Skip to content

Lifecycle Overview

Every package run follows a simple lifecycle: inputs enter through interfaces, domain and application code coordinate the work, and durable artifacts or responses leave the package.

The value of this page is speed. A reader should be able to skim it and leave with one coherent story about how work moves through bijux-proteomics-knowledge from entrypoint to result.

Treat the foundation pages for bijux-proteomics-knowledge as the package's durable self-description. If the package still feels blurry after this section, the boundary story is not clear enough yet.

Visual Summary

flowchart RL
    page["Lifecycle Overview<br/>clarifies: own the right work | name the boundary | compare neighbors"]
    classDef page fill:#dbeafe,stroke:#1d4ed8,color:#1e3a8a,stroke-width:2px;
    classDef positive fill:#dcfce7,stroke:#16a34a,color:#14532d;
    classDef caution fill:#fee2e2,stroke:#dc2626,color:#7f1d1d;
    classDef anchor fill:#ede9fe,stroke:#7c3aed,color:#4c1d95;
    classDef action fill:#fef3c7,stroke:#d97706,color:#7c2d12;
    own1["trace capture, runtime persistence, and execution-store behavior"]
    own1 --> page
    own2["flow execution authority"]
    own2 --> page
    own3["replay and acceptability semantics"]
    own3 --> page
    limit1["repository tooling and release support"]
    page -.keeps outside.-> limit1
    limit2["agent composition policy"]
    page -.keeps outside.-> limit2
    limit3["ingest and index domain ownership"]
    page -.keeps outside.-> limit3
    anchor1["packages/bijux-proteomics-knowledge"]
    page --> anchor1
    anchor2["packages/bijux-proteomics-knowledge/src/bijux_proteomics_knowledge"]
    page --> anchor2
    anchor3["packages/bijux-proteomics-knowledge/tests"]
    page --> anchor3
    class page page;
    class own1,own2,own3 positive;
    class limit1,limit2,limit3 caution;
    class anchor1,anchor2,anchor3 anchor;

Lifecycle Anchors

  • entry surfaces: CLI entrypoint in src/bijux_proteomics_knowledge/evidence.py, HTTP app in src/bijux_proteomics_knowledge/claims.py, knowledge contracts in src/bijux_proteomics_knowledge/schema.py
  • code ownership: src/bijux_proteomics_knowledge/model, src/bijux_proteomics_knowledge/runtime, src/bijux_proteomics_knowledge/application
  • durable outputs: execution store records, replay decision artifacts, non-determinism policy evaluations

Concrete Anchors

  • packages/bijux-proteomics-knowledge as the package root
  • packages/bijux-proteomics-knowledge/src/bijux_proteomics_knowledge as the import boundary
  • packages/bijux-proteomics-knowledge/tests as the package proof surface

Use This Page When

  • you need the package idea before the implementation detail
  • you are deciding whether work belongs here or in a neighboring package
  • you want the shortest honest explanation of what this package is for

Decision Rule

Use Lifecycle Overview to decide whether a change makes bijux-proteomics-knowledge easier or harder to defend as one distinct role in the overall system. If the work makes the package broader without making its role clearer, stop and re-check the boundary before treating the change as a local improvement.

What This Page Answers

  • what problem bijux-proteomics-knowledge is supposed to own on purpose
  • where the package boundary stops, even when nearby code looks tempting
  • which neighboring package seams deserve comparison before the boundary is changed

Reviewer Lens

  • compare the stated boundary with the modules, artifacts, and tests that are supposed to uphold it
  • check that out-of-scope behavior is not quietly re-entering through convenience paths
  • confirm that the package story still matches the real repository layout and neighboring package docs

Honesty Boundary

This page can explain the intended boundary of bijux-proteomics-knowledge, but it cannot prove that boundary by itself. The real proof still lives in the code, tests, and neighboring package seams that either support or contradict the story told here.

Next Checks

  • move to architecture when the question becomes structural rather than boundary-oriented
  • move to interfaces when the question becomes contract-facing
  • move to quality when the question becomes proof or review sufficiency

Purpose

This page keeps the package lifecycle readable before a reader dives into implementation detail.

Stability

Keep it aligned with the current entrypoints and produced outputs.