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What Would Make This Repository Ready

This page is generated from the current release matrix, acceptance dashboard, and package quality reports. It names the exact remaining blockers instead of broad roadmap language.

The important shift is that these blockers now sit on top of a materially stronger repository. The product already has real benchmark, runtime, grounding, recommendation, and consequence depth. These blockers exist because the release sentence still has to be narrower than the strongest current code and artifact surfaces in several places.

  • source of truth: packages/bijux-proteomics-dev/src/bijux_proteomics_dev/release/governance/hostile_review_pages.py

Blocking artifacts

These blockers keep the repository from claiming cleaner release posture because tracked artifacts, runtime evidence, or generated evidence are still not strong enough.

  • faithful-rerun-refused: dda still refuses stronger rerun claims: faithful rerun still stops at imported MaxQuant and comparator exports because the repository does not own a raw DDA search execution lane; external-engine behavior remains proprietary or out-of-repository for the strongest DDA package
  • faithful-rerun-refused: dia still refuses stronger rerun claims: the shipped DIA lane is raw-executable in runtime terms but still depends on library-conditioned exported reports rather than chromatogram-native replay
  • faithful-rerun-refused: multiplex still refuses stronger rerun claims: multiplex remains below outsider-auditable trust because runtime rerun strength still outruns family-level consequence and challenge closure
  • black-box-language-outruns-rerun-evidence: dda still requests outsider_auditable_bounded but the black-box benchmark dashboard only defends review_grade_bounded
  • ssot-readiness-blocked: scientific release dossier is blocked until SSOT readiness is clean: duplicate-model-ownership: structured model 'BeliefAuditEntry' is owned by multiple canonical packages: bijux-proteomics-core:bijux_proteomics/review/belief/belief_audit_models.py, bijux-proteomics-intelligence:bijux_proteomics_intelligence/belief_audit.py
  • ssot-readiness-blocked: scientific release dossier is blocked until SSOT readiness is clean: duplicate-model-ownership: structured model 'BeliefAuditReport' is owned by multiple canonical packages: bijux-proteomics-core:bijux_proteomics/review/belief/belief_audit_models.py, bijux-proteomics-intelligence:bijux_proteomics_intelligence/belief_audit.py
  • ssot-readiness-blocked: scientific release dossier is blocked until SSOT readiness is clean: duplicate-model-ownership: structured model 'BeliefAuditSummary' is owned by multiple canonical packages: bijux-proteomics-core:bijux_proteomics/review/belief/belief_audit_models.py, bijux-proteomics-intelligence:bijux_proteomics_intelligence/belief_audit.py
  • ssot-readiness-blocked: scientific release dossier is blocked until SSOT readiness is clean: package-substance: bijux-proteomics-core exposes 133 thin modules and needs tighter ownership boundaries

How To Read These Blockers

  • artifact blockers mean the public benchmark, rerun, or challenge packet still fails to defend the stronger sentence
  • workflow-family gaps mean a family packet exists, but one visible weakness still narrows released language
  • package-quality gaps mean the public surface or owner boundaries still lag behind the underlying scientific ambition

What A Closure Condition Should Look Like

  • it should name one evidence change that would narrow a current blocker
  • it should make the stronger sentence more defensible without asking the docs to soften the boundary
  • it should remove ambiguity from one live blocker rather than introduce a new summary surface around the same gap

Workflow-family gaps

These blockers still weaken workflow-family trust because the current public sentence would outrun rerun, acceptance, or family-specific evidence.

  • lfq remains review_grade_bounded because acceptance still fails or stays intentionally narrowed: lfq_missingness_burden, lfq_normalization_drift
  • multiplex remains internal_support_only because acceptance still fails or stays intentionally narrowed: multiplex_interference, multiplex_channel_dropout, multiplex_reference_channel_fragility, multiplex_ratio_compression, multiplex_downstream_review_promotion

Package-quality gaps

These blockers show where package maturity or cross-package release coverage still falls short of a repository-wide stronger claim.

  • agentic-proteins is still not architectural-ready
  • bijux-proteomics is still not architectural-ready
  • bijux-proteomics-core is still not architectural-ready
  • bijux-proteomics-dev is still not architectural-ready
  • bijux-proteomics-intelligence is still not architectural-ready
  • bijux-proteomics-knowledge is still not architectural-ready
  • bijux-proteomics-lab is still not architectural-ready
  • bijux-proteomics-runtime is still not architectural-ready
  • proteomics is still not architectural-ready
  • proteomics-core is still not architectural-ready
  • proteomics-foundation is still not architectural-ready
  • proteomics-intelligence is still not architectural-ready
  • proteomics-knowledge is still not architectural-ready
  • proteomics-lab is still not architectural-ready
  • proteomics-runtime is still not architectural-ready
  • agentic-proteins still carries reopened completion pressure: root public breadth still exceeds owner logic depth
  • bijux-proteomics still carries reopened completion pressure: docs and tree still contradict each other; historical topology language still dominates current design; root public breadth still exceeds owner logic depth
  • bijux-proteomics-knowledge still carries reopened completion pressure: root public breadth still exceeds owner logic depth
  • proteomics still carries reopened completion pressure: historical topology language still dominates current design; root public breadth still exceeds owner logic depth; root public module count still rivals the package owner-family count
  • proteomics-core still carries reopened completion pressure: historical topology language still dominates current design; root public breadth still exceeds owner logic depth; root public module count still rivals the package owner-family count
  • proteomics-foundation still carries reopened completion pressure: root public breadth still exceeds owner logic depth
  • proteomics-intelligence still carries reopened completion pressure: root public breadth still exceeds owner logic depth
  • proteomics-knowledge still carries reopened completion pressure: root public breadth still exceeds owner logic depth
  • proteomics-lab still carries reopened completion pressure: root public breadth still exceeds owner logic depth
  • proteomics-runtime still carries reopened completion pressure: historical topology language still dominates current design; root public breadth still exceeds owner logic depth; root public module count still rivals the package owner-family count

Docs failures

These blockers show where public wording, routing, or scrutiny surfaces drift away from the evidence they are supposed to defend.

  • black-box-language-outruns-rerun-evidence: dda still requests outsider_auditable_bounded but the black-box benchmark dashboard only defends review_grade_bounded

Reader Use

  • use this page when the question is not only what is blocked, but what exact evidence would have to change next
  • use it beside the blocker ledger so release closure stays concrete instead of aspirational
  • use it to distinguish real scientific or runtime closure from cleaner docs wording

Why This Page Is Better Than A Generic Roadmap

  • it names exact release blockers instead of aspirational themes
  • it keeps stronger current product depth from being mistaken for broader release readiness
  • it shows where docs, package boundaries, and family packets still need to converge before the public sentence widens