qwen-sci 0.2.2__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
  297. src/harness/src/openharness/engine/cost_tracker.py +24 -0
  298. src/harness/src/openharness/engine/messages.py +222 -0
  299. src/harness/src/openharness/engine/query.py +1188 -0
  300. src/harness/src/openharness/engine/query_engine.py +313 -0
  301. src/harness/src/openharness/engine/stream_events.py +90 -0
  302. src/harness/src/openharness/hooks/__init__.py +50 -0
  303. src/harness/src/openharness/hooks/events.py +20 -0
  304. src/harness/src/openharness/hooks/executor.py +242 -0
  305. src/harness/src/openharness/hooks/hot_reload.py +31 -0
  306. src/harness/src/openharness/hooks/loader.py +68 -0
  307. src/harness/src/openharness/hooks/schemas.py +66 -0
  308. src/harness/src/openharness/hooks/types.py +38 -0
  309. src/harness/src/openharness/keybindings/__init__.py +14 -0
  310. src/harness/src/openharness/keybindings/default_bindings.py +11 -0
  311. src/harness/src/openharness/keybindings/loader.py +22 -0
  312. src/harness/src/openharness/keybindings/parser.py +18 -0
  313. src/harness/src/openharness/keybindings/resolver.py +13 -0
  314. src/harness/src/openharness/mcp/__init__.py +79 -0
  315. src/harness/src/openharness/mcp/client.py +298 -0
  316. src/harness/src/openharness/mcp/config.py +16 -0
  317. src/harness/src/openharness/mcp/types.py +76 -0
  318. src/harness/src/openharness/memory/__init__.py +25 -0
  319. src/harness/src/openharness/memory/agent.py +91 -0
  320. src/harness/src/openharness/memory/manager.py +183 -0
  321. src/harness/src/openharness/memory/memdir.py +52 -0
  322. src/harness/src/openharness/memory/migrate.py +137 -0
  323. src/harness/src/openharness/memory/paths.py +22 -0
  324. src/harness/src/openharness/memory/relevance.py +145 -0
  325. src/harness/src/openharness/memory/scan.py +116 -0
  326. src/harness/src/openharness/memory/schema.py +443 -0
  327. src/harness/src/openharness/memory/search.py +71 -0
  328. src/harness/src/openharness/memory/team.py +90 -0
  329. src/harness/src/openharness/memory/types.py +33 -0
  330. src/harness/src/openharness/memory/usage.py +153 -0
  331. src/harness/src/openharness/output_styles/__init__.py +5 -0
  332. src/harness/src/openharness/output_styles/loader.py +42 -0
  333. src/harness/src/openharness/permissions/__init__.py +26 -0
  334. src/harness/src/openharness/permissions/checker.py +200 -0
  335. src/harness/src/openharness/permissions/modes.py +13 -0
  336. src/harness/src/openharness/personalization/__init__.py +6 -0
  337. src/harness/src/openharness/personalization/extractor.py +138 -0
  338. src/harness/src/openharness/personalization/rules.py +64 -0
  339. src/harness/src/openharness/personalization/session_hook.py +65 -0
  340. src/harness/src/openharness/platforms.py +86 -0
  341. src/harness/src/openharness/plugins/__init__.py +53 -0
  342. src/harness/src/openharness/plugins/bundled/__init__.py +0 -0
  343. src/harness/src/openharness/plugins/installer.py +39 -0
  344. src/harness/src/openharness/plugins/loader.py +730 -0
  345. src/harness/src/openharness/plugins/schemas.py +24 -0
  346. src/harness/src/openharness/plugins/types.py +59 -0
  347. src/harness/src/openharness/prompts/__init__.py +14 -0
  348. src/harness/src/openharness/prompts/claudemd.py +48 -0
  349. src/harness/src/openharness/prompts/context.py +187 -0
  350. src/harness/src/openharness/prompts/environment.py +135 -0
  351. src/harness/src/openharness/prompts/system_prompt.py +109 -0
  352. src/harness/src/openharness/sandbox/Dockerfile +6 -0
  353. src/harness/src/openharness/sandbox/__init__.py +33 -0
  354. src/harness/src/openharness/sandbox/adapter.py +148 -0
  355. src/harness/src/openharness/sandbox/docker_backend.py +232 -0
  356. src/harness/src/openharness/sandbox/docker_image.py +103 -0
  357. src/harness/src/openharness/sandbox/path_validator.py +37 -0
  358. src/harness/src/openharness/sandbox/session.py +63 -0
  359. src/harness/src/openharness/services/__init__.py +30 -0
  360. src/harness/src/openharness/services/autodream/__init__.py +34 -0
  361. src/harness/src/openharness/services/autodream/backup.py +104 -0
  362. src/harness/src/openharness/services/autodream/lock.py +138 -0
  363. src/harness/src/openharness/services/autodream/prompt.py +128 -0
  364. src/harness/src/openharness/services/autodream/service.py +313 -0
  365. src/harness/src/openharness/services/compact/__init__.py +1725 -0
  366. src/harness/src/openharness/services/cron.py +137 -0
  367. src/harness/src/openharness/services/cron_scheduler.py +595 -0
  368. src/harness/src/openharness/services/lsp/__init__.py +216 -0
  369. src/harness/src/openharness/services/memory_extract/__init__.py +261 -0
  370. src/harness/src/openharness/services/oauth/__init__.py +0 -0
  371. src/harness/src/openharness/services/session_backend.py +97 -0
  372. src/harness/src/openharness/services/session_memory/__init__.py +139 -0
  373. src/harness/src/openharness/services/session_storage.py +230 -0
  374. src/harness/src/openharness/services/token_estimation.py +15 -0
  375. src/harness/src/openharness/services/tool_outputs.py +55 -0
  376. src/harness/src/openharness/skills/__init__.py +44 -0
  377. src/harness/src/openharness/skills/_frontmatter.py +97 -0
  378. src/harness/src/openharness/skills/bundled/__init__.py +75 -0
  379. src/harness/src/openharness/skills/bundled/content/commit.md +25 -0
  380. src/harness/src/openharness/skills/bundled/content/debug.md +25 -0
  381. src/harness/src/openharness/skills/bundled/content/diagnose.md +35 -0
  382. src/harness/src/openharness/skills/bundled/content/plan.md +39 -0
  383. src/harness/src/openharness/skills/bundled/content/review.md +33 -0
  384. src/harness/src/openharness/skills/bundled/content/simplify.md +26 -0
  385. src/harness/src/openharness/skills/bundled/content/skill-creator.md +175 -0
  386. src/harness/src/openharness/skills/bundled/content/test.md +38 -0
  387. src/harness/src/openharness/skills/loader.py +229 -0
  388. src/harness/src/openharness/skills/registry.py +29 -0
  389. src/harness/src/openharness/skills/types.py +24 -0
  390. src/harness/src/openharness/state/__init__.py +6 -0
  391. src/harness/src/openharness/state/app_state.py +30 -0
  392. src/harness/src/openharness/state/store.py +40 -0
  393. src/harness/src/openharness/swarm/__init__.py +70 -0
  394. src/harness/src/openharness/swarm/in_process.py +693 -0
  395. src/harness/src/openharness/swarm/lockfile.py +24 -0
  396. src/harness/src/openharness/swarm/mailbox.py +522 -0
  397. src/harness/src/openharness/swarm/permission_sync.py +1168 -0
  398. src/harness/src/openharness/swarm/registry.py +410 -0
  399. src/harness/src/openharness/swarm/spawn_utils.py +229 -0
  400. src/harness/src/openharness/swarm/subprocess_backend.py +171 -0
  401. src/harness/src/openharness/swarm/team_lifecycle.py +910 -0
  402. src/harness/src/openharness/swarm/types.py +398 -0
  403. src/harness/src/openharness/swarm/worktree.py +315 -0
  404. src/harness/src/openharness/tasks/__init__.py +18 -0
  405. src/harness/src/openharness/tasks/local_agent_task.py +28 -0
  406. src/harness/src/openharness/tasks/local_shell_task.py +17 -0
  407. src/harness/src/openharness/tasks/manager.py +475 -0
  408. src/harness/src/openharness/tasks/stop_task.py +11 -0
  409. src/harness/src/openharness/tasks/types.py +32 -0
  410. src/harness/src/openharness/themes/__init__.py +21 -0
  411. src/harness/src/openharness/themes/builtin.py +89 -0
  412. src/harness/src/openharness/themes/loader.py +55 -0
  413. src/harness/src/openharness/themes/schema.py +54 -0
  414. src/harness/src/openharness/tools/__init__.py +107 -0
  415. src/harness/src/openharness/tools/agent_tool.py +141 -0
  416. src/harness/src/openharness/tools/ask_user_question_tool.py +46 -0
  417. src/harness/src/openharness/tools/base.py +80 -0
  418. src/harness/src/openharness/tools/bash_tool.py +259 -0
  419. src/harness/src/openharness/tools/brief_tool.py +33 -0
  420. src/harness/src/openharness/tools/config_tool.py +54 -0
  421. src/harness/src/openharness/tools/cron_create_tool.py +105 -0
  422. src/harness/src/openharness/tools/cron_delete_tool.py +32 -0
  423. src/harness/src/openharness/tools/cron_list_tool.py +69 -0
  424. src/harness/src/openharness/tools/cron_toggle_tool.py +37 -0
  425. src/harness/src/openharness/tools/enter_plan_mode_tool.py +28 -0
  426. src/harness/src/openharness/tools/enter_worktree_tool.py +80 -0
  427. src/harness/src/openharness/tools/exit_plan_mode_tool.py +28 -0
  428. src/harness/src/openharness/tools/exit_worktree_tool.py +42 -0
  429. src/harness/src/openharness/tools/file_edit_tool.py +95 -0
  430. src/harness/src/openharness/tools/file_read_tool.py +72 -0
  431. src/harness/src/openharness/tools/file_write_tool.py +87 -0
  432. src/harness/src/openharness/tools/glob_tool.py +175 -0
  433. src/harness/src/openharness/tools/grep_tool.py +374 -0
  434. src/harness/src/openharness/tools/image_generation_tool.py +447 -0
  435. src/harness/src/openharness/tools/image_to_text_tool.py +237 -0
  436. src/harness/src/openharness/tools/list_mcp_resources_tool.py +36 -0
  437. src/harness/src/openharness/tools/lsp_tool.py +154 -0
  438. src/harness/src/openharness/tools/mcp_auth_tool.py +71 -0
  439. src/harness/src/openharness/tools/mcp_tool.py +72 -0
  440. src/harness/src/openharness/tools/notebook_edit_tool.py +97 -0
  441. src/harness/src/openharness/tools/read_mcp_resource_tool.py +38 -0
  442. src/harness/src/openharness/tools/remote_trigger_tool.py +74 -0
  443. src/harness/src/openharness/tools/send_message_tool.py +58 -0
  444. src/harness/src/openharness/tools/skill_tool.py +43 -0
  445. src/harness/src/openharness/tools/sleep_tool.py +32 -0
  446. src/harness/src/openharness/tools/task_create_tool.py +56 -0
  447. src/harness/src/openharness/tools/task_get_tool.py +33 -0
  448. src/harness/src/openharness/tools/task_list_tool.py +35 -0
  449. src/harness/src/openharness/tools/task_output_tool.py +35 -0
  450. src/harness/src/openharness/tools/task_stop_tool.py +30 -0
  451. src/harness/src/openharness/tools/task_update_tool.py +50 -0
  452. src/harness/src/openharness/tools/team_create_tool.py +31 -0
  453. src/harness/src/openharness/tools/team_delete_tool.py +30 -0
  454. src/harness/src/openharness/tools/todo_write_tool.py +46 -0
  455. src/harness/src/openharness/tools/tool_search_tool.py +38 -0
  456. src/harness/src/openharness/tools/web_fetch_tool.py +117 -0
  457. src/harness/src/openharness/tools/web_search_tool.py +119 -0
  458. src/harness/src/openharness/ui/__init__.py +5 -0
  459. src/harness/src/openharness/ui/app.py +320 -0
  460. src/harness/src/openharness/ui/backend_host.py +941 -0
  461. src/harness/src/openharness/ui/coordinator_drain.py +198 -0
  462. src/harness/src/openharness/ui/input.py +32 -0
  463. src/harness/src/openharness/ui/output.py +265 -0
  464. src/harness/src/openharness/ui/permission_dialog.py +14 -0
  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
  469. src/harness/src/openharness/utils/__init__.py +0 -0
  470. src/harness/src/openharness/utils/file_lock.py +86 -0
  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
  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
  487. src/memory/__init__.py +2 -0
  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
  494. src/memory/api/symbolic_memory_system_api.py +572 -0
  495. src/memory/memory_system/__init__.py +48 -0
  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
  503. src/pipeline/__init__.py +129 -0
  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 +1,166 @@
1
+ """End-to-end, design-only Research Plan TeX/PDF rendering orchestration."""
2
+
3
+ from __future__ import annotations
4
+
5
+ from dataclasses import dataclass
6
+ from pathlib import Path
7
+ from collections.abc import Mapping
8
+ from typing import Any
9
+
10
+ from .latex_compiler import LatexCompilerError, compile_latex_project, resolve_executable
11
+ from .pdf_validator import PdfValidationError, PdfValidationResult, validate_pdf
12
+ from .render_artifacts import AuthorRenderArtifactPaths, AuthorRenderArtifactWriter, RenderArtifactError
13
+ from .template_profile import TemplateProfileError, load_template_profile
14
+ from .tex_renderer import TexRenderError, TexRenderResult, render_tex_project
15
+
16
+
17
+ class AuthorRenderingError(RuntimeError):
18
+ """Typed render failure with retained source/diagnostic artifacts."""
19
+
20
+ def __init__(self, stage: str, message: str, *, paths: AuthorRenderArtifactPaths | None = None) -> None:
21
+ super().__init__(f"{stage}: {message}")
22
+ self.stage = stage
23
+ self.paths = paths
24
+
25
+
26
+ @dataclass(frozen=True)
27
+ class AuthorRenderingResult:
28
+ artifacts: AuthorRenderArtifactPaths
29
+ tex: TexRenderResult
30
+ pdf_validation: PdfValidationResult
31
+
32
+
33
+ def _mapping(value: object) -> dict[str, Any]:
34
+ return dict(value) if isinstance(value, Mapping) else {}
35
+
36
+
37
+ def _text(value: object) -> str:
38
+ return str(value or "").strip()
39
+
40
+
41
+ def render_research_plan_document(
42
+ document: Mapping[str, Any],
43
+ *,
44
+ output_dir: str | Path,
45
+ timestamp: str,
46
+ preparation_collision_index: int,
47
+ template_dir: str | Path,
48
+ template_profile: str | Path | None = None,
49
+ template_main: str | None = None,
50
+ latex_engine: str | Path | None = None,
51
+ bibtex: str | Path | None = None,
52
+ pdf_renderer: str | Path | None = None,
53
+ compile_timeout_seconds: int = 180,
54
+ configured_rendering: Mapping[str, Any] | None = None,
55
+ author_name: str = "Anonymous Research Plan Author",
56
+ logger: Any | None = None,
57
+ ) -> AuthorRenderingResult:
58
+ """Render, compile, and validate a proposal PDF without an execution fallback."""
59
+
60
+ settings = _mapping(configured_rendering)
61
+ writer = AuthorRenderArtifactWriter(output_dir)
62
+ paths = writer.allocate(timestamp=timestamp, preparation_collision_index=preparation_collision_index)
63
+ try:
64
+ profile = load_template_profile(template_profile or _text(settings.get("template_profile")) or "markers_v1", main_tex=template_main or _text(settings.get("main_tex")) or None)
65
+ except TemplateProfileError as error:
66
+ raise AuthorRenderingError("template", str(error), paths=paths) from error
67
+ try:
68
+ if logger is not None:
69
+ logger.emit("tex_render", "started", status="RUNNING", profile_id=profile.profile_id)
70
+ tex = render_tex_project(
71
+ document,
72
+ template_dir=template_dir,
73
+ project_dir=paths.project_dir,
74
+ profile=profile,
75
+ author_name=author_name,
76
+ )
77
+ writer.publish_sources(tex, paths)
78
+ if logger is not None:
79
+ logger.emit(
80
+ "tex_render",
81
+ "completed",
82
+ status="COMPLETED",
83
+ profile_id=profile.profile_id,
84
+ emitted_bibliography_count=len(tex.bibliography.emitted_keys),
85
+ bibliography_needs_completion_count=len(tex.bibliography.needs_completion),
86
+ )
87
+ except (TexRenderError, RenderArtifactError) as error:
88
+ if logger is not None:
89
+ logger.emit("tex_render", "failed", level="ERROR", status="FAILED", error=str(error))
90
+ raise AuthorRenderingError("tex_render", str(error), paths=paths) from error
91
+ try:
92
+ engine = resolve_executable(
93
+ explicit=latex_engine,
94
+ environment_variable="SCIENCE_LATEX_ENGINE",
95
+ configured=settings.get("engine"),
96
+ fallback="pdflatex",
97
+ label="LaTeX engine",
98
+ )
99
+ bibtex_engine = None
100
+ if tex.bibliography.emitted_keys:
101
+ bibtex_engine = resolve_executable(
102
+ explicit=bibtex,
103
+ environment_variable="SCIENCE_BIBTEX",
104
+ configured=settings.get("bibtex"),
105
+ fallback="bibtex",
106
+ label="BibTeX engine",
107
+ )
108
+ except LatexCompilerError as error:
109
+ raise AuthorRenderingError("latex_compile", str(error), paths=paths) from error
110
+ try:
111
+ compile_result = compile_latex_project(
112
+ tex.project_dir,
113
+ main_tex=tex.main_tex,
114
+ latex_engine=engine,
115
+ bibtex=bibtex_engine,
116
+ run_bibtex=bool(tex.bibliography.emitted_keys),
117
+ timeout_seconds=max(1, int(compile_timeout_seconds)),
118
+ staged_pdf_path=paths.staged_pdf,
119
+ logger=logger,
120
+ )
121
+ except LatexCompilerError as error:
122
+ writer.discard_staged_pdf(paths)
123
+ raise AuthorRenderingError("latex_compile", str(error), paths=paths) from error
124
+ try:
125
+ writer.publish_compile_diagnostics(paths, report=compile_result.report, log_text=compile_result.log_text)
126
+ except RenderArtifactError as error:
127
+ writer.discard_staged_pdf(paths)
128
+ raise AuthorRenderingError("artifacts", str(error), paths=paths) from error
129
+ if not compile_result.success:
130
+ writer.discard_staged_pdf(paths)
131
+ raise AuthorRenderingError(
132
+ "latex_compile",
133
+ "LaTeX compilation failed; retained compile log and structured diagnostics",
134
+ paths=paths,
135
+ )
136
+ try:
137
+ renderer = resolve_executable(
138
+ explicit=pdf_renderer,
139
+ environment_variable="SCIENCE_PDF_RENDERER",
140
+ configured=settings.get("pdf_renderer"),
141
+ fallback="pdftoppm",
142
+ label="PDF renderer",
143
+ )
144
+ validation = validate_pdf(
145
+ paths.staged_pdf,
146
+ renderer=renderer,
147
+ timeout_seconds=max(1, int(settings.get("pdf_validation_timeout_seconds") or 60)),
148
+ logger=logger,
149
+ )
150
+ writer.publish_pdf_validation(paths, validation.report)
151
+ except (PdfValidationError, LatexCompilerError, RenderArtifactError) as error:
152
+ if isinstance(error, PdfValidationError) and error.report is not None:
153
+ try:
154
+ writer.publish_pdf_validation(paths, error.report)
155
+ except RenderArtifactError:
156
+ pass
157
+ writer.discard_staged_pdf(paths)
158
+ raise AuthorRenderingError("pdf_validation", str(error), paths=paths) from error
159
+ try:
160
+ writer.publish_validated_pdf(paths)
161
+ except RenderArtifactError as error:
162
+ raise AuthorRenderingError("artifacts", str(error), paths=paths) from error
163
+ return AuthorRenderingResult(artifacts=paths, tex=tex, pdf_validation=validation)
164
+
165
+
166
+ __all__ = ["AuthorRenderingError", "AuthorRenderingResult", "render_research_plan_document"]
@@ -0,0 +1,187 @@
1
+ """Atomic, non-overwriting publication of Author TeX/PDF render artifacts."""
2
+
3
+ from __future__ import annotations
4
+
5
+ from dataclasses import dataclass
6
+ import json
7
+ import os
8
+ from pathlib import Path
9
+ import tempfile
10
+ from typing import Any, Mapping
11
+
12
+ from .tex_renderer import TexRenderResult
13
+
14
+
15
+ class RenderArtifactError(RuntimeError):
16
+ """Raised when a render artifact cannot be allocated or published safely."""
17
+
18
+
19
+ @dataclass(frozen=True)
20
+ class AuthorRenderArtifactPaths:
21
+ timestamp: str
22
+ preparation_collision_index: int
23
+ render_collision_index: int
24
+ project_dir: Path
25
+ tex: Path
26
+ bibtex: Path
27
+ bibliography_needs_completion: Path
28
+ render_manifest: Path
29
+ compile_log: Path
30
+ compile_json: Path
31
+ pdf_validation_json: Path
32
+ pdf: Path
33
+ staged_pdf: Path
34
+
35
+ def as_dict(self) -> dict[str, str | int]:
36
+ return {
37
+ "timestamp": self.timestamp,
38
+ "preparation_collision_index": self.preparation_collision_index,
39
+ "render_collision_index": self.render_collision_index,
40
+ "project_dir": str(self.project_dir),
41
+ "tex": str(self.tex),
42
+ "bibtex": str(self.bibtex),
43
+ "bibliography_needs_completion": str(self.bibliography_needs_completion),
44
+ "render_manifest": str(self.render_manifest),
45
+ "compile_log": str(self.compile_log),
46
+ "compile_json": str(self.compile_json),
47
+ "pdf_validation_json": str(self.pdf_validation_json),
48
+ "pdf": str(self.pdf),
49
+ }
50
+
51
+
52
+ def _json_text(payload: object) -> str:
53
+ return json.dumps(payload, ensure_ascii=False, sort_keys=True, indent=2, allow_nan=False) + "\n"
54
+
55
+
56
+ def _write_bytes_without_overwrite(path: Path, content: bytes) -> None:
57
+ temporary: Path | None = None
58
+ try:
59
+ path.parent.mkdir(parents=True, exist_ok=True)
60
+ descriptor, raw_path = tempfile.mkstemp(prefix=f".{path.name}.", suffix=".tmp", dir=path.parent)
61
+ temporary = Path(raw_path)
62
+ with os.fdopen(descriptor, "wb") as handle:
63
+ handle.write(content)
64
+ handle.flush()
65
+ os.fsync(handle.fileno())
66
+ try:
67
+ os.link(temporary, path)
68
+ except FileExistsError as error:
69
+ raise RenderArtifactError(f"artifact target already exists: {path}") from error
70
+ except OSError:
71
+ descriptor = os.open(path, os.O_WRONLY | os.O_CREAT | os.O_EXCL)
72
+ with os.fdopen(descriptor, "wb") as handle, temporary.open("rb") as source:
73
+ handle.write(source.read())
74
+ handle.flush()
75
+ os.fsync(handle.fileno())
76
+ except OSError as error:
77
+ raise RenderArtifactError(f"cannot publish artifact '{path.name}': {error}") from error
78
+ finally:
79
+ if temporary is not None:
80
+ temporary.unlink(missing_ok=True)
81
+
82
+
83
+ def _write_text_without_overwrite(path: Path, content: str) -> None:
84
+ _write_bytes_without_overwrite(path, content.encode("utf-8"))
85
+
86
+
87
+ class AuthorRenderArtifactWriter:
88
+ """Reserve one timestamped artifact family and publish it without overwrites."""
89
+
90
+ def __init__(self, output_dir: str | Path) -> None:
91
+ self.output_dir = Path(output_dir).expanduser().resolve()
92
+
93
+ def allocate(
94
+ self,
95
+ *,
96
+ timestamp: str,
97
+ preparation_collision_index: int,
98
+ ) -> AuthorRenderArtifactPaths:
99
+ try:
100
+ self.output_dir.mkdir(parents=True, exist_ok=True)
101
+ except OSError as error:
102
+ raise RenderArtifactError(f"cannot create Author render output directory: {error}") from error
103
+ preparation_suffix = "" if preparation_collision_index == 0 else f"_{preparation_collision_index}"
104
+ for render_collision_index in range(1000):
105
+ render_suffix = "" if render_collision_index == 0 else f"_render{render_collision_index}"
106
+ stem = f"research_plan_{timestamp}{preparation_suffix}{render_suffix}"
107
+ paths = AuthorRenderArtifactPaths(
108
+ timestamp=timestamp,
109
+ preparation_collision_index=preparation_collision_index,
110
+ render_collision_index=render_collision_index,
111
+ project_dir=self.output_dir / f"{stem}_project",
112
+ tex=self.output_dir / f"{stem}.tex",
113
+ bibtex=self.output_dir / f"references_{timestamp}{preparation_suffix}{render_suffix}.bib",
114
+ bibliography_needs_completion=self.output_dir
115
+ / f"bibliography_needs_completion_{timestamp}{preparation_suffix}{render_suffix}.json",
116
+ render_manifest=self.output_dir / f"research_plan_render_{timestamp}{preparation_suffix}{render_suffix}.json",
117
+ compile_log=self.output_dir / f"compile_{timestamp}{preparation_suffix}{render_suffix}.log",
118
+ compile_json=self.output_dir / f"compile_{timestamp}{preparation_suffix}{render_suffix}.json",
119
+ pdf_validation_json=self.output_dir / f"pdf_validation_{timestamp}{preparation_suffix}{render_suffix}.json",
120
+ pdf=self.output_dir / f"{stem}.pdf",
121
+ staged_pdf=self.output_dir / f".{stem}.pdf.staging",
122
+ )
123
+ targets = [
124
+ paths.project_dir,
125
+ paths.tex,
126
+ paths.bibtex,
127
+ paths.bibliography_needs_completion,
128
+ paths.render_manifest,
129
+ paths.compile_log,
130
+ paths.compile_json,
131
+ paths.pdf_validation_json,
132
+ paths.pdf,
133
+ paths.staged_pdf,
134
+ ]
135
+ if not any(target.exists() for target in targets):
136
+ return paths
137
+ raise RenderArtifactError(f"could not allocate an unused render artifact family for timestamp '{timestamp}'")
138
+
139
+ def publish_sources(self, rendered: TexRenderResult, paths: AuthorRenderArtifactPaths) -> None:
140
+ if rendered.project_dir.resolve() != paths.project_dir.resolve():
141
+ raise RenderArtifactError("rendered TeX project does not match its allocated artifact directory")
142
+ try:
143
+ _write_bytes_without_overwrite(paths.tex, rendered.main_tex.read_bytes())
144
+ _write_bytes_without_overwrite(paths.bibtex, rendered.bibtex.read_bytes())
145
+ _write_text_without_overwrite(
146
+ paths.bibliography_needs_completion,
147
+ _json_text(
148
+ {
149
+ "schema_version": "research_plan_author_bibliography_completion_v1",
150
+ "needs_completion": list(rendered.bibliography.needs_completion),
151
+ }
152
+ ),
153
+ )
154
+ _write_text_without_overwrite(paths.render_manifest, _json_text(rendered.as_dict()))
155
+ except OSError as error:
156
+ raise RenderArtifactError(f"cannot publish generated TeX/BibTeX sources: {error}") from error
157
+
158
+ def publish_compile_diagnostics(
159
+ self,
160
+ paths: AuthorRenderArtifactPaths,
161
+ *,
162
+ report: Mapping[str, Any],
163
+ log_text: str,
164
+ ) -> None:
165
+ _write_text_without_overwrite(paths.compile_log, str(log_text))
166
+ _write_text_without_overwrite(paths.compile_json, _json_text(dict(report)))
167
+
168
+ def publish_pdf_validation(self, paths: AuthorRenderArtifactPaths, report: Mapping[str, Any]) -> None:
169
+ _write_text_without_overwrite(paths.pdf_validation_json, _json_text(dict(report)))
170
+
171
+ def publish_validated_pdf(self, paths: AuthorRenderArtifactPaths) -> None:
172
+ if not paths.staged_pdf.is_file():
173
+ raise RenderArtifactError("validated PDF staging file does not exist")
174
+ try:
175
+ _write_bytes_without_overwrite(paths.pdf, paths.staged_pdf.read_bytes())
176
+ finally:
177
+ paths.staged_pdf.unlink(missing_ok=True)
178
+
179
+ def discard_staged_pdf(self, paths: AuthorRenderArtifactPaths) -> None:
180
+ paths.staged_pdf.unlink(missing_ok=True)
181
+
182
+
183
+ __all__ = [
184
+ "AuthorRenderArtifactPaths",
185
+ "AuthorRenderArtifactWriter",
186
+ "RenderArtifactError",
187
+ ]