petri-grow 0.2.1

An agent orchestration framework to grow your AI's context.

Image Credit: Gemini Pro, April 2026

Petri

An agent orchestration framework to grow your AI's context. Decomposes claims into DAGs of logical units and validates them bottom-up through a multi-agent adversarial review pipeline.

Cost Warning

Petri uses Claude via Claude Code, which costs money. Each node goes through 13 agents across multiple iterations, generating significant token usage. A single colony with 10+ nodes can produce thousands of LLM calls across Socratic analysis, research, critique, debate, red team, and evaluation phases.

The default model is claude-sonnet-4-6. You can switch models in petri.yaml or the setup wizard:

model:
  name: claude-opus-4-6  # most capable, higher cost

Monitor your usage. Start with small claims to understand the cost profile before running large colonies.

Prerequisites

1. Python 3.11+

Petri requires Python 3.11 or later. Check your version:

python3 --version

If you need a newer version, uv can install one for you:

# Install uv (package manager)
curl -LsSf https://astral.sh/uv/install.sh | sh

# Create a virtual environment with Python 3.11
uv venv --python 3.11 .venv
source .venv/bin/activate    # macOS/Linux
# .venv\Scripts\activate     # Windows

2. Claude Code

Petri uses Claude Code as its agentic harness for inference.

Install: https://docs.anthropic.com/en/docs/claude-code

Verify it's working:

claude --version

Verify everything

petri inspect

This checks all prerequisites and reports what's missing.

Install

# Recommended (with uv)
uv pip install petri-grow

# Or with pip
pip install petri-grow

This installs the CLI and core library. Claude Code must be authenticated (see above).

Quickstart

# 1. Initialize a petri dish
mkdir my-research && cd my-research
petri init
# → Initialized petri dish 'my-research' at /path/to/my-research
#   Model: claude-sonnet-4-6

# 2. Seed a colony from a claim
petri seed "A hotdog is a sandwich" --no-questions
# → Colony 'hotdog-sandwich' created with 6 nodes across 3 levels

# 3. Check status
petri check
# → Shows a table of all nodes with status PENDING

# 4. Grow nodes through the validation pipeline
petri grow --all
# → Processes nodes bottom-up: Socratic → Research → Critique → Red Team → Evaluation

# 5. Feed new evidence (requires nodes that have completed validation)
petri feed https://arxiv.org/abs/2026.12345
# → Ingests content, matches to relevant nodes, flags for re-validation

# 6. Analyze
petri analyze --graph       # text tree / DOT export
petri analyze --dashboard   # REST + SSE API on port 8090
petri analyze --scan --fix  # contradiction scanner
# → --graph shows the colony DAG; --dashboard opens a live web UI

# 7. Stop
petri stop
# → Gracefully halts any active processing

See ARCHITECTURE.md for the full pipeline and state machine details.

CLI Reference

petri --help

Command	Description	Key Flags
petri init	Create .petri/ directory with defaults	--name
petri seed <claim>	Decompose a claim into a colony DAG	--no-questions, --colony
petri check	Show node statuses across colonies	--colony, --node, --json
petri grow	Run nodes through the validation pipeline	--all, --colony, --dry-run, --max-concurrent
petri feed <source>	Ingest new evidence and flag affected nodes	--colony, --auto-reopen
petri analyze	Visualization and diagnostics	--graph, --dashboard, --scan, --fix
petri stop	Gracefully halt active processing	--force
petri inspect	Check that all prerequisites are installed

Typical workflow:

1. petri init -- one-time setup
2. petri seed "your claim" -- decompose into a colony
3. petri grow --all -- validate bottom-up (cells first, then parents)
4. petri check -- inspect progress
5. petri feed <url> -- add evidence, re-open affected nodes
6. petri grow --all -- re-validate impacted nodes
7. petri analyze --graph -- view the final colony structure

Note: petri grow --all processes all currently eligible nodes. For multi-level colonies, run it multiple times until all levels are resolved — cells validate first, unlocking their parents.

How It Works

Each node in the colony goes through:

1. Socratic questioning -- Clarify terms, challenge assumptions, identify what evidence is needed
2. Research phase -- Investigator gathers evidence, Freshness Checker verifies currency, Dependency Auditor checks prerequisites
3. Critique phase -- Specialist agents assess in parallel, Node Lead mediates structured debates
4. Convergence check -- All blocking verdicts must pass (mechanical check, no LLM)
5. Circuit breaker -- Max 3 iterations per cycle; if not converged, flags for human guidance
6. Red Team -- Dedicated adversarial phase builds the strongest case against the node
7. Evidence Evaluation -- Neutral weighing of all evidence: VALIDATED, DISPROVEN, or DEFER

Every action is logged as an immutable event in the node's JSONL file, identified by a composite key ({dish}-{colony}-{level}-{seq}-{8hex}).

Architecture

• Multi-agent pipeline: lead orchestrators + specialists (blocking and advisory)
• Event sourcing: append-only JSONL per node, rolled up to SQLite for the dashboard
• Queue state machine: enforced transitions, file-locked for concurrency
• Harness-agnostic: core uses only stdlib + Pydantic; adapters bridge to Claude Code and future harnesses

See ARCHITECTURE.md for the full design, state machine diagram, and agent details.

Development

uv pip install -e ".[all]"
uv run pytest tests/