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Module map

agentic-proteins is a compatibility distribution for historical runtime imports and the agentic-proteins command. Its source tree preserves the old namespace while canonical implementations live in bijux_proteomics_runtime. In the current package, 111 of 117 Python modules import from runtime; that ratio is the architectural fact readers need before mistaking this tree for a second execution engine.

flowchart LR
    legacy["Historical agentic_proteins import"]
    facade["Compatibility module"]
    runtime["bijux_proteomics_runtime owner"]
    core["bijux_proteomics scientific core"]

    legacy --> facade --> runtime --> core

Compatibility families

Historical namespace Canonical runtime owner Preserved responsibility
package root runtime package root AppConfig, RunManager, cli, create_app
interfaces runtime.api CLI, HTTP application, middleware, routes, and schemas
agents runtime.execution.agents planning, coordination, analysis, verification, and reporting imports
execution runtime.execution and runtime.runs compiler, engine, evaluation, validation, state, artifacts, logging, and telemetry
orchestration runtime.execution, runtime.runs, and runtime governance historical orchestration spelling plus bridge contracts
providers runtime.providers provider contracts, selection, capabilities, local and remote adapters
state runtime.state, runtime.runs, and runtime support snapshots, lifecycle, context, output, request, and workspace imports
tools runtime.execution.tools tool contracts, catalog, schemas, and heuristic tool

Why both execution and orchestration exist

They preserve two historical import families. Both forward to the same runtime owners and must not evolve as parallel implementations. New execution behavior belongs in runtime. A compatibility change here is justified only when it keeps an existing import working, records a bridge contract, or makes retirement safer.

Small bridge-owned surface

The package root resolves its four public names lazily from runtime. orchestration.bridge_contracts exposes runtime-owned inventories and retirement budgets used to audit the bridge. The distribution metadata and console-script declaration remain local because PyPI installation and the historical executable name are themselves compatibility surfaces.

  • An old Python import fails: locate the historical path, then its runtime target in the table above.
  • The legacy command differs from the runtime command: inspect interfaces.cli and the package script entrypoint.
  • A provider extra no longer resolves: compare the legacy optional dependency with the matching runtime extra.
  • A bridge path appears to contain new behavior: treat that as ownership drift and move the implementation to runtime before extending it.

The compatibility inventory and tests are the behavioral evidence. Directory size is not evidence of independent product ownership.