Runtime Artifact Stability

Artifact stability separates exact bytes, semantic values, reviewer interpretation, and permitted environment metadata. Treating all drift alike would either reject harmless run identity changes or conceal meaningful contract movement.

stability class	required invariant
bit stable	governed fixture bytes remain identical
value stable	named semantic values retain the same meaning
review stable	authorized claim scope and interpretation remain unchanged
permitted environment drift	named execution metadata may vary without changing the proof surface

flowchart LR
    R["repeated run"] --> B["byte comparison"]
    R --> V["semantic value comparison"]
    R --> Q["review interpretation"]
    R --> E["environment metadata"]
    E --> P["allow only declared drift"]

Classify Drift Before Comparing Runs

flowchart TD
    pair["baseline and candidate run bundles"] --> identity{"same package and comparison contract?"}
    identity -->|no| incomparable["incomparable; explain identity mismatch"]
    identity -->|yes| inventory["compare artifact inventories"]
    inventory --> bytes["bit-stable paths"]
    inventory --> values["value-stable fields"]
    inventory --> review["review-stable interpretation"]
    inventory --> environment["declared environment drift"]
    bytes --> verdict{"all differences classified?"}
    values --> verdict
    review --> verdict
    environment --> verdict
    verdict -->|yes| comparable["comparable verdict"]
    verdict -->|no| refused["stability refusal"]

Classification is ordered. Package or contract identity is checked before bytes; artifact inventory is checked before field values; review meaning is checked even when the numeric comparison passes. An unclassified difference is a failed comparison, not permitted drift.

Drift example	Class	Required response
changed governed fixture byte	bit stability	fail until the fixture change and its owner are reviewed
reordered representation with unchanged governed value	value stability	prove canonical value equivalence and explain byte drift
changed blocker, claim scope, or invalidation reason	review stability	treat as contract movement even if result values match
new run ID or artifact directory	permitted environment drift	accept only when explicitly named and non-authoritative
missing required artifact	inventory failure	refuse comparison; absence cannot be normalized away
new artifact with unknown role	unclassified drift	assign ownership and stability class before acceptance

Family Stability Contracts

dda

• bit-stable paths: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/stage_lineage.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/failure_replay.json
• value-stable surfaces: runtime package id dda-maxquant-pipeline-corpus, run mode import_only, remaining blockers none
• review-stable surfaces: authorized claim scope in the runtime bundle, family-specific replay invalidation reasons, downstream owner links carried by the checked runtime bundle
• permitted environment drift: run_id, environment.environment_id, run_summary.artifacts_dir

dia

• bit-stable paths: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/stage_lineage.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/failure_replay.json
• value-stable surfaces: runtime package id dia-diann-pipeline-corpus, run mode raw_executable, remaining blockers none
• review-stable surfaces: authorized claim scope in the runtime bundle, family-specific replay invalidation reasons, downstream owner links carried by the checked runtime bundle
• permitted environment drift: run_id, environment.environment_id, run_summary.artifacts_dir

lfq

• bit-stable paths: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/stage_lineage.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/failure_replay.json
• value-stable surfaces: runtime package id lfq-cohort-review-corpus, run mode raw_executable, remaining blockers none
• review-stable surfaces: authorized claim scope in the runtime bundle, family-specific replay invalidation reasons, downstream owner links carried by the checked runtime bundle
• permitted environment drift: run_id, environment.environment_id, run_summary.artifacts_dir

multiplex

• bit-stable paths: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/stage_lineage.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/failure_replay.json
• value-stable surfaces: runtime package id multiplex-tmtpro-review-corpus, run mode raw_executable, remaining blockers none
• review-stable surfaces: authorized claim scope in the runtime bundle, family-specific replay invalidation reasons, downstream owner links carried by the checked runtime bundle
• permitted environment drift: run_id, environment.environment_id, run_summary.artifacts_dir

ptm

• bit-stable paths: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/stage_lineage.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/failure_replay.json
• value-stable surfaces: runtime package id ptm-localization-review-corpus, run mode raw_executable, remaining blockers none
• review-stable surfaces: authorized claim scope in the runtime bundle, family-specific replay invalidation reasons, downstream owner links carried by the checked runtime bundle
• permitted environment drift: run_id, environment.environment_id, run_summary.artifacts_dir

targeted

• bit-stable paths: packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/run_bundle.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/stage_lineage.json, packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/failure_replay.json
• value-stable surfaces: runtime package id targeted-transition-review-corpus, run mode raw_executable, remaining blockers none
• review-stable surfaces: authorized claim scope in the runtime bundle, family-specific replay invalidation reasons, downstream owner links carried by the checked runtime bundle
• permitted environment drift: run_id, environment.environment_id, run_summary.artifacts_dir

Change Rule

A bit-stable path changes only through an intentional governed fixture update. Value-stable or review-stable surfaces change only when the underlying runtime or scientific boundary changes in the same reviewable edit. Permitted environment drift never authorizes a claim, blocker, or lineage change.

Stable execution protects rerun honesty; it does not enlarge biological, analytical, vendor-parity, recommendation, or lab authority.

A stability verdict must retain both run identities, the comparison contract, artifact inventories, classified differences, comparison-tool identity, and the final disposition. A bare “same” or “changed” result is not reviewable.

Minimum comparison record

Record field	Why it is required
baseline and candidate identities	prevents comparison against the wrong run or contract
artifact inventories	exposes missing, added, and role-changed outputs before value comparison
stability policy revision	fixes which paths, fields, meanings, and environment values were governed
classified differences	separates byte, value, review, permitted-environment, and unresolved drift
comparator identity and tolerances	makes numeric and semantic equivalence reproducible
disposition and authority	records who accepted, refused, or escalated the comparison and why

Comparison is refused when either run identity is unresolved, a required artifact is absent, a governed difference has no class, or review meaning moves without an explicit contract decision. Permitted environment drift never absorbs a changed result, blocker, or claim.