Hypothesis full review

hypothesis-full-review

Goal:

• Run the full literature-grounded review for a hypothesis.

Inputs:

• research_plan/RESEARCH_PLAN.json
• hypotheses/<id>/HYPOTHESIS.json
• literature/queries/<query_id>/EVIDENCE_BUNDLE.json produced by tools.search_literature(...)
• optional run-level review guidance from meta/INSIGHTS_FROM_REVIEWS.json

Outputs:

• hypotheses/<id>/REVIEW/FULL_REVIEW.json
• literature/queries/<query_id>/* search bridge artifacts when a new evidence query is required

Context Loading:

• Open skills/shared-references/schema-index.md.
• Open skills/shared-references/literature-search-contract.md.
• Open skills/shared-references/codex-reviewer-routing.md before using any optional Codex reviewer subagent route.
• Read packages/agent_contracts/literature.py before building or consuming search bridge artifacts.
• Read research_plan/RESEARCH_PLAN.json.
• Use research_goal as the review anchor.
• Use preferences as the detailed quality criteria.
• Use constraints as non-negotiable boundaries.
• Read hypotheses/<id>/HYPOTHESIS.json.
• If meta-review guidance exists, use it to calibrate recurring failure patterns without replacing local evidence.

Execution Prompt Contract:

• System Intent:
  • You are performing a thorough literature-grounded review of one hypothesis.
• Required Reasoning Focus:
  • Use tools.search_literature(run_dir, request) to gather the minimum external evidence needed to evaluate the hypothesis claims unless an existing evidence bundle already covers the same query.
  • If Codex reviewer subagents are available and explicitly useful for the review, they may inspect the same canonical artifacts, but the main thread must still validate and persist the canonical FULL_REVIEW.json.
  • If subagents are unavailable, execute the same review contract in the main thread and record reviewerRoute = local_main_thread when a reviewer route trace is written.
  • Treat the returned EvidenceBundleContract as the only formal external literature input.
  • Read retrieval_metadata.status before writing evidence-backed judgments.
  • If retrieval_metadata.status is partial, preserve the partial-source limitation in the affected review points instead of describing the review as comprehensive literature coverage.
  • Judge each preference axis with evidence-backed reasoning.
  • Judge each constraint with evidence-backed reasoning.
  • Be rigorous but fair; separate refinable issues from fundamental problems.
• Do Not Do:
  • Do not quote large parts of the hypothesis back verbatim.
  • Do not emit raw literature notes without turning them into structured review points.
  • Do not treat unsupported intuition as if it were grounded evidence.
  • Do not invent papers, DOIs, arXiv IDs, venues, citation counts, abstracts, or literature claims not present in the evidence bundle.
  • Do not use model memory as a substitute for search bridge artifacts.
  • Do not let a reviewer subagent write deterministic mechanics artifacts or bypass schema validation.
• Review Quality Floor:
  • A status = completed full review must include concrete preferences or constraints that name hypothesis-specific mechanisms, materials, reaction conditions, feasibility limits, evidence gaps, or experimental tests.
  • If external literature support is claimed, retrieval_results, evidence_bundle_ids, and literature_query_ids must remain traceable to search bridge artifacts.
  • If no external evidence can be retrieved, write specific non-literature constraints from the hypothesis and research plan; do not claim literature grounding.
  • Do not use placeholder review phrases such as Viable evolved hypothesis, Refined from parent, Must outperform parent, or Benchmark against parent as substantive review content.
• Output Shape:
  • Produce a structured review with the exact field shape of FullReviewContract from packages/agent_contracts/review.py:
    • preferences
    • constraints
  • Each point should be short, evidence-oriented, and useful to downstream refinement.

Execution Steps:

1. Open skills/shared-references/schema-index.md, skills/shared-references/literature-search-contract.md, and skills/shared-references/codex-reviewer-routing.md, then read packages/agent_contracts/review.py and packages/agent_contracts/literature.py before writing FULL_REVIEW.json, reviewer traces, or consuming search bridge artifacts.
2. Read the research plan and current hypothesis.
3. Build a focused SearchRequestContract for the hypothesis claims and call tools.search_literature(run_dir, request) unless a matching evidence bundle already exists.
4. If retrieval_metadata.status is blocked, write only a degraded review that explicitly says external evidence retrieval was blocked; do not claim literature grounding.
5. If retrieval_metadata.status is partial, continue only when each evidence-dependent critique preserves that limitation and avoids comprehensive-coverage language.
6. Assess the hypothesis against each preference axis using the evidence bundle and the research plan.
7. Assess the hypothesis against each constraint using the evidence bundle and the research plan.
8. Write hypotheses/<id>/REVIEW/FULL_REVIEW.json.
9. Validate before declaring completion.

Artifact Rules:

• FULL_REVIEW.json must remain structured and concise enough for downstream summarization.
• External evidence should be distilled into review points rather than dumped as an appendix inside the review artifact.
• Any retrieval_results entries must be derived from literature/queries/<query_id>/EVIDENCE_BUNDLE.json.
• Partial evidence bundles must remain visible in the review rationale; do not upgrade partial retrieval into full literature support.

Completion Rule:

• This skill is complete only when FULL_REVIEW.json exists, any external evidence claims are traceable to a search bridge evidence bundle, and the artifact is valid for downstream synthesis.