)
Storage	in-mem · mmap · disk (1B+ edges)	in-mem · disk (columnar)	in-mem	in-mem	in-mem · disk (JVM)
Bulk-load from pandas	one-liner	via Arrow	manual	manual	via driver
MCP server for LLM agents	bundled in the kglite wheel	separate mcp-server-ladybug install	—	—	—
describe() schema for LLM prompts	✅	—	—	—	—
Embeddable in Rust (no Python in build)	pure-Rust kglite crate	lbug bindings to the C++ engine	—	✅	—
License	MIT	MIT	BSD-3	Apache-2	GPLv3

Pick KGLite when you want one embedded package that combines Python and pure-Rust Cypher APIs with a bundled MCP binary, prompt-shaped describe(), and agent-contract primitives: role-scoped writes (write_scope), ownership layers, set_instructions, and CALL ready_set(...) — with companion projects (codingest, kglite-datasets) that build code and public-registry graphs it serves. Pick LadybugDB when columnar analytical scans and its broader language ecosystem are the priority; it also provides Rust bindings and a separately installed MCP server. Pick NetworkX when you need its enormous graph-algorithm library and your data fits in RAM. Pick rustworkx when you want a Rust-backed Python graph API with no query language. Pick Neo4j Embedded when you've standardised on server-mode Cypher and want the in-process driver for tests.

📊 Benchmarks → — wall-to-wall time per topic (load, filter/aggregate, traversal, pathfinding, algorithms, mutations) against other embedded graph engines, NetworkX, rustworkx, igraph, and DuckDB on one shared synthetic graph. Reproduce with python benchmarks/benchmark.py.

Quick Start

# Python (the headline distribution path)
pip install kglite

# Optional extras
pip install 'kglite[pandas]'   # DataFrame loading used in the walkthrough below
pip install fastembed            # (or sentence-transformers) embedding models for text_score() — bring your own
pip install 'kglite[neo4j]'      # Neo4j Python driver for Bolt-server tests

import pandas as pd
import kglite

# Three storage modes — pick by graph size:
#   default (in-memory)   — small/medium graphs, fastest queries
#   storage="mapped"      — mmap columns, RAM-friendly as you grow
#   storage="disk", path=…  — 100M+ nodes, Wikidata-scale, loaded lazily
graph = kglite.KnowledgeGraph()

# Bulk-load nodes from a DataFrame.
people = pd.DataFrame({
    "id":   ["alice", "bob", "eve"],
    "name": ["Alice", "Bob", "Eve"],
    "age":  [28, 35, 41],
    "city": ["Oslo", "Bergen", "Trondheim"],
})
graph.add_nodes(people, node_type="Person", unique_id_field="id", node_title_field="name")

# Bulk-load relationships the same way.
knows = pd.DataFrame({"src": ["alice", "bob"], "tgt": ["bob", "eve"]})
graph.add_connections(knows, connection_type="KNOWS",
                      source_type="Person", source_id_field="src",
                      target_type="Person", target_id_field="tgt")

# Query — returns a ResultView (lazy; data stays in Rust until accessed).
for row in graph.cypher("""
    MATCH (p:Person) WHERE p.age > 30
    RETURN p.name AS name, p.city AS city
    ORDER BY p.age DESC
"""):
    print(row['name'], row['city'])

# Or get a pandas DataFrame directly.
df = graph.cypher("MATCH (p:Person) RETURN p.name, p.age ORDER BY p.age", to_df=True)

# Persist to disk and reload. save() is atomic + fsync by default (crash-safe —
# no torn file); load() raises a typed kglite.FileFormatError on a corrupt file.
graph.save("my_graph.kgl")
loaded = kglite.load("my_graph.kgl")

# Or serialize to/from bytes (no filesystem path):
blob = graph.to_bytes(); loaded = kglite.from_bytes(blob)

# Share read-only across threads with an immutable, lock-free snapshot:
snapshot = graph.freeze()        # concurrent snapshot.cypher(...) from many threads

# No data yet? Generate a realistic demo graph in one line (bundled, no extra deps):
demo = kglite.graphgen("medium")               # ~25k nodes, ready to query
# kglite.graphgen("huge", out="/tmp/g")        # stream millions of nodes to CSV, bounded memory

→ Getting Started guide · Cypher reference · API reference.

Prefer a runnable file? examples/csv_to_graph.py loads real CSVs end to end.

Serve it to an agent

The skill above is the zero-configuration review path. Use the MCP server when you want a graph kept warm across many calls, typed tool schemas, watch-mode refresh, root switching, or cached public-repository and source tools.

One command — any .kgl becomes an MCP server

kglite-mcp-server --graph path/to/graph.kgl

The server exposes cypher_query, graph_overview, schema introspection, structural validators, and source-file tools over MCP stdio. Drop it into Claude Desktop / Cursor / any MCP-capable client and your graph is queryable. Works on every graph kglite can build — your own, Wikidata, Sodir, code graphs.

When you register it, point command at the absolute path to the binary (/abs/path/to/venv/bin/kglite-mcp-server), not a bare name — a bare command can silently launch an older PATH-shadowing install. Then confirm it with kglite-mcp-server --selftest --graph path/to/graph.kgl, which drives a real handshake and prints green/red per capability.

Two ready-made code-intelligence recipes ship in examples/ — both build code graphs, so run them under codingest-mcp (it embeds this same tool surface and injects the builder):

• Clone-and-explore GitHub repos — open_source_workspace_mcp.yaml: the agent calls repo_management('org/repo') to clone and build a code graph on demand.
• Review a local directory — local_code_review_mcp.yaml: point it at a checked-out tree, set_root_dir(path) to swap roots, watch-mode auto-rebuild.

Customise with a YAML manifest

Drop <basename>_mcp.yaml next to the graph (e.g. wikidata_mcp.yaml beside wikidata.kgl) and the server auto-loads it at boot.

name: Wikidata Explorer
source_root: /path/to/related/source        # exposes read/grep/list
trust:
  allow_embedder: true
extensions:
  embedder: { library: fastembed, model: BAAI/bge-small-en-v1.5 }  # enables text_score()
  csv_http_server: true                              # bulk CSV exports
tools:                                               # inline parameterised Cypher
  - name: who_invented
    cypher: |
      MATCH (i:Q5)-[:P61]->(t {label:$thing})
      RETURN i.label LIMIT 5

No fork required for most customisation. → MCP server guide.

Teach the MCP agent with bundled tool skills

Markdown skill files (<basename>.skills/*.md) ship methodology for each tool. The agent reads cypher_query.md at session start to learn your schema conventions, read_code_source.md to know when to drill into source vs. query the graph, etc. Three layers compose: kglite-bundled defaults + your project's .skills/ overrides + operator-declared domain packs. Skills with applies_when: predicates only activate when the graph contains the relevant node types — so a non-code graph never sees read_code_source methodology.

Net effect: the agent comes pre-loaded with how to use your graph, rather than discovering it through trial-and-error. → AI Agents guide.

Public datasets

Pre-packaged loaders that turn well-known public sources into queryable graphs — SEC EDGAR filings (insider transactions, institutional holdings, board composition, XBRL financials), Wikidata (the full latest-truthy RDF dump, parallel-decoded and built into a billion-edge graph), and Sodir (Norwegian Offshore Directorate petroleum data) — live in the companion kglite-datasets project. Each handles the fetch + build + cache cycle and returns a KnowledgeGraph you can cypher() against; kglite serves and queries the graphs they produce. The kglite engine itself links zero network code — the loaders are an opt-in companion install.

Recipes

Short patterns for the most-common shapes. Each is self-contained.

Hybrid semantic + structural retrieval

Combine vector similarity (text_score()) with Cypher pattern matching in one query:

graph.cypher("""
    MATCH (c:Chunk)-[:IN_DOC]->(d:Document)
    RETURN c.text, d.title,
           text_score(c.embedding, $query_vec) AS score
    ORDER BY score DESC LIMIT 5
""", params={"query_vec": query_embedding})

Vector embeddings via a bring-your-own embedder — pip install fastembed (or sentence-transformers) and pass it to g.set_embedder(...). → Semantic Search guide.

Structural validators — surface data-integrity gaps

Fourteen built-in CALL procedures find the gaps that aren't visible from normal queries: orphan nodes, missing-required-edge violations, two-step cycles, duplicate titles, parallel edges, cardinality violations, more. They compose with the rest of Cypher.

# Wellbores in our sodir graph that lack a production licence
graph.cypher("""
    CALL missing_required_edge({type: 'Wellbore', edge: 'IN_LICENCE'}) YIELD node
    RETURN node.id, node.title
""")

missing_required_edge and missing_inbound_edge validate the (type, edge) direction against the graph's actual schema and refuse to execute when misused. → Full procedure list in the Cypher reference.

Graph algorithms

Shortest path (BFS or Dijkstra), centrality, community detection, clustering — all in Cypher:

graph.cypher("""
    MATCH path = shortestPath((a:User {name:'Alice'})-[*]-(b:User {name:'Eve'}))
    RETURN path
""")

→ Graph algorithms guide · Traversal patterns · Recipes index.

Use from Rust

The same engine is available as a pure-Rust crate — embed it in a Rust binary without the Python wheel in your build:

# Cargo.toml
[dependencies]
kglite = "0.10"

use kglite::api::{load_file, session, Value};
use std::collections::HashMap;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let graph = load_file("my_graph.kgl")?;     // same .kgl as Python writes
    let params = HashMap::new();
    let opts = session::ExecuteOptions {
        params: &params, deadline: None, max_rows: None,
        lazy_eligible: false, disabled_passes: None, embedder: None,
    };
    let outcome = session::execute_read(
        &graph,
        "MATCH (p:Person) RETURN p.name LIMIT 5",
        &opts,
    )?;
    for row in &outcome.result.rows {
        if let Some(Value::String(name)) = row.first() {
            println!("{}", name);
        }
    }
    Ok(())
}

Zero PyO3 in the dependency tree: cargo tree -p your-crate | grep pyo3 → empty.

• Rust quickstart — load + query + transaction examples.
• Embedding guide — workspace layout, the kglite::api::* surface, cgo / napi / JNI sketches.
• Session abstraction — binding-implementer reference for the canonical Cypher pipeline.
• API reference (docs.rs) — per-symbol Rust API docs.

The Bolt server (crates/kglite-bolt-server) and the Rust MCP server (crates/kglite-mcp-server) are standalone binaries built on the same engine — see the Operators guide for deployment.

For non-Rust language bindings (Go via cgo, JavaScript via napi, JVM via JNI, .NET via P/Invoke), the crates/kglite-c crate exposes the engine through a stable C ABI — 35 extern "C" functions covering lifecycle / Cypher / embedder, plus a cbindgen-generated kglite.h. See docs/rust/c-abi.md for the design and docs/rust/implementing-a-binding.md for cgo / napi / JNI worked examples.

Examples

The examples/ directory has runnable, self-contained artifacts:

• open_source_workspace_mcp.yaml — annotated workspace-mode manifest for the github-clone-tracker pattern. Walked through in the workspace manifest example.
• csv_to_graph.py — minimal pd.read_csv → add_nodes / add_connections walkthrough on a tiny org chart, with a few Cypher queries. The fastest way in.
• incremental_update.py — merge a second data snapshot into an existing graph with add_nodes(conflict_handling='update').
• legal_graph.py — end-to-end add_nodes / add_connections from pandas DataFrames, covering laws, regulations, court decisions with citation edges.
• spatial_graph.py — declarative CSV→graph loading via a JSON blueprint; lat/lon coordinates and pipeline-path traversal queries.
• crates/kglite-mcp-server/ — Rust-native single-binary MCP server (built on rmcp + the mcp-methods framework). Reach for it when the manifest doesn't express what you need; the binary is the reference for layering domain-specific tools on top of the generic surface.

Benchmarks

KGLite builds and queries Wikidata-scale graphs on a laptop. Measured with benchmarks/wiki_benchmark.py on an M-series MacBook.

Ingest — full pipeline from compressed N-Triples to a queryable graph:

dataset	triples	nodes	edges	ingest	throughput	peak RAM
wiki100m	100 M	938 K	748 K	29 s	3.4 M triples/s	1.3 GB
wiki500m	500 M	5.6 M	6.7 M	157 s	3.2 M triples/s	5.2 GB
wiki1000m	1 B	14.7 M	15.4 M	395 s	2.5 M triples/s	7.0 GB

Reloading a saved 1 B-triple graph from disk (7 GB on-disk): 3.5 s.

Query latency on the 1 B-triple graph (mapped storage):

Cypher	wall
MATCH (n)-[:P31]->(:human) RETURN count(n) — typed aggregation	0.5 ms
MATCH (a)-[:P31]->(b)-[:P279]->(c) LIMIT 10 — 2-hop typed	0.9 ms
MATCH (a)-[:P31]->(b {nid:'Q64'}) RETURN a LIMIT 20 — pivot	1 ms
MATCH (a)-[:P31]->(:human) MATCH (a)-[:P27]->(c) LIMIT 10 — join	44 ms

Disk and mapped storage build at the same speed; mapped wins on small-result queries (in-memory inverted index), disk wins on unbounded typed traversals (sorted-CSR mmap I/O). No server, no tuning, same Python process as your code.

Key Features

Quick reference. Each links into the appropriate guide.

Feature	Description
Cypher	MATCH, CREATE, SET, DELETE, MERGE, UNION/INTERSECT/EXCEPT, aggregations (incl. median, percentile_cont, variance), reduce(), ORDER BY, LIMIT, SKIP
Semantic search	Vector embeddings + text_score() for similarity ranking. Bring your own embedder (pip install fastembed or sentence-transformers).
Text predicates	text_edit_distance, text_normalize, text_jaccard, text_ngrams, text_contains_any / text_starts_with_any
Graph algorithms	Shortest path (BFS or Dijkstra), centrality, community detection, clustering
Structural validators	14 CALL procedures: orphan_node, missing_required_edge, cycle_2step, inverse_violation, cardinality_violation, parallel_edges, null_property, more — agent-discoverable integrity checks composable with Cypher
Spatial	Coordinates, WKT geometry, distance + containment, kg_knn k-nearest-neighbour. Pragmatic primitives, not a full GIS stack.
Timeseries	Time-indexed values with ts_*() Cypher functions. For graphs whose nodes carry value-over-time series.
Bulk loading	add_nodes / add_connections for DataFrames
Blueprints	Declarative CSV-to-graph loading via JSON config
Import/Export	Save/load snapshots (.kgl), GraphML, CSV export
AI integration	describe() introspection, MCP server, agent prompts
Code analysis	serve + query 14-language code graphs built by the codingest project — functions, classes, calls, imports, web-framework routes
OKF ingestion	Markdown + YAML-frontmatter bundles (kglite.okf) — Open Knowledge Format, Claude memory dirs, skills, Obsidian vaults → frontmatter as properties, links as typed edges
Public dataset loaders	Fetch-build-cache loaders for public sources — SEC EDGAR filings, Wikidata, Sodir (Norwegian Offshore Directorate) — live in the companion kglite-datasets project; each returns a queryable KnowledgeGraph kglite serves

Documentation

Full docs at kglite.readthedocs.io — five tracks by audience.

Python track — pip install kglite

• Getting Started — installation, first graph, core concepts
• Cypher Guide — MATCH, MERGE, mutations, parameters, validators
• Data Loading — DataFrames in, DataFrames out
• Graph algorithms — shortest path, PageRank, community detection
• Semantic Search — embeddings, vector search, hybrid retrieval
• OKF ingestion — okf.build, markdown knowledge bases & agent memory
• MCP server config — manifests, skills, extensions
• Spatial · Timeseries · Blueprints · Import/Export · Traversal & hierarchy · AI Agents
• Recipes index — copy-paste patterns for common shapes

Rust track — cargo add kglite

• Rust quickstart — load, query, transactions
• Embedding kglite — surface tour, language-binding sketches
• Session abstraction — pipeline + CoW transactions
• API manifest + per-symbol docs.rs

Operators — running the protocol servers

• Bolt server — Neo4j wire compat for cluster-aware drivers

Reference — cross-binding

• Cypher reference — the supported Cypher subset
• Fluent API reference — programmatic graph construction
• Python API (auto) — auto-generated from stubs

Concepts — architecture + contributor docs

• Architecture · Design decisions · Cypher conformance · Concurrency

Requirements

CPython 3.10+ | macOS (arm64/x86_64), Linux (glibc/musl; x86_64 and best-effort aarch64), Windows (x86_64). The base wheel has no Python runtime dependencies; integrations install their named extras. See the artifact support policy for the tested/build-only tiers, libc floors, PyPy status, and source-build fallback.

Stability

KGLite is Beta software, versioned under SemVer. The Python API surface and the supported Cypher dialect have been largely stable across the 0.9 → 0.10 line; the occasional breaking change (e.g. the 0.10.10 node-id semantics unification) is called out prominently in the changelog. The Beta label reflects API maturity, not engine reliability — the storage and query engine are covered by parity oracles and a differential Cypher corpus on every change. Breaking changes are announced in CHANGELOG.md.

License

MIT — see LICENSE for details.