Local development

agentic-proteins is a compatibility bridge, not a second workflow runtime. Local work therefore begins by identifying the canonical owner in bijux-proteomics-runtime or bijux-proteomics-core, then proving that the legacy route still forwards to that owner without acquiring new behavior.

Prepare the repository environment

Run package commands from the repository root. The dispatcher installs the package, its canonical dependencies, and the shared development toolkit into the repository check environment.

make lint PACKAGE=agentic-proteins
make test PACKAGE=agentic-proteins
make quality PACKAGE=agentic-proteins
make api PACKAGE=agentic-proteins

Use make build PACKAGE=agentic-proteins when packaging metadata, forwarding modules, or included artifacts change. Generated reports and distributions are written beneath artifacts/; they do not belong beside source files.

Follow the ownership route

flowchart LR
    legacy["legacy import, CLI, or HTTP route"]
    bridge["agentic-proteins forwarding layer"]
    owner["canonical runtime or core owner"]
    proof["identity and behavior proof"]
    legacy --> bridge --> owner --> proof

For a root import, compare src/agentic_proteins/__init__.py with the public exports of bijux_proteomics_runtime. For CLI or HTTP work, inspect interfaces/cli.py or interfaces/http/app.py and the canonical entrypoint it delegates to. Provider, execution, state, and persistence behavior belongs to Runtime even when a historical module still exposes the old path.

Choose the smallest meaningful proof

Change	Required evidence
lazy root export	imported object is the canonical object, including identity where promised
CLI forwarding	legacy invocation reaches the canonical command and preserves exit semantics
HTTP forwarding	route, schema, status, and error behavior match the canonical API contract
package metadata	canonical dependencies install and wheel/sdist contents remain bridge-only
deprecation text	migration destination and retirement state agree with the migration ledger

Run the narrow test module while editing, then the package test and API gates before committing. A test that only proves the bridge imports is insufficient when the change affects a callable route.

Keep the bridge narrow

Do not add local policy, retries, provider selection, state transitions, or artifact interpretation to make an old caller easier to support. Put the behavior in its canonical owner and forward to it. If an old signature cannot map exactly, expose the incompatibility through a documented migration or an explicit error instead of silently changing meaning.

The change is ready when the canonical owner contains the behavior, the bridge contains only adaptation or forwarding, legacy and canonical routes agree, and the compatibility ledger describes any narrowed promise.