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Documentation Standards

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

For bijux-proteomics-knowledge, documentation should expose contradiction handling directly and show reviewed knowledge state rather than stopping at raw evidence inputs.

Documentation Model

flowchart TB
    evidence["raw evidence input"]
    review["reviewed knowledge state"]
    contradiction["certainty ends and contradiction stays visible"]
    reader["reader can see what is known and what is unresolved"]

    evidence --> review
    review --> contradiction
    contradiction --> reader

This page should keep knowledge docs from becoming too clean. If the prose hides where certainty ends, it stops describing the package honestly.

Review Rules

  • docs should expose contradiction handling directly
  • examples should show reviewed knowledge state, not just raw evidence input
  • quality pages should state where certainty ends

First Proof Check

  • packages/bijux-proteomics-knowledge/tests
  • src/bijux_proteomics_knowledge/claims.py and evidence.py
  • src/bijux_proteomics_knowledge/confidence/segments.py and review.py

Design Pressure

The common mistake is to document the storage path clearly while leaving contradiction handling and uncertainty boundaries vague.