Local development

Lab owns the boundary between advisory follow-up and reviewed physical work: assay planning, experimental design, batching, readiness, handoffs, outcomes, and reconciliation. Local changes must preserve who authorized execution, what was expected, what was actually observed, and why a run was refused or altered.

Run package-scoped gates

Use root package dispatch:

make lint PACKAGE=bijux-proteomics-lab
make test PACKAGE=bijux-proteomics-lab
make quality PACKAGE=bijux-proteomics-lab
make api PACKAGE=bijux-proteomics-lab

Run make build PACKAGE=bijux-proteomics-lab when root exports, handoff artifacts, compatibility forwarding, package data, or metadata changes. Store generated examples and reports under artifacts/.

Trace authority and observation

flowchart LR
    advice["advisory follow-up"]
    review["human review and readiness"]
    execution["authorized instructions"]
    observed["observed outcome"]
    reconcile["deviation and follow-up"]
    advice --> review --> execution --> observed --> reconcile

Start in the owning domain: planning/ for assay intent and batches, design/ for protocols and experimental structure, readiness/ for execution gates, handoffs/ for operator payloads, outcomes/ for observations, and reconciliation/ for comparison and follow-up. Serialization preserves these contracts; it must not promote advice into executable instructions.

Prove operational boundaries

Change	Required evidence
advisory plan	remains non-executable and carries rationale and blockers
readiness gate	ready, not-ready, missing-resource, and review-backlog cases
executable handoff	authority, protocol, materials, controls, and preflight remain explicit
scheduling or batching	dependency, capacity, delay, cycle, and infeasible cases
outcome model	raw values, units, QC, censoring, deviations, and failures survive round trip
reconciliation	expected and observed states remain separate and prior records stay immutable

Use computational fixtures for contract logic. Do not describe them as evidence that an instrument, protocol, or assay performs successfully in the physical world. Operational performance claims require measured laboratory evidence.

Preserve refusal and ownership

Refusal is correct when materials, controls, evidence, staffing, instrument capacity, or review authority are insufficient. Do not replace it with a default plan that appears executable. Lab consumes scientific and advisory inputs but does not redefine Core calculations, Knowledge evidence, or Intelligence recommendations.

The change is ready when advisory and executable states cannot be confused, authority is recoverable, idempotent handoff behavior is tested, observations remain distinct from expectations, and reconciliation records every meaningful deviation without rewriting history.