Dependency Governance

Dependencies must strengthen judgment without transferring another package's authority into Intelligence. The installed graph is intentionally one-way: Foundation, Core, and Knowledge provide contracts or evidence; Intelligence produces decision artifacts for downstream consequence review.

flowchart LR
    P["Pydantic"] --> I["Intelligence"]
    N["NumPy"] --> I
    G["Loguru"] --> I
    F["Foundation"] --> I
    C["Core"] --> I
    K["Knowledge"] --> I
    I -. "must not import" .-> X["Runtime"]
    I -. "must not import" .-> L["Lab"]

Current Dependency Contract

Dependency	Permitted role	Boundary to protect
bijux-proteomics-foundation	shared identifiers, provenance, stable contracts	do not fork shared meanings locally
bijux-proteomics-core	scientific result types and computations used by judgment	do not make Intelligence an alternate scientific engine
bijux-proteomics-knowledge	claims, evidence, citations, lineage, contradiction records	do not mutate custody or redefine evidence truth
Pydantic	validation and serialization of decision artifacts	model shape must not substitute for semantic ownership
NumPy	bounded numeric evaluation and ranking support	record orientation, missingness, tolerance, and deterministic behavior
Loguru	observable diagnostics	logs are not retained decision evidence

Runtime and Lab are deliberately absent. Importing either would let decision policy control execution or consequence recording and would create a cycle in the product flow.

Admission Test

A dependency is acceptable only when:

1. Its role maps to an owned decision capability.
2. It does not introduce a second representation of an upstream contract.
3. Its optional or failure behavior is explicit at the public boundary.
4. Numeric behavior is deterministic or its variability is captured.
5. It does not pull Runtime, Lab, network access, or storage policy into the recommendation layer.
6. Focused tests prove the seam and dependency checks prove the graph.

Prefer a narrow typed input over importing a neighbor's application service. Prefer a recorded evidence reference over reaching into Knowledge storage. Prefer returning a decision artifact over invoking a downstream action.

Rejection Signals

Reject or redesign a dependency that requires hidden global state, changes ranking through an unrecorded default, owns evidence persistence, starts work, records laboratory outcomes, or duplicates a model already owned upstream. Convenience is not sufficient justification for crossing an authority boundary.