Integration Seams

Agentic Proteins has one governing seam: a legacy caller enters through the agentic_proteins namespace and execution continues in bijux_proteomics_runtime. The bridge preserves supported names and call contracts; it does not own a second lifecycle, provider registry, workspace, or HTTP implementation.

flowchart LR
    L[Legacy Python, CLI, or HTTP caller] --> B[Agentic compatibility surface]
    B --> R[Canonical runtime]
    R --> C[Core scientific contracts]
    R --> I[Intelligence decisions]
    R --> K[Knowledge evidence]
    R --> A[Lab handoffs]
    R --> P[Providers and local tools]
    R --> O[Run artifacts and diagnostics]

Seam contracts

Seam	Agentic obligation	Neighbor obligation
Package root	Forward the four supported facade exports without eager runtime side effects	Runtime preserves their documented contracts or publishes a migration
CLI and HTTP	Preserve accepted routes, command behavior, schemas, and error envelopes while forwarding	Runtime owns implementation, lifecycle state, and new surface design
Execution and orchestration aliases	Resolve legacy module paths to one runtime behavior	Runtime keeps run, graph, artifact, telemetry, and validation semantics coherent
Agent and tool aliases	Preserve named contracts and catalogs still covered by compatibility policy	Runtime owns planning, coordination, verification, tool execution, and registration
Provider aliases	Preserve supported provider names and capability queries	Runtime owns provider selection, assurance, credentials, and execution
State aliases	Preserve compatible record and snapshot imports	Runtime owns persistence layout, lifecycle, and workspace integrity

Boundary rules

New behavior enters the canonical runtime or a lower scientific owner. Agentic Proteins changes only when a legacy surface must forward more accurately, report a migration clearly, or be retired under evidence. Adding local business logic would cause the same import to behave differently from its runtime replacement.

Compatibility also does not erase lower-package ownership. Core defines scientific data and analysis meaning; intelligence owns advisory judgment; knowledge owns curated evidence; lab owns operational handoffs. Runtime may coordinate those packages, and Agentic Proteins may expose the runtime path, but neither bridge may reinterpret their contracts.

Change impact

When a runtime export moves, review the corresponding root, interface, execution, orchestration, provider, agent, tool, and state aliases. Test both the legacy import and the canonical import against the same observable result. A bridge change is safe only when callers can migrate without losing error, artifact, lifecycle, or provider semantics—and when no new runtime dependency points back into Agentic Proteins.