agentic-proteins¶

agentic-proteins is the strict compatibility package in bijux-proteomics. It preserves legacy runtime imports and entrypoints long enough for callers to migrate to bijux-proteomics-runtime. Its value is not new capability. Its value is controlled continuity while the old surface is retired without breaking downstream users in the dark.

flowchart LR
    callers["legacy callers<br/>imports, CLI paths, API usage"]
    bridge["agentic-proteins<br/>compatibility forwarding"]
    runtime["bijux-proteomics-runtime<br/>canonical execution"]
    lower["foundation, core, knowledge,<br/>intelligence, lab"]

    callers --> bridge
    bridge --> runtime
    runtime --> lower
    bridge -. retire when callers move .-> runtime

Why This Package Still Matters¶

it absorbs migration pain so the canonical runtime can keep moving
it keeps legacy entrypoints visible instead of burying them in silent shims
it provides a defensible retirement surface: each preserved path should have a reason to exist, not only inertia

What It Owns¶

compatibility forwarding for legacy runtime imports
preserved legacy CLI and API entrypoints while migration is still justified
the proof bar for keeping or retiring those preserved surfaces

Start With¶

Open Foundation when you need the package boundary first.
Open Interfaces when the question is a preserved import, CLI, API, or compatibility contract.
Open bijux-proteomics-runtime as soon as the question becomes current execution behavior rather than legacy forwarding.

What Should Make A Reader Suspicious¶

a feature that is attractive even without any legacy caller
business logic growing inside the bridge instead of inside runtime
compatibility wording that no longer points to a real migration path

First Proof Check¶

packages/agentic-proteins
packages/agentic-proteins/src/agentic_proteins
packages/agentic-proteins/tests

Boundary¶

If the behavior would still be desirable after legacy callers disappear, it probably belongs in the canonical runtime package instead of here.