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Documentation Standards

Documentation standards should protect the reader from filler, drift, and false confidence.

For bijux-proteomics-intelligence, documentation should privilege explanation quality over breadth and end examples at reviewable outputs rather than hidden internal scores.

Documentation Model

flowchart TB
    logic["decision logic and uncertainty"]
    examples["examples end at reviewable outputs"]
    contradiction["uncertainty and contradiction stay visible"]
    reader["reader can justify a recommendation path"]

    logic --> examples
    examples --> contradiction
    contradiction --> reader

This page should keep the package from sounding smarter than it is. Good docs make readers inspect the reasoning path, not merely admire the result surface.

Review Rules

  • docs should prioritize explanation quality over breadth
  • examples should end with reviewable outputs
  • quality pages should make uncertainty and contradiction visible

First Proof Check

  • packages/bijux-proteomics-intelligence/tests
  • src/bijux_proteomics_intelligence/policies.py and evaluators.py
  • src/bijux_proteomics_intelligence/report/ and outcomes.py

Design Pressure

The easy failure is to write persuasive output prose that hides how much uncertainty and evidence-shape still matter underneath.