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Architecture

bijux-proteomics-core architecture is where the repository's governing domain rules become explicit. This section should help a reader see how protein programs, lifecycle checks, assays, reviews, and execution contracts fit together before runtime or intelligence packages act on them.

flowchart LR
    targets["targets and sequences"]
    programs["program specs<br/>programs, context"]
    assays["assays and criteria"]
    reviews["reviews and liabilities"]
    lifecycle["lifecycle and validation"]
    execution["execution contracts"]
    adapters["runtime adapter<br/>repository seams"]

    targets --> programs
    assays --> lifecycle
    programs --> lifecycle
    reviews --> lifecycle
    lifecycle --> execution --> adapters

Architectural Promise

  • program meaning is decided here before orchestration starts
  • lifecycle progression should be explainable from explicit contracts, not from incidental runtime behavior
  • downstream packages may consume these rules, but they should not have to reinvent them

Start With

  • open Execution Model when the question is how program state becomes execution readiness without collapsing into runtime orchestration
  • open Module Map when you need the owning domain files for a concrete noun such as review, assay, program, or target
  • open Integration Seams when a change seems to pull runtime control or recommendation logic inward

Read This Section To Answer

First Proof Check

  • src/bijux_proteomics/program_spec.py, programs.py, and targets.py for durable contracts
  • src/bijux_proteomics/lifecycle.py, validation.py, and execution_contracts.py for readiness and execution rules
  • src/bijux_proteomics/biology/, domain/, and runtime_adapter.py for structural seams to neighboring concerns

Boundary Test

If a rule changes who may advance a program or what counts as ready, the answer should be obvious in this package before any runtime workflow is consulted.