rhizo-core 0.1.2

Data, connected. Content-addressable storage with cross-table ACID transactions.

Rhizo

From the rhizome — a root system with no center, where any point connects to any other.

In 1980, Deleuze and Guattari contrasted the rhizome with the tree: hierarchies vs networks, central authority vs emergent coherence. Traditional databases are trees — leaders, followers, coordination. Rhizo is rhizomatic: every node commits locally, consistency emerges mathematically.

The first database where coordination is optional.

Metric	Rhizo	Industry Standard	Improvement
Transaction latency	0.022ms	100ms (consensus)	31,000x faster
Energy per transaction	2.2e-11 kWh	2.1e-6 kWh	97,943x less
Branch overhead	280 bytes	14.7 MB (Delta Lake)	52,500x smaller
OLAP queries	0.9ms	23ms (DuckDB)	26x faster

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The Problem

Distributed databases require consensus. Consensus adds latency, complexity, and energy cost — even when the operation doesn't need it.

Lakehouses (Delta Lake, Iceberg, Hudi) improve storage but can't solve:

Limitation	What It Costs You
Single-table transactions	No atomic updates across related data
No deduplication	Paying for storage you don't need
No real branching	Can't experiment without copying everything
Consensus overhead	100ms+ latency on every write

Rhizo can.

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Benchmarks

OLAP Performance vs Industry (100K rows)

With the new DataFusion-powered OLAP engine, Rhizo delivers industry-leading query performance:

Metric	Rhizo OLAP	DuckDB	Delta Lake	Parquet	Winner
Read	0.9ms	23.8ms	23.9ms	6.3ms	Rhizo (26x)
Filtered (5%)	1.2ms	1.8ms	19.9ms	7.0ms	Rhizo
Projection	0.7ms	1.4ms	14.5ms	3.5ms	Rhizo (2x)
Complex Query	2.9ms	6.6ms	30.5ms	18.5ms	Rhizo (2.3x)
Storage	3.67MB	6.26MB	63.10MB	3.73MB	Rhizo (17x vs Delta)

Rhizo wins 4/6 performance categories with built-in lakehouse features no competitor matches.

JOIN Performance (10K users x 100K orders)

Operation	Rhizo OLAP	DuckDB	Delta Lake
Simple JOIN	2.9ms	7.5ms	31.5ms
JOIN + Filter	3.0ms	5.9ms	33.4ms
JOIN + Aggregate	4.2ms	5.6ms	34.0ms

Rhizo wins all JOIN categories.

Scale Performance (1M rows)

Metric	Rhizo OLAP	DuckDB	Speedup
Read	5.1ms	257.2ms	50x faster
Filter	1.9ms	14.2ms	7.5x faster
Write	415ms	625ms	1.5x faster

Unique Features (No Competitor Has All)

Feature	Rhizo	Delta Lake	DuckDB	Iceberg
OLAP Query Speed	Yes	No	Yes	No
Time Travel SQL	Yes (VERSION 5)	API only	No	API only
Branch Queries	Yes (@branch)	No	No	No
Changelog SQL	Yes (__changelog)	No	No	No
Cross-table ACID	Yes	No	No	No
Content Dedup	Yes	No	No	No
Merkle Integrity	Yes	No	No	No
Arrow Chunk Cache	Yes (15x speedup)	No	No	No
Algebraic Merge	Yes (4M+ ops/sec)	No	No	No

Core Operations

Operation	Performance	Notes
OLAP read (cached)	0.9ms	26x faster than DuckDB
Arrow cache read	0.24ms	15x faster than uncached
Write throughput	211 MB/s	Native Rust Parquet encoding
Branch creation	<10 ms	Zero-copy, 280 bytes overhead
Time travel query	0.5ms	O(1) version lookup
Cache hit rate	97.2%	LRU eviction, no invalidation

Incremental Deduplication (Merkle Tree Storage)

Change Percentage	Chunk Reuse	Storage Savings
1% change	98.8% reuse	~49% vs naive
5% change	95.0% reuse	~47% vs naive
10% change	90.0% reuse	~45% vs naive

O(change) storage instead of O(n) per version.

Feature Comparison

Feature	Rhizo	Delta Lake	Iceberg	Hudi
Cross-table ACID	Yes	No	No	No
Zero-copy branching	Yes	No	No*	No
Global deduplication	Yes	No	No	No
Merkle tree dedup	Yes	No	No	No
Corruption detection	Built-in	External	External	External
Time travel	Yes	Yes	Yes	Yes
SQL Query Engine	Yes	Yes	Yes	Yes
Cloud Storage	Planned	Yes	Yes	Yes

*Iceberg branching requires Nessie catalog

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Quick Start

Installation

pip install rhizo

Basic Usage

import rhizo
import pandas as pd

# Open or create a database
db = rhizo.open("./mydata")

# Write data
df = pd.DataFrame({
    "id": [1, 2, 3],
    "name": ["Alice", "Bob", "Charlie"],
    "score": [85.5, 92.0, 78.5]
})
db.write("users", df)

# Query with SQL
result = db.sql("SELECT * FROM users WHERE score > 80")
print(result.to_pandas())

# Close when done
db.close()

Or use as a context manager:

with rhizo.open("./mydata") as db:
    db.write("users", df)
    result = db.sql("SELECT * FROM users")

Time Travel

# Query historical versions
result_v1 = db.sql(
    "SELECT AVG(score) FROM users",
    versions={"users": 1}
)

# Read specific version directly
old_data = db.read("users", version=1)

# Compare versions (via engine for advanced features)
diff = db.engine.diff_versions("users", 1, 2, key_columns=["id"])

Branching

# Access branching through the engine
engine = db.engine

# Create branch (instant, zero-copy)
engine.create_branch("experiment/new-scoring")
engine.checkout("experiment/new-scoring")

# Modify on branch (production unchanged)
db.write("scores", updated_df)

# Query both branches
main_result = db.sql("SELECT * FROM scores")  # current branch
engine.checkout("main")
main_result = db.sql("SELECT * FROM scores")  # main branch

# Merge when ready
engine.merge_branch("experiment/new-scoring", into="main")

Cross-Table Transactions

with db.engine.transaction() as tx:
    tx.write_table("customers", updated_customers)
    tx.write_table("orders", new_order)
    tx.write_table("audit_log", audit_entry)
    # All commit together, or all rollback

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Architecture

Application Layer
    Python (rhizo) | Rust | CLI (planned)
    TableWriter | TableReader | QueryEngine (DuckDB)
                            |
                            v
                      FileCatalog
    Versioned table metadata | Time travel queries | Atomic commits
                            |
                            v
                       ChunkStore
    Content-addressed storage (BLAKE3) | Automatic deduplication
    Atomic writes | Integrity verification
                            |
                            v
                       File System
    2-level directory tree | JSON metadata | Parquet chunks

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Current Status

Phase	Description	Status
Phase 1: Storage	Content-addressable chunk store with BLAKE3 hashing	Complete
Phase 2: Catalog	Versioned file catalog with time travel	Complete
Phase 3: Query	DuckDB integration with SQL and time travel	Complete
Phase 4: Branching	Git-like branching with zero-copy semantics	Complete
Phase 5: Transactions	Cross-table ACID with recovery	Complete
Phase 6: Changelog	Unified batch/stream via subscriptions	Complete
Phase A: Merkle Storage	O(change) deduplication via Merkle trees	Complete
Phase P: Performance	Native Rust Parquet, parallel I/O	Complete

All phases complete. 632 tests passing (370 Rust + 262 Python).

Performance Optimization Journey

Phase	Optimization	Result
P.1	Parallel chunk I/O (Rayon)	3-5x batch throughput
P.2	Memory-mapped reads	Infrastructure for zero-copy
P.3	Parallel Parquet parsing	2.1x multi-chunk speedup
P.4	Native Rust Parquet encoder	2.3x write improvement
P.5	Arrow chunk cache	15x faster repeated reads

Phase P.5 leverages content-addressed storage for cache-friendly reads. Since chunk hashes never change, cached Arrow RecordBatches require no invalidation and are shared across tables, versions, and branches. Cache hits bypass both disk I/O and Parquet decoding.

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Project Structure

rhizo/
├── rhizo_core/                 # Rust core library
│   └── src/
│       ├── chunk_store/      # Content-addressable storage
│       ├── catalog/          # Versioned catalog
│       ├── branch/           # Git-like branching
│       ├── transaction/      # Cross-table ACID
│       ├── changelog/        # Change tracking
│       └── merkle/           # Merkle tree deduplication
│
├── rhizo_python/               # PyO3 bindings
├── python/rhizo/  # Python query layer
├── tests/                    # Test suites
└── examples/                 # Interactive demos

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Design Principles

1. Immutability — All data is immutable once written. Updates create new versions.
2. Content Addressing — Data identified by BLAKE3 hash enables automatic deduplication.
3. Atomic Operations — Write-to-temp-rename pattern prevents corruption.
4. Layered Architecture — ChunkStore, FileCatalog, and BranchManager are independent and composable.
5. Time Travel by Default — Every version is preserved and queryable.
6. Zero-Copy Branching — Branches are pointers to table versions, not data copies.

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Documentation

• Technical Foundations — Mathematical proofs and complexity analysis
• Roadmap — Current status and what's next
• Changelog — Version history
• Origin Story — Why I built Rhizo
• Contributing — How to contribute

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License

MIT — See LICENSE for details.