getting_started

Scope: Single install and run path.
Audience: Users running the CLI.
Guarantees: One reproducible path with fixed assumptions.
Non-Goals: Alternative setups or options.
Why: This doc exists to record its single responsibility for review.

Overview

Getting started defines one install and run path.
Read Core Concepts for vocabulary.
Read Dependencies for dependency constraints.
Architecture components are defined in Architecture.

Contracts

Install with pipx install agentic-proteins.
Run with agentic-proteins run --sequence "ACDEFGHIKLMNPQRSTVWY".
Artifacts are stored under artifacts/<run_id>/.

Invariants

Local filesystem permissions prevent cross-tenant access.
Providers return deterministic results for fixed inputs.
CI artifacts are not tampered with between steps.

Failure Modes

Missing allowlist dependencies in Dependencies break this path.
Assumptions are tracked in Threat Model.
Invalid sequences fail validation.

Extension Points

Changes update Cli.
Dependency changes update Dependencies.
Vocabulary changes update Core Concepts.

Exit Criteria

This doc becomes obsolete when a generated entrypoint replaces it.
The replacement is Index.
Obsolete docs are removed.

Code refs: tests/integration/test_cli.py.