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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  465. src/harness/src/openharness/ui/protocol.py +247 -0
  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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  471. src/harness/src/openharness/utils/fs.py +98 -0
  472. src/harness/src/openharness/utils/helpers.py +77 -0
  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
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  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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  488. src/memory/api/__init__.py +1 -0
  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
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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 +1,738 @@
1
+ """Shared helper functions for MCTS parsing, normalization, fallback logic, and formatting."""
2
+
3
+ import re
4
+
5
+ from typing import Any, Dict, List, Sequence, Set, Tuple
6
+
7
+ from src.agents.idea_agent.utils.core.json_utils import compact_json
8
+ from src.agents.idea_agent.utils.prompting.prompt_views import format_analysis_prompt_view
9
+ from src.pipeline.discipline_taxonomy import (
10
+ canonicalize_discipline_key,
11
+ resolve_discipline_taxonomy,
12
+ taxonomy_catalog_labels,
13
+ )
14
+
15
+
16
+ ROOT_DOMAIN_CATALOG: Dict[str, str] = taxonomy_catalog_labels()
17
+ _CONTROL_CORE_RE = re.compile(
18
+ r"\b(threshold\w*|gat\w*|suppress\w*|quota\w*|controller\w*|control\w*)\b",
19
+ re.IGNORECASE,
20
+ )
21
+ _FORBIDDEN_QUERY_TERM_RE = re.compile(
22
+ r"\b(threshold\w*|gat\w*|suppress\w*|quota\w*)\b",
23
+ re.IGNORECASE,
24
+ )
25
+ _EXECUTION_PATH_SCOPE_RE = re.compile(
26
+ r"\b(path|branch|fallback|route|routing|pipeline|repair|recovery|speculat\w*)\b",
27
+ re.IGNORECASE,
28
+ )
29
+ _BROAD_ARCHITECTURE_SCOPE_RE = re.compile(
30
+ r"\b(hierarch\w*|architecture|system|multi scale|multiscale|coordinat\w*|global)\b",
31
+ re.IGNORECASE,
32
+ )
33
+ _MULTI_PATH_SHAPE_RE = re.compile(
34
+ r"\b(path|branch|fallback|repair|hierarch\w*|multi scale|multiscale|feedback|monitor|speculat\w*)\b",
35
+ re.IGNORECASE,
36
+ )
37
+ _TRAINING_FREE_RE = re.compile(
38
+ r"\b(training free|inference time|no training|without training|frozen)\b",
39
+ re.IGNORECASE,
40
+ )
41
+ _SCOPE_KIND_BY_DEFECT: Dict[str, Set[str]] = {
42
+ "existing_component": {
43
+ "stagnant_novelty",
44
+ "unclear_mechanism",
45
+ "validation_gap",
46
+ "feature_dumping",
47
+ "harder_to_ablate",
48
+ },
49
+ "existing_subsystem": {
50
+ "theory_gap",
51
+ "weak_generalization",
52
+ },
53
+ "execution_path": {
54
+ "brittle_single_path",
55
+ "rare_regime_failure",
56
+ "weak_fallback_behavior",
57
+ "silent_failure",
58
+ "drift",
59
+ "open_loop_fragility",
60
+ "over_conservative_execution",
61
+ "rollback_blindspot",
62
+ "latency_bottleneck",
63
+ },
64
+ "broad_architecture": {
65
+ "monolithic_design",
66
+ "scale_mismatch",
67
+ "coordination_failure",
68
+ "responsibility_entanglement",
69
+ },
70
+ }
71
+ _SCOPE_KIND_PRIORITY: Dict[str, int] = {
72
+ "existing_subsystem": 0,
73
+ "existing_component": 1,
74
+ "execution_path": 2,
75
+ "broad_architecture": 3,
76
+ }
77
+ def normalize_term_scan_text(text: str) -> str:
78
+ normalized = re.sub(r"([a-z0-9])([A-Z])", r"\1 \2", str(text))
79
+ normalized = normalized.replace("_", " ").replace("-", " ")
80
+ return normalized.lower()
81
+
82
+
83
+ def _parent_state_text(parent_state: Any) -> str:
84
+ return "\n".join(
85
+ [
86
+ parent_state.title,
87
+ parent_state.abstract,
88
+ parent_state.core_contribution,
89
+ parent_state.method,
90
+ " ".join(parent_state.components or []),
91
+ " ".join((parent_state.component_explanations or {}).values()),
92
+ ]
93
+ )
94
+
95
+
96
+ def parent_centers_control_surface(parent_state: Any) -> bool:
97
+ return bool(_CONTROL_CORE_RE.search(normalize_term_scan_text(_parent_state_text(parent_state))))
98
+
99
+
100
+ def text_uses_forbidden_query_terms(text: str) -> bool:
101
+ return bool(_FORBIDDEN_QUERY_TERM_RE.search(normalize_term_scan_text(text)))
102
+
103
+
104
+ def _infer_scope_kind_from_defects(defect_tags: Sequence[str]) -> str:
105
+ counts = {scope_kind: 0 for scope_kind in _SCOPE_KIND_BY_DEFECT}
106
+ for defect in defect_tags or []:
107
+ normalized = str(defect).strip().lower()
108
+ if not normalized:
109
+ continue
110
+ for scope_kind, tagged_defects in _SCOPE_KIND_BY_DEFECT.items():
111
+ if normalized in tagged_defects:
112
+ counts[scope_kind] += 1
113
+ break
114
+
115
+ ranked = [
116
+ (count, _SCOPE_KIND_PRIORITY[scope_kind], scope_kind)
117
+ for scope_kind, count in counts.items()
118
+ if count > 0
119
+ ]
120
+ if not ranked:
121
+ return ""
122
+ return max(ranked)[2]
123
+
124
+
125
+ def build_structural_profile(
126
+ parent_state: Any,
127
+ *,
128
+ refinement_scope: str,
129
+ mature_idea: str,
130
+ defect_tags: Sequence[str] = (),
131
+ profile_id: str = "generic_scientific",
132
+ ) -> Dict[str, Any]:
133
+ normalized_profile = str(profile_id or "generic_scientific").strip().lower()
134
+ scope_text = normalize_term_scan_text(refinement_scope or "")
135
+ component_names = [
136
+ normalize_term_scan_text(component)
137
+ for component in parent_state.components
138
+ if str(component).strip()
139
+ ]
140
+ parent_text = normalize_term_scan_text(_parent_state_text(parent_state))
141
+ if scope_text and any(name and name in scope_text for name in component_names):
142
+ scope_kind = "existing_component"
143
+ elif normalized_profile == "computational_algorithmic" and scope_text and _BROAD_ARCHITECTURE_SCOPE_RE.search(scope_text):
144
+ scope_kind = "broad_architecture"
145
+ elif normalized_profile == "computational_algorithmic" and scope_text and _EXECUTION_PATH_SCOPE_RE.search(scope_text):
146
+ scope_kind = "execution_path"
147
+ elif scope_text:
148
+ scope_kind = "existing_subsystem"
149
+ else:
150
+ defect_scope_kind = (
151
+ _infer_scope_kind_from_defects(defect_tags)
152
+ if normalized_profile == "computational_algorithmic"
153
+ else ""
154
+ )
155
+ if defect_scope_kind:
156
+ scope_kind = defect_scope_kind
157
+ elif normalized_profile == "computational_algorithmic" and _MULTI_PATH_SHAPE_RE.search(parent_text):
158
+ scope_kind = "execution_path"
159
+ else:
160
+ scope_kind = "existing_subsystem"
161
+ native_structure = "scientific_object_relation"
162
+ if normalized_profile == "computational_algorithmic":
163
+ native_structure = (
164
+ "multi_path_algorithmic_structure"
165
+ if _MULTI_PATH_SHAPE_RE.search(parent_text)
166
+ else "algorithmic_subsystem"
167
+ )
168
+ elif normalized_profile == "formal_theoretical":
169
+ native_structure = "assumption_proposition_proof_structure"
170
+ elif normalized_profile in {"clinical_health", "life_molecular_mechanistic"}:
171
+ native_structure = "intervention_mechanism_measurement_structure"
172
+ elif normalized_profile in {"physical_materials_chemical", "earth_environment_agro"}:
173
+ native_structure = "condition_process_observation_structure"
174
+ return {
175
+ "profile_id": normalized_profile,
176
+ "native_structure": native_structure,
177
+ "control_centered": bool(
178
+ normalized_profile == "computational_algorithmic"
179
+ and parent_centers_control_surface(parent_state)
180
+ ),
181
+ "has_multi_path_shape": bool(
182
+ normalized_profile == "computational_algorithmic"
183
+ and _MULTI_PATH_SHAPE_RE.search(parent_text)
184
+ ),
185
+ "scope_kind": scope_kind,
186
+ "training_free_like": bool(
187
+ normalized_profile == "computational_algorithmic"
188
+ and _TRAINING_FREE_RE.search(normalize_term_scan_text(mature_idea or parent_state.method))
189
+ ),
190
+ }
191
+
192
+
193
+ def format_analysis_blob(analysis: List[Any]) -> str:
194
+ return format_analysis_prompt_view(analysis)
195
+
196
+
197
+ def clip_text(value: Any, limit: int = 800) -> str:
198
+ text = "" if value is None else str(value).strip()
199
+ if limit <= 0:
200
+ return text
201
+ if len(text) <= limit:
202
+ return text
203
+ return text[: max(1, limit - 1)] + "..."
204
+
205
+
206
+ def clip_metric_score(value: Any, *, lower: float = 0.0, upper: float = 5.0) -> float:
207
+ return max(lower, min(upper, _safe_float_default(value, lower)))
208
+
209
+
210
+ def coerce_integer_metric_score(
211
+ value: Any,
212
+ *,
213
+ lower: int = 0,
214
+ upper: int = 5,
215
+ ) -> int:
216
+ clipped = clip_metric_score(value, lower=float(lower), upper=float(upper))
217
+ return max(lower, min(upper, int(round(clipped))))
218
+
219
+
220
+ def normalize_score_weights(
221
+ weights: Dict[str, Any],
222
+ fields: Sequence[str],
223
+ ) -> Dict[str, float]:
224
+ cleaned: Dict[str, float] = {}
225
+ for field_name in fields:
226
+ try:
227
+ cleaned[field_name] = max(0.0, float(weights.get(field_name, 0.0)))
228
+ except (TypeError, ValueError):
229
+ cleaned[field_name] = 0.0
230
+
231
+ total = sum(cleaned.values())
232
+ if total <= 1e-9:
233
+ uniform = 1.0 / max(len(fields), 1)
234
+ return {field_name: uniform for field_name in fields}
235
+ return {field_name: value / total for field_name, value in cleaned.items()}
236
+
237
+
238
+ def apply_normalized_score_weights(target: Any, fields: Sequence[str]) -> None:
239
+ normalized = normalize_score_weights(
240
+ {field_name: getattr(target, field_name, 0.0) for field_name in fields},
241
+ fields,
242
+ )
243
+ for field_name, value in normalized.items():
244
+ setattr(target, field_name, value)
245
+
246
+
247
+ def _normalize_root_domains(items: Sequence[str]) -> List[str]:
248
+ ordered: List[str] = []
249
+ seen: Set[str] = set()
250
+ for item in items:
251
+ canonical_key = canonicalize_discipline_key(item)
252
+ if not canonical_key or canonical_key in seen:
253
+ continue
254
+ seen.add(canonical_key)
255
+ ordered.append(canonical_key)
256
+ return ordered[:2]
257
+
258
+
259
+ def _format_root_domains_for_prompt(domains: Sequence[str]) -> str:
260
+ normalized = _normalize_root_domains(domains)
261
+ if not normalized:
262
+ return "Unspecified"
263
+ return ", ".join(
264
+ f"{key} ({ROOT_DOMAIN_CATALOG[key]})"
265
+ for key in normalized
266
+ )
267
+
268
+
269
+ def _infer_root_domains_heuristically(topic: str, text: str) -> List[str]:
270
+ resolution = resolve_discipline_taxonomy(topic, query=text)
271
+ return _normalize_root_domains(resolution.get("discipline_ids") or [])
272
+
273
+ def _humanize_component_name(component: str) -> str:
274
+ raw = str(component).strip()
275
+ if not raw:
276
+ return "component"
277
+ raw = re.sub(r"([a-z0-9])([A-Z])", r"\1 \2", raw)
278
+ raw = re.sub(r"[^A-Za-z0-9]+", " ", raw)
279
+ tokens = [token for token in raw.split() if token]
280
+ return " ".join(tokens) if tokens else "component"
281
+
282
+
283
+ def _coerce_component_name(value: Any) -> str:
284
+ if value is None:
285
+ return ""
286
+ if isinstance(value, str):
287
+ return value.strip()
288
+ if isinstance(value, dict):
289
+ preferred_keys = ("component", "name", "target", "value", "label", "title", "id")
290
+ for key in preferred_keys:
291
+ text = _coerce_component_name(value.get(key))
292
+ if text:
293
+ return text
294
+ for item in value.values():
295
+ text = _coerce_component_name(item)
296
+ if text:
297
+ return text
298
+ return ""
299
+ if isinstance(value, (list, tuple, set)):
300
+ for item in value:
301
+ text = _coerce_component_name(item)
302
+ if text:
303
+ return text
304
+ return ""
305
+ return str(value).strip()
306
+
307
+
308
+ def _normalize_component_mapping(raw_mapping: Any) -> Dict[str, str]:
309
+ if not isinstance(raw_mapping, dict):
310
+ return {}
311
+
312
+ normalized: Dict[str, str] = {}
313
+ for raw_key, raw_value in raw_mapping.items():
314
+ key = _coerce_component_name(raw_key)
315
+ value = _coerce_component_name(raw_value)
316
+ if key and value:
317
+ normalized[key] = value
318
+ return normalized
319
+
320
+
321
+ def _extract_component_mapping_keys_from_plan(plan: Any) -> List[str]:
322
+ ordered: List[str] = []
323
+ seen: Set[str] = set()
324
+ for edit in getattr(plan, "component_edits", []) or []:
325
+ for raw_name in (
326
+ getattr(edit, "component", ""),
327
+ getattr(edit, "target", ""),
328
+ ):
329
+ name = _coerce_component_name(raw_name)
330
+ lowered = name.lower()
331
+ if not name or lowered in seen:
332
+ continue
333
+ seen.add(lowered)
334
+ ordered.append(name)
335
+ return ordered
336
+
337
+
338
+ def _filter_component_mapping_to_plan_keys(raw_mapping: Any, plan: Any) -> Dict[str, str]:
339
+ normalized = _normalize_component_mapping(raw_mapping)
340
+ allowed_keys = {
341
+ key.lower()
342
+ for key in _extract_component_mapping_keys_from_plan(plan)
343
+ if str(key).strip()
344
+ }
345
+ if not allowed_keys:
346
+ return {}
347
+ return {
348
+ key: value
349
+ for key, value in normalized.items()
350
+ if key.lower() in allowed_keys
351
+ }
352
+
353
+
354
+ def _clean_component_explanation(explanation: Any, fallback_component: str) -> str:
355
+ fallback_label = _humanize_component_name(fallback_component)
356
+
357
+ def _flatten(value: Any) -> str:
358
+ if value is None:
359
+ return ""
360
+ if isinstance(value, str):
361
+ return value
362
+ if isinstance(value, dict):
363
+ preferred_keys = (
364
+ "explanation",
365
+ "description",
366
+ "summary",
367
+ "detail",
368
+ "details",
369
+ "role",
370
+ "rationale",
371
+ "purpose",
372
+ )
373
+ ordered_chunks: List[str] = []
374
+ seen_chunks: Set[str] = set()
375
+ for key in preferred_keys:
376
+ raw = value.get(key)
377
+ text = _flatten(raw).strip()
378
+ norm = text.lower()
379
+ if text and norm not in seen_chunks:
380
+ ordered_chunks.append(text)
381
+ seen_chunks.add(norm)
382
+ if ordered_chunks:
383
+ return " ".join(ordered_chunks)
384
+ return compact_json(value)
385
+ if isinstance(value, (list, tuple, set)):
386
+ parts: List[str] = []
387
+ seen_parts: Set[str] = set()
388
+ for item in value:
389
+ text = _flatten(item).strip()
390
+ norm = text.lower()
391
+ if text and norm not in seen_parts:
392
+ parts.append(text)
393
+ seen_parts.add(norm)
394
+ return " ".join(parts)
395
+ return str(value)
396
+
397
+ text = _flatten(explanation).strip()
398
+ placeholder_values = {
399
+ "",
400
+ "n/a",
401
+ "na",
402
+ "none",
403
+ "null",
404
+ "unknown",
405
+ "unspecified",
406
+ "not provided",
407
+ "no explanation",
408
+ "no explanation provided",
409
+ "no specific explanation provided",
410
+ "tbd",
411
+ }
412
+ if text.lower() in placeholder_values:
413
+ return f"No specific explanation provided for {fallback_label}."
414
+
415
+ text = re.sub(r"\s+", " ", text)
416
+ text = text.strip(" \t\r\n-*:;,.")
417
+ text = re.sub(r"^['\"`]+|['\"`]+$", "", text).strip()
418
+
419
+ prefix_patterns = [
420
+ rf"^{re.escape(str(fallback_component).strip())}\s*[:\-]\s*",
421
+ rf"^{re.escape(fallback_label)}\s*[:\-]\s*",
422
+ r"^(component|module|role|purpose|description|explanation)\s*[:\-]\s*",
423
+ ]
424
+ for pattern in prefix_patterns:
425
+ text = re.sub(pattern, "", text, flags=re.IGNORECASE).strip()
426
+
427
+ if not text:
428
+ return f"No specific explanation provided for {fallback_label}."
429
+
430
+ text = clip_text(text, limit=3000)
431
+ if text[-1] not in ".!?":
432
+ text += "."
433
+ return text
434
+
435
+
436
+ def normalize_component_explanations(
437
+ components: Sequence[str],
438
+ raw_explanations: Any,
439
+ ) -> Dict[str, str]:
440
+ normalized_components: List[str] = []
441
+ seen: Set[str] = set()
442
+ for component in components:
443
+ name = str(component).strip()
444
+ if not name or name.lower() in seen:
445
+ continue
446
+ seen.add(name.lower())
447
+ normalized_components.append(name)
448
+
449
+ lookup: Dict[str, str] = {}
450
+ if isinstance(raw_explanations, dict):
451
+ for key, value in raw_explanations.items():
452
+ name = str(key).strip()
453
+ if not name:
454
+ continue
455
+ lookup[name] = _clean_component_explanation(value, fallback_component=name)
456
+ elif isinstance(raw_explanations, list):
457
+ for item in raw_explanations:
458
+ if not isinstance(item, dict):
459
+ continue
460
+ name = str(item.get("component") or item.get("name") or "").strip()
461
+ if not name:
462
+ continue
463
+ lookup[name] = _clean_component_explanation(
464
+ item.get("explanation", ""),
465
+ fallback_component=name,
466
+ )
467
+
468
+ return {
469
+ component: lookup.get(component, _clean_component_explanation("", fallback_component=component))
470
+ for component in normalized_components
471
+ }
472
+
473
+
474
+ def component_inventory_payload(
475
+ components: Sequence[str],
476
+ component_explanations: Any,
477
+ ) -> List[Dict[str, str]]:
478
+ normalized = normalize_component_explanations(components, component_explanations)
479
+ return [
480
+ {
481
+ "component": component,
482
+ "explanation": normalized.get(component, _clean_component_explanation("", component)),
483
+ }
484
+ for component in normalized
485
+ ]
486
+
487
+
488
+ def parse_component_bundle_payload(
489
+ payload: Any,
490
+ *,
491
+ max_components: int,
492
+ ) -> Tuple[List[str], Dict[str, str]]:
493
+ if not isinstance(payload, dict):
494
+ return [], {}
495
+
496
+ raw_components = payload.get("components", [])
497
+ ordered_components: List[str] = []
498
+ explanations: Dict[str, str] = {}
499
+ seen: Set[str] = set()
500
+
501
+ if isinstance(raw_components, list):
502
+ for item in raw_components:
503
+ if len(ordered_components) >= max_components:
504
+ break
505
+ if isinstance(item, dict):
506
+ name = str(item.get("name") or item.get("component") or "").strip()
507
+ explanation = item.get("explanation", "")
508
+ else:
509
+ name = str(item).strip()
510
+ explanation = ""
511
+ key = name.lower()
512
+ if not name or key in seen:
513
+ continue
514
+ seen.add(key)
515
+ ordered_components.append(name)
516
+ if explanation:
517
+ explanations[name] = _clean_component_explanation(
518
+ explanation,
519
+ fallback_component=name,
520
+ )
521
+
522
+ external_explanations = normalize_component_explanations(
523
+ ordered_components,
524
+ payload.get("component_explanations"),
525
+ )
526
+ explanations = {
527
+ component: explanations.get(component)
528
+ or external_explanations.get(component)
529
+ or _clean_component_explanation("", fallback_component=component)
530
+ for component in ordered_components
531
+ }
532
+ return ordered_components, explanations
533
+
534
+
535
+ def _dedupe_keep_order_strings(items: Sequence[str]) -> List[str]:
536
+ seen: Set[str] = set()
537
+ ordered: List[str] = []
538
+ for item in items:
539
+ text = str(item).strip()
540
+ key = text.lower()
541
+ if not text or key in seen:
542
+ continue
543
+ seen.add(key)
544
+ ordered.append(text)
545
+ return ordered
546
+
547
+ def _safe_float_default(value: Any, fallback: float = 0.0) -> float:
548
+ try:
549
+ return float(value)
550
+ except (TypeError, ValueError):
551
+ return fallback
552
+
553
+
554
+ def normalize_theory_transfer_query_payload(
555
+ payload: Any,
556
+ *,
557
+ fallback: Dict[str, str],
558
+ clip_limit: int,
559
+ ) -> Dict[str, str]:
560
+ if not isinstance(payload, dict):
561
+ return fallback
562
+
563
+ query = clip_text(str(payload.get("query") or "").strip(), clip_limit)
564
+ needed_content = clip_text(str(payload.get("needed_content") or "").strip(), clip_limit)
565
+ expected_role = clip_text(str(payload.get("expected_role") or "").strip(), clip_limit)
566
+ if not query:
567
+ return fallback
568
+ return {
569
+ "query": query,
570
+ "needed_content": needed_content or fallback["needed_content"],
571
+ "expected_role": expected_role or fallback["expected_role"],
572
+ }
573
+
574
+
575
+ def normalize_mechanism_commit_query_payload(
576
+ payload: Any,
577
+ *,
578
+ fallback: Dict[str, str],
579
+ clip_limit: int,
580
+ ) -> Dict[str, str]:
581
+ if not isinstance(payload, dict):
582
+ return fallback
583
+
584
+ query = clip_text(str(payload.get("query") or "").strip(), clip_limit)
585
+ mechanism_gap = clip_text(str(payload.get("mechanism_gap") or "").strip(), clip_limit)
586
+ expected_role = clip_text(str(payload.get("expected_role") or "").strip(), clip_limit)
587
+ if not query:
588
+ return fallback
589
+ return {
590
+ "query": query,
591
+ "mechanism_gap": mechanism_gap or fallback["mechanism_gap"],
592
+ "expected_role": expected_role or fallback["expected_role"],
593
+ }
594
+
595
+
596
+ def format_theory_transfer_references(
597
+ query_payload: Dict[str, str],
598
+ hits: Sequence[Dict[str, Any]],
599
+ *,
600
+ clip_limit: int,
601
+ ) -> str:
602
+ if not hits:
603
+ return "None"
604
+ lines = [
605
+ f"Transfer need: {query_payload.get('needed_content') or 'Unspecified'}",
606
+ f"Expected role: {query_payload.get('expected_role') or 'Unspecified'}",
607
+ "Cross-domain core references:",
608
+ ]
609
+ for idx, hit in enumerate(hits, start=1):
610
+ core_node = hit.get("core_node") if isinstance(hit.get("core_node"), dict) else {}
611
+ label = (
612
+ core_node.get("full_name")
613
+ or core_node.get("paper_title")
614
+ or hit.get("node_id")
615
+ or f"core_{idx}"
616
+ )
617
+ paper_title = str(core_node.get("paper_title") or "").strip()
618
+ paper_domain = str(core_node.get("paper_domain") or "").strip() or "unknown"
619
+ lines.append(
620
+ f"{idx}. {label} | domain={paper_domain} | score={float(hit.get('score') or 0.0):.3f}"
621
+ )
622
+ if paper_title:
623
+ lines.append(f" paper: {clip_text(paper_title, clip_limit)}")
624
+ summary = clip_text(str(core_node.get("summary") or "").strip(), clip_limit)
625
+ insight = clip_text(str(core_node.get("insight") or "").strip(), clip_limit)
626
+ if summary:
627
+ lines.append(f" summary: {summary}")
628
+ if insight:
629
+ lines.append(f" insight: {insight}")
630
+ matched_components = (
631
+ hit.get("matched_components") if isinstance(hit.get("matched_components"), list) else []
632
+ )
633
+ for matched in matched_components[:2]:
634
+ component_name = clip_text(
635
+ str(matched.get("component_name") or "").strip(),
636
+ clip_limit,
637
+ )
638
+ component_summary = clip_text(
639
+ str(matched.get("component_summary") or "").strip(),
640
+ clip_limit,
641
+ )
642
+ if component_name or component_summary:
643
+ lines.append(
644
+ f" matched_component: {component_name or 'unknown'} | {component_summary}"
645
+ )
646
+ lines.append(
647
+ "Use these nodes only as references for transferable mechanisms. Do not copy them verbatim and do not change the root domain(s)."
648
+ )
649
+ return "\n".join(lines)
650
+
651
+
652
+ def format_mechanism_commit_references(
653
+ query_payload: Dict[str, str],
654
+ hits: Sequence[Dict[str, Any]],
655
+ *,
656
+ clip_limit: int,
657
+ ) -> str:
658
+ if not hits:
659
+ return "None"
660
+ lines = [
661
+ f"Mechanism gap: {query_payload.get('mechanism_gap') or 'Unspecified'}",
662
+ f"Expected role: {query_payload.get('expected_role') or 'Unspecified'}",
663
+ "Retrieved core references for mechanism grounding:",
664
+ ]
665
+ for idx, hit in enumerate(hits, start=1):
666
+ core_node = hit.get("core_node") if isinstance(hit.get("core_node"), dict) else {}
667
+ label = (
668
+ core_node.get("full_name")
669
+ or core_node.get("paper_title")
670
+ or hit.get("node_id")
671
+ or f"core_{idx}"
672
+ )
673
+ paper_title = str(core_node.get("paper_title") or "").strip()
674
+ paper_domain = str(core_node.get("paper_domain") or "").strip() or "unknown"
675
+ lines.append(
676
+ f"{idx}. {label} | domain={paper_domain} | score={float(hit.get('score') or 0.0):.3f}"
677
+ )
678
+ if paper_title:
679
+ lines.append(f" paper: {clip_text(paper_title, clip_limit)}")
680
+ summary = clip_text(str(core_node.get("summary") or "").strip(), clip_limit)
681
+ insight = clip_text(str(core_node.get("insight") or "").strip(), clip_limit)
682
+ if summary:
683
+ lines.append(f" summary: {summary}")
684
+ if insight:
685
+ lines.append(f" insight: {insight}")
686
+ matched_components = (
687
+ hit.get("matched_components") if isinstance(hit.get("matched_components"), list) else []
688
+ )
689
+ for matched in matched_components[:2]:
690
+ component_name = clip_text(
691
+ str(matched.get("component_name") or "").strip(),
692
+ clip_limit,
693
+ )
694
+ component_summary = clip_text(
695
+ str(matched.get("component_summary") or "").strip(),
696
+ clip_limit,
697
+ )
698
+ if component_name or component_summary:
699
+ lines.append(
700
+ f" matched_component: {component_name or 'unknown'} | {component_summary}"
701
+ )
702
+ lines.append(
703
+ "Use these nodes to ground the concrete mechanism choice and execution path details."
704
+ )
705
+ lines.append(
706
+ "Use them as grounding patterns, not as modules to copy verbatim."
707
+ )
708
+ return "\n".join(lines)
709
+
710
+
711
+ def plan_to_method_text(plan: Any) -> str:
712
+ lines: List[str] = []
713
+ for idx, edit in enumerate(getattr(plan, "component_edits", []) or [], start=1):
714
+ op = getattr(getattr(edit, "op", None), "value", getattr(edit, "op", ""))
715
+ target = f" -> {getattr(edit, 'target', '')}" if getattr(edit, "target", "") else ""
716
+ condition = (
717
+ f" [condition: {getattr(edit, 'condition', '')}]"
718
+ if getattr(edit, "condition", "")
719
+ else ""
720
+ )
721
+ details = f"; {getattr(edit, 'details', '')}" if getattr(edit, "details", "") else ""
722
+ lines.append(f"{idx}. {op}({getattr(edit, 'component', '')}{target}){condition}{details}")
723
+ return "\n".join(lines)
724
+
725
+
726
+ def plan_to_experiment_text(plan: Any) -> str:
727
+ blocks: List[str] = []
728
+ validation = getattr(plan, "validation", None)
729
+ regression_tests = getattr(validation, "regression_tests", []) if validation else []
730
+ ablation_tests = getattr(validation, "ablation_tests", []) if validation else []
731
+ stress_tests = getattr(validation, "stress_tests", []) if validation else []
732
+ if regression_tests:
733
+ blocks.append("Regression:\n- " + "\n- ".join(regression_tests))
734
+ if ablation_tests:
735
+ blocks.append("Ablation:\n- " + "\n- ".join(ablation_tests))
736
+ if stress_tests:
737
+ blocks.append("Stress:\n- " + "\n- ".join(stress_tests))
738
+ return "\n\n".join(blocks)