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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  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
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  477. src/harness/src/openharness/voice/__init__.py +7 -0
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  483. src/llm/provider_registry.py +419 -0
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  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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  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 +1,52 @@
1
+ """Memory prompt helpers."""
2
+
3
+ from __future__ import annotations
4
+
5
+ from pathlib import Path
6
+
7
+ from openharness.memory.paths import get_memory_entrypoint, get_project_memory_dir
8
+ from openharness.memory.schema import (
9
+ MAX_ENTRYPOINT_BYTES,
10
+ MEMORY_POLICY_LINES,
11
+ truncate_entrypoint_content,
12
+ )
13
+
14
+
15
+ def load_memory_prompt(
16
+ cwd: str | Path,
17
+ *,
18
+ max_entrypoint_lines: int = 200,
19
+ max_entrypoint_bytes: int = MAX_ENTRYPOINT_BYTES,
20
+ ) -> str | None:
21
+ """Return the memory prompt section for the current project."""
22
+ memory_dir = get_project_memory_dir(cwd)
23
+ entrypoint = get_memory_entrypoint(cwd)
24
+ lines = [
25
+ "# Memory",
26
+ f"- Persistent memory directory: {memory_dir}",
27
+ "- Use this directory to store durable project and repository context that should survive future sessions.",
28
+ "- Prefer concise topic files plus an index entry in MEMORY.md.",
29
+ "",
30
+ *MEMORY_POLICY_LINES,
31
+ ]
32
+
33
+ if entrypoint.exists():
34
+ raw = entrypoint.read_text(encoding="utf-8", errors="replace")
35
+ view = truncate_entrypoint_content(
36
+ raw,
37
+ max_lines=max_entrypoint_lines,
38
+ max_bytes=max_entrypoint_bytes,
39
+ )
40
+ content = view.content.strip()
41
+ if content:
42
+ lines.extend(["", "## MEMORY.md", "```md", content, "```"])
43
+ else:
44
+ lines.extend(
45
+ [
46
+ "",
47
+ "## MEMORY.md",
48
+ "(not created yet)",
49
+ ]
50
+ )
51
+
52
+ return "\n".join(lines)
@@ -0,0 +1,137 @@
1
+ """Migration utilities for schema-v1 memory frontmatter."""
2
+
3
+ from __future__ import annotations
4
+
5
+ import argparse
6
+ import json
7
+ import shutil
8
+ from dataclasses import asdict, dataclass
9
+ from pathlib import Path
10
+
11
+ from openharness.memory.paths import get_project_memory_dir
12
+ from openharness.memory.schema import (
13
+ memory_metadata_from_path,
14
+ render_memory_file,
15
+ split_memory_file,
16
+ utc_now,
17
+ )
18
+ from openharness.utils.fs import atomic_write_text
19
+
20
+
21
+ @dataclass(frozen=True)
22
+ class MigrationSummary:
23
+ """Summary returned by a memory schema migration run."""
24
+
25
+ scanned: int
26
+ changed: int
27
+ unchanged: int
28
+ failed: int
29
+ dry_run: bool
30
+ backup_dir: str
31
+ changed_files: tuple[str, ...]
32
+ failed_files: tuple[str, ...]
33
+
34
+ def as_dict(self) -> dict[str, object]:
35
+ return asdict(self)
36
+
37
+
38
+ def migrate_memory(
39
+ cwd: str | Path,
40
+ *,
41
+ memory_dir: str | Path | None = None,
42
+ default_type: str = "project",
43
+ default_category: str = "knowledge",
44
+ apply: bool = False,
45
+ ) -> MigrationSummary:
46
+ """Backfill schema-v1 frontmatter for top-level memory markdown files."""
47
+
48
+ root = Path(memory_dir).expanduser().resolve() if memory_dir is not None else get_project_memory_dir(cwd)
49
+ root.mkdir(parents=True, exist_ok=True)
50
+ files = sorted(path for path in root.glob("*.md") if path.name != "MEMORY.md")
51
+ changed_payloads: list[tuple[Path, str]] = []
52
+ failed_files: list[str] = []
53
+ seen_ids: set[str] = set()
54
+ now = utc_now()
55
+
56
+ for path in files:
57
+ try:
58
+ content = path.read_text(encoding="utf-8")
59
+ metadata, body, _, _ = split_memory_file(content)
60
+ migrated = memory_metadata_from_path(
61
+ path,
62
+ metadata,
63
+ body,
64
+ now=now,
65
+ source="migration",
66
+ default_type=default_type,
67
+ default_category=default_category,
68
+ seen_ids=seen_ids,
69
+ )
70
+ rendered = render_memory_file(migrated, body)
71
+ if rendered != content:
72
+ changed_payloads.append((path, rendered))
73
+ except OSError:
74
+ failed_files.append(path.name)
75
+
76
+ backup_dir = ""
77
+ if apply and changed_payloads:
78
+ backup_path = _create_migration_backup(root)
79
+ backup_dir = str(backup_path)
80
+ for path, rendered in changed_payloads:
81
+ atomic_write_text(path, rendered)
82
+
83
+ changed_files = tuple(path.name for path, _ in changed_payloads)
84
+ return MigrationSummary(
85
+ scanned=len(files),
86
+ changed=len(changed_payloads),
87
+ unchanged=len(files) - len(changed_payloads) - len(failed_files),
88
+ failed=len(failed_files),
89
+ dry_run=not apply,
90
+ backup_dir=backup_dir,
91
+ changed_files=changed_files,
92
+ failed_files=tuple(failed_files),
93
+ )
94
+
95
+
96
+ def main(argv: list[str] | None = None) -> int:
97
+ """Command-line entrypoint for one-off memory migrations."""
98
+
99
+ parser = argparse.ArgumentParser(description="Backfill OpenHarness memory schema metadata.")
100
+ parser.add_argument("--cwd", default=".", help="Project cwd whose memory store should be migrated.")
101
+ parser.add_argument("--memory-dir", default=None, help="Explicit memory directory to migrate.")
102
+ parser.add_argument("--default-type", default="project", help="Type for legacy files without one.")
103
+ parser.add_argument("--default-category", default="knowledge", help="Category for legacy files without one.")
104
+ parser.add_argument("--dry-run", action="store_true", help="Report files that would change.")
105
+ parser.add_argument("--apply", action="store_true", help="Write migrated files and create a backup.")
106
+ args = parser.parse_args(argv)
107
+ if args.dry_run == args.apply:
108
+ parser.error("pass exactly one of --dry-run or --apply")
109
+ summary = migrate_memory(
110
+ args.cwd,
111
+ memory_dir=args.memory_dir,
112
+ default_type=args.default_type,
113
+ default_category=args.default_category,
114
+ apply=args.apply,
115
+ )
116
+ print(json.dumps(summary.as_dict(), indent=2, ensure_ascii=False))
117
+ return 0
118
+
119
+
120
+ def _create_migration_backup(memory_dir: Path) -> Path:
121
+ timestamp = utc_now().strftime("%Y%m%d-%H%M%S")
122
+ backup_dir = memory_dir / "backups" / f"migration-{timestamp}"
123
+ suffix = 2
124
+ while backup_dir.exists():
125
+ backup_dir = memory_dir / "backups" / f"migration-{timestamp}-{suffix}"
126
+ suffix += 1
127
+ backup_dir.mkdir(parents=True, exist_ok=False)
128
+ for path in sorted(memory_dir.glob("*.md")):
129
+ shutil.copy2(path, backup_dir / path.name)
130
+ usage_index = memory_dir / "usage_index.json"
131
+ if usage_index.exists():
132
+ shutil.copy2(usage_index, backup_dir / usage_index.name)
133
+ return backup_dir
134
+
135
+
136
+ if __name__ == "__main__":
137
+ raise SystemExit(main())
@@ -0,0 +1,22 @@
1
+ """Paths for persistent project memory."""
2
+
3
+ from __future__ import annotations
4
+
5
+ from hashlib import sha1
6
+ from pathlib import Path
7
+
8
+ from openharness.config.paths import get_data_dir
9
+
10
+
11
+ def get_project_memory_dir(cwd: str | Path) -> Path:
12
+ """Return the persistent memory directory for a project."""
13
+ path = Path(cwd).resolve()
14
+ digest = sha1(str(path).encode("utf-8")).hexdigest()[:12]
15
+ memory_dir = get_data_dir() / "memory" / f"{path.name}-{digest}"
16
+ memory_dir.mkdir(parents=True, exist_ok=True)
17
+ return memory_dir
18
+
19
+
20
+ def get_memory_entrypoint(cwd: str | Path) -> Path:
21
+ """Return the project memory entrypoint file."""
22
+ return get_project_memory_dir(cwd) / "MEMORY.md"
@@ -0,0 +1,145 @@
1
+ """Relevant memory selection and formatting."""
2
+
3
+ from __future__ import annotations
4
+
5
+ import json
6
+ from dataclasses import dataclass
7
+ from pathlib import Path
8
+ from typing import Callable, Iterable
9
+
10
+ from openharness.memory.scan import scan_memory_files
11
+ from openharness.memory.schema import memory_age_label, memory_freshness_text
12
+ from openharness.memory.search import find_relevant_memories
13
+ from openharness.memory.types import MemoryHeader
14
+
15
+
16
+ @dataclass(frozen=True)
17
+ class RelevantMemory:
18
+ """A memory selected for prompt injection."""
19
+
20
+ header: MemoryHeader
21
+ freshness: str = ""
22
+
23
+
24
+ MemorySelector = Callable[[str, list[MemoryHeader]], list[str]]
25
+
26
+
27
+ def build_memory_manifest(headers: Iterable[MemoryHeader]) -> str:
28
+ """Render a compact manifest for selector prompts and diagnostics."""
29
+
30
+ lines: list[str] = []
31
+ for header in headers:
32
+ prefix = f"[{header.memory_type or 'memory'}]"
33
+ bits = [
34
+ prefix,
35
+ header.relative_path or header.path.name,
36
+ f"({memory_age_label(header.modified_at)})",
37
+ ]
38
+ if header.description:
39
+ bits.append(f"- {header.description}")
40
+ lines.append(" ".join(bits))
41
+ return "\n".join(lines)
42
+
43
+
44
+ def select_relevant_memories(
45
+ query: str,
46
+ cwd: str | Path,
47
+ *,
48
+ max_results: int = 5,
49
+ already_surfaced: set[str] | None = None,
50
+ selector: MemorySelector | None = None,
51
+ ) -> list[RelevantMemory]:
52
+ """Return relevant memories with duplicate and freshness handling.
53
+
54
+ ``selector`` is an optional side-query style reranker. It receives the query
55
+ and a heuristic shortlist, and returns relative paths in desired order.
56
+ """
57
+
58
+ surfaced = already_surfaced or set()
59
+ heuristic = [
60
+ header
61
+ for header in find_relevant_memories(query, cwd, max_results=max(10, max_results * 3))
62
+ if (header.relative_path or str(header.path)) not in surfaced
63
+ ]
64
+ selected = _apply_selector(query, heuristic, selector=selector, max_results=max_results)
65
+ result: list[RelevantMemory] = []
66
+ for header in selected[:max_results]:
67
+ result.append(RelevantMemory(header=header, freshness=memory_freshness_text(header.modified_at)))
68
+ return result
69
+
70
+
71
+ def select_manifest_memories(
72
+ query: str,
73
+ cwd: str | Path,
74
+ *,
75
+ max_results: int = 5,
76
+ selector: MemorySelector | None = None,
77
+ ) -> list[RelevantMemory]:
78
+ """Select from the full manifest instead of heuristic matches only."""
79
+
80
+ headers = scan_memory_files(cwd, max_files=200)
81
+ selected = _apply_selector(query, headers, selector=selector, max_results=max_results)
82
+ return [
83
+ RelevantMemory(header=header, freshness=memory_freshness_text(header.modified_at))
84
+ for header in selected[:max_results]
85
+ ]
86
+
87
+
88
+ def format_relevant_memories(memories: Iterable[RelevantMemory], *, max_chars: int = 8000) -> str:
89
+ """Render selected memories for prompt context."""
90
+
91
+ lines = ["# Relevant Memories"]
92
+ for item in memories:
93
+ header = item.header
94
+ content = header.path.read_text(encoding="utf-8", errors="replace").strip()
95
+ if item.freshness:
96
+ lines.extend(["", f"## {header.relative_path or header.path.name}", f"> {item.freshness}"])
97
+ else:
98
+ lines.extend(["", f"## {header.relative_path or header.path.name}"])
99
+ lines.extend(["```md", content[:max_chars], "```"])
100
+ return "\n".join(lines)
101
+
102
+
103
+ def json_selector_from_text(text: str) -> list[str]:
104
+ """Parse a selector response as either JSON list or newline paths."""
105
+
106
+ stripped = text.strip()
107
+ if not stripped:
108
+ return []
109
+ try:
110
+ payload = json.loads(stripped)
111
+ except json.JSONDecodeError:
112
+ return [line.strip("- ").strip() for line in stripped.splitlines() if line.strip()]
113
+ if isinstance(payload, list):
114
+ return [str(item).strip() for item in payload if str(item).strip()]
115
+ if isinstance(payload, dict) and isinstance(payload.get("paths"), list):
116
+ return [str(item).strip() for item in payload["paths"] if str(item).strip()]
117
+ return []
118
+
119
+
120
+ def _apply_selector(
121
+ query: str,
122
+ headers: list[MemoryHeader],
123
+ *,
124
+ selector: MemorySelector | None,
125
+ max_results: int,
126
+ ) -> list[MemoryHeader]:
127
+ if not headers or selector is None:
128
+ return headers[:max_results]
129
+ requested = selector(query, headers)
130
+ by_path = {header.relative_path or header.path.name: header for header in headers}
131
+ selected: list[MemoryHeader] = []
132
+ seen: set[str] = set()
133
+ for path in requested:
134
+ header = by_path.get(path)
135
+ if header is None or path in seen:
136
+ continue
137
+ selected.append(header)
138
+ seen.add(path)
139
+ if len(selected) < max_results:
140
+ selected.extend(
141
+ header
142
+ for header in headers
143
+ if (header.relative_path or header.path.name) not in seen
144
+ )
145
+ return selected[:max_results]
@@ -0,0 +1,116 @@
1
+ """Scan project memory files."""
2
+
3
+ from __future__ import annotations
4
+
5
+ from pathlib import Path
6
+
7
+ from openharness.memory.paths import get_project_memory_dir
8
+ from openharness.memory.schema import (
9
+ coerce_bool,
10
+ coerce_int,
11
+ coerce_optional_int,
12
+ coerce_str_list,
13
+ first_content_line,
14
+ is_memory_expired,
15
+ split_memory_file,
16
+ )
17
+ from openharness.memory.types import MemoryHeader
18
+
19
+
20
+ def scan_memory_files(
21
+ cwd: str | Path,
22
+ *,
23
+ max_files: int | None = 50,
24
+ include_disabled: bool = False,
25
+ include_expired: bool = False,
26
+ memory_dir: str | Path | None = None,
27
+ ) -> list[MemoryHeader]:
28
+ """Return memory headers sorted by newest first."""
29
+ memory_dir = Path(memory_dir) if memory_dir is not None else get_project_memory_dir(cwd)
30
+ headers: list[MemoryHeader] = []
31
+ for path in memory_dir.glob("*.md"):
32
+ if path.name == "MEMORY.md":
33
+ continue
34
+ try:
35
+ text = path.read_text(encoding="utf-8")
36
+ except OSError:
37
+ continue
38
+ header = _parse_memory_file(path, text)
39
+ if header.disabled and not include_disabled:
40
+ continue
41
+ if is_memory_expired(_metadata_from_header(header)) and not include_expired:
42
+ continue
43
+ headers.append(header)
44
+ headers.sort(key=lambda item: item.modified_at, reverse=True)
45
+ if max_files is None:
46
+ return headers
47
+ return headers[:max_files]
48
+
49
+
50
+ def _parse_memory_file(path: Path, content: str) -> MemoryHeader:
51
+ """Parse a memory file, extracting YAML frontmatter when present."""
52
+ metadata, body, _, _ = split_memory_file(content)
53
+ lines = body.splitlines()
54
+ title = path.stem
55
+ description = ""
56
+ memory_type = ""
57
+ if metadata.get("name"):
58
+ title = str(metadata["name"])
59
+ if metadata.get("description"):
60
+ description = str(metadata["description"])
61
+ if metadata.get("type"):
62
+ memory_type = str(metadata["type"])
63
+
64
+ # Fallback: first non-empty, non-frontmatter line as description
65
+ desc_line_idx: int | None = None
66
+ if not description:
67
+ fallback = first_content_line("\n".join(lines[:10]))
68
+ if fallback:
69
+ description = fallback
70
+ for idx, line in enumerate(lines[:10]):
71
+ stripped = line.strip()
72
+ if stripped[:200] == description:
73
+ desc_line_idx = idx
74
+ break
75
+
76
+ # Build body preview from content after frontmatter, excluding the
77
+ # line already used as description so search scoring stays consistent.
78
+ body_lines = [
79
+ line.strip()
80
+ for idx, line in enumerate(lines)
81
+ if line.strip()
82
+ and not line.strip().startswith("#")
83
+ and idx != desc_line_idx
84
+ ]
85
+ body_preview = " ".join(body_lines)[:300]
86
+
87
+ return MemoryHeader(
88
+ path=path,
89
+ title=title,
90
+ description=description,
91
+ modified_at=path.stat().st_mtime,
92
+ memory_type=memory_type,
93
+ body_preview=body_preview,
94
+ id=str(metadata.get("id") or ""),
95
+ schema_version=coerce_int(metadata.get("schema_version"), default=0),
96
+ category=str(metadata.get("category") or ""),
97
+ importance=coerce_int(metadata.get("importance"), default=0),
98
+ source=str(metadata.get("source") or ""),
99
+ signature=str(metadata.get("signature") or ""),
100
+ created_at=str(metadata.get("created_at") or ""),
101
+ updated_at=str(metadata.get("updated_at") or ""),
102
+ ttl_days=coerce_optional_int(metadata.get("ttl_days")),
103
+ disabled=coerce_bool(metadata.get("disabled"), default=False),
104
+ supersedes=coerce_str_list(metadata.get("supersedes")),
105
+ relative_path=path.name,
106
+ tags=coerce_str_list(metadata.get("tags")),
107
+ frontmatter=metadata,
108
+ )
109
+
110
+
111
+ def _metadata_from_header(header: MemoryHeader) -> dict[str, object]:
112
+ return {
113
+ "created_at": header.created_at,
114
+ "updated_at": header.updated_at,
115
+ "ttl_days": header.ttl_days,
116
+ }