Runtime Handbook¶

bijux-proteomics-runtime is the canonical execution package for the proteomics family. It owns how work is invoked, orchestrated, replayed, and made inspectable after the run. This is where the system becomes operational: operators touch it, providers plug into it, state moves through it, and runs leave artifacts behind that a reviewer can inspect later.

flowchart LR
    operators["operators<br/>CLI, HTTP, automation"]
    bridge["agentic-proteins<br/>legacy paths"]
    runtime["runtime<br/>orchestration and control"]
    providers["providers and tools"]
    state["state, memory, registry"]
    validation["validation and replay"]
    artifacts["run artifacts and execution record"]

    operators --> runtime
    bridge -. migrate .-> runtime
    runtime --> providers
    runtime --> state
    runtime --> validation
    validation --> artifacts
    providers --> artifacts
    state --> artifacts

Why This Package Is Central¶

it is the place where abstract package contracts become concrete runs
it keeps execution reviewable instead of letting provider calls disappear into opaque side effects
it holds the operational seam between the product family and the outside world

Start With¶

open agentic-proteins when the question starts from a legacy import, CLI path, or API surface
open Migration Ledger when the question is whether a legacy module still belongs in runtime ownership
open the lower package handbooks when the disputed behavior is really domain, evidence, recommendation, or lab meaning

What Runtime Owns¶

operator entrypoints such as CLI and HTTP surfaces
provider binding, execution adapters, and workspace control
run orchestration, replay, determinism, and state transitions
runtime artifacts and execution-lifecycle records

What Runtime Refuses¶

canonical domain and biology semantics
evidence, confidence, contradiction, and review semantics
recommendation policy, scoring, and design-loop meaning
planning and outcome-promotion meaning from the lab layer

First Proof Check¶

packages/bijux-proteomics-runtime/src/bijux_proteomics_runtime/interfaces/cli.py
packages/bijux-proteomics-runtime/src/bijux_proteomics_runtime/api/
packages/bijux-proteomics-runtime/src/bijux_proteomics_runtime/runtime/, providers/, and validation/
packages/bijux-proteomics-runtime/tests

Migration References¶

Boundary¶

Runtime should explain execution clearly, but it should not quietly absorb the meaning of evidence, recommendation, or lab intent just because those meanings eventually move through a run.