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.
- qwen_sci-0.2.2.dist-info/METADATA +492 -0
- qwen_sci-0.2.2.dist-info/RECORD +549 -0
- qwen_sci-0.2.2.dist-info/WHEEL +4 -0
- qwen_sci-0.2.2.dist-info/entry_points.txt +6 -0
- qwen_sci-0.2.2.dist-info/licenses/LICENSE +21 -0
- src/1.txt +1 -0
- src/__init__.py +1 -0
- src/__main__.py +5 -0
- src/agents/__init__.py +1 -0
- src/agents/experiment_design_agent/__init__.py +268 -0
- src/agents/experiment_design_agent/artifacts.py +747 -0
- src/agents/experiment_design_agent/cache.py +319 -0
- src/agents/experiment_design_agent/completeness.py +130 -0
- src/agents/experiment_design_agent/contracts.py +771 -0
- src/agents/experiment_design_agent/counterexample_analyzer.py +187 -0
- src/agents/experiment_design_agent/design_evidence_paper_screener.py +470 -0
- src/agents/experiment_design_agent/discipline_catalog.py +178 -0
- src/agents/experiment_design_agent/evidence_cards.py +338 -0
- src/agents/experiment_design_agent/evidence_planner.py +452 -0
- src/agents/experiment_design_agent/formal_reasoning_planner.py +884 -0
- src/agents/experiment_design_agent/fulltext_acquisition.py +863 -0
- src/agents/experiment_design_agent/idea_adapter.py +100 -0
- src/agents/experiment_design_agent/idea_intake.py +87 -0
- src/agents/experiment_design_agent/llm_json.py +328 -0
- src/agents/experiment_design_agent/orchestrator.py +1220 -0
- src/agents/experiment_design_agent/reasoning_context.py +183 -0
- src/agents/experiment_design_agent/reasoning_validation.py +546 -0
- src/agents/experiment_design_agent/run.py +481 -0
- src/agents/experiment_design_agent/run_logging.py +292 -0
- src/agents/experiment_design_agent/scope_gate.py +198 -0
- src/agents/experiment_design_agent/study_type_composer.py +1360 -0
- src/agents/experiment_design_agent/survey_evidence.py +1381 -0
- src/agents/experiment_design_agent/template_router.py +195 -0
- src/agents/experiment_design_agent/variable_claim_extractor.py +93 -0
- src/agents/idea_agent/__init__.py +1 -0
- src/agents/idea_agent/agent/__init__.py +6 -0
- src/agents/idea_agent/agent/artifacts.py +308 -0
- src/agents/idea_agent/agent/base.py +122 -0
- src/agents/idea_agent/agent/ligagent.py +488 -0
- src/agents/idea_agent/agent/mcts.py +2060 -0
- src/agents/idea_agent/agent/prompts/__init__.py +48 -0
- src/agents/idea_agent/agent/prompts/advanced_analysis.py +235 -0
- src/agents/idea_agent/agent/prompts/algorithm_alignment.py +55 -0
- src/agents/idea_agent/agent/prompts/algorithm_structuring.py +48 -0
- src/agents/idea_agent/agent/prompts/component_extraction.py +62 -0
- src/agents/idea_agent/agent/prompts/component_novelty_evaluation.py +54 -0
- src/agents/idea_agent/agent/prompts/experiment_findings_extraction.py +39 -0
- src/agents/idea_agent/agent/prompts/idea_fusion.py +295 -0
- src/agents/idea_agent/agent/prompts/idea_introduction.py +30 -0
- src/agents/idea_agent/agent/prompts/idea_result_alignment.py +39 -0
- src/agents/idea_agent/agent/prompts/input_interpreter.py +52 -0
- src/agents/idea_agent/agent/prompts/keynote_ops.py +78 -0
- src/agents/idea_agent/agent/prompts/mcts_evaluation.py +235 -0
- src/agents/idea_agent/agent/prompts/mcts_generation.py +140 -0
- src/agents/idea_agent/agent/prompts/mechanism_commit_query.py +99 -0
- src/agents/idea_agent/agent/prompts/memory_selection.py +0 -0
- src/agents/idea_agent/agent/prompts/prompt_modes.py +16 -0
- src/agents/idea_agent/agent/prompts/rag_query.py +34 -0
- src/agents/idea_agent/agent/prompts/re_analysis_replan.py +48 -0
- src/agents/idea_agent/agent/prompts/reference_grounding.py +34 -0
- src/agents/idea_agent/agent/prompts/root_domain_classification.py +32 -0
- src/agents/idea_agent/agent/prompts/scientific_debate.py +88 -0
- src/agents/idea_agent/agent/prompts/scientific_materialization.py +45 -0
- src/agents/idea_agent/agent/prompts/skill_instantiation.py +193 -0
- src/agents/idea_agent/agent/prompts/theory_transfer_query.py +93 -0
- src/agents/idea_agent/agent/prompts/topic_background.py +15 -0
- src/agents/idea_agent/agent/skills/DEFAULT_SKILL_TEMPLATES.json +263 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/alternative-path-contrast/SKILL.md +40 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/alternative-path-contrast/references/contrast_patterns.md +22 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/feedback-closed-loop/SKILL.md +40 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/feedback-closed-loop/references/mechanism_cards.md +24 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/hierarchical-decomposition/SKILL.md +39 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/hierarchical-decomposition/references/hierarchy_patterns.md +22 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/mechanism-commit-innovation/SKILL.md +39 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/mechanism-commit-innovation/references/mechanism_commit_patterns.md +24 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/multi-scale-coordinator/SKILL.md +39 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/multi-scale-coordinator/references/coordination_patterns.md +22 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/speculative-execution-with-repair/SKILL.md +41 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/speculative-execution-with-repair/references/speculation_patterns.md +22 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/surgical-modularity/SKILL.md +39 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/surgical-modularity/references/modularity_patterns.md +22 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/theory-transfer-injection/SKILL.md +40 -0
- src/agents/idea_agent/agent/skills/edit_operator_skills/theory-transfer-injection/references/transfer_patterns.md +24 -0
- src/agents/idea_agent/example/idea_result.json +900 -0
- src/agents/idea_agent/run.py +276 -0
- src/agents/idea_agent/tests/test_advanced_analysis_contract.py +90 -0
- src/agents/idea_agent/tests/test_gap_hypothesis_bridge.py +166 -0
- src/agents/idea_agent/tests/test_idea_debate.py +480 -0
- src/agents/idea_agent/tests/test_idea_result_v5.py +99 -0
- src/agents/idea_agent/tests/test_idea_synthesis.py +92 -0
- src/agents/idea_agent/tests/test_mature_idea_sources.py +27 -0
- src/agents/idea_agent/tests/test_multimodal_idea_integration.py +386 -0
- src/agents/idea_agent/tests/test_profile_materialization_and_scoring.py +219 -0
- src/agents/idea_agent/tests/test_profile_native_skill_rendering.py +122 -0
- src/agents/idea_agent/tests/test_result_persistence.py +183 -0
- src/agents/idea_agent/tests/test_scientific_intervention_profiles.py +241 -0
- src/agents/idea_agent/tests/test_scientific_rubric_and_prompts.py +559 -0
- src/agents/idea_agent/tests/test_strict_json_object_responses.py +48 -0
- src/agents/idea_agent/utils/core/__init__.py +1 -0
- src/agents/idea_agent/utils/core/ablation_inputs.py +60 -0
- src/agents/idea_agent/utils/core/chat_errors.py +95 -0
- src/agents/idea_agent/utils/core/chat_router.py +130 -0
- src/agents/idea_agent/utils/core/chat_transport.py +188 -0
- src/agents/idea_agent/utils/core/config_loader.py +166 -0
- src/agents/idea_agent/utils/core/json_utils.py +28 -0
- src/agents/idea_agent/utils/core/logger.py +287 -0
- src/agents/idea_agent/utils/core/progress.py +58 -0
- src/agents/idea_agent/utils/core/response_parsing.py +57 -0
- src/agents/idea_agent/utils/core/run_inputs.py +198 -0
- src/agents/idea_agent/utils/mcts/__init__.py +1 -0
- src/agents/idea_agent/utils/mcts/component_novelty.py +342 -0
- src/agents/idea_agent/utils/mcts/defect_registry.py +302 -0
- src/agents/idea_agent/utils/mcts/idea_routes.py +61 -0
- src/agents/idea_agent/utils/mcts/idea_taste_presets.py +312 -0
- src/agents/idea_agent/utils/mcts/mcts_helpers.py +738 -0
- src/agents/idea_agent/utils/mcts/mcts_runtime.py +3000 -0
- src/agents/idea_agent/utils/mcts/scientific_intervention_ontology.py +1561 -0
- src/agents/idea_agent/utils/mcts/scientific_rubric.py +211 -0
- src/agents/idea_agent/utils/mcts/skill_parsing.py +92 -0
- src/agents/idea_agent/utils/papers/__init__.py +1 -0
- src/agents/idea_agent/utils/papers/paper_graph_vector_store.py +499 -0
- src/agents/idea_agent/utils/papers/paper_repository.py +372 -0
- src/agents/idea_agent/utils/prompting/__init__.py +1 -0
- src/agents/idea_agent/utils/prompting/prompt_views.py +637 -0
- src/agents/idea_agent/utils/workflow/__init__.py +1 -0
- src/agents/idea_agent/utils/workflow/advanced_analysis_contract.py +244 -0
- src/agents/idea_agent/utils/workflow/gap_hypothesis_bridge.py +461 -0
- src/agents/idea_agent/utils/workflow/idea_contract.py +426 -0
- src/agents/idea_agent/utils/workflow/idea_debate.py +1238 -0
- src/agents/idea_agent/utils/workflow/idea_diversity.py +163 -0
- src/agents/idea_agent/utils/workflow/idea_fusion.py +889 -0
- src/agents/idea_agent/utils/workflow/idea_helpers.py +478 -0
- src/agents/idea_agent/utils/workflow/idea_portfolio.py +422 -0
- src/agents/idea_agent/utils/workflow/idea_synthesis.py +482 -0
- src/agents/idea_agent/utils/workflow/ligagent_flow.py +581 -0
- src/agents/idea_agent/utils/workflow/ligagent_handlers.py +1836 -0
- src/agents/idea_agent/utils/workflow/ligagent_helpers.py +1331 -0
- src/agents/idea_agent/utils/workflow/ligagent_utils.py +322 -0
- src/agents/idea_agent/utils/workflow/mature_idea_sources.py +648 -0
- src/agents/idea_agent/utils/workflow/multimodal_data_anchoring.py +578 -0
- src/agents/idea_agent/utils/workflow/result_persistence.py +774 -0
- src/agents/idea_agent/utils/workflow/stage_contract.py +76 -0
- src/agents/idea_agent/utils/workflow/workflow_runtime.py +288 -0
- src/agents/research_plan_author/__init__.py +50 -0
- src/agents/research_plan_author/artifacts.py +270 -0
- src/agents/research_plan_author/authoring_blueprint.py +1246 -0
- src/agents/research_plan_author/bibtex_renderer.py +252 -0
- src/agents/research_plan_author/contract_repair.py +131 -0
- src/agents/research_plan_author/contracts.py +745 -0
- src/agents/research_plan_author/cross_section_editor.py +232 -0
- src/agents/research_plan_author/document_quality.py +987 -0
- src/agents/research_plan_author/idea_evolution.py +223 -0
- src/agents/research_plan_author/input_loader.py +76 -0
- src/agents/research_plan_author/latex_compiler.py +260 -0
- src/agents/research_plan_author/latex_safety.py +159 -0
- src/agents/research_plan_author/llm_json.py +74 -0
- src/agents/research_plan_author/markdown_renderer.py +275 -0
- src/agents/research_plan_author/pdf_validator.py +149 -0
- src/agents/research_plan_author/render.py +166 -0
- src/agents/research_plan_author/render_artifacts.py +187 -0
- src/agents/research_plan_author/run.py +765 -0
- src/agents/research_plan_author/run_logging.py +209 -0
- src/agents/research_plan_author/section_cache.py +184 -0
- src/agents/research_plan_author/section_composer.py +1764 -0
- src/agents/research_plan_author/section_router.py +209 -0
- src/agents/research_plan_author/semantic_validator.py +254 -0
- src/agents/research_plan_author/source_bundle.py +46 -0
- src/agents/research_plan_author/source_registry.py +208 -0
- src/agents/research_plan_author/survey_source_loader.py +137 -0
- src/agents/research_plan_author/template_adapter.py +173 -0
- src/agents/research_plan_author/template_profile.py +204 -0
- src/agents/research_plan_author/tex_renderer.py +496 -0
- src/agents/research_plan_author/theory_presentation.py +134 -0
- src/agents/research_plan_author/theory_spine.py +703 -0
- src/agents/survey_agent/Dockerfile +54 -0
- src/agents/survey_agent/README.md +350 -0
- src/agents/survey_agent/config/deep_survey.yaml +217 -0
- src/agents/survey_agent/config/deep_survey_batch.yaml +176 -0
- src/agents/survey_agent/config/deep_survey_fast.yaml +183 -0
- src/agents/survey_agent/config/evaluate_baseline.yaml +197 -0
- src/agents/survey_agent/config/outcomeRAG.yaml +159 -0
- src/agents/survey_agent/env_report.md +348 -0
- src/agents/survey_agent/modules/__init__.py +0 -0
- src/agents/survey_agent/modules/code_collector.py +2194 -0
- src/agents/survey_agent/modules/code_report_generator.py +1282 -0
- src/agents/survey_agent/modules/data_manager.py +1713 -0
- src/agents/survey_agent/modules/database.py +167 -0
- src/agents/survey_agent/modules/fulltext_download_cache.py +462 -0
- src/agents/survey_agent/modules/fulltext_http.py +134 -0
- src/agents/survey_agent/modules/fulltext_resolution.py +749 -0
- src/agents/survey_agent/modules/judge.py +434 -0
- src/agents/survey_agent/modules/outcome_RAG.py +236 -0
- src/agents/survey_agent/modules/paper_graph_retriever.py +1075 -0
- src/agents/survey_agent/modules/pe.py +1729 -0
- src/agents/survey_agent/modules/pseudo_creator.py +782 -0
- src/agents/survey_agent/modules/pseudo_reviser.py +537 -0
- src/agents/survey_agent/modules/refine_agent.py +1952 -0
- src/agents/survey_agent/modules/survey_generator.py +5691 -0
- src/agents/survey_agent/modules/survey_visualizer.py +1817 -0
- src/agents/survey_agent/modules/visual_prompts.py +327 -0
- src/agents/survey_agent/modules/work_analyzer.py +2750 -0
- src/agents/survey_agent/modules/work_collector.py +5649 -0
- src/agents/survey_agent/scripts/baseline_evaluation.py +411 -0
- src/agents/survey_agent/scripts/run_deep_survey.py +224 -0
- src/agents/survey_agent/scripts/run_deep_survey_adapter.py +407 -0
- src/agents/survey_agent/scripts/run_deep_survey_adapter_with_input.py +409 -0
- src/agents/survey_agent/scripts/run_deep_survey_batch.py +228 -0
- src/agents/survey_agent/scripts/run_deep_survey_batch_arg.py +243 -0
- src/agents/survey_agent/scripts/run_deep_survey_batch_settings.py +218 -0
- src/agents/survey_agent/scripts/run_keynotes_gen.py +128 -0
- src/agents/survey_agent/scripts/run_work_clusters.py +140 -0
- src/agents/survey_agent/utils/__init__.py +0 -0
- src/agents/survey_agent/utils/ablation_utils.py +317 -0
- src/agents/survey_agent/utils/api_call.py +2518 -0
- src/agents/survey_agent/utils/chat_utils.py +82 -0
- src/agents/survey_agent/utils/config_utils.py +70 -0
- src/agents/survey_agent/utils/convert_to_md.py +29 -0
- src/agents/survey_agent/utils/err_info.py +24 -0
- src/agents/survey_agent/utils/file_utils.py +176 -0
- src/agents/survey_agent/utils/gpu_utils.py +145 -0
- src/agents/survey_agent/utils/graph_visualizer.py +279 -0
- src/agents/survey_agent/utils/html_utils.py +181 -0
- src/agents/survey_agent/utils/latex_generator_intra_cluster.py +529 -0
- src/agents/survey_agent/utils/latex_generator_relation_table.py +193 -0
- src/agents/survey_agent/utils/mineru_section_packer.py +334 -0
- src/agents/survey_agent/utils/mineru_utils.py +396 -0
- src/agents/survey_agent/utils/paper.py +144 -0
- src/agents/survey_agent/utils/read_yaml.py +15 -0
- src/agents/survey_agent/utils/repo_utils.py +167 -0
- src/agents/survey_agent/utils/rich_logger.py +77 -0
- src/agents/survey_agent/utils/step2v2.py +874 -0
- src/agents/survey_agent/utils/step2v2_extractor.py +856 -0
- src/agents/survey_agent/utils/topic_survey_storage.py +309 -0
- src/agents/survey_agent/utils/utils.py +118 -0
- src/agents/survey_agent/utils/work.py +2 -0
- src/cli.py +1611 -0
- src/config/__init__.py +213 -0
- src/config/default.yaml +1122 -0
- src/harness/LICENSE +21 -0
- src/harness/VENDORED.md +14 -0
- src/harness/src/__init__.py +0 -0
- src/harness/src/openharness/__init__.py +0 -0
- src/harness/src/openharness/__main__.py +6 -0
- src/harness/src/openharness/api/__init__.py +21 -0
- src/harness/src/openharness/api/client.py +281 -0
- src/harness/src/openharness/api/codex_client.py +407 -0
- src/harness/src/openharness/api/copilot_auth.py +240 -0
- src/harness/src/openharness/api/copilot_client.py +134 -0
- src/harness/src/openharness/api/errors.py +19 -0
- src/harness/src/openharness/api/openai_client.py +577 -0
- src/harness/src/openharness/api/provider.py +186 -0
- src/harness/src/openharness/api/registry.py +437 -0
- src/harness/src/openharness/api/usage.py +17 -0
- src/harness/src/openharness/auth/__init__.py +29 -0
- src/harness/src/openharness/auth/external.py +610 -0
- src/harness/src/openharness/auth/flows.py +189 -0
- src/harness/src/openharness/auth/manager.py +482 -0
- src/harness/src/openharness/auth/storage.py +269 -0
- src/harness/src/openharness/autopilot/__init__.py +23 -0
- src/harness/src/openharness/autopilot/service.py +2239 -0
- src/harness/src/openharness/autopilot/types.py +91 -0
- src/harness/src/openharness/bridge/__init__.py +20 -0
- src/harness/src/openharness/bridge/manager.py +106 -0
- src/harness/src/openharness/bridge/session_runner.py +46 -0
- src/harness/src/openharness/bridge/types.py +37 -0
- src/harness/src/openharness/bridge/work_secret.py +41 -0
- src/harness/src/openharness/channels/UPSTREAM +6 -0
- src/harness/src/openharness/channels/__init__.py +22 -0
- src/harness/src/openharness/channels/adapter.py +131 -0
- src/harness/src/openharness/channels/bus/__init__.py +6 -0
- src/harness/src/openharness/channels/bus/events.py +38 -0
- src/harness/src/openharness/channels/bus/queue.py +44 -0
- src/harness/src/openharness/channels/impl/__init__.py +6 -0
- src/harness/src/openharness/channels/impl/base.py +141 -0
- src/harness/src/openharness/channels/impl/dingtalk.py +445 -0
- src/harness/src/openharness/channels/impl/discord.py +311 -0
- src/harness/src/openharness/channels/impl/email.py +410 -0
- src/harness/src/openharness/channels/impl/feishu.py +1342 -0
- src/harness/src/openharness/channels/impl/manager.py +257 -0
- src/harness/src/openharness/channels/impl/matrix.py +700 -0
- src/harness/src/openharness/channels/impl/mochat.py +897 -0
- src/harness/src/openharness/channels/impl/qq.py +141 -0
- src/harness/src/openharness/channels/impl/slack.py +284 -0
- src/harness/src/openharness/channels/impl/telegram.py +525 -0
- src/harness/src/openharness/channels/impl/whatsapp.py +159 -0
- src/harness/src/openharness/cli.py +2551 -0
- src/harness/src/openharness/commands/__init__.py +21 -0
- src/harness/src/openharness/commands/registry.py +2783 -0
- src/harness/src/openharness/config/__init__.py +34 -0
- src/harness/src/openharness/config/paths.py +160 -0
- src/harness/src/openharness/config/schema.py +119 -0
- src/harness/src/openharness/config/settings.py +1104 -0
- src/harness/src/openharness/coordinator/__init__.py +12 -0
- src/harness/src/openharness/coordinator/agent_definitions.py +975 -0
- src/harness/src/openharness/coordinator/coordinator_mode.py +520 -0
- src/harness/src/openharness/engine/__init__.py +80 -0
- src/harness/src/openharness/engine/cost_tracker.py +24 -0
- src/harness/src/openharness/engine/messages.py +222 -0
- src/harness/src/openharness/engine/query.py +1188 -0
- src/harness/src/openharness/engine/query_engine.py +313 -0
- src/harness/src/openharness/engine/stream_events.py +90 -0
- src/harness/src/openharness/hooks/__init__.py +50 -0
- src/harness/src/openharness/hooks/events.py +20 -0
- src/harness/src/openharness/hooks/executor.py +242 -0
- src/harness/src/openharness/hooks/hot_reload.py +31 -0
- src/harness/src/openharness/hooks/loader.py +68 -0
- src/harness/src/openharness/hooks/schemas.py +66 -0
- src/harness/src/openharness/hooks/types.py +38 -0
- src/harness/src/openharness/keybindings/__init__.py +14 -0
- src/harness/src/openharness/keybindings/default_bindings.py +11 -0
- src/harness/src/openharness/keybindings/loader.py +22 -0
- src/harness/src/openharness/keybindings/parser.py +18 -0
- src/harness/src/openharness/keybindings/resolver.py +13 -0
- src/harness/src/openharness/mcp/__init__.py +79 -0
- src/harness/src/openharness/mcp/client.py +298 -0
- src/harness/src/openharness/mcp/config.py +16 -0
- src/harness/src/openharness/mcp/types.py +76 -0
- src/harness/src/openharness/memory/__init__.py +25 -0
- src/harness/src/openharness/memory/agent.py +91 -0
- src/harness/src/openharness/memory/manager.py +183 -0
- src/harness/src/openharness/memory/memdir.py +52 -0
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- src/harness/src/openharness/services/token_estimation.py +15 -0
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- src/harness/src/openharness/skills/_frontmatter.py +97 -0
- src/harness/src/openharness/skills/bundled/__init__.py +75 -0
- src/harness/src/openharness/skills/bundled/content/commit.md +25 -0
- src/harness/src/openharness/skills/bundled/content/debug.md +25 -0
- src/harness/src/openharness/skills/bundled/content/diagnose.md +35 -0
- src/harness/src/openharness/skills/bundled/content/plan.md +39 -0
- src/harness/src/openharness/skills/bundled/content/review.md +33 -0
- src/harness/src/openharness/skills/bundled/content/simplify.md +26 -0
- src/harness/src/openharness/skills/bundled/content/skill-creator.md +175 -0
- src/harness/src/openharness/skills/bundled/content/test.md +38 -0
- src/harness/src/openharness/skills/loader.py +229 -0
- src/harness/src/openharness/skills/registry.py +29 -0
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- src/harness/src/openharness/state/app_state.py +30 -0
- src/harness/src/openharness/state/store.py +40 -0
- src/harness/src/openharness/swarm/__init__.py +70 -0
- src/harness/src/openharness/swarm/in_process.py +693 -0
- src/harness/src/openharness/swarm/lockfile.py +24 -0
- src/harness/src/openharness/swarm/mailbox.py +522 -0
- src/harness/src/openharness/swarm/permission_sync.py +1168 -0
- src/harness/src/openharness/swarm/registry.py +410 -0
- src/harness/src/openharness/swarm/spawn_utils.py +229 -0
- src/harness/src/openharness/swarm/subprocess_backend.py +171 -0
- src/harness/src/openharness/swarm/team_lifecycle.py +910 -0
- src/harness/src/openharness/swarm/types.py +398 -0
- src/harness/src/openharness/swarm/worktree.py +315 -0
- src/harness/src/openharness/tasks/__init__.py +18 -0
- src/harness/src/openharness/tasks/local_agent_task.py +28 -0
- src/harness/src/openharness/tasks/local_shell_task.py +17 -0
- src/harness/src/openharness/tasks/manager.py +475 -0
- src/harness/src/openharness/tasks/stop_task.py +11 -0
- src/harness/src/openharness/tasks/types.py +32 -0
- src/harness/src/openharness/themes/__init__.py +21 -0
- src/harness/src/openharness/themes/builtin.py +89 -0
- src/harness/src/openharness/themes/loader.py +55 -0
- src/harness/src/openharness/themes/schema.py +54 -0
- src/harness/src/openharness/tools/__init__.py +107 -0
- src/harness/src/openharness/tools/agent_tool.py +141 -0
- src/harness/src/openharness/tools/ask_user_question_tool.py +46 -0
- src/harness/src/openharness/tools/base.py +80 -0
- src/harness/src/openharness/tools/bash_tool.py +259 -0
- src/harness/src/openharness/tools/brief_tool.py +33 -0
- src/harness/src/openharness/tools/config_tool.py +54 -0
- src/harness/src/openharness/tools/cron_create_tool.py +105 -0
- src/harness/src/openharness/tools/cron_delete_tool.py +32 -0
- src/harness/src/openharness/tools/cron_list_tool.py +69 -0
- src/harness/src/openharness/tools/cron_toggle_tool.py +37 -0
- src/harness/src/openharness/tools/enter_plan_mode_tool.py +28 -0
- src/harness/src/openharness/tools/enter_worktree_tool.py +80 -0
- src/harness/src/openharness/tools/exit_plan_mode_tool.py +28 -0
- src/harness/src/openharness/tools/exit_worktree_tool.py +42 -0
- src/harness/src/openharness/tools/file_edit_tool.py +95 -0
- src/harness/src/openharness/tools/file_read_tool.py +72 -0
- src/harness/src/openharness/tools/file_write_tool.py +87 -0
- src/harness/src/openharness/tools/glob_tool.py +175 -0
- src/harness/src/openharness/tools/grep_tool.py +374 -0
- src/harness/src/openharness/tools/image_generation_tool.py +447 -0
- src/harness/src/openharness/tools/image_to_text_tool.py +237 -0
- src/harness/src/openharness/tools/list_mcp_resources_tool.py +36 -0
- src/harness/src/openharness/tools/lsp_tool.py +154 -0
- src/harness/src/openharness/tools/mcp_auth_tool.py +71 -0
- src/harness/src/openharness/tools/mcp_tool.py +72 -0
- src/harness/src/openharness/tools/notebook_edit_tool.py +97 -0
- src/harness/src/openharness/tools/read_mcp_resource_tool.py +38 -0
- src/harness/src/openharness/tools/remote_trigger_tool.py +74 -0
- src/harness/src/openharness/tools/send_message_tool.py +58 -0
- src/harness/src/openharness/tools/skill_tool.py +43 -0
- src/harness/src/openharness/tools/sleep_tool.py +32 -0
- src/harness/src/openharness/tools/task_create_tool.py +56 -0
- src/harness/src/openharness/tools/task_get_tool.py +33 -0
- src/harness/src/openharness/tools/task_list_tool.py +35 -0
- src/harness/src/openharness/tools/task_output_tool.py +35 -0
- src/harness/src/openharness/tools/task_stop_tool.py +30 -0
- src/harness/src/openharness/tools/task_update_tool.py +50 -0
- src/harness/src/openharness/tools/team_create_tool.py +31 -0
- src/harness/src/openharness/tools/team_delete_tool.py +30 -0
- src/harness/src/openharness/tools/todo_write_tool.py +46 -0
- src/harness/src/openharness/tools/tool_search_tool.py +38 -0
- src/harness/src/openharness/tools/web_fetch_tool.py +117 -0
- src/harness/src/openharness/tools/web_search_tool.py +119 -0
- src/harness/src/openharness/ui/__init__.py +5 -0
- src/harness/src/openharness/ui/app.py +320 -0
- src/harness/src/openharness/ui/backend_host.py +941 -0
- src/harness/src/openharness/ui/coordinator_drain.py +198 -0
- src/harness/src/openharness/ui/input.py +32 -0
- src/harness/src/openharness/ui/output.py +265 -0
- src/harness/src/openharness/ui/permission_dialog.py +14 -0
- src/harness/src/openharness/ui/protocol.py +247 -0
- src/harness/src/openharness/ui/react_launcher.py +179 -0
- src/harness/src/openharness/ui/runtime.py +799 -0
- src/harness/src/openharness/ui/textual_app.py +495 -0
- src/harness/src/openharness/utils/__init__.py +0 -0
- src/harness/src/openharness/utils/file_lock.py +86 -0
- src/harness/src/openharness/utils/fs.py +98 -0
- src/harness/src/openharness/utils/helpers.py +77 -0
- src/harness/src/openharness/utils/network_guard.py +340 -0
- src/harness/src/openharness/utils/shell.py +147 -0
- src/harness/src/openharness/vim/__init__.py +5 -0
- src/harness/src/openharness/vim/transitions.py +8 -0
- src/harness/src/openharness/voice/__init__.py +7 -0
- src/harness/src/openharness/voice/keyterms.py +10 -0
- src/harness/src/openharness/voice/stream_stt.py +8 -0
- src/harness/src/openharness/voice/voice_mode.py +44 -0
- src/llm/__init__.py +29 -0
- src/llm/image_generation.py +402 -0
- src/llm/provider_registry.py +419 -0
- src/llm/runtime_env.py +64 -0
- src/llm/structured_output.py +131 -0
- src/llm/vision.py +198 -0
- src/memory/__init__.py +2 -0
- src/memory/api/__init__.py +1 -0
- src/memory/api/base_memory_system_api.py +98 -0
- src/memory/api/base_symbolic_memory_system_api.py +190 -0
- src/memory/api/base_vector_memory_system_api.py +116 -0
- src/memory/api/faiss_memory_system_api.py +228 -0
- src/memory/api/slot_process_api.py +827 -0
- src/memory/api/symbolic_memory_system_api.py +572 -0
- src/memory/memory_system/__init__.py +48 -0
- src/memory/memory_system/component_taxonomy.py +430 -0
- src/memory/memory_system/llm.py +437 -0
- src/memory/memory_system/models.py +168 -0
- src/memory/memory_system/user_prompt.py +418 -0
- src/memory/memory_system/utils.py +282 -0
- src/memory/memory_system/vectorstore.py +311 -0
- src/memory/memory_system/working_slot.py +99 -0
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- src/pipeline/contracts.py +531 -0
- src/pipeline/discipline_taxonomy.py +916 -0
- src/pipeline/evidence_coverage_ledger.py +1150 -0
- src/pipeline/evidence_refinement.py +620 -0
- src/pipeline/experiment_to_symbolic.py +137 -0
- src/pipeline/multimodal_evidence/__init__.py +28 -0
- src/pipeline/multimodal_evidence/capabilities.py +107 -0
- src/pipeline/multimodal_evidence/claims.py +135 -0
- src/pipeline/multimodal_evidence/contract.py +291 -0
- src/pipeline/multimodal_evidence/data_sh_compiler.py +505 -0
- src/pipeline/multimodal_evidence/handoff_binding.py +135 -0
- src/pipeline/multimodal_evidence/manifest.py +254 -0
- src/pipeline/multimodal_evidence/native_analysis.py +479 -0
- src/pipeline/multimodal_evidence/perception.py +277 -0
- src/pipeline/multimodal_evidence/query_binding.py +65 -0
- src/pipeline/multimodal_evidence/rendering.py +120 -0
- src/pipeline/multimodal_evidence/safety.py +42 -0
- src/pipeline/multimodal_evidence/sampling.py +69 -0
- src/pipeline/multimodal_evidence/service.py +148 -0
- src/pipeline/multimodal_evidence/survey_integration.py +460 -0
- src/pipeline/paper_identity.py +52 -0
- src/pipeline/research_design_inventory.py +338 -0
- src/pipeline/research_domain_resolution.py +669 -0
- src/pipeline/research_identity.py +548 -0
- src/pipeline/research_question_contract.py +646 -0
- src/pipeline/retrieval_lanes.py +889 -0
- src/pipeline/run_loop.py +862 -0
- src/pipeline/science_events.py +30 -0
- src/pipeline/science_manifests.py +602 -0
- src/pipeline/science_run.py +918 -0
- src/pipeline/science_stages.py +709 -0
- src/pipeline/science_workflow.py +807 -0
- src/pipeline/sh_cluster_projection.py +306 -0
- src/pipeline/sh_graph_provenance.py +648 -0
- src/pipeline/subhypothesis_decomposition.py +392 -0
- src/pipeline/subhypothesis_evidence.py +856 -0
- src/pipeline/survey_evidence_plan.py +858 -0
- src/pipeline/survey_gap_adjudication.py +647 -0
- src/pipeline/survey_gap_candidates.py +840 -0
- src/pipeline/survey_gap_ledger.py +683 -0
- src/pipeline/survey_gap_triage.py +401 -0
- src/pipeline/survey_handoff_persistence.py +481 -0
- src/pipeline/survey_handoff_projection.py +457 -0
- src/pipeline/survey_idea_handoff.py +1112 -0
- src/pipeline/survey_idea_loader.py +289 -0
- src/research_run_ids.py +11 -0
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"""Shared helper functions for MCTS parsing, normalization, fallback logic, and formatting."""
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return bool(_FORBIDDEN_QUERY_TERM_RE.search(normalize_term_scan_text(text)))
|
|
102
|
+
|
|
103
|
+
|
|
104
|
+
def _infer_scope_kind_from_defects(defect_tags: Sequence[str]) -> str:
|
|
105
|
+
counts = {scope_kind: 0 for scope_kind in _SCOPE_KIND_BY_DEFECT}
|
|
106
|
+
for defect in defect_tags or []:
|
|
107
|
+
normalized = str(defect).strip().lower()
|
|
108
|
+
if not normalized:
|
|
109
|
+
continue
|
|
110
|
+
for scope_kind, tagged_defects in _SCOPE_KIND_BY_DEFECT.items():
|
|
111
|
+
if normalized in tagged_defects:
|
|
112
|
+
counts[scope_kind] += 1
|
|
113
|
+
break
|
|
114
|
+
|
|
115
|
+
ranked = [
|
|
116
|
+
(count, _SCOPE_KIND_PRIORITY[scope_kind], scope_kind)
|
|
117
|
+
for scope_kind, count in counts.items()
|
|
118
|
+
if count > 0
|
|
119
|
+
]
|
|
120
|
+
if not ranked:
|
|
121
|
+
return ""
|
|
122
|
+
return max(ranked)[2]
|
|
123
|
+
|
|
124
|
+
|
|
125
|
+
def build_structural_profile(
|
|
126
|
+
parent_state: Any,
|
|
127
|
+
*,
|
|
128
|
+
refinement_scope: str,
|
|
129
|
+
mature_idea: str,
|
|
130
|
+
defect_tags: Sequence[str] = (),
|
|
131
|
+
profile_id: str = "generic_scientific",
|
|
132
|
+
) -> Dict[str, Any]:
|
|
133
|
+
normalized_profile = str(profile_id or "generic_scientific").strip().lower()
|
|
134
|
+
scope_text = normalize_term_scan_text(refinement_scope or "")
|
|
135
|
+
component_names = [
|
|
136
|
+
normalize_term_scan_text(component)
|
|
137
|
+
for component in parent_state.components
|
|
138
|
+
if str(component).strip()
|
|
139
|
+
]
|
|
140
|
+
parent_text = normalize_term_scan_text(_parent_state_text(parent_state))
|
|
141
|
+
if scope_text and any(name and name in scope_text for name in component_names):
|
|
142
|
+
scope_kind = "existing_component"
|
|
143
|
+
elif normalized_profile == "computational_algorithmic" and scope_text and _BROAD_ARCHITECTURE_SCOPE_RE.search(scope_text):
|
|
144
|
+
scope_kind = "broad_architecture"
|
|
145
|
+
elif normalized_profile == "computational_algorithmic" and scope_text and _EXECUTION_PATH_SCOPE_RE.search(scope_text):
|
|
146
|
+
scope_kind = "execution_path"
|
|
147
|
+
elif scope_text:
|
|
148
|
+
scope_kind = "existing_subsystem"
|
|
149
|
+
else:
|
|
150
|
+
defect_scope_kind = (
|
|
151
|
+
_infer_scope_kind_from_defects(defect_tags)
|
|
152
|
+
if normalized_profile == "computational_algorithmic"
|
|
153
|
+
else ""
|
|
154
|
+
)
|
|
155
|
+
if defect_scope_kind:
|
|
156
|
+
scope_kind = defect_scope_kind
|
|
157
|
+
elif normalized_profile == "computational_algorithmic" and _MULTI_PATH_SHAPE_RE.search(parent_text):
|
|
158
|
+
scope_kind = "execution_path"
|
|
159
|
+
else:
|
|
160
|
+
scope_kind = "existing_subsystem"
|
|
161
|
+
native_structure = "scientific_object_relation"
|
|
162
|
+
if normalized_profile == "computational_algorithmic":
|
|
163
|
+
native_structure = (
|
|
164
|
+
"multi_path_algorithmic_structure"
|
|
165
|
+
if _MULTI_PATH_SHAPE_RE.search(parent_text)
|
|
166
|
+
else "algorithmic_subsystem"
|
|
167
|
+
)
|
|
168
|
+
elif normalized_profile == "formal_theoretical":
|
|
169
|
+
native_structure = "assumption_proposition_proof_structure"
|
|
170
|
+
elif normalized_profile in {"clinical_health", "life_molecular_mechanistic"}:
|
|
171
|
+
native_structure = "intervention_mechanism_measurement_structure"
|
|
172
|
+
elif normalized_profile in {"physical_materials_chemical", "earth_environment_agro"}:
|
|
173
|
+
native_structure = "condition_process_observation_structure"
|
|
174
|
+
return {
|
|
175
|
+
"profile_id": normalized_profile,
|
|
176
|
+
"native_structure": native_structure,
|
|
177
|
+
"control_centered": bool(
|
|
178
|
+
normalized_profile == "computational_algorithmic"
|
|
179
|
+
and parent_centers_control_surface(parent_state)
|
|
180
|
+
),
|
|
181
|
+
"has_multi_path_shape": bool(
|
|
182
|
+
normalized_profile == "computational_algorithmic"
|
|
183
|
+
and _MULTI_PATH_SHAPE_RE.search(parent_text)
|
|
184
|
+
),
|
|
185
|
+
"scope_kind": scope_kind,
|
|
186
|
+
"training_free_like": bool(
|
|
187
|
+
normalized_profile == "computational_algorithmic"
|
|
188
|
+
and _TRAINING_FREE_RE.search(normalize_term_scan_text(mature_idea or parent_state.method))
|
|
189
|
+
),
|
|
190
|
+
}
|
|
191
|
+
|
|
192
|
+
|
|
193
|
+
def format_analysis_blob(analysis: List[Any]) -> str:
|
|
194
|
+
return format_analysis_prompt_view(analysis)
|
|
195
|
+
|
|
196
|
+
|
|
197
|
+
def clip_text(value: Any, limit: int = 800) -> str:
|
|
198
|
+
text = "" if value is None else str(value).strip()
|
|
199
|
+
if limit <= 0:
|
|
200
|
+
return text
|
|
201
|
+
if len(text) <= limit:
|
|
202
|
+
return text
|
|
203
|
+
return text[: max(1, limit - 1)] + "..."
|
|
204
|
+
|
|
205
|
+
|
|
206
|
+
def clip_metric_score(value: Any, *, lower: float = 0.0, upper: float = 5.0) -> float:
|
|
207
|
+
return max(lower, min(upper, _safe_float_default(value, lower)))
|
|
208
|
+
|
|
209
|
+
|
|
210
|
+
def coerce_integer_metric_score(
|
|
211
|
+
value: Any,
|
|
212
|
+
*,
|
|
213
|
+
lower: int = 0,
|
|
214
|
+
upper: int = 5,
|
|
215
|
+
) -> int:
|
|
216
|
+
clipped = clip_metric_score(value, lower=float(lower), upper=float(upper))
|
|
217
|
+
return max(lower, min(upper, int(round(clipped))))
|
|
218
|
+
|
|
219
|
+
|
|
220
|
+
def normalize_score_weights(
|
|
221
|
+
weights: Dict[str, Any],
|
|
222
|
+
fields: Sequence[str],
|
|
223
|
+
) -> Dict[str, float]:
|
|
224
|
+
cleaned: Dict[str, float] = {}
|
|
225
|
+
for field_name in fields:
|
|
226
|
+
try:
|
|
227
|
+
cleaned[field_name] = max(0.0, float(weights.get(field_name, 0.0)))
|
|
228
|
+
except (TypeError, ValueError):
|
|
229
|
+
cleaned[field_name] = 0.0
|
|
230
|
+
|
|
231
|
+
total = sum(cleaned.values())
|
|
232
|
+
if total <= 1e-9:
|
|
233
|
+
uniform = 1.0 / max(len(fields), 1)
|
|
234
|
+
return {field_name: uniform for field_name in fields}
|
|
235
|
+
return {field_name: value / total for field_name, value in cleaned.items()}
|
|
236
|
+
|
|
237
|
+
|
|
238
|
+
def apply_normalized_score_weights(target: Any, fields: Sequence[str]) -> None:
|
|
239
|
+
normalized = normalize_score_weights(
|
|
240
|
+
{field_name: getattr(target, field_name, 0.0) for field_name in fields},
|
|
241
|
+
fields,
|
|
242
|
+
)
|
|
243
|
+
for field_name, value in normalized.items():
|
|
244
|
+
setattr(target, field_name, value)
|
|
245
|
+
|
|
246
|
+
|
|
247
|
+
def _normalize_root_domains(items: Sequence[str]) -> List[str]:
|
|
248
|
+
ordered: List[str] = []
|
|
249
|
+
seen: Set[str] = set()
|
|
250
|
+
for item in items:
|
|
251
|
+
canonical_key = canonicalize_discipline_key(item)
|
|
252
|
+
if not canonical_key or canonical_key in seen:
|
|
253
|
+
continue
|
|
254
|
+
seen.add(canonical_key)
|
|
255
|
+
ordered.append(canonical_key)
|
|
256
|
+
return ordered[:2]
|
|
257
|
+
|
|
258
|
+
|
|
259
|
+
def _format_root_domains_for_prompt(domains: Sequence[str]) -> str:
|
|
260
|
+
normalized = _normalize_root_domains(domains)
|
|
261
|
+
if not normalized:
|
|
262
|
+
return "Unspecified"
|
|
263
|
+
return ", ".join(
|
|
264
|
+
f"{key} ({ROOT_DOMAIN_CATALOG[key]})"
|
|
265
|
+
for key in normalized
|
|
266
|
+
)
|
|
267
|
+
|
|
268
|
+
|
|
269
|
+
def _infer_root_domains_heuristically(topic: str, text: str) -> List[str]:
|
|
270
|
+
resolution = resolve_discipline_taxonomy(topic, query=text)
|
|
271
|
+
return _normalize_root_domains(resolution.get("discipline_ids") or [])
|
|
272
|
+
|
|
273
|
+
def _humanize_component_name(component: str) -> str:
|
|
274
|
+
raw = str(component).strip()
|
|
275
|
+
if not raw:
|
|
276
|
+
return "component"
|
|
277
|
+
raw = re.sub(r"([a-z0-9])([A-Z])", r"\1 \2", raw)
|
|
278
|
+
raw = re.sub(r"[^A-Za-z0-9]+", " ", raw)
|
|
279
|
+
tokens = [token for token in raw.split() if token]
|
|
280
|
+
return " ".join(tokens) if tokens else "component"
|
|
281
|
+
|
|
282
|
+
|
|
283
|
+
def _coerce_component_name(value: Any) -> str:
|
|
284
|
+
if value is None:
|
|
285
|
+
return ""
|
|
286
|
+
if isinstance(value, str):
|
|
287
|
+
return value.strip()
|
|
288
|
+
if isinstance(value, dict):
|
|
289
|
+
preferred_keys = ("component", "name", "target", "value", "label", "title", "id")
|
|
290
|
+
for key in preferred_keys:
|
|
291
|
+
text = _coerce_component_name(value.get(key))
|
|
292
|
+
if text:
|
|
293
|
+
return text
|
|
294
|
+
for item in value.values():
|
|
295
|
+
text = _coerce_component_name(item)
|
|
296
|
+
if text:
|
|
297
|
+
return text
|
|
298
|
+
return ""
|
|
299
|
+
if isinstance(value, (list, tuple, set)):
|
|
300
|
+
for item in value:
|
|
301
|
+
text = _coerce_component_name(item)
|
|
302
|
+
if text:
|
|
303
|
+
return text
|
|
304
|
+
return ""
|
|
305
|
+
return str(value).strip()
|
|
306
|
+
|
|
307
|
+
|
|
308
|
+
def _normalize_component_mapping(raw_mapping: Any) -> Dict[str, str]:
|
|
309
|
+
if not isinstance(raw_mapping, dict):
|
|
310
|
+
return {}
|
|
311
|
+
|
|
312
|
+
normalized: Dict[str, str] = {}
|
|
313
|
+
for raw_key, raw_value in raw_mapping.items():
|
|
314
|
+
key = _coerce_component_name(raw_key)
|
|
315
|
+
value = _coerce_component_name(raw_value)
|
|
316
|
+
if key and value:
|
|
317
|
+
normalized[key] = value
|
|
318
|
+
return normalized
|
|
319
|
+
|
|
320
|
+
|
|
321
|
+
def _extract_component_mapping_keys_from_plan(plan: Any) -> List[str]:
|
|
322
|
+
ordered: List[str] = []
|
|
323
|
+
seen: Set[str] = set()
|
|
324
|
+
for edit in getattr(plan, "component_edits", []) or []:
|
|
325
|
+
for raw_name in (
|
|
326
|
+
getattr(edit, "component", ""),
|
|
327
|
+
getattr(edit, "target", ""),
|
|
328
|
+
):
|
|
329
|
+
name = _coerce_component_name(raw_name)
|
|
330
|
+
lowered = name.lower()
|
|
331
|
+
if not name or lowered in seen:
|
|
332
|
+
continue
|
|
333
|
+
seen.add(lowered)
|
|
334
|
+
ordered.append(name)
|
|
335
|
+
return ordered
|
|
336
|
+
|
|
337
|
+
|
|
338
|
+
def _filter_component_mapping_to_plan_keys(raw_mapping: Any, plan: Any) -> Dict[str, str]:
|
|
339
|
+
normalized = _normalize_component_mapping(raw_mapping)
|
|
340
|
+
allowed_keys = {
|
|
341
|
+
key.lower()
|
|
342
|
+
for key in _extract_component_mapping_keys_from_plan(plan)
|
|
343
|
+
if str(key).strip()
|
|
344
|
+
}
|
|
345
|
+
if not allowed_keys:
|
|
346
|
+
return {}
|
|
347
|
+
return {
|
|
348
|
+
key: value
|
|
349
|
+
for key, value in normalized.items()
|
|
350
|
+
if key.lower() in allowed_keys
|
|
351
|
+
}
|
|
352
|
+
|
|
353
|
+
|
|
354
|
+
def _clean_component_explanation(explanation: Any, fallback_component: str) -> str:
|
|
355
|
+
fallback_label = _humanize_component_name(fallback_component)
|
|
356
|
+
|
|
357
|
+
def _flatten(value: Any) -> str:
|
|
358
|
+
if value is None:
|
|
359
|
+
return ""
|
|
360
|
+
if isinstance(value, str):
|
|
361
|
+
return value
|
|
362
|
+
if isinstance(value, dict):
|
|
363
|
+
preferred_keys = (
|
|
364
|
+
"explanation",
|
|
365
|
+
"description",
|
|
366
|
+
"summary",
|
|
367
|
+
"detail",
|
|
368
|
+
"details",
|
|
369
|
+
"role",
|
|
370
|
+
"rationale",
|
|
371
|
+
"purpose",
|
|
372
|
+
)
|
|
373
|
+
ordered_chunks: List[str] = []
|
|
374
|
+
seen_chunks: Set[str] = set()
|
|
375
|
+
for key in preferred_keys:
|
|
376
|
+
raw = value.get(key)
|
|
377
|
+
text = _flatten(raw).strip()
|
|
378
|
+
norm = text.lower()
|
|
379
|
+
if text and norm not in seen_chunks:
|
|
380
|
+
ordered_chunks.append(text)
|
|
381
|
+
seen_chunks.add(norm)
|
|
382
|
+
if ordered_chunks:
|
|
383
|
+
return " ".join(ordered_chunks)
|
|
384
|
+
return compact_json(value)
|
|
385
|
+
if isinstance(value, (list, tuple, set)):
|
|
386
|
+
parts: List[str] = []
|
|
387
|
+
seen_parts: Set[str] = set()
|
|
388
|
+
for item in value:
|
|
389
|
+
text = _flatten(item).strip()
|
|
390
|
+
norm = text.lower()
|
|
391
|
+
if text and norm not in seen_parts:
|
|
392
|
+
parts.append(text)
|
|
393
|
+
seen_parts.add(norm)
|
|
394
|
+
return " ".join(parts)
|
|
395
|
+
return str(value)
|
|
396
|
+
|
|
397
|
+
text = _flatten(explanation).strip()
|
|
398
|
+
placeholder_values = {
|
|
399
|
+
"",
|
|
400
|
+
"n/a",
|
|
401
|
+
"na",
|
|
402
|
+
"none",
|
|
403
|
+
"null",
|
|
404
|
+
"unknown",
|
|
405
|
+
"unspecified",
|
|
406
|
+
"not provided",
|
|
407
|
+
"no explanation",
|
|
408
|
+
"no explanation provided",
|
|
409
|
+
"no specific explanation provided",
|
|
410
|
+
"tbd",
|
|
411
|
+
}
|
|
412
|
+
if text.lower() in placeholder_values:
|
|
413
|
+
return f"No specific explanation provided for {fallback_label}."
|
|
414
|
+
|
|
415
|
+
text = re.sub(r"\s+", " ", text)
|
|
416
|
+
text = text.strip(" \t\r\n-*:;,.")
|
|
417
|
+
text = re.sub(r"^['\"`]+|['\"`]+$", "", text).strip()
|
|
418
|
+
|
|
419
|
+
prefix_patterns = [
|
|
420
|
+
rf"^{re.escape(str(fallback_component).strip())}\s*[:\-]\s*",
|
|
421
|
+
rf"^{re.escape(fallback_label)}\s*[:\-]\s*",
|
|
422
|
+
r"^(component|module|role|purpose|description|explanation)\s*[:\-]\s*",
|
|
423
|
+
]
|
|
424
|
+
for pattern in prefix_patterns:
|
|
425
|
+
text = re.sub(pattern, "", text, flags=re.IGNORECASE).strip()
|
|
426
|
+
|
|
427
|
+
if not text:
|
|
428
|
+
return f"No specific explanation provided for {fallback_label}."
|
|
429
|
+
|
|
430
|
+
text = clip_text(text, limit=3000)
|
|
431
|
+
if text[-1] not in ".!?":
|
|
432
|
+
text += "."
|
|
433
|
+
return text
|
|
434
|
+
|
|
435
|
+
|
|
436
|
+
def normalize_component_explanations(
|
|
437
|
+
components: Sequence[str],
|
|
438
|
+
raw_explanations: Any,
|
|
439
|
+
) -> Dict[str, str]:
|
|
440
|
+
normalized_components: List[str] = []
|
|
441
|
+
seen: Set[str] = set()
|
|
442
|
+
for component in components:
|
|
443
|
+
name = str(component).strip()
|
|
444
|
+
if not name or name.lower() in seen:
|
|
445
|
+
continue
|
|
446
|
+
seen.add(name.lower())
|
|
447
|
+
normalized_components.append(name)
|
|
448
|
+
|
|
449
|
+
lookup: Dict[str, str] = {}
|
|
450
|
+
if isinstance(raw_explanations, dict):
|
|
451
|
+
for key, value in raw_explanations.items():
|
|
452
|
+
name = str(key).strip()
|
|
453
|
+
if not name:
|
|
454
|
+
continue
|
|
455
|
+
lookup[name] = _clean_component_explanation(value, fallback_component=name)
|
|
456
|
+
elif isinstance(raw_explanations, list):
|
|
457
|
+
for item in raw_explanations:
|
|
458
|
+
if not isinstance(item, dict):
|
|
459
|
+
continue
|
|
460
|
+
name = str(item.get("component") or item.get("name") or "").strip()
|
|
461
|
+
if not name:
|
|
462
|
+
continue
|
|
463
|
+
lookup[name] = _clean_component_explanation(
|
|
464
|
+
item.get("explanation", ""),
|
|
465
|
+
fallback_component=name,
|
|
466
|
+
)
|
|
467
|
+
|
|
468
|
+
return {
|
|
469
|
+
component: lookup.get(component, _clean_component_explanation("", fallback_component=component))
|
|
470
|
+
for component in normalized_components
|
|
471
|
+
}
|
|
472
|
+
|
|
473
|
+
|
|
474
|
+
def component_inventory_payload(
|
|
475
|
+
components: Sequence[str],
|
|
476
|
+
component_explanations: Any,
|
|
477
|
+
) -> List[Dict[str, str]]:
|
|
478
|
+
normalized = normalize_component_explanations(components, component_explanations)
|
|
479
|
+
return [
|
|
480
|
+
{
|
|
481
|
+
"component": component,
|
|
482
|
+
"explanation": normalized.get(component, _clean_component_explanation("", component)),
|
|
483
|
+
}
|
|
484
|
+
for component in normalized
|
|
485
|
+
]
|
|
486
|
+
|
|
487
|
+
|
|
488
|
+
def parse_component_bundle_payload(
|
|
489
|
+
payload: Any,
|
|
490
|
+
*,
|
|
491
|
+
max_components: int,
|
|
492
|
+
) -> Tuple[List[str], Dict[str, str]]:
|
|
493
|
+
if not isinstance(payload, dict):
|
|
494
|
+
return [], {}
|
|
495
|
+
|
|
496
|
+
raw_components = payload.get("components", [])
|
|
497
|
+
ordered_components: List[str] = []
|
|
498
|
+
explanations: Dict[str, str] = {}
|
|
499
|
+
seen: Set[str] = set()
|
|
500
|
+
|
|
501
|
+
if isinstance(raw_components, list):
|
|
502
|
+
for item in raw_components:
|
|
503
|
+
if len(ordered_components) >= max_components:
|
|
504
|
+
break
|
|
505
|
+
if isinstance(item, dict):
|
|
506
|
+
name = str(item.get("name") or item.get("component") or "").strip()
|
|
507
|
+
explanation = item.get("explanation", "")
|
|
508
|
+
else:
|
|
509
|
+
name = str(item).strip()
|
|
510
|
+
explanation = ""
|
|
511
|
+
key = name.lower()
|
|
512
|
+
if not name or key in seen:
|
|
513
|
+
continue
|
|
514
|
+
seen.add(key)
|
|
515
|
+
ordered_components.append(name)
|
|
516
|
+
if explanation:
|
|
517
|
+
explanations[name] = _clean_component_explanation(
|
|
518
|
+
explanation,
|
|
519
|
+
fallback_component=name,
|
|
520
|
+
)
|
|
521
|
+
|
|
522
|
+
external_explanations = normalize_component_explanations(
|
|
523
|
+
ordered_components,
|
|
524
|
+
payload.get("component_explanations"),
|
|
525
|
+
)
|
|
526
|
+
explanations = {
|
|
527
|
+
component: explanations.get(component)
|
|
528
|
+
or external_explanations.get(component)
|
|
529
|
+
or _clean_component_explanation("", fallback_component=component)
|
|
530
|
+
for component in ordered_components
|
|
531
|
+
}
|
|
532
|
+
return ordered_components, explanations
|
|
533
|
+
|
|
534
|
+
|
|
535
|
+
def _dedupe_keep_order_strings(items: Sequence[str]) -> List[str]:
|
|
536
|
+
seen: Set[str] = set()
|
|
537
|
+
ordered: List[str] = []
|
|
538
|
+
for item in items:
|
|
539
|
+
text = str(item).strip()
|
|
540
|
+
key = text.lower()
|
|
541
|
+
if not text or key in seen:
|
|
542
|
+
continue
|
|
543
|
+
seen.add(key)
|
|
544
|
+
ordered.append(text)
|
|
545
|
+
return ordered
|
|
546
|
+
|
|
547
|
+
def _safe_float_default(value: Any, fallback: float = 0.0) -> float:
|
|
548
|
+
try:
|
|
549
|
+
return float(value)
|
|
550
|
+
except (TypeError, ValueError):
|
|
551
|
+
return fallback
|
|
552
|
+
|
|
553
|
+
|
|
554
|
+
def normalize_theory_transfer_query_payload(
|
|
555
|
+
payload: Any,
|
|
556
|
+
*,
|
|
557
|
+
fallback: Dict[str, str],
|
|
558
|
+
clip_limit: int,
|
|
559
|
+
) -> Dict[str, str]:
|
|
560
|
+
if not isinstance(payload, dict):
|
|
561
|
+
return fallback
|
|
562
|
+
|
|
563
|
+
query = clip_text(str(payload.get("query") or "").strip(), clip_limit)
|
|
564
|
+
needed_content = clip_text(str(payload.get("needed_content") or "").strip(), clip_limit)
|
|
565
|
+
expected_role = clip_text(str(payload.get("expected_role") or "").strip(), clip_limit)
|
|
566
|
+
if not query:
|
|
567
|
+
return fallback
|
|
568
|
+
return {
|
|
569
|
+
"query": query,
|
|
570
|
+
"needed_content": needed_content or fallback["needed_content"],
|
|
571
|
+
"expected_role": expected_role or fallback["expected_role"],
|
|
572
|
+
}
|
|
573
|
+
|
|
574
|
+
|
|
575
|
+
def normalize_mechanism_commit_query_payload(
|
|
576
|
+
payload: Any,
|
|
577
|
+
*,
|
|
578
|
+
fallback: Dict[str, str],
|
|
579
|
+
clip_limit: int,
|
|
580
|
+
) -> Dict[str, str]:
|
|
581
|
+
if not isinstance(payload, dict):
|
|
582
|
+
return fallback
|
|
583
|
+
|
|
584
|
+
query = clip_text(str(payload.get("query") or "").strip(), clip_limit)
|
|
585
|
+
mechanism_gap = clip_text(str(payload.get("mechanism_gap") or "").strip(), clip_limit)
|
|
586
|
+
expected_role = clip_text(str(payload.get("expected_role") or "").strip(), clip_limit)
|
|
587
|
+
if not query:
|
|
588
|
+
return fallback
|
|
589
|
+
return {
|
|
590
|
+
"query": query,
|
|
591
|
+
"mechanism_gap": mechanism_gap or fallback["mechanism_gap"],
|
|
592
|
+
"expected_role": expected_role or fallback["expected_role"],
|
|
593
|
+
}
|
|
594
|
+
|
|
595
|
+
|
|
596
|
+
def format_theory_transfer_references(
|
|
597
|
+
query_payload: Dict[str, str],
|
|
598
|
+
hits: Sequence[Dict[str, Any]],
|
|
599
|
+
*,
|
|
600
|
+
clip_limit: int,
|
|
601
|
+
) -> str:
|
|
602
|
+
if not hits:
|
|
603
|
+
return "None"
|
|
604
|
+
lines = [
|
|
605
|
+
f"Transfer need: {query_payload.get('needed_content') or 'Unspecified'}",
|
|
606
|
+
f"Expected role: {query_payload.get('expected_role') or 'Unspecified'}",
|
|
607
|
+
"Cross-domain core references:",
|
|
608
|
+
]
|
|
609
|
+
for idx, hit in enumerate(hits, start=1):
|
|
610
|
+
core_node = hit.get("core_node") if isinstance(hit.get("core_node"), dict) else {}
|
|
611
|
+
label = (
|
|
612
|
+
core_node.get("full_name")
|
|
613
|
+
or core_node.get("paper_title")
|
|
614
|
+
or hit.get("node_id")
|
|
615
|
+
or f"core_{idx}"
|
|
616
|
+
)
|
|
617
|
+
paper_title = str(core_node.get("paper_title") or "").strip()
|
|
618
|
+
paper_domain = str(core_node.get("paper_domain") or "").strip() or "unknown"
|
|
619
|
+
lines.append(
|
|
620
|
+
f"{idx}. {label} | domain={paper_domain} | score={float(hit.get('score') or 0.0):.3f}"
|
|
621
|
+
)
|
|
622
|
+
if paper_title:
|
|
623
|
+
lines.append(f" paper: {clip_text(paper_title, clip_limit)}")
|
|
624
|
+
summary = clip_text(str(core_node.get("summary") or "").strip(), clip_limit)
|
|
625
|
+
insight = clip_text(str(core_node.get("insight") or "").strip(), clip_limit)
|
|
626
|
+
if summary:
|
|
627
|
+
lines.append(f" summary: {summary}")
|
|
628
|
+
if insight:
|
|
629
|
+
lines.append(f" insight: {insight}")
|
|
630
|
+
matched_components = (
|
|
631
|
+
hit.get("matched_components") if isinstance(hit.get("matched_components"), list) else []
|
|
632
|
+
)
|
|
633
|
+
for matched in matched_components[:2]:
|
|
634
|
+
component_name = clip_text(
|
|
635
|
+
str(matched.get("component_name") or "").strip(),
|
|
636
|
+
clip_limit,
|
|
637
|
+
)
|
|
638
|
+
component_summary = clip_text(
|
|
639
|
+
str(matched.get("component_summary") or "").strip(),
|
|
640
|
+
clip_limit,
|
|
641
|
+
)
|
|
642
|
+
if component_name or component_summary:
|
|
643
|
+
lines.append(
|
|
644
|
+
f" matched_component: {component_name or 'unknown'} | {component_summary}"
|
|
645
|
+
)
|
|
646
|
+
lines.append(
|
|
647
|
+
"Use these nodes only as references for transferable mechanisms. Do not copy them verbatim and do not change the root domain(s)."
|
|
648
|
+
)
|
|
649
|
+
return "\n".join(lines)
|
|
650
|
+
|
|
651
|
+
|
|
652
|
+
def format_mechanism_commit_references(
|
|
653
|
+
query_payload: Dict[str, str],
|
|
654
|
+
hits: Sequence[Dict[str, Any]],
|
|
655
|
+
*,
|
|
656
|
+
clip_limit: int,
|
|
657
|
+
) -> str:
|
|
658
|
+
if not hits:
|
|
659
|
+
return "None"
|
|
660
|
+
lines = [
|
|
661
|
+
f"Mechanism gap: {query_payload.get('mechanism_gap') or 'Unspecified'}",
|
|
662
|
+
f"Expected role: {query_payload.get('expected_role') or 'Unspecified'}",
|
|
663
|
+
"Retrieved core references for mechanism grounding:",
|
|
664
|
+
]
|
|
665
|
+
for idx, hit in enumerate(hits, start=1):
|
|
666
|
+
core_node = hit.get("core_node") if isinstance(hit.get("core_node"), dict) else {}
|
|
667
|
+
label = (
|
|
668
|
+
core_node.get("full_name")
|
|
669
|
+
or core_node.get("paper_title")
|
|
670
|
+
or hit.get("node_id")
|
|
671
|
+
or f"core_{idx}"
|
|
672
|
+
)
|
|
673
|
+
paper_title = str(core_node.get("paper_title") or "").strip()
|
|
674
|
+
paper_domain = str(core_node.get("paper_domain") or "").strip() or "unknown"
|
|
675
|
+
lines.append(
|
|
676
|
+
f"{idx}. {label} | domain={paper_domain} | score={float(hit.get('score') or 0.0):.3f}"
|
|
677
|
+
)
|
|
678
|
+
if paper_title:
|
|
679
|
+
lines.append(f" paper: {clip_text(paper_title, clip_limit)}")
|
|
680
|
+
summary = clip_text(str(core_node.get("summary") or "").strip(), clip_limit)
|
|
681
|
+
insight = clip_text(str(core_node.get("insight") or "").strip(), clip_limit)
|
|
682
|
+
if summary:
|
|
683
|
+
lines.append(f" summary: {summary}")
|
|
684
|
+
if insight:
|
|
685
|
+
lines.append(f" insight: {insight}")
|
|
686
|
+
matched_components = (
|
|
687
|
+
hit.get("matched_components") if isinstance(hit.get("matched_components"), list) else []
|
|
688
|
+
)
|
|
689
|
+
for matched in matched_components[:2]:
|
|
690
|
+
component_name = clip_text(
|
|
691
|
+
str(matched.get("component_name") or "").strip(),
|
|
692
|
+
clip_limit,
|
|
693
|
+
)
|
|
694
|
+
component_summary = clip_text(
|
|
695
|
+
str(matched.get("component_summary") or "").strip(),
|
|
696
|
+
clip_limit,
|
|
697
|
+
)
|
|
698
|
+
if component_name or component_summary:
|
|
699
|
+
lines.append(
|
|
700
|
+
f" matched_component: {component_name or 'unknown'} | {component_summary}"
|
|
701
|
+
)
|
|
702
|
+
lines.append(
|
|
703
|
+
"Use these nodes to ground the concrete mechanism choice and execution path details."
|
|
704
|
+
)
|
|
705
|
+
lines.append(
|
|
706
|
+
"Use them as grounding patterns, not as modules to copy verbatim."
|
|
707
|
+
)
|
|
708
|
+
return "\n".join(lines)
|
|
709
|
+
|
|
710
|
+
|
|
711
|
+
def plan_to_method_text(plan: Any) -> str:
|
|
712
|
+
lines: List[str] = []
|
|
713
|
+
for idx, edit in enumerate(getattr(plan, "component_edits", []) or [], start=1):
|
|
714
|
+
op = getattr(getattr(edit, "op", None), "value", getattr(edit, "op", ""))
|
|
715
|
+
target = f" -> {getattr(edit, 'target', '')}" if getattr(edit, "target", "") else ""
|
|
716
|
+
condition = (
|
|
717
|
+
f" [condition: {getattr(edit, 'condition', '')}]"
|
|
718
|
+
if getattr(edit, "condition", "")
|
|
719
|
+
else ""
|
|
720
|
+
)
|
|
721
|
+
details = f"; {getattr(edit, 'details', '')}" if getattr(edit, "details", "") else ""
|
|
722
|
+
lines.append(f"{idx}. {op}({getattr(edit, 'component', '')}{target}){condition}{details}")
|
|
723
|
+
return "\n".join(lines)
|
|
724
|
+
|
|
725
|
+
|
|
726
|
+
def plan_to_experiment_text(plan: Any) -> str:
|
|
727
|
+
blocks: List[str] = []
|
|
728
|
+
validation = getattr(plan, "validation", None)
|
|
729
|
+
regression_tests = getattr(validation, "regression_tests", []) if validation else []
|
|
730
|
+
ablation_tests = getattr(validation, "ablation_tests", []) if validation else []
|
|
731
|
+
stress_tests = getattr(validation, "stress_tests", []) if validation else []
|
|
732
|
+
if regression_tests:
|
|
733
|
+
blocks.append("Regression:\n- " + "\n- ".join(regression_tests))
|
|
734
|
+
if ablation_tests:
|
|
735
|
+
blocks.append("Ablation:\n- " + "\n- ".join(ablation_tests))
|
|
736
|
+
if stress_tests:
|
|
737
|
+
blocks.append("Stress:\n- " + "\n- ".join(stress_tests))
|
|
738
|
+
return "\n\n".join(blocks)
|