feat: Add optional setup command to helix.yaml

[amrit110]

Summary

Add support for an optional setup command in helix.yaml that runs once before the first experiment in a session. This allows helices to declare one-time setup steps (e.g. downloading model weights, caching datasets) as part of their configuration, making helix run fully self-contained without requiring manual pre-run steps.

Motivation

Currently, some helices require a one-time setup step to be run manually before helix run can work — for example, uv run prepare.py in helix-inference-opt downloads model weights and caches datasets. There is no way to declare this in helix.yaml, so users must remember to run it themselves on each new machine. This is a poor experience and easy to forget.

Proposed Change

Add an optional setup section to helix.yaml:

setup:
  command: uv run prepare.py

Behaviour

• If setup.command is provided, the runner executes it once at the start of helix run, before the agent is invoked or any experiments are run.
• If setup.command is absent, the runner proceeds as today (no change in behaviour).
• The command runs in the repo root, inheriting the same environment as the evaluate command.
• If the setup command exits non-zero, helix run should abort with a clear error message.

Schema Changes

In config.py, add a new optional SetupConfig model and field on HelixConfig:

class SetupConfig(BaseModel):
    command: str

class HelixConfig(BaseModel):
    ...
    setup: Optional[SetupConfig] = None

Runner Changes

In runner.py, after _preflight() and before launching the agent, add a setup step:

if self.config.setup:
    # run setup.command, stream output, abort on non-zero exit

Example helix.yaml

name: inference-opt
setup:
  command: uv run prepare.py
metrics:
  primary:
    name: tokens_per_sec
    optimize: maximize
  evaluate:
    command: uv run infer.py

Acceptance Criteria

• SetupConfig added to config.py with command field
• HelixConfig.setup is optional (existing helices without it are unaffected)
• Runner executes setup command once per helix run session before the agent starts
• Setup output is streamed to the terminal so the user can see progress
• Non-zero exit aborts the session with a clear error
• Docs/template updated to show the new field