agentic-proteins Canonical Migration Guide

This guide shows how compatibility imports map back to canonical package ownership. The point is not to preserve the bridge forever; it is to make every remaining legacy path reviewable and replaceable.

Migration Decision

flowchart LR
    legacy["legacy import"] --> inventory["live compatibility inventory"]
    inventory --> status{"classification"}
    status -->|wrapper| canonical["move caller to canonical target"]
    status -->|dead| absence["prove caller absence, then delete"]
    status -->|canonical or duplicate| block["release-blocking ownership violation"]
    canonical --> retire["retire compatibility path"]
    absence --> retire

The inventory is a routing authority, not a parity claim. A canonical import still requires surface-specific compatibility evidence before a caller can move safely.

Current Posture

• total compatibility modules: 117
• wrapper modules: 112
• dead modules: 5

Migration Map

legacy module	status	canonical target(s)	migration action
agentic_proteins.__init__	wrapper	bijux_proteomics_runtime	replace agentic_proteins.__init__ with bijux_proteomics_runtime and retire the compat import
agentic_proteins.agents	wrapper	bijux_proteomics_runtime.execution.agents.catalog bijux_proteomics_runtime.execution.agents.contracts	replace agentic_proteins.agents with one of bijux_proteomics_runtime.execution.agents.catalog, bijux_proteomics_runtime.execution.agents.contracts based on the live owner
agentic_proteins.agents.analysis	dead	none declared	delete agentic_proteins.agents.analysis after confirming no callers remain
agentic_proteins.agents.analysis.failure_analysis	wrapper	bijux_proteomics_runtime.execution.agents.analysis.failure_analysis	replace agentic_proteins.agents.analysis.failure_analysis with bijux_proteomics_runtime.execution.agents.analysis.failure_analysis and retire the compat import
agentic_proteins.agents.analysis.sequence_analysis	wrapper	bijux_proteomics_runtime.execution.agents.analysis.sequence_analysis	replace agentic_proteins.agents.analysis.sequence_analysis with bijux_proteomics_runtime.execution.agents.analysis.sequence_analysis and retire the compat import
agentic_proteins.agents.analysis.structure	wrapper	bijux_proteomics_runtime.execution.agents.analysis.structure	replace agentic_proteins.agents.analysis.structure with bijux_proteomics_runtime.execution.agents.analysis.structure and retire the compat import
agentic_proteins.agents.base	wrapper	bijux_proteomics_runtime.execution.agents.base	replace agentic_proteins.agents.base with bijux_proteomics_runtime.execution.agents.base and retire the compat import
agentic_proteins.agents.base.base	wrapper	bijux_proteomics_runtime.execution.agents.base.base	replace agentic_proteins.agents.base.base with bijux_proteomics_runtime.execution.agents.base.base and retire the compat import
agentic_proteins.agents.catalog	wrapper	bijux_proteomics_runtime.execution.agents.catalog	replace agentic_proteins.agents.catalog with bijux_proteomics_runtime.execution.agents.catalog and retire the compat import
agentic_proteins.agents.contracts	wrapper	bijux_proteomics_runtime.execution.agents.contracts	replace agentic_proteins.agents.contracts with bijux_proteomics_runtime.execution.agents.contracts and retire the compat import
agentic_proteins.agents.coordination	wrapper	bijux_proteomics_runtime.execution.agents.coordination.coordinator	replace agentic_proteins.agents.coordination with bijux_proteomics_runtime.execution.agents.coordination.coordinator and retire the compat import
agentic_proteins.agents.coordination.coordinator	wrapper	bijux_proteomics_runtime.execution.agents.coordination.coordinator	replace agentic_proteins.agents.coordination.coordinator with bijux_proteomics_runtime.execution.agents.coordination.coordinator and retire the compat import
agentic_proteins.agents.execution	wrapper	bijux_proteomics_runtime.execution.agents.coordination	replace agentic_proteins.agents.execution with bijux_proteomics_runtime.execution.agents.coordination and retire the compat import
agentic_proteins.agents.execution.coordinator	wrapper	bijux_proteomics_runtime.execution.agents.coordination.coordinator	replace agentic_proteins.agents.execution.coordinator with bijux_proteomics_runtime.execution.agents.coordination.coordinator and retire the compat import
agentic_proteins.agents.planning	dead	none declared	delete agentic_proteins.agents.planning after confirming no callers remain
agentic_proteins.agents.planning.compiler	wrapper	bijux_proteomics_runtime.execution.agents.planning.compiler	replace agentic_proteins.agents.planning.compiler with bijux_proteomics_runtime.execution.agents.planning.compiler and retire the compat import
agentic_proteins.agents.planning.generation	wrapper	bijux_proteomics_runtime.execution.agents.planning.generation	replace agentic_proteins.agents.planning.generation with bijux_proteomics_runtime.execution.agents.planning.generation and retire the compat import
agentic_proteins.agents.planning.planner	wrapper	bijux_proteomics_runtime.execution.agents.planning.planner	replace agentic_proteins.agents.planning.planner with bijux_proteomics_runtime.execution.agents.planning.planner and retire the compat import
agentic_proteins.agents.planning.schemas	wrapper	bijux_proteomics_runtime.execution.agents.planning.schemas	replace agentic_proteins.agents.planning.schemas with bijux_proteomics_runtime.execution.agents.planning.schemas and retire the compat import
agentic_proteins.agents.planning.validation	wrapper	bijux_proteomics_runtime.execution.agents.planning.validation	replace agentic_proteins.agents.planning.validation with bijux_proteomics_runtime.execution.agents.planning.validation and retire the compat import
agentic_proteins.agents.reporting	dead	none declared	delete agentic_proteins.agents.reporting after confirming no callers remain
agentic_proteins.agents.reporting.reporting	wrapper	bijux_proteomics_runtime.execution.agents.reporting.reporting	replace agentic_proteins.agents.reporting.reporting with bijux_proteomics_runtime.execution.agents.reporting.reporting and retire the compat import
agentic_proteins.agents.schemas	wrapper	bijux_proteomics_runtime.execution.agents.schemas	replace agentic_proteins.agents.schemas with bijux_proteomics_runtime.execution.agents.schemas and retire the compat import
agentic_proteins.agents.verification	dead	none declared	delete agentic_proteins.agents.verification after confirming no callers remain
agentic_proteins.agents.verification.critic	wrapper	bijux_proteomics_runtime.execution.agents.verification.critic	replace agentic_proteins.agents.verification.critic with bijux_proteomics_runtime.execution.agents.verification.critic and retire the compat import
agentic_proteins.agents.verification.input_validation	wrapper	bijux_proteomics_runtime.execution.agents.verification.input_validation	replace agentic_proteins.agents.verification.input_validation with bijux_proteomics_runtime.execution.agents.verification.input_validation and retire the compat import
agentic_proteins.agents.verification.quality_control	wrapper	bijux_proteomics_runtime.execution.agents.verification.quality_control	replace agentic_proteins.agents.verification.quality_control with bijux_proteomics_runtime.execution.agents.verification.quality_control and retire the compat import
agentic_proteins.execution	wrapper	bijux_proteomics_runtime.execution.graph_validation bijux_proteomics_runtime.runs.analysis bijux_proteomics_runtime.runs.logging bijux_proteomics_runtime.runs.manager bijux_proteomics_runtime.runs.run_config bijux_proteomics_runtime.runs.telemetry bijux_proteomics_runtime.runs.tool_reliability	replace agentic_proteins.execution with one of bijux_proteomics_runtime.execution.graph_validation, bijux_proteomics_runtime.runs.analysis, bijux_proteomics_runtime.runs.logging, bijux_proteomics_runtime.runs.manager, bijux_proteomics_runtime.runs.run_config, bijux_proteomics_runtime.runs.telemetry, bijux_proteomics_runtime.runs.tool_reliability based on the live owner
agentic_proteins.execution.analysis	wrapper	bijux_proteomics_runtime.runs.analysis	replace agentic_proteins.execution.analysis with bijux_proteomics_runtime.runs.analysis and retire the compat import
agentic_proteins.execution.artifacts	wrapper	bijux_proteomics_runtime.runs.artifacts	replace agentic_proteins.execution.artifacts with bijux_proteomics_runtime.runs.artifacts and retire the compat import
agentic_proteins.execution.compiler	wrapper	bijux_proteomics_runtime.execution.compiler	replace agentic_proteins.execution.compiler with bijux_proteomics_runtime.execution.compiler and retire the compat import
agentic_proteins.execution.compiler.boundary	wrapper	bijux_proteomics_runtime.execution.compiler.boundary	replace agentic_proteins.execution.compiler.boundary with bijux_proteomics_runtime.execution.compiler.boundary and retire the compat import
agentic_proteins.execution.evaluation	wrapper	bijux_proteomics_runtime.execution.evaluation	replace agentic_proteins.execution.evaluation with bijux_proteomics_runtime.execution.evaluation and retire the compat import
agentic_proteins.execution.evaluation.evaluation	wrapper	bijux_proteomics_runtime.execution.evaluation.evaluation	replace agentic_proteins.execution.evaluation.evaluation with bijux_proteomics_runtime.execution.evaluation.evaluation and retire the compat import
agentic_proteins.execution.evaluation.observations	wrapper	bijux_proteomics_runtime.execution.evaluation.observations	replace agentic_proteins.execution.evaluation.observations with bijux_proteomics_runtime.execution.evaluation.observations and retire the compat import
agentic_proteins.execution.evaluation.schemas	wrapper	bijux_proteomics_runtime.execution.evaluation.schemas	replace agentic_proteins.execution.evaluation.schemas with bijux_proteomics_runtime.execution.evaluation.schemas and retire the compat import
agentic_proteins.execution.graphs	wrapper	bijux_proteomics_runtime.execution.graph_validation	replace agentic_proteins.execution.graphs with bijux_proteomics_runtime.execution.graph_validation and retire the compat import
agentic_proteins.execution.logging	wrapper	bijux_proteomics_runtime.runs.logging	replace agentic_proteins.execution.logging with bijux_proteomics_runtime.runs.logging and retire the compat import
agentic_proteins.execution.manager	wrapper	bijux_proteomics_runtime.runs.manager	replace agentic_proteins.execution.manager with bijux_proteomics_runtime.runs.manager and retire the compat import
agentic_proteins.execution.run_config	wrapper	bijux_proteomics_runtime.runs.run_config	replace agentic_proteins.execution.run_config with bijux_proteomics_runtime.runs.run_config and retire the compat import
agentic_proteins.execution.runtime	wrapper	bijux_proteomics_runtime.execution.engine	replace agentic_proteins.execution.runtime with bijux_proteomics_runtime.execution.engine and retire the compat import
agentic_proteins.execution.runtime.executor	wrapper	bijux_proteomics_runtime.execution.engine.executor	replace agentic_proteins.execution.runtime.executor with bijux_proteomics_runtime.execution.engine.executor and retire the compat import
agentic_proteins.execution.runtime.integration	wrapper	bijux_proteomics_runtime.execution.engine.integration	replace agentic_proteins.execution.runtime.integration with bijux_proteomics_runtime.execution.engine.integration and retire the compat import
agentic_proteins.execution.schemas	wrapper	bijux_proteomics_runtime.execution.schemas	replace agentic_proteins.execution.schemas with bijux_proteomics_runtime.execution.schemas and retire the compat import
agentic_proteins.execution.state_machine	wrapper	bijux_proteomics_runtime.runs.state_machine	replace agentic_proteins.execution.state_machine with bijux_proteomics_runtime.runs.state_machine and retire the compat import
agentic_proteins.execution.telemetry	wrapper	bijux_proteomics_runtime.runs.telemetry	replace agentic_proteins.execution.telemetry with bijux_proteomics_runtime.runs.telemetry and retire the compat import
agentic_proteins.execution.tool_reliability	wrapper	bijux_proteomics_runtime.runs.tool_reliability	replace agentic_proteins.execution.tool_reliability with bijux_proteomics_runtime.runs.tool_reliability and retire the compat import
agentic_proteins.execution.validation	wrapper	bijux_proteomics_runtime.execution.validation	replace agentic_proteins.execution.validation with bijux_proteomics_runtime.execution.validation and retire the compat import
agentic_proteins.interfaces	wrapper	bijux_proteomics_runtime.api.app	replace agentic_proteins.interfaces with bijux_proteomics_runtime.api.app and retire the compat import
agentic_proteins.interfaces.cli	wrapper	bijux_proteomics_runtime.api.cli	replace agentic_proteins.interfaces.cli with bijux_proteomics_runtime.api.cli and retire the compat import
agentic_proteins.interfaces.http	wrapper	bijux_proteomics_runtime.api.app	replace agentic_proteins.interfaces.http with bijux_proteomics_runtime.api.app and retire the compat import
agentic_proteins.interfaces.http.app	wrapper	bijux_proteomics_runtime.api.app	replace agentic_proteins.interfaces.http.app with bijux_proteomics_runtime.api.app and retire the compat import
agentic_proteins.interfaces.http.deps	wrapper	bijux_proteomics_runtime.api.deps	replace agentic_proteins.interfaces.http.deps with bijux_proteomics_runtime.api.deps and retire the compat import
agentic_proteins.interfaces.http.errors	wrapper	bijux_proteomics_runtime.api.errors	replace agentic_proteins.interfaces.http.errors with bijux_proteomics_runtime.api.errors and retire the compat import
agentic_proteins.interfaces.http.middleware	wrapper	bijux_proteomics_runtime.api.middleware	replace agentic_proteins.interfaces.http.middleware with bijux_proteomics_runtime.api.middleware and retire the compat import
agentic_proteins.interfaces.http.v1	dead	none declared	delete agentic_proteins.interfaces.http.v1 after confirming no callers remain
agentic_proteins.interfaces.http.v1.endpoints	wrapper	bijux_proteomics_runtime.api.v1.endpoints	replace agentic_proteins.interfaces.http.v1.endpoints with bijux_proteomics_runtime.api.v1.endpoints and retire the compat import
agentic_proteins.interfaces.http.v1.endpoints.compare	wrapper	bijux_proteomics_runtime.api.v1.endpoints.compare	replace agentic_proteins.interfaces.http.v1.endpoints.compare with bijux_proteomics_runtime.api.v1.endpoints.compare and retire the compat import
agentic_proteins.interfaces.http.v1.endpoints.inspect	wrapper	bijux_proteomics_runtime.api.v1.endpoints.inspect	replace agentic_proteins.interfaces.http.v1.endpoints.inspect with bijux_proteomics_runtime.api.v1.endpoints.inspect and retire the compat import
agentic_proteins.interfaces.http.v1.endpoints.resume	wrapper	bijux_proteomics_runtime.api.v1.endpoints.resume	replace agentic_proteins.interfaces.http.v1.endpoints.resume with bijux_proteomics_runtime.api.v1.endpoints.resume and retire the compat import
agentic_proteins.interfaces.http.v1.endpoints.run	wrapper	bijux_proteomics_runtime.api.v1.endpoints.run	replace agentic_proteins.interfaces.http.v1.endpoints.run with bijux_proteomics_runtime.api.v1.endpoints.run and retire the compat import
agentic_proteins.interfaces.http.v1.router	wrapper	bijux_proteomics_runtime.api.v1.router	replace agentic_proteins.interfaces.http.v1.router with bijux_proteomics_runtime.api.v1.router and retire the compat import
agentic_proteins.interfaces.http.v1.schema	wrapper	bijux_proteomics_runtime.api.v1.schema	replace agentic_proteins.interfaces.http.v1.schema with bijux_proteomics_runtime.api.v1.schema and retire the compat import
agentic_proteins.interfaces.structure_reports	wrapper	bijux_proteomics.review.structure_reports bijux_proteomics.review.structure_reports.render	replace agentic_proteins.interfaces.structure_reports with one of bijux_proteomics.review.structure_reports, bijux_proteomics.review.structure_reports.render based on the live owner
agentic_proteins.orchestration	wrapper	bijux_proteomics_runtime.execution bijux_proteomics_runtime.governance.compatibility_bridges bijux_proteomics_runtime.runs	replace agentic_proteins.orchestration with one of bijux_proteomics_runtime.execution, bijux_proteomics_runtime.governance.compatibility_bridges, bijux_proteomics_runtime.runs based on the live owner
agentic_proteins.orchestration.analysis	wrapper	bijux_proteomics_runtime.runs.analysis	replace agentic_proteins.orchestration.analysis with bijux_proteomics_runtime.runs.analysis and retire the compat import
agentic_proteins.orchestration.artifacts	wrapper	bijux_proteomics_runtime.runs.artifacts	replace agentic_proteins.orchestration.artifacts with bijux_proteomics_runtime.runs.artifacts and retire the compat import
agentic_proteins.orchestration.bridge_contracts	wrapper	bijux_proteomics_runtime.governance.compatibility_bridges	replace agentic_proteins.orchestration.bridge_contracts with bijux_proteomics_runtime.governance.compatibility_bridges and retire the compat import
agentic_proteins.orchestration.compiler	wrapper	bijux_proteomics_runtime.execution.compiler	replace agentic_proteins.orchestration.compiler with bijux_proteomics_runtime.execution.compiler and retire the compat import
agentic_proteins.orchestration.compiler.boundary	wrapper	bijux_proteomics_runtime.execution.compiler.boundary	replace agentic_proteins.orchestration.compiler.boundary with bijux_proteomics_runtime.execution.compiler.boundary and retire the compat import
agentic_proteins.orchestration.evaluation	wrapper	bijux_proteomics_runtime.execution.evaluation	replace agentic_proteins.orchestration.evaluation with bijux_proteomics_runtime.execution.evaluation and retire the compat import
agentic_proteins.orchestration.evaluation.evaluation	wrapper	bijux_proteomics_runtime.execution.evaluation.evaluation	replace agentic_proteins.orchestration.evaluation.evaluation with bijux_proteomics_runtime.execution.evaluation.evaluation and retire the compat import
agentic_proteins.orchestration.evaluation.observations	wrapper	bijux_proteomics_runtime.execution.evaluation.observations	replace agentic_proteins.orchestration.evaluation.observations with bijux_proteomics_runtime.execution.evaluation.observations and retire the compat import
agentic_proteins.orchestration.evaluation.schemas	wrapper	bijux_proteomics_runtime.execution.evaluation.schemas	replace agentic_proteins.orchestration.evaluation.schemas with bijux_proteomics_runtime.execution.evaluation.schemas and retire the compat import
agentic_proteins.orchestration.graphs	wrapper	bijux_proteomics_runtime.execution.graph_validation	replace agentic_proteins.orchestration.graphs with bijux_proteomics_runtime.execution.graph_validation and retire the compat import
agentic_proteins.orchestration.logging	wrapper	bijux_proteomics_runtime.runs.logging	replace agentic_proteins.orchestration.logging with bijux_proteomics_runtime.runs.logging and retire the compat import
agentic_proteins.orchestration.manager	wrapper	bijux_proteomics_runtime.runs.manager	replace agentic_proteins.orchestration.manager with bijux_proteomics_runtime.runs.manager and retire the compat import
agentic_proteins.orchestration.run_config	wrapper	bijux_proteomics_runtime.runs.run_config	replace agentic_proteins.orchestration.run_config with bijux_proteomics_runtime.runs.run_config and retire the compat import
agentic_proteins.orchestration.runtime	wrapper	bijux_proteomics_runtime.execution.engine	replace agentic_proteins.orchestration.runtime with bijux_proteomics_runtime.execution.engine and retire the compat import
agentic_proteins.orchestration.runtime.executor	wrapper	bijux_proteomics_runtime.execution.engine.executor	replace agentic_proteins.orchestration.runtime.executor with bijux_proteomics_runtime.execution.engine.executor and retire the compat import
agentic_proteins.orchestration.runtime.integration	wrapper	bijux_proteomics_runtime.execution.engine.integration	replace agentic_proteins.orchestration.runtime.integration with bijux_proteomics_runtime.execution.engine.integration and retire the compat import
agentic_proteins.orchestration.schemas	wrapper	bijux_proteomics_runtime.execution.schemas	replace agentic_proteins.orchestration.schemas with bijux_proteomics_runtime.execution.schemas and retire the compat import
agentic_proteins.orchestration.state_machine	wrapper	bijux_proteomics_runtime.runs.state_machine	replace agentic_proteins.orchestration.state_machine with bijux_proteomics_runtime.runs.state_machine and retire the compat import
agentic_proteins.orchestration.telemetry	wrapper	bijux_proteomics_runtime.runs.telemetry	replace agentic_proteins.orchestration.telemetry with bijux_proteomics_runtime.runs.telemetry and retire the compat import
agentic_proteins.orchestration.tool_reliability	wrapper	bijux_proteomics_runtime.runs.tool_reliability	replace agentic_proteins.orchestration.tool_reliability with bijux_proteomics_runtime.runs.tool_reliability and retire the compat import
agentic_proteins.orchestration.validation	wrapper	bijux_proteomics_runtime.execution.validation	replace agentic_proteins.orchestration.validation with bijux_proteomics_runtime.execution.validation and retire the compat import
agentic_proteins.providers	wrapper	bijux_proteomics_runtime.providers.assurance bijux_proteomics_runtime.providers.builtin.heuristic bijux_proteomics_runtime.providers.capabilities bijux_proteomics_runtime.providers.catalog bijux_proteomics_runtime.providers.contracts bijux_proteomics_runtime.providers.errors bijux_proteomics_runtime.providers.selection	replace agentic_proteins.providers with one of bijux_proteomics_runtime.providers.assurance, bijux_proteomics_runtime.providers.builtin.heuristic, bijux_proteomics_runtime.providers.capabilities, bijux_proteomics_runtime.providers.catalog, bijux_proteomics_runtime.providers.contracts, bijux_proteomics_runtime.providers.errors, bijux_proteomics_runtime.providers.selection based on the live owner
agentic_proteins.providers.base	wrapper	bijux_proteomics_runtime.providers.contracts	replace agentic_proteins.providers.base with bijux_proteomics_runtime.providers.contracts and retire the compat import
agentic_proteins.providers.capabilities	wrapper	bijux_proteomics_runtime.providers.capabilities bijux_proteomics_runtime.providers.catalog	replace agentic_proteins.providers.capabilities with one of bijux_proteomics_runtime.providers.capabilities, bijux_proteomics_runtime.providers.catalog based on the live owner
agentic_proteins.providers.errors	wrapper	bijux_proteomics_runtime.providers.errors	replace agentic_proteins.providers.errors with bijux_proteomics_runtime.providers.errors and retire the compat import
agentic_proteins.providers.experimental	wrapper	bijux_proteomics_runtime.providers.remote	replace agentic_proteins.providers.experimental with bijux_proteomics_runtime.providers.remote and retire the compat import
agentic_proteins.providers.experimental._async_utils	wrapper	bijux_proteomics_runtime.providers.remote._async_utils	replace agentic_proteins.providers.experimental._async_utils with bijux_proteomics_runtime.providers.remote._async_utils and retire the compat import
agentic_proteins.providers.experimental.colabfold	wrapper	bijux_proteomics_runtime.providers.remote.colabfold	replace agentic_proteins.providers.experimental.colabfold with bijux_proteomics_runtime.providers.remote.colabfold and retire the compat import
agentic_proteins.providers.experimental.openprotein	wrapper	bijux_proteomics_runtime.providers.remote.openprotein	replace agentic_proteins.providers.experimental.openprotein with bijux_proteomics_runtime.providers.remote.openprotein and retire the compat import
agentic_proteins.providers.heuristic	wrapper	bijux_proteomics_runtime.providers.builtin.heuristic	replace agentic_proteins.providers.heuristic with bijux_proteomics_runtime.providers.builtin.heuristic and retire the compat import
agentic_proteins.providers.local	wrapper	bijux_proteomics_runtime.providers.local	replace agentic_proteins.providers.local with bijux_proteomics_runtime.providers.local and retire the compat import
agentic_proteins.providers.local.esmfold	wrapper	bijux_proteomics_runtime.providers.local.esmfold	replace agentic_proteins.providers.local.esmfold with bijux_proteomics_runtime.providers.local.esmfold and retire the compat import
agentic_proteins.providers.local.rosettafold	wrapper	bijux_proteomics_runtime.providers.local.rosettafold	replace agentic_proteins.providers.local.rosettafold with bijux_proteomics_runtime.providers.local.rosettafold and retire the compat import
agentic_proteins.providers.remote	wrapper	bijux_proteomics_runtime.providers.remote bijux_proteomics_runtime.providers.remote.colabfold bijux_proteomics_runtime.providers.remote.openprotein	replace agentic_proteins.providers.remote with one of bijux_proteomics_runtime.providers.remote, bijux_proteomics_runtime.providers.remote.colabfold, bijux_proteomics_runtime.providers.remote.openprotein based on the live owner
agentic_proteins.providers.remote._async_utils	wrapper	bijux_proteomics_runtime.providers.remote._async_utils	replace agentic_proteins.providers.remote._async_utils with bijux_proteomics_runtime.providers.remote._async_utils and retire the compat import
agentic_proteins.providers.remote.colabfold	wrapper	bijux_proteomics_runtime.providers.remote.colabfold	replace agentic_proteins.providers.remote.colabfold with bijux_proteomics_runtime.providers.remote.colabfold and retire the compat import
agentic_proteins.providers.remote.openprotein	wrapper	bijux_proteomics_runtime.providers.remote.openprotein	replace agentic_proteins.providers.remote.openprotein with bijux_proteomics_runtime.providers.remote.openprotein and retire the compat import
agentic_proteins.providers.selection	wrapper	bijux_proteomics_runtime.providers.selection	replace agentic_proteins.providers.selection with bijux_proteomics_runtime.providers.selection and retire the compat import
agentic_proteins.state	wrapper	bijux_proteomics_runtime.state.memory_records bijux_proteomics_runtime.state.memory_store bijux_proteomics_runtime.state.schemas bijux_proteomics_runtime.state.snapshot	replace agentic_proteins.state with one of bijux_proteomics_runtime.state.memory_records, bijux_proteomics_runtime.state.memory_store, bijux_proteomics_runtime.state.schemas, bijux_proteomics_runtime.state.snapshot based on the live owner
agentic_proteins.state.context	wrapper	bijux_proteomics_runtime.runs.context	replace agentic_proteins.state.context with bijux_proteomics_runtime.runs.context and retire the compat import
agentic_proteins.state.lifecycle	wrapper	bijux_proteomics_runtime.runs.lifecycle	replace agentic_proteins.state.lifecycle with bijux_proteomics_runtime.runs.lifecycle and retire the compat import
agentic_proteins.state.output	wrapper	bijux_proteomics_runtime.runs.output	replace agentic_proteins.state.output with bijux_proteomics_runtime.runs.output and retire the compat import
agentic_proteins.state.request	wrapper	bijux_proteomics_runtime.runs.request	replace agentic_proteins.state.request with bijux_proteomics_runtime.runs.request and retire the compat import
agentic_proteins.state.schemas	wrapper	bijux_proteomics_runtime.state.schemas	replace agentic_proteins.state.schemas with bijux_proteomics_runtime.state.schemas and retire the compat import
agentic_proteins.state.snapshot	wrapper	bijux_proteomics_runtime.state.snapshot	replace agentic_proteins.state.snapshot with bijux_proteomics_runtime.state.snapshot and retire the compat import
agentic_proteins.state.workspace	wrapper	bijux_proteomics_runtime.support.workspace	replace agentic_proteins.state.workspace with bijux_proteomics_runtime.support.workspace and retire the compat import
agentic_proteins.tools	wrapper	bijux_proteomics_runtime.execution.tools.base bijux_proteomics_runtime.execution.tools.catalog bijux_proteomics_runtime.execution.tools.contracts bijux_proteomics_runtime.execution.tools.heuristic	replace agentic_proteins.tools with one of bijux_proteomics_runtime.execution.tools.base, bijux_proteomics_runtime.execution.tools.catalog, bijux_proteomics_runtime.execution.tools.contracts, bijux_proteomics_runtime.execution.tools.heuristic based on the live owner
agentic_proteins.tools.base	wrapper	bijux_proteomics_runtime.execution.tools.base	replace agentic_proteins.tools.base with bijux_proteomics_runtime.execution.tools.base and retire the compat import
agentic_proteins.tools.catalog	wrapper	bijux_proteomics_runtime.execution.tools.catalog	replace agentic_proteins.tools.catalog with bijux_proteomics_runtime.execution.tools.catalog and retire the compat import
agentic_proteins.tools.contracts	wrapper	bijux_proteomics_runtime.execution.tools.contracts	replace agentic_proteins.tools.contracts with bijux_proteomics_runtime.execution.tools.contracts and retire the compat import
agentic_proteins.tools.heuristic	wrapper	bijux_proteomics_runtime.execution.tools.heuristic	replace agentic_proteins.tools.heuristic with bijux_proteomics_runtime.execution.tools.heuristic and retire the compat import
agentic_proteins.tools.schemas	wrapper	bijux_proteomics_runtime.execution.tools.schemas	replace agentic_proteins.tools.schemas with bijux_proteomics_runtime.execution.tools.schemas and retire the compat import

Reading The Guide

• wrapper means the compatibility module is a narrow bridge and callers should move directly to the named canonical target.
• dead means the module no longer carries meaningful behavior and should be deleted once callers disappear.
• canonical or duplicate would be release-blocking because the compatibility family is not allowed to regain original product logic.

Migration Proof

Migration state	Evidence required before progression
caller still uses a wrapper	canonical target, caller inventory, and observable compatibility comparison
caller moved to canonical owner	updated import plus import, CLI, HTTP, state, or replay proof for the affected surface
wrapper has no callers	repository and declared downstream absence evidence
wrapper removed	compatibility inventory, generated guide, tests, and release notes agree at the same revision

A wrapper row authorizes migration work, not immediate deletion. A dead row identifies absent owned behavior, not proven absence of callers.

Freshness Contract

This reference is generated from the live compatibility inventory. Validate it with:

PYTHONPATH=packages/bijux-proteomics-dev/src .venv/bin/python -m bijux_proteomics_dev.quality.architecture.compatibility_migration_guides --check

When forwarding changes, run the same command without --check, review the generator and guide together, then rerun the compatibility and migration gates. A stale guide cannot support a retirement decision.