Architecture

This section maps the real module layout for bijux-proteomics-knowledge.

The package is not split into runtime/model/application layers. The structure is feature-oriented around evidence, claims, conflict resolution, review, and graph semantics.

Visual Summary

flowchart LR
    evidence["evidence.py"]
    claims["claims.py"]
    resolution["resolution.py"]
    review["review.py"]
    graph["graph.py"]
    repositories["repositories.py"]
    adapters["adapters.py"]
    evidence --> claims
    claims --> resolution
    resolution --> review
    claims --> graph
    repositories --> review
    adapters --> evidence

Pages in This Section

• Module Map
• Dependency Direction
• Execution Model
• State and Persistence
• Integration Seams
• Error Model
• Extensibility Model
• Code Navigation
• Architecture Risks

Read Across the Package

• Foundation when you need the package boundary and ownership story first
• Interfaces when the question becomes caller-facing, schema-facing, or contract-facing
• Operations when the question becomes procedural, environmental, diagnostic, or release-oriented
• Quality when the question becomes proof, risk, trust, or review sufficiency

Concrete Anchors

• src/bijux_proteomics_knowledge/evidence.py for evidence modeling and trust logic
• src/bijux_proteomics_knowledge/claims.py for claim lifecycle and lineage behavior
• src/bijux_proteomics_knowledge/resolution.py for conflict resolution policy behavior
• src/bijux_proteomics_knowledge/review.py for review-packet and readiness summarization

Use This Page When

• you are tracing structure, execution flow, or dependency pressure
• you need to understand how modules fit before refactoring
• you are reviewing design drift rather than one isolated bug

Decision Rule

Use Architecture to decide whether a structural change makes bijux-proteomics-knowledge easier or harder to explain in terms of modules, dependency direction, and execution flow. If the change works only because the design becomes harder to read, the safer answer is redesign rather than acceptance.

What This Page Answers

• how the package is actually decomposed today
• which modules are core dependency hubs
• where structural drift is likely to create caller confusion

Reviewer Lens

• trace the described execution path through the named modules instead of trusting the diagram alone
• look for dependency direction or layering that now contradicts the documented seam
• verify that the structural risks named here still match the current code shape

Honesty Boundary

This page describes the current structural model of bijux-proteomics-knowledge, but it does not guarantee that every import path or runtime path still obeys that model. Readers should treat it as a map that must stay aligned with code and tests, not as an authority above them.

Next Checks

• move to interfaces when the review reaches a public or operator-facing seam
• move to operations when the concern becomes repeatable runtime behavior
• move to quality when you need proof that the documented structure is still protected

Purpose

This page explains how to use the architecture section for bijux-proteomics-knowledge without repeating the detail that belongs on the topic pages beneath it.

Stability

This page is part of the canonical package docs spine. Keep it aligned with the current package boundary and the topic pages in this section.