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Integration Seams

Integration seams are the points where bijux-proteomics-knowledge meets configuration, APIs, operators, or neighboring packages.

This page exists so integration changes do not feel mysterious. A reviewer should be able to say which seams are intentional, which ones carry compatibility risk, and where the package expects outside systems to meet it.

Visual Summary

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

Integration Surfaces

  • ingestion adapters that normalize external inputs (adapters.py)
  • serialization and schema boundaries used by other packages (serialization.py, schema.py)
  • repository protocols and review summaries consumed by downstream decision layers (repositories.py, review.py)

Adjacent Systems

  • governs the other canonical packages instead of replacing their local ownership
  • is the final authority for run acceptance, replay evaluation, and stored evidence

Concrete Anchors

  • src/bijux_proteomics_knowledge/adapters.py
  • src/bijux_proteomics_knowledge/evidence.py
  • src/bijux_proteomics_knowledge/claims.py
  • src/bijux_proteomics_knowledge/resolution.py
  • src/bijux_proteomics_knowledge/review.py

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 Integration Seams 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 bijux-proteomics-knowledge is organized internally in terms a reviewer can follow
  • which modules carry the main execution and dependency story
  • where structural drift would show up before it becomes expensive

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 where to look when integration behavior changes.

Stability

Keep it aligned with real boundary modules and schema files.