ProtocolPilot (RUO)

Convert papers/preprints into draft, research-use-only lab protocols with a structured schema, auto-generated Bill of Materials (BOM), guardrails, and CI. Designed to pair with async agents (e.g., Open SWE) that open pull requests instead of just chatting.

Quick start

Requirements: Python 3.11+, GitHub repo, (optional) Open SWE + Daytona for async runs.

# Clone and set up
uv venv -p 3.11  # or python -m venv .venv
source .venv/bin/activate
pip install -U uv || true
uv pip install -e .
pre-commit install
pytest -q

Typical flow

1. Open a GitHub Issue using the "ProtocolPilot task" template and include links to PDFs/DOIs and constraints.
2. Agent (or you) runs the extractor → planner → programmer → reviewer flow.
3. A PR adds protocols/<slug>.md, env/conda.yaml (optional), tests/ updates, and a BOM JSON/CSV.
4. You edit, request changes, and merge when satisfied.

Open SWE integration (labels)

• Add labels from labels.json to your repo.
• To run with plan approval: label an Issue open-swe.
• To run auto-execute: label open-swe-auto (use sparingly).

Safety & scope

• RUO only; no patient data; no diagnostic/treatment claims.
• PRs include a RUO disclaimer and the guardrails checker blocks unsafe language.

Commands

# Validate a protocol Markdown against the schema
python -m protocol_pilot.extract --validate protocols/examples/qPCR.md

# Generate a BOM stub from a protocol (to JSON)
python -m protocol_pilot.bom protocols/examples/qPCR.md --out bom.json

Contributing

• Keep protocol steps numbered, measurable, and source-cited.
• Prefer SI units and temperatures in °C.
• Use PRs; auto-merge should remain off.