| # 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. | |
| ```bash | |
| # 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 | |
| ```bash | |
| # 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. | |