Foundation¶

The foundation section explains the durable role of bijux-proteomics-core before it explains implementation detail. Use it to resolve why durable workflow rules belong here before evidence, scoring, or execution layers act on them.

flowchart LR
    lifecycle["lifecycle states"]
    gates["gate semantics"]
    workflows["workflow contracts"]
    core["core foundation"]
    intelligence["intelligence"]
    runtime["runtime"]
    lab["lab"]

    lifecycle --> core
    gates --> core
    workflows --> core
    core --> intelligence
    core --> runtime
    core --> lab

What This Section Protects¶

one durable grammar for workflows before downstream packages optimize around it
gate semantics that remain reviewable instead of dissolving into code paths
lifecycle discipline that survives changes in policy or execution tooling

Start With¶

Open Package Overview for the shortest statement of the package role.
Open Ownership Boundary when the question is whether a change belongs here or in a neighbor.
Open Scope and Non-Goals when a proposed change risks broadening the package.
Open Capability Map when you need the concrete work the package is allowed to do.

Section Pages¶

What This Section Settles¶

when a rule is foundational enough to belong in core
how much downstream freedom exists once lifecycle and gate contracts are set
when a proposed change is really policy or execution and should leave this package

First Proof Check¶

packages/bijux-proteomics-core/src/bijux_proteomics
packages/bijux-proteomics-core/tests
neighboring handbooks once the change crosses the local boundary

Neighbors¶

Open bijux-proteomics-foundation when the question leaves program contracts, lifecycle rules, and gate semantics.
Open bijux-proteomics-intelligence when the issue is clearly outside this package's local role.