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Execution

Execution turns an identified public benchmark package into a run bundle that can be rerun, compared, refused, and inspected without private operational knowledge.

bijux-proteomics-runtime owns run-mode declaration, preflight, execution, state history, replay, rerun comparison, artifact integrity, and runtime refusal. A CLI transcript is one view of that evidence, not the execution contract itself.

What Execution Means Here

Execution evidence is narrower than scientific truth and stronger than a convenient demo:

  • it proves what can be rerun or replayed from the current public package set
  • it proves which artifacts, checks, and refusal boundaries still survive without private maintainer glue
  • it does not by itself widen scientific meaning, recommendation posture, or lab-worth claims that belong to other owners

Current Runtime Ceiling By Family

family current runtime lane what the runtime route proves current runtime limiter
dda import_only downstream replay and review remain real and auditable full in-repo live-engine parity is still not the flagship route
dia raw_executable public rerun, replay, and challenge routes are real runtime proof still narrows under library and consequence limits
lfq raw_executable public rerun and comparability routes are real execution strength does not erase missingness and cohort-transfer limits
multiplex raw_executable runtime substance is real and reviewable outsider-facing trust still collapses under the stress packet
ptm raw_executable localization and rerun evidence survive public replay consequence confidence remains narrower than execution strength
targeted raw_executable public rerun and artifact verification are real calibration and interference limits still narrow the broader sentence

Runtime Evidence Flow

flowchart LR
    package["identified benchmark package"] --> preflight["input and environment preflight"]
    preflight --> entrypoint["public Runtime entrypoint"]
    entrypoint --> state["state history and diagnostics"]
    state --> bundle["artifact inventory and checksums"]
    bundle --> replay["replay and companion comparison"]
    replay --> verdict["accepted, degraded, or refused"]
    preflight -. unmet .-> refusal["structured refusal"]
    replay -. unstable .-> refusal

Every arrow has a durable record. A command transcript without input identity cannot establish which benchmark ran. Output files without state history and an artifact inventory cannot establish a run bundle. Similar values without a declared comparison policy cannot establish replay or parity.

Runtime disposition Required record Meaning
accepted request, environment, state history, complete artifact inventory, checks, comparison verdict the declared runtime lane completed and met its runtime contract
degraded completed output plus named instability, missing capability, or permitted narrowing the lane produced reviewable evidence with a reduced runtime claim
refused failed prerequisite or invariant, reason code, retained partial evidence, next admissible route the requested execution claim is unavailable

An accepted runtime disposition cannot promote scientific or experimental authority. A refusal can still be a complete and trustworthy runtime result.

Concrete Runtime Proof Surfaces

runtime surface current substance why outsiders should care
API and entrypoints CLI, HTTP, and package-driven operator routes reruns do not require private maintainer entrypoints
execution engine orchestrated execution, replay, and evaluation control the run path is inspectable instead of ad hoc
providers builtin, local, and remote provider layers execution realism is bounded explicitly
artifacts and checkpoints run bundles, checkpoints, and stability classes rerun claims can be checked after the run
state, resume, and rehydrate persistent execution state and reopening routes operators can prove what was resumed or rebuilt
diff and comparability surfaces run comparison and replay challenges "same result" becomes a tested question instead of a verbal claim

What A Successful Rerun Should Prove

  • which public package pair was actually reopened
  • which run mode was used and why that mode is still the strongest honest lane
  • which artifacts, checkpoints, and verification records were emitted
  • which replay or invalidation challenge the lane still survives
  • which stronger sentence still remains blocked even after the rerun works

Choose By Review Question

Question Route Review closes when
How do I reopen one family? Operator rerun journey package identity, environment, mode, command, outputs, and comparison are recorded
Which public package starts the rerun? Benchmark rerun kits primary and companion package roles and checksums are explicit
Which artifacts must a run emit? Black-box run verification required, optional, absent, and invalid artifacts are classified
Which replay pressure must the lane survive? Runtime replay challenges invalidation, resume, clean-environment, and failure-replay verdicts are visible
When must runtime stop? Runtime rerun refusals the failed condition and next admissible evidence route are named

What Execution Still Does Not Prove

  • scientific truth independent of benchmark and knowledge owners
  • stronger recommendation posture independent of intelligence review
  • downstream assay worth independent of lab consequence
  • vendor-parity or universal production readiness just because one rerun lane is reproducible

Adjacent Authority

Interpretation Boundaries

  • a raw-executable lane is stronger than an import-only lane, but neither lane automatically widens scientific trust on its own
  • a stable run bundle is necessary for outsider review, but it is not the same thing as broader biological truth
  • a successful local rerun does not erase benchmark incompleteness, grounding pressure, or downstream assay burden
  • runtime refusal is part of runtime honesty, not a sign that the package has become weaker or less useful

Boundary

Runtime evidence settles how an identified lane executed, what it emitted, and whether it survived the declared replay pressure. Benchmark authenticity, scientific acceptance, recommendation authority, and laboratory meaning remain separate contracts.