Installation and Setup

Install agentic-proteins only when an existing application still imports the historical package or invokes the legacy command. New integrations should install and call bijux-proteomics-runtime directly.

Requirements

• Python 3.11 or newer
• an isolated Python environment
• the same 0.3.x release family for agentic-proteins, bijux-proteomics-core, and bijux-proteomics-runtime

The base distribution installs Core and Runtime because compatibility modules forward to those canonical owners. It does not carry independent execution implementations.

Install the compatibility bridge

python -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install agentic-proteins

Choose an optional dependency only when the legacy application already requires that capability:

python -m pip install "agentic-proteins[api]"
python -m pip install "agentic-proteins[local-esmfold]"
python -m pip install "agentic-proteins[local-rosettafold]"
python -m pip install "agentic-proteins[nl]"

Each extra delegates to the corresponding Runtime extra. Hardware, model assets, service credentials, and provider availability remain Runtime concerns.

Verify forwarding

Confirm both commands are present:

agentic-proteins --help
bijux-proteomics-runtime --help

Then verify that the historical import resolves to the canonical object:

from agentic_proteins import cli as legacy_cli
from bijux_proteomics_runtime import cli as canonical_cli

assert legacy_cli is canonical_cli

That identity check is more meaningful than a successful import alone: it detects accidental package-local implementations that would split behavior between the bridge and Runtime.

Source checkout

From the repository root, install the package in editable mode when reviewing compatibility changes:

python -m pip install -e "packages/agentic-proteins[test]"
python -m pytest packages/agentic-proteins/tests

Inspect interfaces, orchestration, providers, state, and tools when a legacy path is in scope. A compatibility change is ready only when the old import still works, resolves to its declared canonical owner, and adds no new execution semantics under agentic_proteins.

Remove the bridge when possible

Migration is complete when the consumer imports bijux_proteomics_runtime, invokes bijux-proteomics-runtime, and no longer relies on a historical submodule path. Uninstalling agentic-proteins should then leave the canonical integration functional.