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/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
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- src/memory/api/slot_process_api.py +827 -0
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- 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
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- src/pipeline/sh_cluster_projection.py +306 -0
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- 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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"""Build mature-idea portfolios from heterogeneous sources and scoped evidence."""
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from __future__ import annotations
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from copy import deepcopy
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from itertools import combinations
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from typing import Any, Dict, Iterable, List, Mapping, Sequence
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from src.agents.idea_agent.utils.workflow.idea_contract import (
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normalize_mature_ideas,
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)
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from src.agents.idea_agent.utils.workflow.idea_diversity import (
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filter_independent_mature_ideas,
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)
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"survey_gap": "survey_gap",
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"history": "prior_candidate",
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"prior": "prior_candidate",
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"prior_candidate": "prior_candidate",
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"experiment": "experiment_feedback",
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"experiment_feedback": "experiment_feedback",
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"generated": "problem_reframing",
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"problem_reframing": "problem_reframing",
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"adversarial": "adversarial_generation",
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"user": "user_input",
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source = _canonical_source(source)
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lineage = lineage if lineage is not None else source
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record["idea_source"] = source
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record["lineage"] = lineage
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record["source_lineage"] = [{"idea_source": source, "lineage": deepcopy(lineage)}]
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return record
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107
|
+
|
|
108
|
+
def _gap_rows(survey_handoff: Any, gap_triage: Any = None) -> List[Dict[str, Any]]:
|
|
109
|
+
handoff = survey_handoff if isinstance(survey_handoff, Mapping) else {}
|
|
110
|
+
triage_candidate = gap_triage if isinstance(gap_triage, Mapping) else handoff.get("gap_triage")
|
|
111
|
+
triage = dict(triage_candidate) if isinstance(triage_candidate, Mapping) else {}
|
|
112
|
+
triage_by_id = {
|
|
113
|
+
_text(row.get("gap_id")): row
|
|
114
|
+
for row in _list(triage.get("gaps"))
|
|
115
|
+
if isinstance(row, Mapping) and _text(row.get("gap_id"))
|
|
116
|
+
}
|
|
117
|
+
rows: List[Dict[str, Any]] = []
|
|
118
|
+
for row in _list(handoff.get("gaps")):
|
|
119
|
+
if not isinstance(row, Mapping):
|
|
120
|
+
continue
|
|
121
|
+
gap_id = _text(row.get("gap_id"))
|
|
122
|
+
triage_row = triage_by_id.get(gap_id, {})
|
|
123
|
+
route = _text(triage_row.get("eligibility_route") or row.get("eligibility_route"))
|
|
124
|
+
if route and route not in _ACTIVE_GAP_ROUTES:
|
|
125
|
+
continue
|
|
126
|
+
rows.append({**dict(row), **dict(triage_row)})
|
|
127
|
+
if rows:
|
|
128
|
+
return rows
|
|
129
|
+
return [dict(row) for row in triage_by_id.values()]
|
|
130
|
+
|
|
131
|
+
|
|
132
|
+
def _survey_gap_ideas(survey_handoff: Any, gap_triage: Any = None, *, limit: int = 4) -> List[Dict[str, Any]]:
|
|
133
|
+
ideas: List[Dict[str, Any]] = []
|
|
134
|
+
gap_rows = _gap_rows(survey_handoff, gap_triage)[:limit]
|
|
135
|
+
for index, gap in enumerate(gap_rows):
|
|
136
|
+
gap_id = _text(gap.get("gap_id"))
|
|
137
|
+
statement = _text(gap.get("statement") or gap.get("gap") or gap.get("description"))
|
|
138
|
+
target_object = gap.get("target_object") or gap.get("scientific_object") or gap.get("object")
|
|
139
|
+
mechanism = _text(gap.get("mechanism") or gap.get("missing_mechanism") or gap.get("target_slot"))
|
|
140
|
+
evidence = gap.get("evidence_basis") or gap.get("source_anchors") or gap.get("evidence_roles") or []
|
|
141
|
+
ideas.append(
|
|
142
|
+
_source_record(
|
|
143
|
+
{
|
|
144
|
+
"idea_id": f"survey-gap-{gap_id or index + 1}",
|
|
145
|
+
"title": _text(gap.get("title")) or f"Gap route: {gap_id or index + 1}",
|
|
146
|
+
"abstract": statement,
|
|
147
|
+
"hypothesis": statement or f"The unresolved relation associated with {gap_id} is testable.",
|
|
148
|
+
"scientific_object": target_object or {},
|
|
149
|
+
"mechanism": mechanism,
|
|
150
|
+
"mechanism_or_relation": mechanism,
|
|
151
|
+
"target_gap_ids": [gap_id] if gap_id else [],
|
|
152
|
+
"gap_alignment": [{"gap_id": gap_id, "alignment": "survey_gap"}] if gap_id else [],
|
|
153
|
+
"evidence_basis": evidence,
|
|
154
|
+
"refinement_scope": _text(gap.get("target_slot") or gap.get("refinement_scope")),
|
|
155
|
+
"falsifier": _text(gap.get("falsifier") or gap.get("discriminating_observation"))
|
|
156
|
+
or "A result showing the stated gap is resolved without this hypothesis.",
|
|
157
|
+
},
|
|
158
|
+
"survey_gap",
|
|
159
|
+
index=index,
|
|
160
|
+
lineage={"source": "survey", "gap_id": gap_id},
|
|
161
|
+
)
|
|
162
|
+
)
|
|
163
|
+
if len(gap_rows) >= 2:
|
|
164
|
+
for index, pair in enumerate(combinations(gap_rows[:3], 2)):
|
|
165
|
+
gap_ids = [_text(item.get("gap_id")) for item in pair if _text(item.get("gap_id"))]
|
|
166
|
+
statements = [
|
|
167
|
+
_text(item.get("statement") or item.get("gap") or item.get("description"))
|
|
168
|
+
for item in pair
|
|
169
|
+
]
|
|
170
|
+
ideas.append(
|
|
171
|
+
_source_record(
|
|
172
|
+
{
|
|
173
|
+
"idea_id": "survey-gap-combination-" + "-".join(gap_ids),
|
|
174
|
+
"title": "Combined gap route: " + " + ".join(gap_ids),
|
|
175
|
+
"abstract": " | ".join(item for item in statements if item),
|
|
176
|
+
"hypothesis": "The joint constraints represented by " + ", ".join(gap_ids) + " admit a shared mechanism.",
|
|
177
|
+
"scientific_object": [
|
|
178
|
+
_text(item.get("target_object") or item.get("scientific_object"))
|
|
179
|
+
for item in pair
|
|
180
|
+
],
|
|
181
|
+
"mechanism": "Joint mechanism linking the selected gap constraints.",
|
|
182
|
+
"target_gap_ids": gap_ids,
|
|
183
|
+
"gap_alignment": [
|
|
184
|
+
{"gap_id": gap_id, "alignment": "combined_survey_gaps"}
|
|
185
|
+
for gap_id in gap_ids
|
|
186
|
+
],
|
|
187
|
+
"evidence_basis": [
|
|
188
|
+
item.get("evidence_basis") or item.get("source_anchors") or []
|
|
189
|
+
for item in pair
|
|
190
|
+
],
|
|
191
|
+
"falsifier": "Evidence that the selected gaps require mutually incompatible mechanisms.",
|
|
192
|
+
},
|
|
193
|
+
"survey_gap",
|
|
194
|
+
index=limit + index,
|
|
195
|
+
lineage={"source": "survey", "gap_ids": gap_ids, "combination": True},
|
|
196
|
+
)
|
|
197
|
+
)
|
|
198
|
+
return ideas
|
|
199
|
+
|
|
200
|
+
|
|
201
|
+
def _survey_subhypothesis_ideas(survey_handoff: Any, *, limit: int = 6) -> List[Dict[str, Any]]:
|
|
202
|
+
"""Promote independent Survey sub-hypotheses into source records."""
|
|
203
|
+
|
|
204
|
+
handoff = survey_handoff if isinstance(survey_handoff, Mapping) else {}
|
|
205
|
+
raw_rows: List[Any] = []
|
|
206
|
+
for key in ("subhypotheses", "sub_hypotheses", "hypothesis_seeds", "subhypothesis_candidates"):
|
|
207
|
+
value = handoff.get(key)
|
|
208
|
+
if isinstance(value, Mapping):
|
|
209
|
+
value = value.get("items") or value.get("records") or value.get("seeds") or []
|
|
210
|
+
raw_rows.extend(_list(value))
|
|
211
|
+
ideas: List[Dict[str, Any]] = []
|
|
212
|
+
for index, raw in enumerate(raw_rows[:limit]):
|
|
213
|
+
if not isinstance(raw, Mapping):
|
|
214
|
+
continue
|
|
215
|
+
gap_ids = _unique(raw.get("target_gap_ids") or raw.get("gap_ids") or raw.get("gap_id"))
|
|
216
|
+
hypothesis = _text(raw.get("hypothesis") or raw.get("central_hypothesis") or raw.get("statement"))
|
|
217
|
+
if not hypothesis and not _text(raw.get("title")):
|
|
218
|
+
continue
|
|
219
|
+
ideas.append(
|
|
220
|
+
_source_record(
|
|
221
|
+
{
|
|
222
|
+
**dict(raw),
|
|
223
|
+
"idea_id": _text(raw.get("idea_id")) or f"survey-subhypothesis-{index + 1:02d}",
|
|
224
|
+
"title": _text(raw.get("title")) or f"Survey sub-hypothesis {index + 1}",
|
|
225
|
+
"hypothesis": hypothesis,
|
|
226
|
+
"target_gap_ids": gap_ids,
|
|
227
|
+
"evidence_basis": raw.get("evidence_basis") or raw.get("source_anchors") or [],
|
|
228
|
+
},
|
|
229
|
+
"survey_gap",
|
|
230
|
+
index=index,
|
|
231
|
+
lineage={"source": "survey", "subhypothesis_id": _text(raw.get("subhypothesis_id") or raw.get("idea_id"))},
|
|
232
|
+
)
|
|
233
|
+
)
|
|
234
|
+
return ideas
|
|
235
|
+
|
|
236
|
+
|
|
237
|
+
def _prior_candidate_ideas(candidate: Any) -> List[Dict[str, Any]]:
|
|
238
|
+
if isinstance(candidate, Mapping):
|
|
239
|
+
candidates = candidate.get("candidates") or candidate.get("history") or [candidate]
|
|
240
|
+
else:
|
|
241
|
+
candidates = candidate
|
|
242
|
+
ideas: List[Dict[str, Any]] = []
|
|
243
|
+
for index, item in enumerate(_list(candidates)):
|
|
244
|
+
if not isinstance(item, Mapping) or not item:
|
|
245
|
+
continue
|
|
246
|
+
ideas.append(
|
|
247
|
+
_source_record(
|
|
248
|
+
deepcopy(item),
|
|
249
|
+
"prior_candidate",
|
|
250
|
+
index=index,
|
|
251
|
+
lineage={"source": "history", "candidate_id": _text(item.get("idea_id") or item.get("seed_id"))},
|
|
252
|
+
)
|
|
253
|
+
)
|
|
254
|
+
return ideas
|
|
255
|
+
|
|
256
|
+
|
|
257
|
+
def _experiment_feedback_ideas(results: Any, *, limit: int = 4) -> List[Dict[str, Any]]:
|
|
258
|
+
ideas: List[Dict[str, Any]] = []
|
|
259
|
+
if isinstance(results, Mapping):
|
|
260
|
+
results = results.get("results") or results.get("ablations") or results.get("experiments") or []
|
|
261
|
+
for index, item in enumerate(_list(results)[:limit]):
|
|
262
|
+
if not isinstance(item, Mapping):
|
|
263
|
+
continue
|
|
264
|
+
component = _text(item.get("component") or item.get("name"))
|
|
265
|
+
outcome = _text(item.get("result") or item.get("status") or item.get("hypothesis_status"))
|
|
266
|
+
analysis = _text(item.get("analysis") or item.get("finding") or item.get("summary"))
|
|
267
|
+
if not component and not analysis:
|
|
268
|
+
continue
|
|
269
|
+
ideas.append(
|
|
270
|
+
_source_record(
|
|
271
|
+
{
|
|
272
|
+
"idea_id": f"experiment-feedback-{index + 1:02d}",
|
|
273
|
+
"title": f"Experiment feedback: {component or index + 1}",
|
|
274
|
+
"abstract": analysis or outcome,
|
|
275
|
+
"hypothesis": f"The observed feedback for {component or 'the candidate'} identifies a mechanism-level refinement.",
|
|
276
|
+
"scientific_object": component,
|
|
277
|
+
"mechanism": analysis,
|
|
278
|
+
"mechanism_or_relation": analysis,
|
|
279
|
+
"evidence_basis": [analysis, outcome],
|
|
280
|
+
"falsifier": "A repeated controlled result that removes the reported effect.",
|
|
281
|
+
},
|
|
282
|
+
"experiment_feedback",
|
|
283
|
+
index=index,
|
|
284
|
+
lineage={"source": "ablation_results", "component": component, "outcome": outcome},
|
|
285
|
+
)
|
|
286
|
+
)
|
|
287
|
+
return ideas
|
|
288
|
+
|
|
289
|
+
|
|
290
|
+
def _analysis_source_ideas(analysis: Any) -> List[Dict[str, Any]]:
|
|
291
|
+
if not isinstance(analysis, Mapping):
|
|
292
|
+
return []
|
|
293
|
+
ideas: List[Dict[str, Any]] = []
|
|
294
|
+
groups = (
|
|
295
|
+
("problem_reframing", "problem_reframing_ideas"),
|
|
296
|
+
("problem_reframing", "reframed_ideas"),
|
|
297
|
+
("adversarial_generation", "adversarial_idea_seeds"),
|
|
298
|
+
("adversarial_generation", "divergent_idea_seeds"),
|
|
299
|
+
("cross_domain_transfer", "cross_domain_inspiration"),
|
|
300
|
+
)
|
|
301
|
+
counters: Dict[str, int] = {}
|
|
302
|
+
for source, key in groups:
|
|
303
|
+
for raw in _list(analysis.get(key)):
|
|
304
|
+
if not isinstance(raw, Mapping):
|
|
305
|
+
continue
|
|
306
|
+
mapped = dict(raw)
|
|
307
|
+
if source == "cross_domain_transfer":
|
|
308
|
+
mapped.setdefault("title", _text(raw.get("source_field")) or "Cross-domain transfer")
|
|
309
|
+
mapped.setdefault("hypothesis", raw.get("application_hook"))
|
|
310
|
+
mapped.setdefault("mechanism", raw.get("transferable_mechanism"))
|
|
311
|
+
mapped.setdefault("mechanism_or_relation", raw.get("transferable_mechanism"))
|
|
312
|
+
mapped.setdefault("scientific_object", raw.get("source_field"))
|
|
313
|
+
elif source == "adversarial_generation":
|
|
314
|
+
mapped.setdefault("mechanism", raw.get("method_sketch") or raw.get("method"))
|
|
315
|
+
mapped.setdefault("mechanism_or_relation", raw.get("method_sketch") or raw.get("method"))
|
|
316
|
+
mapped.setdefault("falsifier", raw.get("evaluation_plan"))
|
|
317
|
+
elif source == "problem_reframing":
|
|
318
|
+
mapped.setdefault("title", raw.get("reframed_problem") or raw.get("new_question"))
|
|
319
|
+
mapped.setdefault("hypothesis", raw.get("reframed_problem") or raw.get("new_question"))
|
|
320
|
+
mapped.setdefault("mechanism", raw.get("mechanism") or raw.get("mechanism_sketch"))
|
|
321
|
+
mapped.setdefault("mechanism_or_relation", raw.get("mechanism") or raw.get("mechanism_sketch"))
|
|
322
|
+
counters[source] = counters.get(source, 0) + 1
|
|
323
|
+
ideas.append(
|
|
324
|
+
_source_record(
|
|
325
|
+
mapped,
|
|
326
|
+
source,
|
|
327
|
+
index=counters[source] - 1,
|
|
328
|
+
lineage={"source": "advanced_analysis", "field": key},
|
|
329
|
+
)
|
|
330
|
+
)
|
|
331
|
+
return ideas
|
|
332
|
+
|
|
333
|
+
|
|
334
|
+
def collect_mature_idea_sources(
|
|
335
|
+
*,
|
|
336
|
+
existing: Any = None,
|
|
337
|
+
survey_handoff: Any = None,
|
|
338
|
+
gap_triage: Any = None,
|
|
339
|
+
prior_candidate: Any = None,
|
|
340
|
+
experiment_results: Any = None,
|
|
341
|
+
analysis: Any = None,
|
|
342
|
+
max_ideas: int = 12,
|
|
343
|
+
allow_problem_reframing: bool = True,
|
|
344
|
+
allow_unanchored_seed: bool = True,
|
|
345
|
+
allow_high_risk_seed: bool = True,
|
|
346
|
+
multimodal_evidence_projection: Mapping[str, Any] | None = None,
|
|
347
|
+
) -> List[Dict[str, Any]]:
|
|
348
|
+
"""Collect, structurally deduplicate, and annotate mature ideas by lineage."""
|
|
349
|
+
|
|
350
|
+
records: List[Dict[str, Any]] = []
|
|
351
|
+
for raw in normalize_mature_ideas(existing, default_source="user_input"):
|
|
352
|
+
records.append(
|
|
353
|
+
_source_record(
|
|
354
|
+
raw,
|
|
355
|
+
_canonical_source(raw.get("idea_source"), "user_input"),
|
|
356
|
+
lineage=raw.get("lineage") or "user_input",
|
|
357
|
+
)
|
|
358
|
+
)
|
|
359
|
+
records.extend(_survey_gap_ideas(survey_handoff, gap_triage))
|
|
360
|
+
records.extend(_survey_subhypothesis_ideas(survey_handoff))
|
|
361
|
+
records.extend(_prior_candidate_ideas(prior_candidate))
|
|
362
|
+
records.extend(_experiment_feedback_ideas(experiment_results))
|
|
363
|
+
records.extend(_analysis_source_ideas(analysis))
|
|
364
|
+
records = [
|
|
365
|
+
annotate_data_anchored_mature_idea(
|
|
366
|
+
record,
|
|
367
|
+
survey_idea_handoff=survey_handoff if isinstance(survey_handoff, Mapping) else {},
|
|
368
|
+
multimodal_evidence_projection=multimodal_evidence_projection,
|
|
369
|
+
)
|
|
370
|
+
for record in records
|
|
371
|
+
]
|
|
372
|
+
|
|
373
|
+
independent = filter_independent_mature_ideas(records)
|
|
374
|
+
enriched: List[Dict[str, Any]] = []
|
|
375
|
+
for record in independent:
|
|
376
|
+
maturity = assess_mature_idea_maturity(record, independent=True)
|
|
377
|
+
record["maturity"] = maturity
|
|
378
|
+
record["maturity_status"] = maturity["maturity_status"]
|
|
379
|
+
record["maturity_is_not_rank"] = True
|
|
380
|
+
source = _canonical_source(record.get("idea_source"), "user_input")
|
|
381
|
+
if not allow_problem_reframing and source == "problem_reframing":
|
|
382
|
+
continue
|
|
383
|
+
if not allow_unanchored_seed and (
|
|
384
|
+
bool(record.get("anti_anchor")) or source in {"problem_reframing", "adversarial_generation"}
|
|
385
|
+
):
|
|
386
|
+
continue
|
|
387
|
+
if not allow_high_risk_seed and (
|
|
388
|
+
maturity.get("maturity_status") in {"exploratory", "needs_grounding"}
|
|
389
|
+
or _text(record.get("risk")).casefold() in {"high", "major"}
|
|
390
|
+
):
|
|
391
|
+
continue
|
|
392
|
+
enriched.append(record)
|
|
393
|
+
limit = max(1, int(max_ideas or 12))
|
|
394
|
+
if len(enriched) <= limit:
|
|
395
|
+
return enriched
|
|
396
|
+
selected: List[Dict[str, Any]] = []
|
|
397
|
+
selected_ids = set()
|
|
398
|
+
for source in MATURE_IDEA_SOURCES:
|
|
399
|
+
item = next((record for record in enriched if record.get("idea_source") == source), None)
|
|
400
|
+
if item is not None:
|
|
401
|
+
selected.append(item)
|
|
402
|
+
selected_ids.add(id(item))
|
|
403
|
+
if len(selected) >= limit:
|
|
404
|
+
return selected[:limit]
|
|
405
|
+
for item in enriched:
|
|
406
|
+
if id(item) in selected_ids:
|
|
407
|
+
continue
|
|
408
|
+
selected.append(item)
|
|
409
|
+
if len(selected) >= limit:
|
|
410
|
+
break
|
|
411
|
+
return selected
|
|
412
|
+
|
|
413
|
+
|
|
414
|
+
def assess_mature_idea_maturity(
|
|
415
|
+
idea: Mapping[str, Any],
|
|
416
|
+
*,
|
|
417
|
+
evidence_context: Mapping[str, Any] | None = None,
|
|
418
|
+
independent: bool = True,
|
|
419
|
+
) -> Dict[str, Any]:
|
|
420
|
+
"""Score maturity dimensions independently; no single winner is selected."""
|
|
421
|
+
|
|
422
|
+
evidence_context = evidence_context if isinstance(evidence_context, Mapping) else {}
|
|
423
|
+
specificity = sum(
|
|
424
|
+
bool(idea.get(field))
|
|
425
|
+
for field in ("title", "hypothesis", "scientific_object", "target_gap_ids")
|
|
426
|
+
) / 4.0
|
|
427
|
+
mechanism_complete = sum(
|
|
428
|
+
bool(idea.get(field))
|
|
429
|
+
for field in ("mechanism", "mechanism_or_relation", "intervention_or_transformation", "assumptions")
|
|
430
|
+
) / 4.0
|
|
431
|
+
evidence_support = 1.0 if idea.get("evidence_basis") or evidence_context.get("evidence_subset") else 0.0
|
|
432
|
+
falsifiability = 1.0 if idea.get("falsifier") or idea.get("discriminating_observation") else 0.0
|
|
433
|
+
scope_clarity = 1.0 if idea.get("refinement_scope") or idea.get("claim_scope") else 0.0
|
|
434
|
+
executability = 1.0 if evidence_context.get("validation_targets") or (evidence_support and falsifiability) else 0.0
|
|
435
|
+
independence_score = 1.0 if independent else 0.0
|
|
436
|
+
dimensions = {
|
|
437
|
+
"specificity": round(specificity, 3),
|
|
438
|
+
"mechanism_completeness": round(mechanism_complete, 3),
|
|
439
|
+
"evidence_support": round(evidence_support, 3),
|
|
440
|
+
"falsifiability": round(falsifiability, 3),
|
|
441
|
+
"scope_clarity": round(scope_clarity, 3),
|
|
442
|
+
"executability": round(executability, 3),
|
|
443
|
+
"independence": round(independence_score, 3),
|
|
444
|
+
}
|
|
445
|
+
average = sum(dimensions.values()) / len(dimensions)
|
|
446
|
+
minimum = min(dimensions.values())
|
|
447
|
+
source_status = _text(idea.get("maturity_status")).lower()
|
|
448
|
+
if source_status == "rejected":
|
|
449
|
+
status = "rejected"
|
|
450
|
+
elif average >= 0.68 and minimum >= 0.45:
|
|
451
|
+
status = "mature"
|
|
452
|
+
elif average >= 0.42:
|
|
453
|
+
status = "provisional"
|
|
454
|
+
elif evidence_support == 0.0:
|
|
455
|
+
status = "needs_grounding"
|
|
456
|
+
else:
|
|
457
|
+
status = "exploratory"
|
|
458
|
+
return {
|
|
459
|
+
"dimensions": dimensions,
|
|
460
|
+
"aggregate": round(average, 3),
|
|
461
|
+
"maturity_status": status,
|
|
462
|
+
"maturity_is_not_rank": True,
|
|
463
|
+
}
|
|
464
|
+
|
|
465
|
+
|
|
466
|
+
def build_mature_idea_evidence_context(
|
|
467
|
+
idea: Mapping[str, Any],
|
|
468
|
+
*,
|
|
469
|
+
topic: str = "",
|
|
470
|
+
survey_handoff: Any = None,
|
|
471
|
+
references: Sequence[Mapping[str, Any]] | None = None,
|
|
472
|
+
ablation_results: Any = None,
|
|
473
|
+
public_facts: Any = None,
|
|
474
|
+
multimodal_evidence_projection: Mapping[str, Any] | None = None,
|
|
475
|
+
) -> Dict[str, Any]:
|
|
476
|
+
"""Create public, idea-specific, and anti-anchor evidence layers."""
|
|
477
|
+
|
|
478
|
+
handoff = dict(survey_handoff) if isinstance(survey_handoff, Mapping) else {}
|
|
479
|
+
source = _canonical_source(idea.get("idea_source"), "user_input")
|
|
480
|
+
anti_anchor = source in {"problem_reframing", "adversarial_generation"} or _text(idea.get("anchor_policy")) == "reframe_without_default_problem_anchor"
|
|
481
|
+
gap_ids = set(_text(item) for item in _list(idea.get("target_gap_ids")))
|
|
482
|
+
gaps = [
|
|
483
|
+
dict(row)
|
|
484
|
+
for row in _gap_rows(handoff)
|
|
485
|
+
if gap_ids and _text(row.get("gap_id")) in gap_ids
|
|
486
|
+
]
|
|
487
|
+
data_evidence = scoped_multimodal_evidence_for_idea(
|
|
488
|
+
idea,
|
|
489
|
+
survey_idea_handoff=handoff,
|
|
490
|
+
multimodal_evidence_projection=multimodal_evidence_projection,
|
|
491
|
+
)
|
|
492
|
+
keywords = set(
|
|
493
|
+
_text(value).casefold()
|
|
494
|
+
for value in (
|
|
495
|
+
idea.get("title"),
|
|
496
|
+
idea.get("hypothesis"),
|
|
497
|
+
idea.get("mechanism"),
|
|
498
|
+
idea.get("mechanism_or_relation"),
|
|
499
|
+
)
|
|
500
|
+
if _text(value)
|
|
501
|
+
)
|
|
502
|
+
evidence_subset: List[Dict[str, Any]] = []
|
|
503
|
+
target_anchor_ids = {
|
|
504
|
+
_text(anchor_id)
|
|
505
|
+
for gap in gaps
|
|
506
|
+
for anchor_id in _list(gap.get("anchor_ids"))
|
|
507
|
+
if _text(anchor_id)
|
|
508
|
+
}
|
|
509
|
+
scoped_anchors = [
|
|
510
|
+
anchor
|
|
511
|
+
for anchor in _list(handoff.get("anchors"))
|
|
512
|
+
if isinstance(anchor, Mapping)
|
|
513
|
+
and (
|
|
514
|
+
_text(anchor.get("anchor_id")) in target_anchor_ids
|
|
515
|
+
or anchor in data_evidence.get("source_anchors", [])
|
|
516
|
+
)
|
|
517
|
+
]
|
|
518
|
+
scoped_paper_ids = {
|
|
519
|
+
_text(_mapping(anchor.get("source_pointer")).get("paper_id"))
|
|
520
|
+
for anchor in scoped_anchors
|
|
521
|
+
if _text(_mapping(anchor.get("source_pointer")).get("paper_id"))
|
|
522
|
+
}
|
|
523
|
+
target_subhypotheses_for_papers = {_text(gap.get("subhypothesis_id")) for gap in gaps}
|
|
524
|
+
for role in _list(handoff.get("evidence_roles")):
|
|
525
|
+
if not isinstance(role, Mapping) or _text(role.get("subhypothesis_id")) not in target_subhypotheses_for_papers:
|
|
526
|
+
continue
|
|
527
|
+
scoped_paper_ids.update(
|
|
528
|
+
paper_id
|
|
529
|
+
for paper_id in _unique(
|
|
530
|
+
[
|
|
531
|
+
role.get("paper_id"),
|
|
532
|
+
*_list(role.get("paper_ids")),
|
|
533
|
+
*_list(role.get("qualified_paper_ids")),
|
|
534
|
+
*_list(role.get("background_paper_ids")),
|
|
535
|
+
]
|
|
536
|
+
)
|
|
537
|
+
if paper_id
|
|
538
|
+
)
|
|
539
|
+
scoped_paper_ids.update(
|
|
540
|
+
_text(assessment.get("paper_id"))
|
|
541
|
+
for assessment in _list(data_evidence.get("paper_assessments"))
|
|
542
|
+
if isinstance(assessment, Mapping) and _text(assessment.get("paper_id"))
|
|
543
|
+
)
|
|
544
|
+
for reference in references or []:
|
|
545
|
+
if not isinstance(reference, Mapping):
|
|
546
|
+
continue
|
|
547
|
+
ref_text = " ".join(_text(reference.get(field)) for field in ("title", "abstract", "summary", "tldr")).casefold()
|
|
548
|
+
if _text(reference.get("paper_id")) in scoped_paper_ids or any(
|
|
549
|
+
gap_id.casefold() in ref_text for gap_id in gap_ids
|
|
550
|
+
) or any(
|
|
551
|
+
keyword and keyword in ref_text for keyword in keywords
|
|
552
|
+
):
|
|
553
|
+
evidence_subset.append(dict(reference))
|
|
554
|
+
evidence_subset = evidence_subset[:8]
|
|
555
|
+
ablation_subset = [
|
|
556
|
+
dict(item)
|
|
557
|
+
for item in _list(ablation_results)
|
|
558
|
+
if isinstance(item, Mapping)
|
|
559
|
+
and idea.get("scientific_object")
|
|
560
|
+
and _text(item.get("component") or item.get("name")).casefold()
|
|
561
|
+
in _text(idea.get("scientific_object")).casefold()
|
|
562
|
+
][:6]
|
|
563
|
+
scoped_handoff = {
|
|
564
|
+
key: deepcopy(value)
|
|
565
|
+
for key, value in handoff.items()
|
|
566
|
+
if key not in {"gaps", "gap_triage", "source_anchors", "evidence_roles"}
|
|
567
|
+
}
|
|
568
|
+
scoped_handoff["gaps"] = gaps
|
|
569
|
+
raw_gap_triage = handoff.get("gap_triage")
|
|
570
|
+
raw_gap_triage_rows = (
|
|
571
|
+
raw_gap_triage.get("gaps")
|
|
572
|
+
if isinstance(raw_gap_triage, Mapping)
|
|
573
|
+
else raw_gap_triage
|
|
574
|
+
)
|
|
575
|
+
scoped_handoff["gap_triage"] = {
|
|
576
|
+
"gaps": [
|
|
577
|
+
row
|
|
578
|
+
for row in _list(raw_gap_triage_rows)
|
|
579
|
+
if isinstance(row, Mapping)
|
|
580
|
+
and (
|
|
581
|
+
gap_ids and _text(row.get("gap_id")) in gap_ids
|
|
582
|
+
)
|
|
583
|
+
]
|
|
584
|
+
}
|
|
585
|
+
target_subhypotheses = {_text(gap.get("subhypothesis_id")) for gap in gaps}
|
|
586
|
+
scoped_handoff["anchors"] = [
|
|
587
|
+
deepcopy(anchor)
|
|
588
|
+
for anchor in scoped_anchors
|
|
589
|
+
]
|
|
590
|
+
scoped_handoff["evidence_roles"] = [
|
|
591
|
+
deepcopy(role)
|
|
592
|
+
for role in _list(handoff.get("evidence_roles"))
|
|
593
|
+
if isinstance(role, Mapping)
|
|
594
|
+
and (
|
|
595
|
+
_text(role.get("subhypothesis_id")) in target_subhypotheses
|
|
596
|
+
or bool(
|
|
597
|
+
set(_unique(role.get("anchor_ids")))
|
|
598
|
+
& {_text(anchor.get("anchor_id")) for anchor in scoped_anchors}
|
|
599
|
+
)
|
|
600
|
+
)
|
|
601
|
+
]
|
|
602
|
+
result = {
|
|
603
|
+
"public_facts": deepcopy(public_facts) if isinstance(public_facts, (Mapping, list, str)) else {},
|
|
604
|
+
"idea_id": _text(idea.get("idea_id")),
|
|
605
|
+
"idea_source": source,
|
|
606
|
+
"gap_explanation": gaps,
|
|
607
|
+
"evidence_subset": evidence_subset,
|
|
608
|
+
"retrieval_queries": _unique(
|
|
609
|
+
[topic, idea.get("title"), idea.get("hypothesis"), idea.get("mechanism_or_relation")]
|
|
610
|
+
),
|
|
611
|
+
"counterexamples": _list(idea.get("counterexamples") or idea.get("negative_evidence")) + ablation_subset,
|
|
612
|
+
"mechanism_chain": _unique(
|
|
613
|
+
[idea.get("scientific_object"), idea.get("hypothesis"), idea.get("mechanism_or_relation"), idea.get("falsifier")]
|
|
614
|
+
),
|
|
615
|
+
"validation_targets": _unique(
|
|
616
|
+
[idea.get("falsifier"), idea.get("discriminating_observation"), idea.get("refinement_scope")]
|
|
617
|
+
),
|
|
618
|
+
"survey_handoff": scoped_handoff,
|
|
619
|
+
"anchor_policy": "reframe_without_default_problem_anchor" if anti_anchor else "scoped_survey_anchor",
|
|
620
|
+
"anti_anchor": anti_anchor,
|
|
621
|
+
"anti_anchor_reason": (
|
|
622
|
+
"This idea challenges the default problem definition and therefore receives public facts only; "
|
|
623
|
+
"Survey gaps and evidence are included only when explicitly targeted."
|
|
624
|
+
if anti_anchor
|
|
625
|
+
else "Evidence is scoped to the idea's selected gaps and mechanism."
|
|
626
|
+
),
|
|
627
|
+
}
|
|
628
|
+
if data_evidence:
|
|
629
|
+
result["multimodal_evidence_context"] = data_evidence
|
|
630
|
+
result["counterexamples"] = _list(result["counterexamples"]) + [
|
|
631
|
+
*data_evidence.get("competing_explanations", []),
|
|
632
|
+
*data_evidence.get("claim_limits", []),
|
|
633
|
+
]
|
|
634
|
+
result["validation_targets"] = _unique(
|
|
635
|
+
[
|
|
636
|
+
*result["validation_targets"],
|
|
637
|
+
*data_evidence.get("measurement_needs", []),
|
|
638
|
+
]
|
|
639
|
+
)
|
|
640
|
+
return result
|
|
641
|
+
|
|
642
|
+
|
|
643
|
+
__all__ = [
|
|
644
|
+
"MATURE_IDEA_SOURCES",
|
|
645
|
+
"collect_mature_idea_sources",
|
|
646
|
+
"assess_mature_idea_maturity",
|
|
647
|
+
"build_mature_idea_evidence_context",
|
|
648
|
+
]
|