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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  549. src/research_run_ids.py +11 -0
@@ -0,0 +1,703 @@
1
+ """Compile frozen theory artifacts into a deterministic audit registry.
2
+
3
+ The compiler deliberately creates only document-local labels. It never adds
4
+ scientific content, bibliography records, or upstream identifiers; every
5
+ compiled unit retains reverse references to the frozen Author handoff.
6
+ """
7
+
8
+ from __future__ import annotations
9
+
10
+ from collections.abc import Mapping, Sequence
11
+ from copy import deepcopy
12
+ import json
13
+ import re
14
+ from typing import Any
15
+
16
+ from jsonschema import Draft202012Validator
17
+
18
+
19
+ THEORY_SPINE_SCHEMA_VERSION = "research_plan_theory_spine_v1"
20
+
21
+ _NONEMPTY = {"type": "string", "minLength": 1}
22
+ _STRING_LIST = {"type": "array", "items": _NONEMPTY, "uniqueItems": True}
23
+ _LOCAL_LEMMA_ID = re.compile(r"^TS-L-[1-9][0-9]*$")
24
+ _LOCAL_PROOF_OBLIGATION_ID = re.compile(r"^TS-PO-[1-9][0-9]*$")
25
+ _LOCAL_FALSIFIER_ID = re.compile(r"^TS-F-[1-9][0-9]*$")
26
+ _LOCAL_BRANCH_ID = re.compile(r"^TS-BR-[A-Z0-9][A-Z0-9_-]*$")
27
+ _VISIBLE_LOCAL_ID = re.compile(r"(?<![A-Za-z0-9_-])TS-(?:L|PO|F|BR)-[A-Za-z0-9_-]+(?![A-Za-z0-9_-])")
28
+ _UNRESOLVED_STATUSES = {
29
+ "missing",
30
+ "needs_human_input",
31
+ "requires_human_review",
32
+ "review_required",
33
+ "unresolved",
34
+ }
35
+
36
+
37
+ THEORY_SPINE_SCHEMA: dict[str, Any] = {
38
+ "$schema": "https://json-schema.org/draft/2020-12/schema",
39
+ "title": "Research Plan Theory Spine v1",
40
+ "type": "object",
41
+ "additionalProperties": False,
42
+ "required": [
43
+ "schema_version",
44
+ "template_family",
45
+ "enabled",
46
+ "compiler_status",
47
+ "lemma_units",
48
+ "proof_obligations",
49
+ "falsifiers",
50
+ "decision_branches",
51
+ ],
52
+ "properties": {
53
+ "schema_version": {"const": THEORY_SPINE_SCHEMA_VERSION},
54
+ "template_family": _NONEMPTY,
55
+ "enabled": {"type": "boolean"},
56
+ "compiler_status": {"enum": ["ready", "no_auditable_lemma_input", "not_applicable"]},
57
+ "lemma_units": {"type": "array", "items": {"type": "object"}},
58
+ "proof_obligations": {"type": "array", "items": {"type": "object"}},
59
+ "falsifiers": {"type": "array", "items": {"type": "object"}},
60
+ "decision_branches": {"type": "array", "items": {"type": "object"}},
61
+ },
62
+ }
63
+
64
+
65
+ class TheorySpineError(ValueError):
66
+ """Raised when a deterministic theory registry cannot be source-bounded."""
67
+
68
+
69
+ def _mapping(value: object) -> dict[str, Any]:
70
+ return dict(value) if isinstance(value, Mapping) else {}
71
+
72
+
73
+ def _text(value: object) -> str:
74
+ return str(value or "").strip()
75
+
76
+
77
+ def _canonical_json(value: object) -> str:
78
+ return json.dumps(value, ensure_ascii=False, sort_keys=True, separators=(",", ":"), allow_nan=False)
79
+
80
+
81
+ def _text_list(value: object) -> list[str]:
82
+ if isinstance(value, str):
83
+ return [_text(value)] if _text(value) else []
84
+ if not isinstance(value, Sequence) or isinstance(value, (bytes, bytearray)):
85
+ return []
86
+ return sorted({_text(item) for item in value if _text(item)})
87
+
88
+
89
+ def _record_references(record: Mapping[str, Any], *field_names: str) -> set[str]:
90
+ references: set[str] = set()
91
+ for field_name in field_names:
92
+ references.update(_text_list(record.get(field_name)))
93
+ return references
94
+
95
+
96
+ def _reference_tokens(record: Mapping[str, Any]) -> set[str]:
97
+ return {
98
+ *(_record_references(record, "symbol_references", "symbols")),
99
+ *(_record_references(record, "variable_references", "variables")),
100
+ }
101
+
102
+
103
+ def _stable_records(records: object, *, identifier_field: str) -> list[dict[str, Any]]:
104
+ if not isinstance(records, list):
105
+ return []
106
+ values = [dict(record) for record in records if isinstance(record, Mapping) and _text(record.get(identifier_field))]
107
+ return sorted(values, key=lambda record: (_text(record.get(identifier_field)), _canonical_json(record)))
108
+
109
+
110
+ def _formal_records(author_context: Mapping[str, Any]) -> tuple[dict[str, dict[str, Any]], dict[str, str]]:
111
+ formal_reasoning = _mapping(author_context.get("formal_reasoning"))
112
+ records: dict[str, dict[str, Any]] = {}
113
+ kinds: dict[str, str] = {}
114
+ collections = (
115
+ ("definitions", "definition_id", "definition"),
116
+ ("assumptions", "assumption_id", "assumption"),
117
+ ("propositions", "proposition_id", "proposition"),
118
+ ("proof_obligations", "obligation_id", "proof_obligation"),
119
+ )
120
+ for collection, identifier_field, kind in collections:
121
+ for record in _stable_records(formal_reasoning.get(collection), identifier_field=identifier_field):
122
+ identifier = _text(record.get(identifier_field))
123
+ records.setdefault(identifier, record)
124
+ kinds.setdefault(identifier, kind)
125
+ derivation = _mapping(formal_reasoning.get("forward_derivation"))
126
+ for record in _stable_records(derivation.get("steps"), identifier_field="step_id"):
127
+ identifier = _text(record.get("step_id"))
128
+ records.setdefault(identifier, record)
129
+ kinds.setdefault(identifier, "forward_derivation_step")
130
+ return records, kinds
131
+
132
+
133
+ def _unknown_records(
134
+ preparation: Mapping[str, Any],
135
+ source_registry: Mapping[str, Any] | None,
136
+ ) -> list[dict[str, Any]]:
137
+ """Return source-registry unknown IDs plus their frozen records.
138
+
139
+ ``source_registry`` is available in Author preparation. Direct library
140
+ callers receive the same canonical ``unknown-N`` IDs by constructing the
141
+ frozen registry from the supplied preparation rather than minting a local
142
+ unknown-item identifier.
143
+ """
144
+
145
+ resolved_registry = source_registry
146
+ if not isinstance(resolved_registry, Mapping):
147
+ from .source_registry import build_frozen_source_registry
148
+
149
+ resolved_registry = build_frozen_source_registry(preparation)
150
+ records = [
151
+ {
152
+ "source_item_id": _text(record.get("source_item_id")),
153
+ "original_item": deepcopy(_mapping(record.get("original_item"))),
154
+ }
155
+ for record in resolved_registry.get("unknown_items") or []
156
+ if isinstance(record, Mapping) and _text(record.get("source_item_id"))
157
+ ]
158
+ return sorted(records, key=lambda record: (_text(_mapping(record["original_item"]).get("field_path")), record["source_item_id"]))
159
+
160
+
161
+ def _formal_reference_for_unknown(record: Mapping[str, Any], formal_ids: set[str]) -> str:
162
+ field_path = _text(record.get("field_path"))
163
+ match = re.search(r"(?:definitions|assumptions|propositions|proof_obligations|forward_derivation(?:\.steps)?)\.([A-Za-z][A-Za-z0-9_-]*)", field_path)
164
+ if match and match.group(1) in formal_ids:
165
+ return match.group(1)
166
+ return ""
167
+
168
+
169
+ def _status(value: object) -> str:
170
+ raw = _text(value).casefold()
171
+ if raw in {"candidate_formalization", "proposed", "user_declared"}:
172
+ return "candidate"
173
+ return "unverified"
174
+
175
+
176
+ def _local_branch_token(identifier: str) -> str:
177
+ token = re.sub(r"[^A-Z0-9]+", "-", identifier.upper()).strip("-")
178
+ return token or "UPSTREAM"
179
+
180
+
181
+ def _outcome_branch_id(outcome_ids: set[str], *candidates: str) -> list[str]:
182
+ return [candidate for candidate in candidates if candidate in outcome_ids][:1]
183
+
184
+
185
+ def _explicit_formal_references(record: Mapping[str, Any], formal_ids: set[str]) -> set[str]:
186
+ references = _record_references(
187
+ record,
188
+ "premises",
189
+ "depends_on",
190
+ "assumption_ids",
191
+ "formal_reference_ids",
192
+ "required_formal_reference_ids",
193
+ )
194
+ return references & formal_ids
195
+
196
+
197
+ def _matching_formal_ids(
198
+ record: Mapping[str, Any],
199
+ *,
200
+ candidates: Mapping[str, Mapping[str, Any]],
201
+ ) -> set[str]:
202
+ tokens = _reference_tokens(record)
203
+ if not tokens:
204
+ return set()
205
+ return {
206
+ identifier
207
+ for identifier, candidate in candidates.items()
208
+ if tokens & _reference_tokens(candidate)
209
+ }
210
+
211
+
212
+ def _counterexample_classification(record: Mapping[str, Any]) -> str:
213
+ validity = _text(record.get("validity")).casefold()
214
+ conclusion = _mapping(record.get("conclusion_check"))
215
+ conclusion_result = _text(conclusion.get("result")).casefold()
216
+ if validity in {"valid_counterexample", "valid", "all_assumptions_satisfied"} and conclusion_result in {
217
+ "counterexample",
218
+ "contradicted",
219
+ "refuted",
220
+ "violated",
221
+ }:
222
+ return "would_falsify"
223
+ if validity == "boundary_case":
224
+ return "scope_delimiter"
225
+ if validity == "assumptions_not_satisfied":
226
+ return "assumptions_not_satisfied"
227
+ return "no_information"
228
+
229
+
230
+ def build_theory_spine(
231
+ preparation: Mapping[str, Any],
232
+ *,
233
+ routing: Mapping[str, Any],
234
+ source_registry: Mapping[str, Any] | None = None,
235
+ ) -> dict[str, Any]:
236
+ """Compile frozen mathematical-theory records into local audit units.
237
+
238
+ Internal IDs such as ``TS-L-1`` and ``TS-BR-PO1-NO_INFORMATION`` are
239
+ document-local. Their reader-facing ``display_label`` values retain the
240
+ conventional ``L1``/``PO1``/``F1`` notation, while source-reference fields
241
+ contain exclusively IDs supplied by the frozen handoff records.
242
+ """
243
+
244
+ template_family = _text(routing.get("template_family"))
245
+ empty_spine = {
246
+ "schema_version": THEORY_SPINE_SCHEMA_VERSION,
247
+ "template_family": template_family,
248
+ "enabled": False,
249
+ "compiler_status": "not_applicable",
250
+ "lemma_units": [],
251
+ "proof_obligations": [],
252
+ "falsifiers": [],
253
+ "decision_branches": [],
254
+ }
255
+ if template_family != "mathematics_theory":
256
+ return empty_spine
257
+
258
+ author_context = _mapping(_mapping(preparation.get("source_bundle")).get("author_context"))
259
+ formal_reasoning = _mapping(author_context.get("formal_reasoning"))
260
+ formal_by_id, formal_kinds = _formal_records(author_context)
261
+ formal_ids = set(formal_by_id)
262
+ assumption_records = {
263
+ identifier: record
264
+ for identifier, record in formal_by_id.items()
265
+ if formal_kinds.get(identifier) == "assumption"
266
+ }
267
+ proof_records = {
268
+ identifier: record
269
+ for identifier, record in formal_by_id.items()
270
+ if formal_kinds.get(identifier) == "proof_obligation"
271
+ }
272
+ unknown_records = _unknown_records(preparation, source_registry)
273
+ unknown_ids_by_formal_id: dict[str, list[str]] = {}
274
+ for unknown in unknown_records:
275
+ original_item = _mapping(unknown.get("original_item"))
276
+ formal_reference_id = _formal_reference_for_unknown(original_item, formal_ids)
277
+ if formal_reference_id:
278
+ unknown_ids_by_formal_id.setdefault(formal_reference_id, []).append(_text(unknown.get("source_item_id")))
279
+ for unknown_ids in unknown_ids_by_formal_id.values():
280
+ unknown_ids.sort()
281
+
282
+ outcomes = _stable_records(author_context.get("outcome_branches"), identifier_field="branch_id")
283
+ outcome_ids = {_text(record.get("branch_id")) for record in outcomes}
284
+
285
+ lemma_sources = [
286
+ (identifier, record)
287
+ for identifier, record in formal_by_id.items()
288
+ if formal_kinds.get(identifier) in {"proposition", "forward_derivation_step"}
289
+ ]
290
+ lemma_sources.sort(key=lambda item: (0 if formal_kinds[item[0]] == "proposition" else 1, item[0], _canonical_json(item[1])))
291
+ lemma_units: list[dict[str, Any]] = []
292
+ lemma_id_by_source_id: dict[str, str] = {}
293
+ for index, (source_id, record) in enumerate(lemma_sources, start=1):
294
+ lemma_id = f"TS-L-{index}"
295
+ lemma_id_by_source_id[source_id] = lemma_id
296
+ premise_ids = _explicit_formal_references(record, formal_ids)
297
+ premise_ids.update(_matching_formal_ids(record, candidates=assumption_records))
298
+ related_proof_ids = _matching_formal_ids(record, candidates=proof_records)
299
+ lemma_units.append(
300
+ {
301
+ "lemma_id": lemma_id,
302
+ "display_label": f"L{index}",
303
+ "source_kind": formal_kinds[source_id],
304
+ "source_formal_reference_ids": [source_id],
305
+ "premise_ids": sorted(premise_ids),
306
+ "status": _status(record.get("status")),
307
+ "source_status": _text(record.get("status")),
308
+ "proof_obligation_ids": sorted(related_proof_ids),
309
+ "falsifier_ids": [],
310
+ "decision_branch_ids": [],
311
+ }
312
+ )
313
+
314
+ no_information_reference_ids = {
315
+ identifier
316
+ for identifier, record in formal_by_id.items()
317
+ if _text(record.get("status")).casefold() in _UNRESOLVED_STATUSES
318
+ }
319
+ no_information_reference_ids.update(unknown_ids_by_formal_id)
320
+ decision_branches: list[dict[str, Any]] = []
321
+ for outcome in outcomes:
322
+ outcome_id = _text(outcome.get("branch_id"))
323
+ decision_branches.append(
324
+ {
325
+ "branch_id": f"TS-BR-OUTCOME-{_local_branch_token(outcome_id)}",
326
+ "display_label": f"Branch {outcome_id}",
327
+ "branch_kind": "upstream_outcome_branch",
328
+ "source_formal_reference_ids": [],
329
+ "source_counterexample_ids": [],
330
+ "source_outcome_branch_ids": [outcome_id],
331
+ "source_unknown_item_ids": [],
332
+ "status": "expected_not_observed",
333
+ "conclusion_policy": "defer_to_upstream_outcome_branch",
334
+ }
335
+ )
336
+ no_information_branch_by_formal_id: dict[str, str] = {}
337
+ for source_id in sorted(no_information_reference_ids):
338
+ branch_id = f"TS-BR-{_local_branch_token(source_id)}-NO_INFORMATION"
339
+ no_information_branch_by_formal_id[source_id] = branch_id
340
+ decision_branches.append(
341
+ {
342
+ "branch_id": branch_id,
343
+ "display_label": f"No-information: {source_id}",
344
+ "branch_kind": "no_information",
345
+ "source_formal_reference_ids": [source_id] if source_id in formal_ids else [],
346
+ "source_counterexample_ids": [],
347
+ "source_outcome_branch_ids": _outcome_branch_id(outcome_ids, "uninformative_or_invalid"),
348
+ "source_unknown_item_ids": sorted(unknown_ids_by_formal_id.get(source_id) or []),
349
+ "status": "no_information",
350
+ "conclusion_policy": "withhold_theorem_status_update",
351
+ "next_action": "resolve_or_review_upstream_input",
352
+ }
353
+ )
354
+
355
+ proof_obligations: list[dict[str, Any]] = []
356
+ for index, (source_id, record) in enumerate(sorted(proof_records.items()), start=1):
357
+ local_id = f"TS-PO-{index}"
358
+ matching_dependencies = _matching_formal_ids(record, candidates={
359
+ identifier: candidate
360
+ for identifier, candidate in formal_by_id.items()
361
+ if formal_kinds.get(identifier) in {"definition", "assumption", "proposition", "forward_derivation_step"}
362
+ })
363
+ matching_dependencies.update(_explicit_formal_references(record, formal_ids))
364
+ related_lemma_ids = sorted(
365
+ lemma_id
366
+ for lemma_source_id, lemma_id in lemma_id_by_source_id.items()
367
+ if lemma_source_id in matching_dependencies
368
+ or source_id in set(next(
369
+ unit["proof_obligation_ids"]
370
+ for unit in lemma_units
371
+ if unit["lemma_id"] == lemma_id
372
+ ))
373
+ )
374
+ proof_obligations.append(
375
+ {
376
+ "proof_obligation_id": local_id,
377
+ "display_label": f"PO{index}",
378
+ "source_formal_reference_ids": [source_id],
379
+ "required_formal_reference_ids": sorted(matching_dependencies),
380
+ "related_lemma_ids": related_lemma_ids,
381
+ "source_unknown_item_ids": sorted(unknown_ids_by_formal_id.get(source_id) or []),
382
+ "status": _status(record.get("status")),
383
+ "source_status": _text(record.get("status")),
384
+ "if_unavailable_branch_id": no_information_branch_by_formal_id.get(source_id, ""),
385
+ }
386
+ )
387
+
388
+ local_proof_id_by_source_id = {
389
+ source_id: proof_obligation["proof_obligation_id"]
390
+ for source_id, proof_obligation in zip(sorted(proof_records), proof_obligations, strict=True)
391
+ }
392
+ for unit in lemma_units:
393
+ unit["proof_obligation_ids"] = [
394
+ local_proof_id_by_source_id[source_id]
395
+ for source_id in unit["proof_obligation_ids"]
396
+ if source_id in local_proof_id_by_source_id
397
+ ]
398
+ related_source_ids = set(unit["source_formal_reference_ids"]) | set(unit["premise_ids"])
399
+ unit["decision_branch_ids"] = sorted(
400
+ branch_id
401
+ for source_id, branch_id in no_information_branch_by_formal_id.items()
402
+ if source_id in related_source_ids
403
+ or source_id in {
404
+ proof_obligation["source_formal_reference_ids"][0]
405
+ for proof_obligation in proof_obligations
406
+ if set(proof_obligation["related_lemma_ids"]) & {unit["lemma_id"]}
407
+ }
408
+ )
409
+
410
+ counterexample_analysis = _mapping(author_context.get("counterexample_analysis"))
411
+ counterexamples = _stable_records(counterexample_analysis.get("candidate_counterexamples"), identifier_field="counterexample_id")
412
+ counterexample_target_id = _text(counterexample_analysis.get("target_claim_id"))
413
+ target_lemma_ids = [lemma_id_by_source_id[counterexample_target_id]] if counterexample_target_id in lemma_id_by_source_id else []
414
+ falsifiers: list[dict[str, Any]] = []
415
+ outcome_candidates_by_classification = {
416
+ "would_falsify": ("null_or_contradictory",),
417
+ "scope_delimiter": ("partial_or_heterogeneous",),
418
+ "assumptions_not_satisfied": ("uninformative_or_invalid",),
419
+ "no_information": ("uninformative_or_invalid",),
420
+ }
421
+ for index, record in enumerate(counterexamples, start=1):
422
+ counterexample_id = _text(record.get("counterexample_id"))
423
+ classification = _counterexample_classification(record)
424
+ falsifier_id = f"TS-F-{index}"
425
+ falsifiers.append(
426
+ {
427
+ "falsifier_id": falsifier_id,
428
+ "display_label": f"F{index}",
429
+ "source_counterexample_ids": [counterexample_id],
430
+ "target_formal_reference_ids": [counterexample_target_id] if counterexample_target_id in formal_ids else [],
431
+ "target_lemma_ids": target_lemma_ids,
432
+ "classification": classification,
433
+ "source_outcome_branch_ids": _outcome_branch_id(
434
+ outcome_ids,
435
+ *outcome_candidates_by_classification[classification],
436
+ ),
437
+ }
438
+ )
439
+ for falsifier in falsifiers:
440
+ for lemma_id in falsifier["target_lemma_ids"]:
441
+ for unit in lemma_units:
442
+ if unit["lemma_id"] == lemma_id:
443
+ unit["falsifier_ids"].append(falsifier["falsifier_id"])
444
+
445
+ if not lemma_units:
446
+ decision_branches.append(
447
+ {
448
+ "branch_id": "TS-BR-MISSING-DERIVATION-INPUT-NO_INFORMATION",
449
+ "display_label": "No-information: derivation input",
450
+ "branch_kind": "compiler_no_information",
451
+ "source_formal_reference_ids": [],
452
+ "source_counterexample_ids": [],
453
+ "source_outcome_branch_ids": _outcome_branch_id(outcome_ids, "uninformative_or_invalid"),
454
+ "source_unknown_item_ids": [],
455
+ "status": "no_information",
456
+ "conclusion_policy": "withhold_theorem_status_update",
457
+ "next_action": "supply_upstream_proposition_or_derivation_input",
458
+ "reason_code": "missing_upstream_derivation_input",
459
+ }
460
+ )
461
+ spine = {
462
+ "schema_version": THEORY_SPINE_SCHEMA_VERSION,
463
+ "template_family": template_family,
464
+ "enabled": True,
465
+ "compiler_status": "ready" if lemma_units else "no_auditable_lemma_input",
466
+ "lemma_units": lemma_units,
467
+ "proof_obligations": proof_obligations,
468
+ "falsifiers": falsifiers,
469
+ "decision_branches": decision_branches,
470
+ }
471
+ errors = validate_theory_spine(spine, preparation=preparation, source_registry=source_registry)
472
+ if errors:
473
+ raise TheorySpineError("theory spine compilation failed: " + "; ".join(errors))
474
+ return spine
475
+
476
+
477
+ def validate_theory_spine(
478
+ payload: object,
479
+ *,
480
+ preparation: Mapping[str, Any],
481
+ source_registry: Mapping[str, Any] | None = None,
482
+ ) -> list[str]:
483
+ """Validate local labels and their reverse references to frozen records."""
484
+
485
+ errors: list[str] = []
486
+ for error in Draft202012Validator(THEORY_SPINE_SCHEMA).iter_errors(payload):
487
+ path = "/".join(str(part) for part in error.absolute_path) or "$"
488
+ errors.append(f"{path}: {error.message}")
489
+ if not isinstance(payload, Mapping):
490
+ return sorted(set(errors))
491
+ spine = dict(payload)
492
+ author_context = _mapping(_mapping(preparation.get("source_bundle")).get("author_context"))
493
+ resolved_source_registry = source_registry
494
+ if not isinstance(resolved_source_registry, Mapping):
495
+ from .source_registry import build_frozen_source_registry
496
+
497
+ resolved_source_registry = build_frozen_source_registry(preparation)
498
+ formal_by_id, _formal_kinds = _formal_records(author_context)
499
+ formal_ids = set(formal_by_id)
500
+ counterexample_ids = {
501
+ _text(record.get("counterexample_id"))
502
+ for record in _mapping(author_context.get("counterexample_analysis")).get("candidate_counterexamples") or []
503
+ if isinstance(record, Mapping) and _text(record.get("counterexample_id"))
504
+ }
505
+ outcome_ids = {
506
+ _text(record.get("branch_id"))
507
+ for record in author_context.get("outcome_branches") or []
508
+ if isinstance(record, Mapping) and _text(record.get("branch_id"))
509
+ }
510
+ unknown_ids = {
511
+ _text(record.get("source_item_id"))
512
+ for record in _mapping(resolved_source_registry).get("unknown_items") or []
513
+ if isinstance(record, Mapping) and _text(record.get("source_item_id"))
514
+ }
515
+ collection_specs = (
516
+ ("lemma_units", "lemma_id", _LOCAL_LEMMA_ID),
517
+ ("proof_obligations", "proof_obligation_id", _LOCAL_PROOF_OBLIGATION_ID),
518
+ ("falsifiers", "falsifier_id", _LOCAL_FALSIFIER_ID),
519
+ ("decision_branches", "branch_id", _LOCAL_BRANCH_ID),
520
+ )
521
+ records_by_collection = {
522
+ collection: [record for record in spine.get(collection) or [] if isinstance(record, Mapping)]
523
+ for collection, _identifier_field, _pattern in collection_specs
524
+ }
525
+ local_ids: set[str] = set()
526
+ for collection, identifier_field, pattern in collection_specs:
527
+ seen_ids: set[str] = set()
528
+ for index, record in enumerate(spine.get(collection) or []):
529
+ if not isinstance(record, Mapping):
530
+ errors.append(f"{collection}/{index} must be an object")
531
+ continue
532
+ identifier = _text(record.get(identifier_field))
533
+ if not pattern.fullmatch(identifier):
534
+ errors.append(f"{collection}/{index}/{identifier_field} is not a valid local audit label")
535
+ if identifier in seen_ids or identifier in local_ids:
536
+ errors.append(f"{collection}/{index}/{identifier_field} duplicates a local audit label")
537
+ seen_ids.add(identifier)
538
+ local_ids.add(identifier)
539
+ upstream_ids = {
540
+ *formal_ids,
541
+ *counterexample_ids,
542
+ *outcome_ids,
543
+ *unknown_ids,
544
+ *{
545
+ _text(value)
546
+ for value in _mapping(resolved_source_registry).get("allowed_source_ids") or []
547
+ if _text(value)
548
+ },
549
+ *{
550
+ _text(_mapping(record).get("citation_key"))
551
+ for record in _mapping(resolved_source_registry).get("citation_registry") or []
552
+ if _text(_mapping(record).get("citation_key"))
553
+ },
554
+ }
555
+ if local_ids & upstream_ids:
556
+ errors.append("local theory audit labels collide with frozen upstream identifiers")
557
+
558
+ lemma_ids = {
559
+ _text(record.get("lemma_id")) for record in records_by_collection["lemma_units"] if _text(record.get("lemma_id"))
560
+ }
561
+ proof_obligation_ids = {
562
+ _text(record.get("proof_obligation_id"))
563
+ for record in records_by_collection["proof_obligations"]
564
+ if _text(record.get("proof_obligation_id"))
565
+ }
566
+ falsifier_ids = {
567
+ _text(record.get("falsifier_id")) for record in records_by_collection["falsifiers"] if _text(record.get("falsifier_id"))
568
+ }
569
+ decision_branch_ids = {
570
+ _text(record.get("branch_id"))
571
+ for record in records_by_collection["decision_branches"]
572
+ if _text(record.get("branch_id"))
573
+ }
574
+ for collection, records in records_by_collection.items():
575
+ for index, record in enumerate(records):
576
+ for field, allowed in (
577
+ ("source_formal_reference_ids", formal_ids),
578
+ ("required_formal_reference_ids", formal_ids),
579
+ ("target_formal_reference_ids", formal_ids),
580
+ ("source_counterexample_ids", counterexample_ids),
581
+ ("source_outcome_branch_ids", outcome_ids),
582
+ ):
583
+ values = _text_list(record.get(field))
584
+ if set(values) - allowed:
585
+ errors.append(f"{collection}/{index}/{field} contains an unknown upstream ID")
586
+ unknown_references = _text_list(record.get("source_unknown_item_ids"))
587
+ if set(unknown_references) - unknown_ids:
588
+ errors.append(f"{collection}/{index}/source_unknown_item_ids contains an unknown source item")
589
+ if collection == "lemma_units":
590
+ if set(_text_list(record.get("premise_ids"))) - formal_ids:
591
+ errors.append(f"lemma_units/{index}/premise_ids contains an unknown formal reference")
592
+ if set(_text_list(record.get("proof_obligation_ids"))) - proof_obligation_ids:
593
+ errors.append(f"lemma_units/{index}/proof_obligation_ids contains an unknown local proof obligation")
594
+ if set(_text_list(record.get("falsifier_ids"))) - falsifier_ids:
595
+ errors.append(f"lemma_units/{index}/falsifier_ids contains an unknown local falsifier")
596
+ if set(_text_list(record.get("decision_branch_ids"))) - decision_branch_ids:
597
+ errors.append(f"lemma_units/{index}/decision_branch_ids contains an unknown local decision branch")
598
+ elif collection == "proof_obligations":
599
+ if set(_text_list(record.get("related_lemma_ids"))) - lemma_ids:
600
+ errors.append(f"proof_obligations/{index}/related_lemma_ids contains an unknown local lemma")
601
+ branch_id = _text(record.get("if_unavailable_branch_id"))
602
+ if branch_id and branch_id not in decision_branch_ids:
603
+ errors.append(f"proof_obligations/{index}/if_unavailable_branch_id contains an unknown local decision branch")
604
+ elif collection == "falsifiers" and set(_text_list(record.get("target_lemma_ids"))) - lemma_ids:
605
+ errors.append(f"falsifiers/{index}/target_lemma_ids contains an unknown local lemma")
606
+ return sorted(set(errors))
607
+
608
+
609
+ def theory_spine_context_for_section(
610
+ theory_spine: Mapping[str, Any],
611
+ *,
612
+ section_id: str,
613
+ unit_references: Mapping[str, Any] | None = None,
614
+ ) -> dict[str, Any]:
615
+ """Return the compact, route-owned slice of a theory spine registry."""
616
+
617
+ spine = _mapping(theory_spine)
618
+ if not spine.get("enabled"):
619
+ return {
620
+ "schema_version": _text(spine.get("schema_version")) or THEORY_SPINE_SCHEMA_VERSION,
621
+ "enabled": False,
622
+ "section_id": section_id,
623
+ "mode": "not_applicable",
624
+ "lemma_units": [],
625
+ "proof_obligations": [],
626
+ "falsifiers": [],
627
+ "decision_branches": [],
628
+ }
629
+ references = _mapping(unit_references)
630
+
631
+ def selected(collection: str, identifier_field: str, reference_field: str) -> list[dict[str, Any]]:
632
+ selected_ids = set(_text_list(references.get(reference_field)))
633
+ return [
634
+ deepcopy(dict(record))
635
+ for record in spine.get(collection) or []
636
+ if isinstance(record, Mapping) and _text(record.get(identifier_field)) in selected_ids
637
+ ]
638
+
639
+ return {
640
+ "schema_version": _text(spine.get("schema_version")) or THEORY_SPINE_SCHEMA_VERSION,
641
+ "enabled": True,
642
+ "section_id": section_id,
643
+ "mode": _text(references.get("mode")) or "reference_only",
644
+ "lemma_units": selected("lemma_units", "lemma_id", "lemma_ids"),
645
+ "proof_obligations": selected("proof_obligations", "proof_obligation_id", "proof_obligation_ids"),
646
+ "falsifiers": selected("falsifiers", "falsifier_id", "falsifier_ids"),
647
+ "decision_branches": selected("decision_branches", "branch_id", "decision_branch_ids"),
648
+ }
649
+
650
+
651
+ def theory_spine_display_labels(theory_spine: Mapping[str, Any]) -> dict[str, str]:
652
+ """Return the reader-facing labels for private local theory identifiers."""
653
+
654
+ spine = _mapping(theory_spine)
655
+ labels: dict[str, str] = {}
656
+ for collection, identifier_field in (
657
+ ("lemma_units", "lemma_id"),
658
+ ("proof_obligations", "proof_obligation_id"),
659
+ ("falsifiers", "falsifier_id"),
660
+ ("decision_branches", "branch_id"),
661
+ ):
662
+ for record in spine.get(collection) or []:
663
+ if not isinstance(record, Mapping):
664
+ continue
665
+ identifier = _text(record.get(identifier_field))
666
+ display_label = _text(record.get("display_label"))
667
+ if identifier and display_label:
668
+ labels[identifier] = display_label
669
+ return labels
670
+
671
+
672
+ def replace_theory_spine_internal_ids(text: object, theory_spine: Mapping[str, Any]) -> str:
673
+ """Replace known private audit identifiers with their public labels."""
674
+
675
+ value = str(text or "")
676
+ labels = theory_spine_display_labels(theory_spine)
677
+ if not labels:
678
+ return value
679
+ pattern = re.compile(
680
+ r"(?<![A-Za-z0-9_-])(?:"
681
+ + "|".join(re.escape(identifier) for identifier in sorted(labels, key=len, reverse=True))
682
+ + r")(?![A-Za-z0-9_-])"
683
+ )
684
+ return pattern.sub(lambda match: labels[match.group(0)], value)
685
+
686
+
687
+ def theory_spine_internal_ids_in_text(text: object) -> list[str]:
688
+ """Return local audit identifiers that must never appear in public prose."""
689
+
690
+ return sorted(set(_VISIBLE_LOCAL_ID.findall(str(text or ""))))
691
+
692
+
693
+ __all__ = [
694
+ "THEORY_SPINE_SCHEMA",
695
+ "THEORY_SPINE_SCHEMA_VERSION",
696
+ "TheorySpineError",
697
+ "build_theory_spine",
698
+ "replace_theory_spine_internal_ids",
699
+ "theory_spine_display_labels",
700
+ "theory_spine_context_for_section",
701
+ "theory_spine_internal_ids_in_text",
702
+ "validate_theory_spine",
703
+ ]