Architecture¶

This section explains how bijux_proteomics_foundation is organized so a reviewer can follow structure, dependency direction, and execution flow without guessing.

These pages turn bijux-proteomics-foundation from a directory tree into a readable design map. Use them when a structural change needs to be grounded in named modules and real execution paths.

Treat the architecture pages for bijux-proteomics-foundation as a reviewer-facing map of structure and flow. They should shorten code reading, not try to replace it.

Visual Summary¶

flowchart LR
    page["Architecture<br/>clarifies: trace execution | spot dependency pressure | judge structural drift"]
    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;
    module1["schema and identifier invariants"]
    module1 --> page
    module2["serialization and migration compatibility"]
    module2 --> page
    module3["error taxonomy and package export stability"]
    module3 --> page
    code1["src/bijux_proteomics_foundation/schema.py and ids.py"]
    page --> code1
    code2["src/bijux_proteomics_foundation/serialization.py and migrations.py"]
    page --> code2
    code3["src/bijux_proteomics_foundation/errors.py and __init__.py"]
    page --> code3
    pressure1["tests for document primitives and package-level type contracts"]
    pressure1 -.tests whether this structure still holds.-> page
    pressure2["cross-package tests that consume foundation schemas and ids"]
    pressure2 -.tests whether this structure still holds.-> page
    pressure3["lint and type gates protecting long-lived boundary compatibility"]
    pressure3 -.tests whether this structure still holds.-> page
    class page page;
    class module1,module2,module3 positive;
    class code1,code2,code3 anchor;
    class pressure1,pressure2,pressure3 caution;

Pages in This Section¶

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_foundation/schema.py and ids.py for document and identifier contracts
src/bijux_proteomics_foundation/serialization.py and migrations.py for compatibility flows
src/bijux_proteomics_foundation/errors.py and __init__.py for stable exported boundaries

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-foundation 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-foundation 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-foundation, 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-foundation 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.