Python entry points

bijux-proteomics-foundation is a typed library and deliberately installs no command-line executable. It defines the identity, serialization, hashing, schema-evolution, and outcome contracts used by commands in higher-level packages. A standalone foundation CLI would have to invent application policy: which document to read, which migration registry to load, and where to write the result.

Use the curated package root for the smallest stable surface:

from bijux_proteomics_foundation import (
    DocumentSchema,
    ProgramId,
    hash_payload,
    to_canonical_json,
)

schema = DocumentSchema(
    created_by="review-service",
    document_id="program-demo",
    document_kind="program_spec",
)

payload = {"document_schema": schema.to_dict(), "program_id": "prog-demo"}
canonical = to_canonical_json(payload)
digest = hash_payload(payload)

ProgramId and the other identifier aliases are Pydantic-compatible annotated strings. For prefix construction and classification, import IdentifierKind, build_identifier(), and ensure_identifier_kind() from bijux_proteomics_foundation.identity.

Where command-line behavior belongs

Need	Owning surface
Validate a domain document	The package that defines that document model
Execute or reproduce a run	bijux-proteomics-runtime
Inspect scientific data	bijux-proteomics-core
Check repository contracts	bijux-proteomics-dev maintainer commands
Convert a foundation model to JSON, JSONL, or TSV	JsonModel methods in application code

Foundation raises typed validation, migration, serialization, and optional dependency errors; a consuming CLI decides how those failures map to exit codes and terminal or JSON output. This separation keeps the same contract usable from a notebook, service, batch worker, or command without transport behavior changing its meaning.