Runtime Artifact Stability

This page states what must remain bit-stable, value-stable, or review-stable across repeated flagship reruns. It also names the environment-bound drift that is allowed without pretending the rerun changed meaningfully.

This page exists because reproducibility claims become dishonest when every change is either treated as fatal drift or waved away as harmless noise. The runtime layer needs a sharper contract: which artifacts must match exactly, which semantic surfaces must remain stable, and which small environment-shaped differences are tolerated.

How To Read The Stability Contract

• bit-stable paths: should remain byte-for-byte identical across faithful reruns of the shipped lane
• value-stable surfaces: should preserve meaning even if surrounding metadata evolves
• review-stable surfaces: should keep the same reviewer interpretation unless the repository intentionally changes the runtime or scientific boundary
• permitted environment drift: names the few fields that may change without altering the proof surface

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
• note: Bit-stable paths are checked fixture artifacts. Value-stable and review-stable surfaces may change wording only when the underlying runtime or scientific boundary changes in the same reviewable edit.

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
• note: Bit-stable paths are checked fixture artifacts. Value-stable and review-stable surfaces may change wording only when the underlying runtime or scientific boundary changes in the same reviewable edit.

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
• note: Bit-stable paths are checked fixture artifacts. Value-stable and review-stable surfaces may change wording only when the underlying runtime or scientific boundary changes in the same reviewable edit.

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
• note: Bit-stable paths are checked fixture artifacts. Value-stable and review-stable surfaces may change wording only when the underlying runtime or scientific boundary changes in the same reviewable edit.

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
• note: Bit-stable paths are checked fixture artifacts. Value-stable and review-stable surfaces may change wording only when the underlying runtime or scientific boundary changes in the same reviewable edit.

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
• note: Bit-stable paths are checked fixture artifacts. Value-stable and review-stable surfaces may change wording only when the underlying runtime or scientific boundary changes in the same reviewable edit.

Why Stability Is Not The Same As Bigger Trust

• a perfectly stable import-backed lane is still import-backed
• a raw-executable lane can be stable and still remain bounded by benchmark or consequence limits
• stability protects honest rerun claims; it does not automatically expand biological, analytical, or outsider-facing authority