qwen-sci 0.2.2__py3-none-any.whl

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Files changed (549) hide show
  1. qwen_sci-0.2.2.dist-info/METADATA +492 -0
  2. qwen_sci-0.2.2.dist-info/RECORD +549 -0
  3. qwen_sci-0.2.2.dist-info/WHEEL +4 -0
  4. qwen_sci-0.2.2.dist-info/entry_points.txt +6 -0
  5. qwen_sci-0.2.2.dist-info/licenses/LICENSE +21 -0
  6. src/1.txt +1 -0
  7. src/__init__.py +1 -0
  8. src/__main__.py +5 -0
  9. src/agents/__init__.py +1 -0
  10. src/agents/experiment_design_agent/__init__.py +268 -0
  11. src/agents/experiment_design_agent/artifacts.py +747 -0
  12. src/agents/experiment_design_agent/cache.py +319 -0
  13. src/agents/experiment_design_agent/completeness.py +130 -0
  14. src/agents/experiment_design_agent/contracts.py +771 -0
  15. src/agents/experiment_design_agent/counterexample_analyzer.py +187 -0
  16. src/agents/experiment_design_agent/design_evidence_paper_screener.py +470 -0
  17. src/agents/experiment_design_agent/discipline_catalog.py +178 -0
  18. src/agents/experiment_design_agent/evidence_cards.py +338 -0
  19. src/agents/experiment_design_agent/evidence_planner.py +452 -0
  20. src/agents/experiment_design_agent/formal_reasoning_planner.py +884 -0
  21. src/agents/experiment_design_agent/fulltext_acquisition.py +863 -0
  22. src/agents/experiment_design_agent/idea_adapter.py +100 -0
  23. src/agents/experiment_design_agent/idea_intake.py +87 -0
  24. src/agents/experiment_design_agent/llm_json.py +328 -0
  25. src/agents/experiment_design_agent/orchestrator.py +1220 -0
  26. src/agents/experiment_design_agent/reasoning_context.py +183 -0
  27. src/agents/experiment_design_agent/reasoning_validation.py +546 -0
  28. src/agents/experiment_design_agent/run.py +481 -0
  29. src/agents/experiment_design_agent/run_logging.py +292 -0
  30. src/agents/experiment_design_agent/scope_gate.py +198 -0
  31. src/agents/experiment_design_agent/study_type_composer.py +1360 -0
  32. src/agents/experiment_design_agent/survey_evidence.py +1381 -0
  33. src/agents/experiment_design_agent/template_router.py +195 -0
  34. src/agents/experiment_design_agent/variable_claim_extractor.py +93 -0
  35. src/agents/idea_agent/__init__.py +1 -0
  36. src/agents/idea_agent/agent/__init__.py +6 -0
  37. src/agents/idea_agent/agent/artifacts.py +308 -0
  38. src/agents/idea_agent/agent/base.py +122 -0
  39. src/agents/idea_agent/agent/ligagent.py +488 -0
  40. src/agents/idea_agent/agent/mcts.py +2060 -0
  41. src/agents/idea_agent/agent/prompts/__init__.py +48 -0
  42. src/agents/idea_agent/agent/prompts/advanced_analysis.py +235 -0
  43. src/agents/idea_agent/agent/prompts/algorithm_alignment.py +55 -0
  44. src/agents/idea_agent/agent/prompts/algorithm_structuring.py +48 -0
  45. src/agents/idea_agent/agent/prompts/component_extraction.py +62 -0
  46. src/agents/idea_agent/agent/prompts/component_novelty_evaluation.py +54 -0
  47. src/agents/idea_agent/agent/prompts/experiment_findings_extraction.py +39 -0
  48. src/agents/idea_agent/agent/prompts/idea_fusion.py +295 -0
  49. src/agents/idea_agent/agent/prompts/idea_introduction.py +30 -0
  50. src/agents/idea_agent/agent/prompts/idea_result_alignment.py +39 -0
  51. src/agents/idea_agent/agent/prompts/input_interpreter.py +52 -0
  52. src/agents/idea_agent/agent/prompts/keynote_ops.py +78 -0
  53. src/agents/idea_agent/agent/prompts/mcts_evaluation.py +235 -0
  54. src/agents/idea_agent/agent/prompts/mcts_generation.py +140 -0
  55. src/agents/idea_agent/agent/prompts/mechanism_commit_query.py +99 -0
  56. src/agents/idea_agent/agent/prompts/memory_selection.py +0 -0
  57. src/agents/idea_agent/agent/prompts/prompt_modes.py +16 -0
  58. src/agents/idea_agent/agent/prompts/rag_query.py +34 -0
  59. src/agents/idea_agent/agent/prompts/re_analysis_replan.py +48 -0
  60. src/agents/idea_agent/agent/prompts/reference_grounding.py +34 -0
  61. src/agents/idea_agent/agent/prompts/root_domain_classification.py +32 -0
  62. src/agents/idea_agent/agent/prompts/scientific_debate.py +88 -0
  63. src/agents/idea_agent/agent/prompts/scientific_materialization.py +45 -0
  64. src/agents/idea_agent/agent/prompts/skill_instantiation.py +193 -0
  65. src/agents/idea_agent/agent/prompts/theory_transfer_query.py +93 -0
  66. src/agents/idea_agent/agent/prompts/topic_background.py +15 -0
  67. src/agents/idea_agent/agent/skills/DEFAULT_SKILL_TEMPLATES.json +263 -0
  68. src/agents/idea_agent/agent/skills/edit_operator_skills/alternative-path-contrast/SKILL.md +40 -0
  69. src/agents/idea_agent/agent/skills/edit_operator_skills/alternative-path-contrast/references/contrast_patterns.md +22 -0
  70. src/agents/idea_agent/agent/skills/edit_operator_skills/feedback-closed-loop/SKILL.md +40 -0
  71. src/agents/idea_agent/agent/skills/edit_operator_skills/feedback-closed-loop/references/mechanism_cards.md +24 -0
  72. src/agents/idea_agent/agent/skills/edit_operator_skills/hierarchical-decomposition/SKILL.md +39 -0
  73. src/agents/idea_agent/agent/skills/edit_operator_skills/hierarchical-decomposition/references/hierarchy_patterns.md +22 -0
  74. src/agents/idea_agent/agent/skills/edit_operator_skills/mechanism-commit-innovation/SKILL.md +39 -0
  75. src/agents/idea_agent/agent/skills/edit_operator_skills/mechanism-commit-innovation/references/mechanism_commit_patterns.md +24 -0
  76. src/agents/idea_agent/agent/skills/edit_operator_skills/multi-scale-coordinator/SKILL.md +39 -0
  77. src/agents/idea_agent/agent/skills/edit_operator_skills/multi-scale-coordinator/references/coordination_patterns.md +22 -0
  78. src/agents/idea_agent/agent/skills/edit_operator_skills/speculative-execution-with-repair/SKILL.md +41 -0
  79. src/agents/idea_agent/agent/skills/edit_operator_skills/speculative-execution-with-repair/references/speculation_patterns.md +22 -0
  80. src/agents/idea_agent/agent/skills/edit_operator_skills/surgical-modularity/SKILL.md +39 -0
  81. src/agents/idea_agent/agent/skills/edit_operator_skills/surgical-modularity/references/modularity_patterns.md +22 -0
  82. src/agents/idea_agent/agent/skills/edit_operator_skills/theory-transfer-injection/SKILL.md +40 -0
  83. src/agents/idea_agent/agent/skills/edit_operator_skills/theory-transfer-injection/references/transfer_patterns.md +24 -0
  84. src/agents/idea_agent/example/idea_result.json +900 -0
  85. src/agents/idea_agent/run.py +276 -0
  86. src/agents/idea_agent/tests/test_advanced_analysis_contract.py +90 -0
  87. src/agents/idea_agent/tests/test_gap_hypothesis_bridge.py +166 -0
  88. src/agents/idea_agent/tests/test_idea_debate.py +480 -0
  89. src/agents/idea_agent/tests/test_idea_result_v5.py +99 -0
  90. src/agents/idea_agent/tests/test_idea_synthesis.py +92 -0
  91. src/agents/idea_agent/tests/test_mature_idea_sources.py +27 -0
  92. src/agents/idea_agent/tests/test_multimodal_idea_integration.py +386 -0
  93. src/agents/idea_agent/tests/test_profile_materialization_and_scoring.py +219 -0
  94. src/agents/idea_agent/tests/test_profile_native_skill_rendering.py +122 -0
  95. src/agents/idea_agent/tests/test_result_persistence.py +183 -0
  96. src/agents/idea_agent/tests/test_scientific_intervention_profiles.py +241 -0
  97. src/agents/idea_agent/tests/test_scientific_rubric_and_prompts.py +559 -0
  98. src/agents/idea_agent/tests/test_strict_json_object_responses.py +48 -0
  99. src/agents/idea_agent/utils/core/__init__.py +1 -0
  100. src/agents/idea_agent/utils/core/ablation_inputs.py +60 -0
  101. src/agents/idea_agent/utils/core/chat_errors.py +95 -0
  102. src/agents/idea_agent/utils/core/chat_router.py +130 -0
  103. src/agents/idea_agent/utils/core/chat_transport.py +188 -0
  104. src/agents/idea_agent/utils/core/config_loader.py +166 -0
  105. src/agents/idea_agent/utils/core/json_utils.py +28 -0
  106. src/agents/idea_agent/utils/core/logger.py +287 -0
  107. src/agents/idea_agent/utils/core/progress.py +58 -0
  108. src/agents/idea_agent/utils/core/response_parsing.py +57 -0
  109. src/agents/idea_agent/utils/core/run_inputs.py +198 -0
  110. src/agents/idea_agent/utils/mcts/__init__.py +1 -0
  111. src/agents/idea_agent/utils/mcts/component_novelty.py +342 -0
  112. src/agents/idea_agent/utils/mcts/defect_registry.py +302 -0
  113. src/agents/idea_agent/utils/mcts/idea_routes.py +61 -0
  114. src/agents/idea_agent/utils/mcts/idea_taste_presets.py +312 -0
  115. src/agents/idea_agent/utils/mcts/mcts_helpers.py +738 -0
  116. src/agents/idea_agent/utils/mcts/mcts_runtime.py +3000 -0
  117. src/agents/idea_agent/utils/mcts/scientific_intervention_ontology.py +1561 -0
  118. src/agents/idea_agent/utils/mcts/scientific_rubric.py +211 -0
  119. src/agents/idea_agent/utils/mcts/skill_parsing.py +92 -0
  120. src/agents/idea_agent/utils/papers/__init__.py +1 -0
  121. src/agents/idea_agent/utils/papers/paper_graph_vector_store.py +499 -0
  122. src/agents/idea_agent/utils/papers/paper_repository.py +372 -0
  123. src/agents/idea_agent/utils/prompting/__init__.py +1 -0
  124. src/agents/idea_agent/utils/prompting/prompt_views.py +637 -0
  125. src/agents/idea_agent/utils/workflow/__init__.py +1 -0
  126. src/agents/idea_agent/utils/workflow/advanced_analysis_contract.py +244 -0
  127. src/agents/idea_agent/utils/workflow/gap_hypothesis_bridge.py +461 -0
  128. src/agents/idea_agent/utils/workflow/idea_contract.py +426 -0
  129. src/agents/idea_agent/utils/workflow/idea_debate.py +1238 -0
  130. src/agents/idea_agent/utils/workflow/idea_diversity.py +163 -0
  131. src/agents/idea_agent/utils/workflow/idea_fusion.py +889 -0
  132. src/agents/idea_agent/utils/workflow/idea_helpers.py +478 -0
  133. src/agents/idea_agent/utils/workflow/idea_portfolio.py +422 -0
  134. src/agents/idea_agent/utils/workflow/idea_synthesis.py +482 -0
  135. src/agents/idea_agent/utils/workflow/ligagent_flow.py +581 -0
  136. src/agents/idea_agent/utils/workflow/ligagent_handlers.py +1836 -0
  137. src/agents/idea_agent/utils/workflow/ligagent_helpers.py +1331 -0
  138. src/agents/idea_agent/utils/workflow/ligagent_utils.py +322 -0
  139. src/agents/idea_agent/utils/workflow/mature_idea_sources.py +648 -0
  140. src/agents/idea_agent/utils/workflow/multimodal_data_anchoring.py +578 -0
  141. src/agents/idea_agent/utils/workflow/result_persistence.py +774 -0
  142. src/agents/idea_agent/utils/workflow/stage_contract.py +76 -0
  143. src/agents/idea_agent/utils/workflow/workflow_runtime.py +288 -0
  144. src/agents/research_plan_author/__init__.py +50 -0
  145. src/agents/research_plan_author/artifacts.py +270 -0
  146. src/agents/research_plan_author/authoring_blueprint.py +1246 -0
  147. src/agents/research_plan_author/bibtex_renderer.py +252 -0
  148. src/agents/research_plan_author/contract_repair.py +131 -0
  149. src/agents/research_plan_author/contracts.py +745 -0
  150. src/agents/research_plan_author/cross_section_editor.py +232 -0
  151. src/agents/research_plan_author/document_quality.py +987 -0
  152. src/agents/research_plan_author/idea_evolution.py +223 -0
  153. src/agents/research_plan_author/input_loader.py +76 -0
  154. src/agents/research_plan_author/latex_compiler.py +260 -0
  155. src/agents/research_plan_author/latex_safety.py +159 -0
  156. src/agents/research_plan_author/llm_json.py +74 -0
  157. src/agents/research_plan_author/markdown_renderer.py +275 -0
  158. src/agents/research_plan_author/pdf_validator.py +149 -0
  159. src/agents/research_plan_author/render.py +166 -0
  160. src/agents/research_plan_author/render_artifacts.py +187 -0
  161. src/agents/research_plan_author/run.py +765 -0
  162. src/agents/research_plan_author/run_logging.py +209 -0
  163. src/agents/research_plan_author/section_cache.py +184 -0
  164. src/agents/research_plan_author/section_composer.py +1764 -0
  165. src/agents/research_plan_author/section_router.py +209 -0
  166. src/agents/research_plan_author/semantic_validator.py +254 -0
  167. src/agents/research_plan_author/source_bundle.py +46 -0
  168. src/agents/research_plan_author/source_registry.py +208 -0
  169. src/agents/research_plan_author/survey_source_loader.py +137 -0
  170. src/agents/research_plan_author/template_adapter.py +173 -0
  171. src/agents/research_plan_author/template_profile.py +204 -0
  172. src/agents/research_plan_author/tex_renderer.py +496 -0
  173. src/agents/research_plan_author/theory_presentation.py +134 -0
  174. src/agents/research_plan_author/theory_spine.py +703 -0
  175. src/agents/survey_agent/Dockerfile +54 -0
  176. src/agents/survey_agent/README.md +350 -0
  177. src/agents/survey_agent/config/deep_survey.yaml +217 -0
  178. src/agents/survey_agent/config/deep_survey_batch.yaml +176 -0
  179. src/agents/survey_agent/config/deep_survey_fast.yaml +183 -0
  180. src/agents/survey_agent/config/evaluate_baseline.yaml +197 -0
  181. src/agents/survey_agent/config/outcomeRAG.yaml +159 -0
  182. src/agents/survey_agent/env_report.md +348 -0
  183. src/agents/survey_agent/modules/__init__.py +0 -0
  184. src/agents/survey_agent/modules/code_collector.py +2194 -0
  185. src/agents/survey_agent/modules/code_report_generator.py +1282 -0
  186. src/agents/survey_agent/modules/data_manager.py +1713 -0
  187. src/agents/survey_agent/modules/database.py +167 -0
  188. src/agents/survey_agent/modules/fulltext_download_cache.py +462 -0
  189. src/agents/survey_agent/modules/fulltext_http.py +134 -0
  190. src/agents/survey_agent/modules/fulltext_resolution.py +749 -0
  191. src/agents/survey_agent/modules/judge.py +434 -0
  192. src/agents/survey_agent/modules/outcome_RAG.py +236 -0
  193. src/agents/survey_agent/modules/paper_graph_retriever.py +1075 -0
  194. src/agents/survey_agent/modules/pe.py +1729 -0
  195. src/agents/survey_agent/modules/pseudo_creator.py +782 -0
  196. src/agents/survey_agent/modules/pseudo_reviser.py +537 -0
  197. src/agents/survey_agent/modules/refine_agent.py +1952 -0
  198. src/agents/survey_agent/modules/survey_generator.py +5691 -0
  199. src/agents/survey_agent/modules/survey_visualizer.py +1817 -0
  200. src/agents/survey_agent/modules/visual_prompts.py +327 -0
  201. src/agents/survey_agent/modules/work_analyzer.py +2750 -0
  202. src/agents/survey_agent/modules/work_collector.py +5649 -0
  203. src/agents/survey_agent/scripts/baseline_evaluation.py +411 -0
  204. src/agents/survey_agent/scripts/run_deep_survey.py +224 -0
  205. src/agents/survey_agent/scripts/run_deep_survey_adapter.py +407 -0
  206. src/agents/survey_agent/scripts/run_deep_survey_adapter_with_input.py +409 -0
  207. src/agents/survey_agent/scripts/run_deep_survey_batch.py +228 -0
  208. src/agents/survey_agent/scripts/run_deep_survey_batch_arg.py +243 -0
  209. src/agents/survey_agent/scripts/run_deep_survey_batch_settings.py +218 -0
  210. src/agents/survey_agent/scripts/run_keynotes_gen.py +128 -0
  211. src/agents/survey_agent/scripts/run_work_clusters.py +140 -0
  212. src/agents/survey_agent/utils/__init__.py +0 -0
  213. src/agents/survey_agent/utils/ablation_utils.py +317 -0
  214. src/agents/survey_agent/utils/api_call.py +2518 -0
  215. src/agents/survey_agent/utils/chat_utils.py +82 -0
  216. src/agents/survey_agent/utils/config_utils.py +70 -0
  217. src/agents/survey_agent/utils/convert_to_md.py +29 -0
  218. src/agents/survey_agent/utils/err_info.py +24 -0
  219. src/agents/survey_agent/utils/file_utils.py +176 -0
  220. src/agents/survey_agent/utils/gpu_utils.py +145 -0
  221. src/agents/survey_agent/utils/graph_visualizer.py +279 -0
  222. src/agents/survey_agent/utils/html_utils.py +181 -0
  223. src/agents/survey_agent/utils/latex_generator_intra_cluster.py +529 -0
  224. src/agents/survey_agent/utils/latex_generator_relation_table.py +193 -0
  225. src/agents/survey_agent/utils/mineru_section_packer.py +334 -0
  226. src/agents/survey_agent/utils/mineru_utils.py +396 -0
  227. src/agents/survey_agent/utils/paper.py +144 -0
  228. src/agents/survey_agent/utils/read_yaml.py +15 -0
  229. src/agents/survey_agent/utils/repo_utils.py +167 -0
  230. src/agents/survey_agent/utils/rich_logger.py +77 -0
  231. src/agents/survey_agent/utils/step2v2.py +874 -0
  232. src/agents/survey_agent/utils/step2v2_extractor.py +856 -0
  233. src/agents/survey_agent/utils/topic_survey_storage.py +309 -0
  234. src/agents/survey_agent/utils/utils.py +118 -0
  235. src/agents/survey_agent/utils/work.py +2 -0
  236. src/cli.py +1611 -0
  237. src/config/__init__.py +213 -0
  238. src/config/default.yaml +1122 -0
  239. src/harness/LICENSE +21 -0
  240. src/harness/VENDORED.md +14 -0
  241. src/harness/src/__init__.py +0 -0
  242. src/harness/src/openharness/__init__.py +0 -0
  243. src/harness/src/openharness/__main__.py +6 -0
  244. src/harness/src/openharness/api/__init__.py +21 -0
  245. src/harness/src/openharness/api/client.py +281 -0
  246. src/harness/src/openharness/api/codex_client.py +407 -0
  247. src/harness/src/openharness/api/copilot_auth.py +240 -0
  248. src/harness/src/openharness/api/copilot_client.py +134 -0
  249. src/harness/src/openharness/api/errors.py +19 -0
  250. src/harness/src/openharness/api/openai_client.py +577 -0
  251. src/harness/src/openharness/api/provider.py +186 -0
  252. src/harness/src/openharness/api/registry.py +437 -0
  253. src/harness/src/openharness/api/usage.py +17 -0
  254. src/harness/src/openharness/auth/__init__.py +29 -0
  255. src/harness/src/openharness/auth/external.py +610 -0
  256. src/harness/src/openharness/auth/flows.py +189 -0
  257. src/harness/src/openharness/auth/manager.py +482 -0
  258. src/harness/src/openharness/auth/storage.py +269 -0
  259. src/harness/src/openharness/autopilot/__init__.py +23 -0
  260. src/harness/src/openharness/autopilot/service.py +2239 -0
  261. src/harness/src/openharness/autopilot/types.py +91 -0
  262. src/harness/src/openharness/bridge/__init__.py +20 -0
  263. src/harness/src/openharness/bridge/manager.py +106 -0
  264. src/harness/src/openharness/bridge/session_runner.py +46 -0
  265. src/harness/src/openharness/bridge/types.py +37 -0
  266. src/harness/src/openharness/bridge/work_secret.py +41 -0
  267. src/harness/src/openharness/channels/UPSTREAM +6 -0
  268. src/harness/src/openharness/channels/__init__.py +22 -0
  269. src/harness/src/openharness/channels/adapter.py +131 -0
  270. src/harness/src/openharness/channels/bus/__init__.py +6 -0
  271. src/harness/src/openharness/channels/bus/events.py +38 -0
  272. src/harness/src/openharness/channels/bus/queue.py +44 -0
  273. src/harness/src/openharness/channels/impl/__init__.py +6 -0
  274. src/harness/src/openharness/channels/impl/base.py +141 -0
  275. src/harness/src/openharness/channels/impl/dingtalk.py +445 -0
  276. src/harness/src/openharness/channels/impl/discord.py +311 -0
  277. src/harness/src/openharness/channels/impl/email.py +410 -0
  278. src/harness/src/openharness/channels/impl/feishu.py +1342 -0
  279. src/harness/src/openharness/channels/impl/manager.py +257 -0
  280. src/harness/src/openharness/channels/impl/matrix.py +700 -0
  281. src/harness/src/openharness/channels/impl/mochat.py +897 -0
  282. src/harness/src/openharness/channels/impl/qq.py +141 -0
  283. src/harness/src/openharness/channels/impl/slack.py +284 -0
  284. src/harness/src/openharness/channels/impl/telegram.py +525 -0
  285. src/harness/src/openharness/channels/impl/whatsapp.py +159 -0
  286. src/harness/src/openharness/cli.py +2551 -0
  287. src/harness/src/openharness/commands/__init__.py +21 -0
  288. src/harness/src/openharness/commands/registry.py +2783 -0
  289. src/harness/src/openharness/config/__init__.py +34 -0
  290. src/harness/src/openharness/config/paths.py +160 -0
  291. src/harness/src/openharness/config/schema.py +119 -0
  292. src/harness/src/openharness/config/settings.py +1104 -0
  293. src/harness/src/openharness/coordinator/__init__.py +12 -0
  294. src/harness/src/openharness/coordinator/agent_definitions.py +975 -0
  295. src/harness/src/openharness/coordinator/coordinator_mode.py +520 -0
  296. src/harness/src/openharness/engine/__init__.py +80 -0
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  466. src/harness/src/openharness/ui/react_launcher.py +179 -0
  467. src/harness/src/openharness/ui/runtime.py +799 -0
  468. src/harness/src/openharness/ui/textual_app.py +495 -0
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  473. src/harness/src/openharness/utils/network_guard.py +340 -0
  474. src/harness/src/openharness/utils/shell.py +147 -0
  475. src/harness/src/openharness/vim/__init__.py +5 -0
  476. src/harness/src/openharness/vim/transitions.py +8 -0
  477. src/harness/src/openharness/voice/__init__.py +7 -0
  478. src/harness/src/openharness/voice/keyterms.py +10 -0
  479. src/harness/src/openharness/voice/stream_stt.py +8 -0
  480. src/harness/src/openharness/voice/voice_mode.py +44 -0
  481. src/llm/__init__.py +29 -0
  482. src/llm/image_generation.py +402 -0
  483. src/llm/provider_registry.py +419 -0
  484. src/llm/runtime_env.py +64 -0
  485. src/llm/structured_output.py +131 -0
  486. src/llm/vision.py +198 -0
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  489. src/memory/api/base_memory_system_api.py +98 -0
  490. src/memory/api/base_symbolic_memory_system_api.py +190 -0
  491. src/memory/api/base_vector_memory_system_api.py +116 -0
  492. src/memory/api/faiss_memory_system_api.py +228 -0
  493. src/memory/api/slot_process_api.py +827 -0
  494. src/memory/api/symbolic_memory_system_api.py +572 -0
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  496. src/memory/memory_system/component_taxonomy.py +430 -0
  497. src/memory/memory_system/llm.py +437 -0
  498. src/memory/memory_system/models.py +168 -0
  499. src/memory/memory_system/user_prompt.py +418 -0
  500. src/memory/memory_system/utils.py +282 -0
  501. src/memory/memory_system/vectorstore.py +311 -0
  502. src/memory/memory_system/working_slot.py +99 -0
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  504. src/pipeline/contracts.py +531 -0
  505. src/pipeline/discipline_taxonomy.py +916 -0
  506. src/pipeline/evidence_coverage_ledger.py +1150 -0
  507. src/pipeline/evidence_refinement.py +620 -0
  508. src/pipeline/experiment_to_symbolic.py +137 -0
  509. src/pipeline/multimodal_evidence/__init__.py +28 -0
  510. src/pipeline/multimodal_evidence/capabilities.py +107 -0
  511. src/pipeline/multimodal_evidence/claims.py +135 -0
  512. src/pipeline/multimodal_evidence/contract.py +291 -0
  513. src/pipeline/multimodal_evidence/data_sh_compiler.py +505 -0
  514. src/pipeline/multimodal_evidence/handoff_binding.py +135 -0
  515. src/pipeline/multimodal_evidence/manifest.py +254 -0
  516. src/pipeline/multimodal_evidence/native_analysis.py +479 -0
  517. src/pipeline/multimodal_evidence/perception.py +277 -0
  518. src/pipeline/multimodal_evidence/query_binding.py +65 -0
  519. src/pipeline/multimodal_evidence/rendering.py +120 -0
  520. src/pipeline/multimodal_evidence/safety.py +42 -0
  521. src/pipeline/multimodal_evidence/sampling.py +69 -0
  522. src/pipeline/multimodal_evidence/service.py +148 -0
  523. src/pipeline/multimodal_evidence/survey_integration.py +460 -0
  524. src/pipeline/paper_identity.py +52 -0
  525. src/pipeline/research_design_inventory.py +338 -0
  526. src/pipeline/research_domain_resolution.py +669 -0
  527. src/pipeline/research_identity.py +548 -0
  528. src/pipeline/research_question_contract.py +646 -0
  529. src/pipeline/retrieval_lanes.py +889 -0
  530. src/pipeline/run_loop.py +862 -0
  531. src/pipeline/science_events.py +30 -0
  532. src/pipeline/science_manifests.py +602 -0
  533. src/pipeline/science_run.py +918 -0
  534. src/pipeline/science_stages.py +709 -0
  535. src/pipeline/science_workflow.py +807 -0
  536. src/pipeline/sh_cluster_projection.py +306 -0
  537. src/pipeline/sh_graph_provenance.py +648 -0
  538. src/pipeline/subhypothesis_decomposition.py +392 -0
  539. src/pipeline/subhypothesis_evidence.py +856 -0
  540. src/pipeline/survey_evidence_plan.py +858 -0
  541. src/pipeline/survey_gap_adjudication.py +647 -0
  542. src/pipeline/survey_gap_candidates.py +840 -0
  543. src/pipeline/survey_gap_ledger.py +683 -0
  544. src/pipeline/survey_gap_triage.py +401 -0
  545. src/pipeline/survey_handoff_persistence.py +481 -0
  546. src/pipeline/survey_handoff_projection.py +457 -0
  547. src/pipeline/survey_idea_handoff.py +1112 -0
  548. src/pipeline/survey_idea_loader.py +289 -0
  549. src/research_run_ids.py +11 -0
@@ -0,0 +1,646 @@
1
+ """Domain-neutral, lightweight contracts for scientific sub-hypotheses.
2
+
3
+ This module is intentionally limited to declaring an evidence-searchable
4
+ research question. It does not model a full evidence graph or attempt to
5
+ repair an underspecified question. Invalid contracts stay invalid and must be
6
+ regenerated or corrected by their producer.
7
+ """
8
+
9
+ from __future__ import annotations
10
+
11
+ import re
12
+ from collections.abc import Mapping, Sequence
13
+ from typing import Any
14
+
15
+ from src.pipeline.research_design_inventory import (
16
+ RESEARCH_DESIGN_INVENTORY_SCHEMA_VERSION,
17
+ validate_research_design_inventory,
18
+ )
19
+ from src.pipeline.discipline_taxonomy import canonicalize_discipline_key
20
+
21
+
22
+ SCIENCE_SUBHYPOTHESIS_SCHEMA_VERSION = "science_subhypothesis_v2"
23
+ MAX_RETRIEVAL_QUERY_VARIANTS_PER_SLOT = 5
24
+ MIN_RETRIEVAL_QUERY_TERMS_PER_VARIANT = 2
25
+ MAX_RETRIEVAL_QUERY_TERMS_PER_VARIANT = 6
26
+
27
+ SUPPORTED_QUESTION_KINDS = frozenset(
28
+ {
29
+ "EMPIRICAL_COVERAGE",
30
+ "COMPARATIVE_EVALUATION",
31
+ "MECHANISM_EXPLANATION",
32
+ "BOUNDARY_HETEROGENEITY",
33
+ "REPLICATION_CONTRADICTION",
34
+ "MEASUREMENT_VALIDITY",
35
+ "GENERALIZATION_TRANSPORT",
36
+ "METHOD_DESIGN",
37
+ "DATA_COVERAGE",
38
+ "THEORY_MODEL_VALIDITY",
39
+ }
40
+ )
41
+ SUPPORTED_RESEARCH_ROLES = frozenset(
42
+ {
43
+ "PRIMARY_QUESTION",
44
+ "BASELINE_ENABLER",
45
+ "BOUNDARY_TEST",
46
+ "FALSIFICATION_RULE",
47
+ "FOUNDATIONAL_CONTEXT",
48
+ }
49
+ )
50
+ _RESEARCH_ROLE_ALIASES = {
51
+ "PRIMARY": "PRIMARY_QUESTION",
52
+ "CORE_QUESTION": "PRIMARY_QUESTION",
53
+ "COMPARATIVE_ANALYSIS": "PRIMARY_QUESTION",
54
+ "EVALUATION": "PRIMARY_QUESTION",
55
+ "BASELINE": "BASELINE_ENABLER",
56
+ "ENABLER": "BASELINE_ENABLER",
57
+ "MECHANISTIC_ENABLER": "BASELINE_ENABLER",
58
+ "METHOD_ENABLER": "BASELINE_ENABLER",
59
+ "BOUNDARY": "BOUNDARY_TEST",
60
+ "LIMITATION_TEST": "BOUNDARY_TEST",
61
+ "SAFETY_BOUNDARY": "BOUNDARY_TEST",
62
+ "COUNTEREVIDENCE": "FALSIFICATION_RULE",
63
+ "COUNTEREVIDENCE_TEST": "FALSIFICATION_RULE",
64
+ "CONTRADICTION_TEST": "FALSIFICATION_RULE",
65
+ "BACKGROUND": "FOUNDATIONAL_CONTEXT",
66
+ "CONTEXT": "FOUNDATIONAL_CONTEXT",
67
+ "EVIDENCE_LANDSCAPE": "FOUNDATIONAL_CONTEXT",
68
+ }
69
+ _RESEARCH_ROLE_FALLBACKS = {
70
+ "BOUNDARY_HETEROGENEITY": "BOUNDARY_TEST",
71
+ "REPLICATION_CONTRADICTION": "FALSIFICATION_RULE",
72
+ "GENERALIZATION_TRANSPORT": "BOUNDARY_TEST",
73
+ "MECHANISM_EXPLANATION": "BASELINE_ENABLER",
74
+ "MEASUREMENT_VALIDITY": "BASELINE_ENABLER",
75
+ "METHOD_DESIGN": "BASELINE_ENABLER",
76
+ "THEORY_MODEL_VALIDITY": "BASELINE_ENABLER",
77
+ "DATA_COVERAGE": "FOUNDATIONAL_CONTEXT",
78
+ }
79
+ SCIENTIFIC_SCOPE_KEYS = frozenset(
80
+ {
81
+ "research_object",
82
+ "population_or_system",
83
+ "condition_or_regime",
84
+ "intervention_or_input",
85
+ "comparison_frame",
86
+ "outcome_or_construct",
87
+ "measurement_or_endpoint",
88
+ "method_or_design",
89
+ "dataset_or_corpus",
90
+ "time_or_scale",
91
+ "theoretical_assumptions",
92
+ "deployment_context",
93
+ }
94
+ )
95
+ QUESTION_KIND_SPECS: dict[str, dict[str, tuple[str, ...]]] = {
96
+ "EMPIRICAL_COVERAGE": {
97
+ "required_slots": (
98
+ "phenomenon",
99
+ "target_object",
100
+ "target_condition",
101
+ "direct_observation",
102
+ ),
103
+ "required_scope": (
104
+ "research_object",
105
+ "condition_or_regime",
106
+ "outcome_or_construct",
107
+ ),
108
+ },
109
+ "COMPARATIVE_EVALUATION": {
110
+ "required_slots": (
111
+ "candidate",
112
+ "comparator",
113
+ "comparison_condition",
114
+ "comparable_endpoint",
115
+ ),
116
+ "required_scope": (
117
+ "research_object",
118
+ "comparison_frame",
119
+ "outcome_or_construct",
120
+ ),
121
+ },
122
+ "MECHANISM_EXPLANATION": {
123
+ "required_slots": (
124
+ "input_or_condition",
125
+ "common_outcome",
126
+ "candidate_mechanism",
127
+ "discriminating_observation",
128
+ ),
129
+ "required_scope": (
130
+ "research_object",
131
+ "intervention_or_input",
132
+ "outcome_or_construct",
133
+ ),
134
+ },
135
+ "BOUNDARY_HETEROGENEITY": {
136
+ "required_slots": (
137
+ "base_relation",
138
+ "boundary_variable",
139
+ "condition_a",
140
+ "condition_b",
141
+ "comparable_endpoint",
142
+ ),
143
+ "required_scope": (
144
+ "research_object",
145
+ "condition_or_regime",
146
+ "outcome_or_construct",
147
+ ),
148
+ },
149
+ "REPLICATION_CONTRADICTION": {
150
+ "required_slots": (
151
+ "shared_claim",
152
+ "result_a",
153
+ "result_b",
154
+ "comparability_axes",
155
+ ),
156
+ "required_scope": ("research_object", "outcome_or_construct"),
157
+ },
158
+ "MEASUREMENT_VALIDITY": {
159
+ "required_slots": (
160
+ "construct",
161
+ "proxy_or_measure",
162
+ "reference_or_target_measure",
163
+ "mapping_or_calibration",
164
+ ),
165
+ "required_scope": (
166
+ "research_object",
167
+ "outcome_or_construct",
168
+ "measurement_or_endpoint",
169
+ ),
170
+ },
171
+ "GENERALIZATION_TRANSPORT": {
172
+ "required_slots": (
173
+ "source_system",
174
+ "target_system",
175
+ "shift_or_variation",
176
+ "external_validation",
177
+ ),
178
+ "required_scope": (
179
+ "research_object",
180
+ "population_or_system",
181
+ "condition_or_regime",
182
+ "outcome_or_construct",
183
+ ),
184
+ },
185
+ "METHOD_DESIGN": {
186
+ "required_slots": (
187
+ "current_method_or_design",
188
+ "failure_or_bias",
189
+ "alternative_design",
190
+ "evaluation_criterion",
191
+ ),
192
+ "required_scope": (
193
+ "research_object",
194
+ "method_or_design",
195
+ "outcome_or_construct",
196
+ ),
197
+ },
198
+ "DATA_COVERAGE": {
199
+ "required_slots": (
200
+ "required_variable",
201
+ "coverage_range",
202
+ "missing_range",
203
+ "impact_on_claim",
204
+ ),
205
+ "required_scope": (
206
+ "research_object",
207
+ "dataset_or_corpus",
208
+ "outcome_or_construct",
209
+ ),
210
+ },
211
+ "THEORY_MODEL_VALIDITY": {
212
+ "required_slots": (
213
+ "formal_claim",
214
+ "assumption",
215
+ "validity_domain",
216
+ "falsification_or_counterexample",
217
+ ),
218
+ "required_scope": (
219
+ "research_object",
220
+ "theoretical_assumptions",
221
+ "outcome_or_construct",
222
+ ),
223
+ },
224
+ }
225
+
226
+ _ALLOWED_FIELDS = frozenset(
227
+ {
228
+ "schema_version",
229
+ "sub_hypothesis_id",
230
+ "title",
231
+ "question",
232
+ "question_kind",
233
+ "scientific_scope",
234
+ "required_slots",
235
+ "slot_definitions",
236
+ "research_role",
237
+ "challenge_target",
238
+ "design_basis_ids",
239
+ "allowed_evidence_scope",
240
+ "excluded_evidence_scope",
241
+ "exclusion_terms",
242
+ }
243
+ )
244
+ _SLOT_DEFINITION_FIELDS = frozenset(
245
+ {
246
+ "meaning",
247
+ "retrieval_concepts",
248
+ "retrieval_query_variants",
249
+ "minimum_evidence",
250
+ "admission_rule",
251
+ }
252
+ )
253
+ _RETRIEVAL_QUERY_VARIANT_FIELDS = frozenset(
254
+ {"variant_id", "purpose", "query_terms", "preferred_disciplines"}
255
+ )
256
+
257
+
258
+ def _text(value: Any, *, limit: int = 1000) -> str:
259
+ return re.sub(r"\s+", " ", str(value or "").strip())[:limit]
260
+
261
+
262
+ def _mapping(value: Any) -> dict[str, Any]:
263
+ return dict(value) if isinstance(value, Mapping) else {}
264
+
265
+
266
+ def _texts(value: Any, *, limit: int = 12) -> list[str]:
267
+ values = value if isinstance(value, Sequence) and not isinstance(value, (str, bytes)) else [value]
268
+ result: list[str] = []
269
+ seen: set[str] = set()
270
+ for value in values:
271
+ item = _text(value, limit=240)
272
+ key = item.casefold()
273
+ if not item or key in seen:
274
+ continue
275
+ seen.add(key)
276
+ result.append(item)
277
+ if len(result) >= limit:
278
+ break
279
+ return result
280
+
281
+
282
+ def _variant_id(value: Any, *, fallback: str) -> str:
283
+ normalized = re.sub(r"[^a-z0-9]+", "_", _text(value, limit=100).casefold()).strip("_")
284
+ return normalized[:80] or fallback
285
+
286
+
287
+ def _retrieval_query_variants(
288
+ value: Any,
289
+ *,
290
+ slot: str,
291
+ errors: list[str],
292
+ warnings: list[str],
293
+ ) -> list[dict[str, Any]]:
294
+ """Normalize optional, alternative retrieval paths for one SH slot.
295
+
296
+ Variants are candidate-discovery entry points. They must remain short and
297
+ independently meaningful, so they never encode an all-concepts evidence
298
+ requirement for a paper.
299
+ """
300
+
301
+ if value is None:
302
+ return []
303
+ if not isinstance(value, Sequence) or isinstance(value, (str, bytes)):
304
+ errors.append(f"retrieval_query_variants_must_be_a_list:{slot}")
305
+ return []
306
+ if len(value) > MAX_RETRIEVAL_QUERY_VARIANTS_PER_SLOT:
307
+ errors.append(f"too_many_retrieval_query_variants:{slot}")
308
+
309
+ variants: list[dict[str, Any]] = []
310
+ seen_ids: set[str] = set()
311
+ for index, raw_variant in enumerate(value[:MAX_RETRIEVAL_QUERY_VARIANTS_PER_SLOT], start=1):
312
+ if not isinstance(raw_variant, Mapping):
313
+ errors.append(f"retrieval_query_variant_must_be_an_object:{slot}:{index}")
314
+ continue
315
+ unknown_fields = sorted(
316
+ key for key in raw_variant if key not in _RETRIEVAL_QUERY_VARIANT_FIELDS
317
+ )
318
+ errors.extend(
319
+ f"unsupported_retrieval_query_variant_field:{slot}:{field}"
320
+ for field in unknown_fields
321
+ )
322
+ variant_id = _variant_id(
323
+ raw_variant.get("variant_id"),
324
+ fallback=f"variant_{index}",
325
+ )
326
+ if variant_id in seen_ids:
327
+ errors.append(f"duplicate_retrieval_query_variant_id:{slot}:{variant_id}")
328
+ seen_ids.add(variant_id)
329
+ purpose = _text(raw_variant.get("purpose"), limit=240)
330
+ raw_terms = raw_variant.get("query_terms")
331
+ if not isinstance(raw_terms, Sequence) or isinstance(raw_terms, (str, bytes)):
332
+ errors.append(f"retrieval_query_variant_terms_must_be_a_list:{slot}:{variant_id}")
333
+ query_terms: list[str] = []
334
+ else:
335
+ query_terms = _texts(raw_terms, limit=MAX_RETRIEVAL_QUERY_TERMS_PER_VARIANT)
336
+ supplied_term_count = len(
337
+ [item for item in raw_terms if _text(item, limit=240)]
338
+ )
339
+ if not (
340
+ MIN_RETRIEVAL_QUERY_TERMS_PER_VARIANT
341
+ <= supplied_term_count
342
+ <= MAX_RETRIEVAL_QUERY_TERMS_PER_VARIANT
343
+ ):
344
+ errors.append(f"invalid_retrieval_query_variant_term_count:{slot}:{variant_id}")
345
+
346
+ raw_disciplines = raw_variant.get("preferred_disciplines", [])
347
+ if isinstance(raw_disciplines, (str, bytes)):
348
+ # This is an optional precision hint. A scalar model output must not
349
+ # invalidate an otherwise usable SH or suppress its broad lane.
350
+ raw_disciplines = [raw_disciplines]
351
+ warnings.append(
352
+ f"coerced_retrieval_query_variant_discipline_to_list:{slot}:{variant_id}"
353
+ )
354
+ elif not isinstance(raw_disciplines, Sequence):
355
+ raw_disciplines = []
356
+ warnings.append(
357
+ f"dropped_malformed_retrieval_query_variant_disciplines:{slot}:{variant_id}"
358
+ )
359
+ preferred_disciplines: list[str] = []
360
+ for discipline in _texts(raw_disciplines, limit=3):
361
+ canonical = canonicalize_discipline_key(discipline)
362
+ if not canonical:
363
+ # preferred_disciplines only narrows an optional precision lane.
364
+ # Keep discovery viable by dropping an unrecognised suggestion;
365
+ # the unfiltered broad lane is still generated for this variant.
366
+ warnings.append(
367
+ f"dropped_unsupported_retrieval_query_variant_discipline:{slot}:{discipline}"
368
+ )
369
+ continue
370
+ if canonical not in preferred_disciplines:
371
+ preferred_disciplines.append(canonical)
372
+
373
+ if not purpose:
374
+ errors.append(f"missing_retrieval_query_variant_purpose:{slot}:{variant_id}")
375
+ if not query_terms:
376
+ errors.append(f"missing_retrieval_query_variant_terms:{slot}:{variant_id}")
377
+ variants.append(
378
+ {
379
+ "variant_id": variant_id,
380
+ "purpose": purpose,
381
+ "query_terms": query_terms,
382
+ "preferred_disciplines": preferred_disciplines,
383
+ }
384
+ )
385
+ return variants
386
+
387
+
388
+ def _normalized_research_role(
389
+ value: Any,
390
+ *,
391
+ question_kind: str,
392
+ warnings: list[str],
393
+ ) -> str:
394
+ """Return a supported reporting role without making LLM wording a hard gate."""
395
+
396
+ supplied = _text(value, limit=80).upper()
397
+ normalized = re.sub(r"[^A-Z0-9]+", "_", supplied).strip("_")
398
+ resolved = _RESEARCH_ROLE_ALIASES.get(normalized, normalized)
399
+ if resolved in SUPPORTED_RESEARCH_ROLES:
400
+ if supplied and resolved != supplied:
401
+ warnings.append(f"normalized_research_role:{supplied}:{resolved}")
402
+ return resolved
403
+
404
+ fallback = _RESEARCH_ROLE_FALLBACKS.get(question_kind, "PRIMARY_QUESTION")
405
+ warnings.append(
406
+ f"fallback_research_role:{supplied or '<missing>'}:{fallback}"
407
+ )
408
+ return fallback
409
+
410
+
411
+ def _scope(value: Any) -> tuple[dict[str, list[str]], list[str]]:
412
+ raw = _mapping(value)
413
+ unknown = sorted(key for key in raw if key not in SCIENTIFIC_SCOPE_KEYS)
414
+ return (
415
+ {key: _texts(raw.get(key), limit=8) for key in SCIENTIFIC_SCOPE_KEYS if _texts(raw.get(key), limit=8)},
416
+ unknown,
417
+ )
418
+
419
+
420
+ def _evidence_scope(value: Any) -> dict[str, Any]:
421
+ raw = _mapping(value)
422
+ result: dict[str, Any] = {}
423
+ for key in (
424
+ "date_range",
425
+ "languages",
426
+ "publication_types",
427
+ "providers",
428
+ "source_types",
429
+ "study_designs",
430
+ "contexts",
431
+ "notes",
432
+ ):
433
+ item = raw.get(key)
434
+ if isinstance(item, Sequence) and not isinstance(item, (str, bytes)):
435
+ values = _texts(item, limit=8)
436
+ if values:
437
+ result[key] = values
438
+ elif _text(item, limit=240):
439
+ result[key] = _text(item, limit=240)
440
+ return result
441
+
442
+
443
+ def _question_errors(question: str) -> list[str]:
444
+ normalized = re.sub(r"[^a-z0-9\u4e00-\u9fff]+", " ", question.casefold()).strip()
445
+ if not normalized:
446
+ return ["missing_question"]
447
+ if len(normalized) < 12:
448
+ return ["question_not_independently_answerable"]
449
+ return []
450
+
451
+
452
+ def normalize_science_subhypothesis_v2(
453
+ value: Any,
454
+ *,
455
+ design_inventory: Mapping[str, Any] | None,
456
+ project_context: Mapping[str, Any] | None = None,
457
+ ) -> dict[str, Any]:
458
+ """Validate and normalize only the v2 SH contract; no legacy conversion."""
459
+
460
+ raw = _mapping(value)
461
+ errors: list[str] = []
462
+ warnings: list[str] = []
463
+ if not isinstance(value, Mapping):
464
+ errors.append("subhypothesis_must_be_an_object")
465
+ unknown_fields = sorted(key for key in raw if key not in _ALLOWED_FIELDS)
466
+ errors.extend(f"unsupported_field:{field}" for field in unknown_fields)
467
+ if raw.get("schema_version") != SCIENCE_SUBHYPOTHESIS_SCHEMA_VERSION:
468
+ errors.append("invalid_schema_version")
469
+
470
+ identifier = _text(raw.get("sub_hypothesis_id"), limit=120)
471
+ if not identifier:
472
+ errors.append("missing_sub_hypothesis_id")
473
+ question = _text(raw.get("question"), limit=1800)
474
+ errors.extend(_question_errors(question))
475
+ title = _text(raw.get("title"), limit=180)
476
+
477
+ question_kind = _text(raw.get("question_kind"), limit=80).upper()
478
+ if question_kind not in SUPPORTED_QUESTION_KINDS:
479
+ errors.append("unsupported_question_kind")
480
+ specification = QUESTION_KIND_SPECS.get(question_kind, {})
481
+
482
+ scientific_scope, unknown_scope_fields = _scope(raw.get("scientific_scope"))
483
+ errors.extend(f"unsupported_scope_field:{field}" for field in unknown_scope_fields)
484
+ if not isinstance(raw.get("scientific_scope"), Mapping):
485
+ errors.append("scientific_scope_must_be_an_object")
486
+ for field in specification.get("required_scope", ()):
487
+ if not scientific_scope.get(field):
488
+ errors.append(f"missing_required_scope:{field}")
489
+
490
+ raw_required_slots = raw.get("required_slots")
491
+ required_slot_values = (
492
+ [_text(item, limit=240) for item in raw_required_slots]
493
+ if isinstance(raw_required_slots, Sequence) and not isinstance(raw_required_slots, (str, bytes))
494
+ else []
495
+ )
496
+ required_slots = _texts(required_slot_values, limit=16)
497
+ if not isinstance(raw_required_slots, Sequence) or isinstance(raw_required_slots, (str, bytes)):
498
+ errors.append("required_slots_must_be_a_list")
499
+ nonempty_raw_slots = [item for item in required_slot_values if item]
500
+ if len(nonempty_raw_slots) != len({item.casefold() for item in nonempty_raw_slots}):
501
+ errors.append("duplicate_required_slot")
502
+ for slot in specification.get("required_slots", ()):
503
+ if slot not in required_slots:
504
+ errors.append(f"missing_required_slot:{slot}")
505
+
506
+ raw_definitions = _mapping(raw.get("slot_definitions"))
507
+ if not isinstance(raw.get("slot_definitions"), Mapping):
508
+ errors.append("slot_definitions_must_be_an_object")
509
+ slot_definitions: dict[str, dict[str, Any]] = {}
510
+ for slot in required_slots:
511
+ definition = _mapping(raw_definitions.get(slot))
512
+ if not definition:
513
+ errors.append(f"missing_slot_definition:{slot}")
514
+ continue
515
+ unknown_definition_fields = sorted(
516
+ key for key in definition if key not in _SLOT_DEFINITION_FIELDS
517
+ )
518
+ errors.extend(
519
+ f"unsupported_slot_definition_field:{slot}:{field}"
520
+ for field in unknown_definition_fields
521
+ )
522
+ normalized_definition = {
523
+ "meaning": _text(definition.get("meaning"), limit=700),
524
+ "retrieval_concepts": _texts(definition.get("retrieval_concepts"), limit=10),
525
+ "retrieval_query_variants": _retrieval_query_variants(
526
+ definition.get("retrieval_query_variants"),
527
+ slot=slot,
528
+ errors=errors,
529
+ warnings=warnings,
530
+ ),
531
+ "minimum_evidence": _text(definition.get("minimum_evidence"), limit=700),
532
+ "admission_rule": _text(definition.get("admission_rule"), limit=700),
533
+ }
534
+ for field in ("meaning", "retrieval_concepts", "minimum_evidence", "admission_rule"):
535
+ item = normalized_definition[field]
536
+ if not item:
537
+ errors.append(f"missing_slot_definition_value:{slot}:{field}")
538
+ slot_definitions[slot] = normalized_definition
539
+ for extra_slot in sorted(key for key in raw_definitions if key not in required_slots):
540
+ errors.append(f"unexpected_slot_definition:{extra_slot}")
541
+
542
+ research_role = _normalized_research_role(
543
+ raw.get("research_role"),
544
+ question_kind=question_kind,
545
+ warnings=warnings,
546
+ )
547
+ challenge_target = _text(raw.get("challenge_target"), limit=1200)
548
+ if not challenge_target:
549
+ errors.append("missing_challenge_target")
550
+
551
+ raw_design_basis_ids = raw.get("design_basis_ids")
552
+ raw_basis_id_values = (
553
+ [_text(item, limit=80) for item in raw_design_basis_ids]
554
+ if isinstance(raw_design_basis_ids, Sequence) and not isinstance(raw_design_basis_ids, (str, bytes))
555
+ else []
556
+ )
557
+ design_basis_ids = _texts(raw_basis_id_values, limit=10)
558
+ if not isinstance(raw_design_basis_ids, Sequence) or isinstance(raw_design_basis_ids, (str, bytes)):
559
+ errors.append("design_basis_ids_must_be_a_list")
560
+ nonempty_raw_basis_ids = [item for item in raw_basis_id_values if item]
561
+ if len(nonempty_raw_basis_ids) != len({item.casefold() for item in nonempty_raw_basis_ids}):
562
+ errors.append("duplicate_design_basis_id")
563
+ if not design_basis_ids:
564
+ errors.append("missing_design_basis_ids")
565
+ inventory_ids: set[str] = set()
566
+ try:
567
+ inventory = validate_research_design_inventory(
568
+ design_inventory,
569
+ project_context=project_context,
570
+ )
571
+ inventory_ids = {
572
+ _text(item.get("id"), limit=80)
573
+ for item in inventory.get("design_basis", [])
574
+ if isinstance(item, Mapping)
575
+ }
576
+ except ValueError as exc:
577
+ errors.append(f"invalid_design_inventory:{str(exc)}")
578
+ inventory = {}
579
+ unknown_basis_ids = [identifier for identifier in design_basis_ids if identifier not in inventory_ids]
580
+ errors.extend(f"unknown_design_basis_id:{identifier}" for identifier in unknown_basis_ids)
581
+
582
+ return {
583
+ "schema_version": SCIENCE_SUBHYPOTHESIS_SCHEMA_VERSION,
584
+ "sub_hypothesis_id": identifier,
585
+ "title": title,
586
+ "question": question,
587
+ "question_kind": question_kind,
588
+ "scientific_scope": scientific_scope,
589
+ "required_slots": required_slots,
590
+ "slot_definitions": slot_definitions,
591
+ "research_role": research_role,
592
+ "challenge_target": challenge_target,
593
+ "design_basis_ids": design_basis_ids,
594
+ "allowed_evidence_scope": _evidence_scope(raw.get("allowed_evidence_scope")),
595
+ "excluded_evidence_scope": _evidence_scope(raw.get("excluded_evidence_scope")),
596
+ "exclusion_terms": _texts(raw.get("exclusion_terms"), limit=10),
597
+ "validation": {
598
+ "valid": not errors,
599
+ "errors": errors,
600
+ "warnings": warnings,
601
+ "unknown_fields": unknown_fields,
602
+ "inventory_schema_version": _text(
603
+ _mapping(design_inventory).get("schema_version"), limit=80
604
+ ),
605
+ "required_inventory_schema_version": RESEARCH_DESIGN_INVENTORY_SCHEMA_VERSION,
606
+ },
607
+ }
608
+
609
+
610
+ def science_subhypothesis_v2_prompt_contract() -> dict[str, Any]:
611
+ """Return the literal shape emitted by automatic SH decomposition prompts."""
612
+
613
+ return {
614
+ "schema_version": SCIENCE_SUBHYPOTHESIS_SCHEMA_VERSION,
615
+ "sub_hypothesis_id": "SH1",
616
+ "title": "short evidence-focused title",
617
+ "question": "an independently answerable scientific evidence question",
618
+ "question_kind": "one supported question kind",
619
+ "scientific_scope": {"research_object": ["source-grounded scope value"]},
620
+ "required_slots": ["all slots required by question_kind"],
621
+ "slot_definitions": {
622
+ "one_required_slot": {
623
+ "meaning": "what the slot denotes for this question",
624
+ "retrieval_concepts": ["concise searchable terms"],
625
+ "retrieval_query_variants": [
626
+ {
627
+ "variant_id": "baseline_observation",
628
+ "purpose": "broad candidate recall for this slot",
629
+ "query_terms": [
630
+ "canonical system phrase",
631
+ "canonical outcome phrase",
632
+ ],
633
+ "preferred_disciplines": ["materials_science"],
634
+ }
635
+ ],
636
+ "minimum_evidence": "minimum evidence needed for this slot",
637
+ "admission_rule": "what makes a retrieved work admissible",
638
+ }
639
+ },
640
+ "research_role": "one supported role",
641
+ "challenge_target": "the claim, assumption, or relation this question can challenge",
642
+ "design_basis_ids": ["DB1"],
643
+ "allowed_evidence_scope": {},
644
+ "excluded_evidence_scope": {},
645
+ "exclusion_terms": [],
646
+ }