/setup

name: by:setup
description: Discover and configure compute environment

/setup — Environment Discovery and Configuration

Scan the local system and cloud endpoints to detect available tools, GPU resources, and API keys. Write a complete environment profile.

Instructions

Step 0: Read model profile

MODEL_PROFILE=$(cat .by/config.json 2>/dev/null | grep -o '"model_profile"[[:space:]]*:[[:space:]]*"[^"]*"' | grep -o '"[^"]*"$' | tr -d '"' || echo "balanced")

Model lookup for this command: | Agent | quality | balanced | budget | |-------|---------|----------|--------| | by-environment | sonnet | sonnet | haiku |

Step 1: Ensure config directory

mkdir -p .by
if [ ! -f .by/config.json ]; then
  echo '{"model_profile": "balanced"}' > .by/config.json
fi

Step 2: Spawn by-environment agent

Delegate to a **by-environment** agent (model per profile table above):

> Scan the compute environment and produce a complete inventory. > > **Local tools** — check env vars and PATH for installed tools: > - Protenix: `$PROTEUS_FOLD_DIR` or `which protenix` > - PXDesign: `$PROTEUS_PROT_DIR` or `which pxdesign` > - boltzgen: `$PROTEUS_AB_DIR` or `which boltzgen` > > **GPU** — run `nvidia-smi` if available. Report: > - GPU model, VRAM, driver version, CUDA version > - If no GPU, note "CPU-only — cloud providers required" > > **Python environment** — check for: > - Python version (require 3.10+) > - Key packages: torch, numpy, biopython, boltzgen > > **Cloud providers** — check API key environment variables: > - TAMARIND_API_KEY (Tamarind Bio) > - ADAPTYV_API_KEY (Adaptyv Bio — lab submission) > - Report configured/missing for each (NEVER log key values) > > **SSH tunnels** — check for any active SSH tunnels to GPU nodes > > Write complete results to `.by/environment.json`.

Step 3: Review environment report

Verify the agent produced valid environment.json with all required sections.

Step 4: Select default provider

Based on the environment scan, recommend a compute provider: 1. **Tamarind Bio** if API key is configured (preferred — free tier) 2. **Local GPU** if NVIDIA GPU detected with sufficient VRAM (>=16GB) 3. **None** — warn that no compute provider is available

Step 5: Report to user

Display a formatted environment summary:

• Tools found and their versions
• GPU status
• API keys status (configured/missing)
• Recommended provider
• Any warnings or setup steps needed