namidb 1.3.0

Cloud-native graph database on object storage (Python bindings)

namidb (Python bindings)

Python wrapper around the NamiDB storage and query engine. The heavy lifting is Rust, bridged with pyo3 and built with maturin.

Install

pip install namidb              # released wheel, Python >= 3.9, abi3
pip install 'namidb[pandas]'    # + DataFrame interop
pip install 'namidb[polars]'    # + polars interop

Wheels go out for Linux (x86_64, aarch64), macOS (arm64), and Windows (x86_64) from the python-wheels.yml workflow on every py-v* tag. pyarrow >= 14 is a hard transitive dependency. Intel macOS falls back to the sdist, which is slower to install but behaves the same at runtime.

Build from source

pip install maturin
cd crates/namidb-py
maturin develop --release --extras test

Once maturin develop finishes, namidb imports from any Python >= 3.9 environment:

import uuid
import namidb

client = namidb.Client("memory://acme")

alice = str(uuid.uuid7())
bob = str(uuid.uuid7())

client.upsert_node("Person", alice, {"name": "Alice", "age": 30})
client.upsert_node("Person", bob, {"name": "Bob"})
client.upsert_edge("KNOWS", alice, bob, {"since": 2020})
client.commit()
client.flush()

print(client.lookup_node("Person", alice))
# {'id': '...', 'label': 'Person', 'lsn': 1, 'schema_version': 0,
#  'properties': {'name': 'Alice', 'age': 30}}

print(client.scan_label("Person"))
print(client.out_edges("KNOWS", alice))
print(client.cache_stats())

Cypher queries

Client.cypher(query, params=None) runs a Cypher query against the current namespace and hands back a QueryResult:

client.cypher("CREATE (a:Person {name: 'Alice', age: 30})")
client.cypher("CREATE (a:Person {name: 'Bob',   age: 25})")
client.commit()

result = client.cypher(
    "MATCH (p:Person) WHERE p.age > $min RETURN p.name AS name, p.age AS age",
    params={"min": 26},
)

print(result.columns)   # ['name', 'age']
print(len(result))      # 1
print(result.first())   # {'name': 'Alice', 'age': 30}
for row in result.rows():
    print(row)          # {'name': 'Alice', 'age': 30}

One thing to keep straight: Cypher writes (CREATE / SET / DELETE / MERGE / REMOVE) are durably committed (WAL append plus manifest CAS) before cypher() returns, because the executor calls commit_batch() at the end of every write plan. You still want to call client.flush() now and then to push the memtable into L0 SSTs. That's different from the upsert_node / upsert_edge / tombstone_* API, which stages mutations and waits for an explicit client.commit().

Async API

The same surface is available as a coroutine through Client.acypher, for asyncio / FastAPI / aiohttp:

import asyncio
import namidb


async def main() -> None:
    client = namidb.Client("memory://acme")
    await client.acypher("CREATE (p:Person {name: 'Alice'})")
    client.commit()
    result = await client.acypher(
        "MATCH (p:Person {name: $name}) RETURN p.name AS name",
        params={"name": "Alice"},
    )
    print(result.rows())


asyncio.run(main())

acypher rides the pyo3-async-runtimes tokio bridge. Every call runs on the same multi-threaded tokio runtime that backs the synchronous API, so mixing the two from one Client is fine.

Type mapping (Cypher and Python)

Both cypher parameters and QueryResult.rows() follow the same mapping:

Cypher RuntimeValue	Python type
Null	None
Bool	bool
Integer	int
Float	float
String	str
Bytes	bytes
Vector(Vec<f32>)	list[float]
List	list
Map	dict[str, ...]
Date	datetime.date
DateTime (UTC, microseconds)	datetime.datetime UTC
Node(NodeValue)	{"_kind": "node", "id", "label", "properties"}
Rel(RelValue)	{"_kind": "rel", "edge_type", "src", "dst", "properties"}
Path	list[Node|Rel] alternating

bool is checked before int on purpose, so that Python True / False don't quietly round-trip as Integer(1) / Integer(0).

Bulk inserts

Client.merge_nodes and Client.merge_edges batch a lot of writes behind a single tokio-runtime plus mutex round-trip. They're the right ingestion path once you have thousands of rows, since Cypher CREATE parses, plans and executes once per call:

import uuid
import namidb

client = namidb.Client("memory://acme")

# Bulk insert: each row needs an "id" UUID string + arbitrary properties.
client.merge_nodes(
    "Person",
    [{"id": str(uuid.uuid4()), "name": f"p{i}", "age": 20 + i} for i in range(10_000)],
)
# Edges: each row needs "src" + "dst" UUIDs.
client.merge_edges(
    "KNOWS",
    [
        {"src": "uuid-a", "dst": "uuid-b", "since": 2020},
        {"src": "uuid-b", "dst": "uuid-c", "since": 2021},
    ],
)
client.commit()        # WAL + manifest CAS
client.flush()         # memtable -> L0 SSTs

merge_nodes / merge_edges stage into the current batch (same lifecycle as upsert_*), so call client.commit() to make the mutations durable.

Arrow / pandas / polars output

pyarrow >= 14 is a hard dependency. Every QueryResult can materialise as a pyarrow.Table, and the pandas / polars conversions just delegate to that.

result = client.cypher(
    "MATCH (p:Person) RETURN p.name AS name, p.age AS age ORDER BY p.age DESC"
)

table = result.to_arrow()              # pyarrow.Table
df = result.to_pandas()                # pandas.DataFrame  (needs pandas)
pl_df = result.to_polars()             # polars.DataFrame  (needs polars)

Column order follows the RETURN projection from the parsed plan, not the runtime row's BTreeMap ordering, so RETURN p.name AS name, p.age AS age always gives you columns ["name", "age"] even when nothing matches.

pandas and polars are optional extras:

pip install 'namidb[pandas]'
pip install 'namidb[polars]'

Calling to_polars() without the polars extra raises a clear ImportError that points at the install command.

For label-wide scans you can skip the Cypher round-trip:

table = client.scan_label_arrow("Person")
# Columns: id, label, lsn, schema_version, then the union of property
# keys across the scanned views (missing keys filled with None).

Storage backends

URI scheme	Backend	Status
memory://<ns>	object_store::memory::InMemory	Stable. Ephemeral, single-process.
file:///abs/dir?ns=<ns> (or file://./rel?ns=<ns>)	NamiDB LocalFileObjectStore (wraps LocalFileSystem and adds manifest CAS via flock + atomic rename)	Stable.
s3://<bucket>[/<prefix>]?ns=<ns>...	object_store::aws::AmazonS3	Stable. AWS S3, Cloudflare R2, MinIO, Tigris, LocalStack, any S3-compatible service.
gs://<bucket>[/<prefix>]?ns=<ns>	object_store::gcp::GoogleCloudStorage	Stable. Auth via GOOGLE_APPLICATION_CREDENTIALS or ?service_account=....
az://<account>/<container>[/<prefix>]?ns=<ns>	object_store::azure::MicrosoftAzure	Stable. Auth via AZURE_STORAGE_* env vars; ?use_emulator=true for Azurite.

Local filesystem

For development, single-machine deployments, and CI fixtures. Full manifest CAS via per-namespace flock plus atomic rename, and it passes the same concurrency test suite as s3://.

import namidb

client = namidb.Client("file:///var/lib/namidb?ns=prod")
# or relative
client = namidb.Client("file://./data?ns=dev")

AWS S3

import namidb

client = namidb.Client(
    "s3://my-bucket/data?ns=prod"
    "&region=us-west-2"
)

Credentials come from the standard AWS environment variables (AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, AWS_SESSION_TOKEN, AWS_DEFAULT_REGION). A query-string region=... overrides the env.

Cloudflare R2

import namidb

client = namidb.Client(
    "s3://my-bucket?ns=prod"
    "&endpoint=https://<ACCOUNT_ID>.r2.cloudflarestorage.com"
    "&region=auto"
)

AWS_ACCESS_KEY_ID / AWS_SECRET_ACCESS_KEY should hold the R2 API token credentials.

Google Cloud Storage

import os
os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = "/etc/gcs-key.json"

client = namidb.Client("gs://my-bucket/data?ns=prod")

Azure Blob Storage

import os
os.environ["AZURE_STORAGE_ACCOUNT_NAME"] = "myacct"
os.environ["AZURE_STORAGE_ACCESS_KEY"]   = "..."

client = namidb.Client("az://myacct/mycontainer?ns=prod")

LocalStack (local persistent storage)

docker run -p 4566:4566 -e SERVICES=s3 localstack/localstack
aws --endpoint-url=http://localhost:4566 s3 mb s3://namidb-dev
export AWS_ACCESS_KEY_ID=test
export AWS_SECRET_ACCESS_KEY=test

client = namidb.Client(
    "s3://namidb-dev?ns=local"
    "&endpoint=http://localhost:4566"
    "&allow_http=true"
    "&region=us-east-1"
)

You need allow_http=true because LocalStack doesn't serve TLS by default.

Scope (v0)

• Six storage backends: memory://, file://, s3://, gs://, az://. All five non-memory backends share the same manifest CAS protocol (If-Match on object stores, flock plus atomic rename on the filesystem) and the same single-writer-per-namespace epoch fencing.
• A synchronous Python API plus an async coroutine API (acypher). Under the hood every call drives a tokio runtime owned by the Client; the first call per process pays the bootstrap cost.
• The same SST plus bloom cache the Rust read path uses (SstCache) is exposed through client.cache_stats(), so application dashboards can graph the hit rate.
• Cypher coverage matches the Rust engine: LDBC SNB Interactive IC01 through IC12, with factorized execution toggled by NAMIDB_FACTORIZE=1. See the project README for the engine's surface and the RFCs in docs/rfc/ for the design details.

Running the integration test (optional)

The pytest suite under tests/ ships a LocalStack round-trip test that is @pytest.mark.skipif-guarded on the NAMIDB_TEST_LOCALSTACK_BUCKET env var. To turn it on:

docker run -p 4566:4566 -e SERVICES=s3 localstack/localstack &
aws --endpoint-url=http://localhost:4566 s3 mb s3://namidb-it
export NAMIDB_TEST_LOCALSTACK_BUCKET=namidb-it
export AWS_ACCESS_KEY_ID=test AWS_SECRET_ACCESS_KEY=test
.venv/bin/pytest tests/test_uri.py::test_s3_localstack_round_trip -v

Releasing to PyPI

1. Bump version in crates/namidb-py/pyproject.toml and crates/namidb-py/Cargo.toml (they have to match).
2. Update CHANGELOG.md (or this README's release notes section).
3. Commit, then tag and push:

   git tag py-v0.2.0
   git push origin py-v0.2.0
   

4. python-wheels.yml builds 4 wheels (Linux x86_64/aarch64, macOS arm64, Windows x86_64) plus the sdist, smoke-tests one wheel on Python 3.9 and 3.13, then publishes to PyPI via OIDC trusted publishing (set up once per account at https://pypi.org/manage/account/publishing/).

The py-v* tag prefix keeps Python releases separate from any future v* tags that mark engine or crate releases.