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
- src/harness/src/openharness/memory/migrate.py +137 -0
- src/harness/src/openharness/memory/paths.py +22 -0
- src/harness/src/openharness/memory/relevance.py +145 -0
- src/harness/src/openharness/memory/scan.py +116 -0
- src/harness/src/openharness/memory/schema.py +443 -0
- src/harness/src/openharness/memory/search.py +71 -0
- src/harness/src/openharness/memory/team.py +90 -0
- src/harness/src/openharness/memory/types.py +33 -0
- src/harness/src/openharness/memory/usage.py +153 -0
- src/harness/src/openharness/output_styles/__init__.py +5 -0
- src/harness/src/openharness/output_styles/loader.py +42 -0
- src/harness/src/openharness/permissions/__init__.py +26 -0
- src/harness/src/openharness/permissions/checker.py +200 -0
- src/harness/src/openharness/permissions/modes.py +13 -0
- src/harness/src/openharness/personalization/__init__.py +6 -0
- src/harness/src/openharness/personalization/extractor.py +138 -0
- src/harness/src/openharness/personalization/rules.py +64 -0
- src/harness/src/openharness/personalization/session_hook.py +65 -0
- src/harness/src/openharness/platforms.py +86 -0
- src/harness/src/openharness/plugins/__init__.py +53 -0
- src/harness/src/openharness/plugins/bundled/__init__.py +0 -0
- src/harness/src/openharness/plugins/installer.py +39 -0
- src/harness/src/openharness/plugins/loader.py +730 -0
- src/harness/src/openharness/plugins/schemas.py +24 -0
- src/harness/src/openharness/plugins/types.py +59 -0
- src/harness/src/openharness/prompts/__init__.py +14 -0
- src/harness/src/openharness/prompts/claudemd.py +48 -0
- src/harness/src/openharness/prompts/context.py +187 -0
- src/harness/src/openharness/prompts/environment.py +135 -0
- src/harness/src/openharness/prompts/system_prompt.py +109 -0
- src/harness/src/openharness/sandbox/Dockerfile +6 -0
- src/harness/src/openharness/sandbox/__init__.py +33 -0
- src/harness/src/openharness/sandbox/adapter.py +148 -0
- src/harness/src/openharness/sandbox/docker_backend.py +232 -0
- src/harness/src/openharness/sandbox/docker_image.py +103 -0
- src/harness/src/openharness/sandbox/path_validator.py +37 -0
- src/harness/src/openharness/sandbox/session.py +63 -0
- src/harness/src/openharness/services/__init__.py +30 -0
- src/harness/src/openharness/services/autodream/__init__.py +34 -0
- src/harness/src/openharness/services/autodream/backup.py +104 -0
- src/harness/src/openharness/services/autodream/lock.py +138 -0
- src/harness/src/openharness/services/autodream/prompt.py +128 -0
- src/harness/src/openharness/services/autodream/service.py +313 -0
- src/harness/src/openharness/services/compact/__init__.py +1725 -0
- src/harness/src/openharness/services/cron.py +137 -0
- src/harness/src/openharness/services/cron_scheduler.py +595 -0
- src/harness/src/openharness/services/lsp/__init__.py +216 -0
- src/harness/src/openharness/services/memory_extract/__init__.py +261 -0
- src/harness/src/openharness/services/oauth/__init__.py +0 -0
- src/harness/src/openharness/services/session_backend.py +97 -0
- src/harness/src/openharness/services/session_memory/__init__.py +139 -0
- src/harness/src/openharness/services/session_storage.py +230 -0
- src/harness/src/openharness/services/token_estimation.py +15 -0
- src/harness/src/openharness/services/tool_outputs.py +55 -0
- src/harness/src/openharness/skills/__init__.py +44 -0
- 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
- src/harness/src/openharness/skills/types.py +24 -0
- src/harness/src/openharness/state/__init__.py +6 -0
- 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
- src/pipeline/__init__.py +129 -0
- 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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from __future__ import annotations
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import importlib
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from types import SimpleNamespace
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import pytest
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from src.agents.idea_agent.agent.prompts.component_extraction import (
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COMPONENT_EXTRACTION_PROMPT,
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from src.agents.idea_agent.agent.prompts.advanced_analysis import (
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render_advanced_analysis_prompt,
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from src.agents.idea_agent.agent.prompts.idea_fusion import (
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IDEA_FUSION_PROMPT,
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render_idea_fusion_prompt,
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from src.agents.idea_agent.agent.prompts.mcts_evaluation import (
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MCTS_IDEA_EVALUATION_PROMPT,
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from src.agents.idea_agent.agent.prompts.mcts_generation import (
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from src.agents.idea_agent.agent.prompts.skill_instantiation import (
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from src.agents.idea_agent.utils.mcts.defect_registry import format_defect_registry
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from src.agents.idea_agent.utils.mcts.defect_registry import profile_skill_defect_tags
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from src.agents.idea_agent.utils.mcts.idea_taste_presets import (
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SCORE_WEIGHT_FIELDS,
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get_idea_taste_preset,
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)
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from src.agents.idea_agent.utils.mcts.mcts_runtime import (
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_contract_from_instantiation,
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_direction_prompt_context,
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EditPlan,
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evaluation_prompt_cache_key,
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materialize_child_state,
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merge_hypothesis_contract,
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ValidationProtocol,
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)
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from src.agents.idea_agent.utils.mcts.scientific_intervention_ontology import (
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format_scientific_intervention_profile_for_prompt,
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get_scientific_intervention_profile,
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)
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from src.agents.idea_agent.utils.mcts.scientific_rubric import (
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format_scientific_rubric_for_prompt,
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from src.agents.idea_agent.utils.workflow.idea_contract import normalize_idea_contract
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def _profile_payload(profile_id: str) -> dict[str, object]:
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profile = get_scientific_intervention_profile(profile_id)
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assert profile is not None
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payload = profile.to_payload()
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payload["contribution_mode"] = profile.contribution_modes[0].mode_id
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return payload
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def test_profile_text_is_injected_into_generation_and_extraction_prompts() -> None:
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profile_text = format_scientific_intervention_profile_for_prompt(
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_profile_payload("physical_materials_chemical")
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)
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assert "physical_materials_chemical" in profile_text
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assert "structure_property_mechanism" in profile_text
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69
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generation = MCTS_IDEA_GENERATION_PROMPT.format(
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70
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topic="battery degradation",
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71
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direction_mode="evidence_first",
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direction_summary="Prefer defensible evidence.",
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taste_guidance="Use a narrow mechanism.",
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target_gap_ids="gap-1",
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profile_id="physical_materials_chemical",
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scientific_intervention_profile=profile_text,
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profile_native_object_schema="{}",
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gap_seed_context="seed-1",
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current_summary="parent",
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paper_context="papers",
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memory_bundle="memory",
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edit_operators="ops",
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constraints="constraints",
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max_children=2,
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)
|
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86
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extraction = COMPONENT_EXTRACTION_PROMPT.format(
|
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87
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+
mature_idea="materials idea",
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88
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topic="battery degradation",
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89
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scientific_intervention_profile=profile_text,
|
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90
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prior_components="[]",
|
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91
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component_decisions="[]",
|
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92
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)
|
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93
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+
assert "physical_materials_chemical" in generation
|
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94
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assert "physical_materials_chemical" in extraction
|
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95
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assert "Training signals and model objectives are primary only" in generation
|
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96
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assert "flow_matching_generator" not in COMPONENT_EXTRACTION_PROMPT
|
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97
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+
assert "controllability_gramian" not in COMPONENT_EXTRACTION_PROMPT
|
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98
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assert "proof_obligation" in COMPONENT_EXTRACTION_PROMPT
|
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99
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+
|
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100
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+
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101
|
+
def test_skill_prompt_accepts_profile_native_objects_and_roles() -> None:
|
|
102
|
+
profile_text = format_scientific_intervention_profile_for_prompt(
|
|
103
|
+
_profile_payload("formal_theoretical")
|
|
104
|
+
)
|
|
105
|
+
prompt = SKILL_INSTANTIATION_PROMPT.format(
|
|
106
|
+
topic="mathematical dynamics",
|
|
107
|
+
root_domains="mathematics",
|
|
108
|
+
scientific_intervention_profile=profile_text,
|
|
109
|
+
refinement_scope="theorem assumptions",
|
|
110
|
+
taste_guidance="none",
|
|
111
|
+
mature_idea="theorem",
|
|
112
|
+
parent_summary="parent",
|
|
113
|
+
parent_components="proof_object",
|
|
114
|
+
paper_context="papers",
|
|
115
|
+
memory_bundle="memory",
|
|
116
|
+
skill_references="references",
|
|
117
|
+
additional_retrieval_context="",
|
|
118
|
+
skill_name="mechanism-commit-innovation",
|
|
119
|
+
plan_objective="repair proof gap",
|
|
120
|
+
target_defects="proof_gap",
|
|
121
|
+
component_edits="[]",
|
|
122
|
+
validation_protocols="counterexample",
|
|
123
|
+
guardrails="none",
|
|
124
|
+
)
|
|
125
|
+
assert "formal_theoretical" in prompt
|
|
126
|
+
assert "scientific object, role, mechanism, process, relation" in prompt
|
|
127
|
+
|
|
128
|
+
|
|
129
|
+
def test_profiles_expose_native_contribution_modes() -> None:
|
|
130
|
+
for profile_id in (
|
|
131
|
+
"physical_materials_chemical",
|
|
132
|
+
"clinical_health",
|
|
133
|
+
"formal_theoretical",
|
|
134
|
+
"computational_algorithmic",
|
|
135
|
+
):
|
|
136
|
+
profile = get_scientific_intervention_profile(profile_id)
|
|
137
|
+
assert profile is not None
|
|
138
|
+
assert profile.contribution_modes
|
|
139
|
+
assert all(mode.mode_id for mode in profile.contribution_modes)
|
|
140
|
+
|
|
141
|
+
|
|
142
|
+
def test_non_cs_rubric_does_not_require_training_signal() -> None:
|
|
143
|
+
rubric = format_scientific_rubric_for_prompt(
|
|
144
|
+
_profile_payload("clinical_health")
|
|
145
|
+
)
|
|
146
|
+
assert "not universal quality requirements" not in rubric
|
|
147
|
+
assert "training signal" not in rubric
|
|
148
|
+
assert "native objects" in rubric
|
|
149
|
+
assert "causal" in rubric.lower()
|
|
150
|
+
|
|
151
|
+
|
|
152
|
+
def test_non_cs_early_prompts_use_profile_neutral_vocabulary() -> None:
|
|
153
|
+
advanced = render_advanced_analysis_prompt(
|
|
154
|
+
ADVANCED_ANALYSIS_PROMPT.format(
|
|
155
|
+
topic="clinical endpoint",
|
|
156
|
+
mature_idea="",
|
|
157
|
+
mature_idea_source="empty",
|
|
158
|
+
refinement_scope="",
|
|
159
|
+
refinement_scope_source="empty",
|
|
160
|
+
survey_contents="",
|
|
161
|
+
papers="",
|
|
162
|
+
experiment_findings="None",
|
|
163
|
+
),
|
|
164
|
+
"clinical_health",
|
|
165
|
+
).lower()
|
|
166
|
+
fusion = render_idea_fusion_prompt(
|
|
167
|
+
IDEA_FUSION_PROMPT.format(
|
|
168
|
+
topic="clinical endpoint",
|
|
169
|
+
mature_idea="",
|
|
170
|
+
refinement_scope="",
|
|
171
|
+
root_domains="medicine",
|
|
172
|
+
scientific_intervention_profile="clinical_health",
|
|
173
|
+
scientific_object_schema="{}",
|
|
174
|
+
analysis="",
|
|
175
|
+
mode_count=2,
|
|
176
|
+
candidate_ideas_json="[]",
|
|
177
|
+
),
|
|
178
|
+
"clinical_health",
|
|
179
|
+
).lower()
|
|
180
|
+
for prompt in (advanced, fusion):
|
|
181
|
+
assert "training signals" not in prompt
|
|
182
|
+
assert "task-solving mechanism" not in prompt
|
|
183
|
+
assert "gate/router/controller" not in prompt
|
|
184
|
+
assert "specific computational role" not in prompt
|
|
185
|
+
|
|
186
|
+
|
|
187
|
+
def test_evaluation_prompt_accepts_profile_and_rubric_blocks() -> None:
|
|
188
|
+
rendered = MCTS_IDEA_EVALUATION_PROMPT.format(
|
|
189
|
+
topic="clinical endpoint",
|
|
190
|
+
direction_mode="evidence_first",
|
|
191
|
+
direction_summary="Prefer defensible evidence.",
|
|
192
|
+
taste_guidance="Use a narrow mechanism.",
|
|
193
|
+
target_gap_ids="gap-1",
|
|
194
|
+
profile_id="clinical_health",
|
|
195
|
+
gap_seed_context="seed-1",
|
|
196
|
+
root_domains="medicine",
|
|
197
|
+
mature_idea="causal intervention",
|
|
198
|
+
refinement_scope="mediator identification",
|
|
199
|
+
edit_plan="plan",
|
|
200
|
+
idea="candidate",
|
|
201
|
+
scientific_intervention_profile=format_scientific_intervention_profile_for_prompt(
|
|
202
|
+
_profile_payload("clinical_health")
|
|
203
|
+
),
|
|
204
|
+
profile_native_object_schema="{}",
|
|
205
|
+
scientific_rubric=format_scientific_rubric_for_prompt(
|
|
206
|
+
_profile_payload("clinical_health")
|
|
207
|
+
),
|
|
208
|
+
defect_registry=format_defect_registry("clinical_health"),
|
|
209
|
+
symbolic_memory_hints="none",
|
|
210
|
+
)
|
|
211
|
+
assert '"explanatory_power": 0-5' in rendered
|
|
212
|
+
assert "clinical_health" in rendered
|
|
213
|
+
|
|
214
|
+
|
|
215
|
+
def test_direction_context_exposes_mode_profile_and_gap_seeds() -> None:
|
|
216
|
+
preset = get_idea_taste_preset("evidence_first")
|
|
217
|
+
assert preset is not None
|
|
218
|
+
mcts = SimpleNamespace(
|
|
219
|
+
idea_taste_preset=preset,
|
|
220
|
+
scientific_intervention_profile={
|
|
221
|
+
"profile_id": "physical_materials_chemical",
|
|
222
|
+
"scientific_object_schema": {"object_types": ["material_process"]},
|
|
223
|
+
},
|
|
224
|
+
gap_hypothesis_seeds=[{"gap_id": "gap-1"}],
|
|
225
|
+
gap_seed_context="seed-1",
|
|
226
|
+
)
|
|
227
|
+
state = SimpleNamespace(scientific_intervention={})
|
|
228
|
+
|
|
229
|
+
context = _direction_prompt_context(mcts, state)
|
|
230
|
+
|
|
231
|
+
assert context["direction_mode"] == "evidence_first"
|
|
232
|
+
assert context["profile_id"] == "physical_materials_chemical"
|
|
233
|
+
assert context["target_gap_ids"] == "gap-1"
|
|
234
|
+
assert "seed-1" in context["gap_seed_context"]
|
|
235
|
+
assert "material_process" in context["profile_native_object_schema"]
|
|
236
|
+
|
|
237
|
+
|
|
238
|
+
def test_optional_scientific_contract_fields_are_preserved_without_new_required_fields() -> None:
|
|
239
|
+
normalized = normalize_idea_contract(
|
|
240
|
+
{
|
|
241
|
+
"title": "A hypothesis",
|
|
242
|
+
"abstract": "A concise abstract.",
|
|
243
|
+
"core_contribution": "A scientific claim.",
|
|
244
|
+
"method": "A profile-native method.",
|
|
245
|
+
"direction_mode": "bridge_builder",
|
|
246
|
+
"central_hypothesis": "The relation changes under the condition.",
|
|
247
|
+
"scientific_object": {"object_type": "process"},
|
|
248
|
+
"target_gap_ids": ["gap-1"],
|
|
249
|
+
"gap_alignment": [{"gap_id": "gap-1", "alignment": "direct"}],
|
|
250
|
+
"evidence_basis": ["SURVEY_ANCHOR: mechanism remains unresolved"],
|
|
251
|
+
"experiment_design": "must be discarded",
|
|
252
|
+
}
|
|
253
|
+
)
|
|
254
|
+
|
|
255
|
+
assert normalized["direction_mode"] == "bridge_builder"
|
|
256
|
+
assert normalized["central_hypothesis"] == "The relation changes under the condition."
|
|
257
|
+
assert normalized["scientific_object"] == {"object_type": "process"}
|
|
258
|
+
assert normalized["target_gap_ids"] == ["gap-1"]
|
|
259
|
+
assert normalized["gap_alignment"] == [{"gap_id": "gap-1", "alignment": "direct"}]
|
|
260
|
+
assert normalized["evidence_basis"] == ["SURVEY_ANCHOR: mechanism remains unresolved"]
|
|
261
|
+
assert "experiment_design" not in normalized
|
|
262
|
+
|
|
263
|
+
|
|
264
|
+
def test_instantiation_contract_collects_top_level_scientific_fields() -> None:
|
|
265
|
+
contract = _contract_from_instantiation(
|
|
266
|
+
{
|
|
267
|
+
"central_hypothesis": "A claim",
|
|
268
|
+
"target_gap_ids": ["gap-1"],
|
|
269
|
+
"evidence_basis": ["anchor-1"],
|
|
270
|
+
"scientific_contract": {"direction_mode": "moonshot_inventor"},
|
|
271
|
+
}
|
|
272
|
+
)
|
|
273
|
+
|
|
274
|
+
assert contract == {
|
|
275
|
+
"direction_mode": "moonshot_inventor",
|
|
276
|
+
"central_hypothesis": "A claim",
|
|
277
|
+
"target_gap_ids": ["gap-1"],
|
|
278
|
+
"evidence_basis": ["anchor-1"],
|
|
279
|
+
}
|
|
280
|
+
|
|
281
|
+
|
|
282
|
+
def test_child_contract_inherits_parent_fields_without_treating_blanks_as_clears() -> None:
|
|
283
|
+
parent_contract = {
|
|
284
|
+
"central_hypothesis": "The relation changes under a bounded condition.",
|
|
285
|
+
"mechanism_or_relation": "A native mediator links the intervention to the outcome.",
|
|
286
|
+
"target_gap_ids": ["gap-1"],
|
|
287
|
+
"claim_scope": "The measured operating regime.",
|
|
288
|
+
}
|
|
289
|
+
child_contract = {
|
|
290
|
+
"central_hypothesis": "",
|
|
291
|
+
"claim_scope": "A narrower operating regime.",
|
|
292
|
+
}
|
|
293
|
+
|
|
294
|
+
merged = merge_hypothesis_contract(parent_contract, child_contract)
|
|
295
|
+
|
|
296
|
+
assert merged["central_hypothesis"] == parent_contract["central_hypothesis"]
|
|
297
|
+
assert merged["mechanism_or_relation"] == parent_contract["mechanism_or_relation"]
|
|
298
|
+
assert merged["target_gap_ids"] == ["gap-1"]
|
|
299
|
+
assert merged["claim_scope"] == "A narrower operating regime."
|
|
300
|
+
|
|
301
|
+
|
|
302
|
+
def test_route_specific_omission_is_marked_instead_of_being_silently_inherited() -> None:
|
|
303
|
+
parent_contract = {
|
|
304
|
+
"scientific_object": {"object_type": "parent_object"},
|
|
305
|
+
"mechanism_or_relation": "parent mechanism",
|
|
306
|
+
"expected_mechanism": "parent expectation",
|
|
307
|
+
}
|
|
308
|
+
|
|
309
|
+
assert _route_contract_incomplete_fields(
|
|
310
|
+
"mechanism_replacement",
|
|
311
|
+
parent_contract,
|
|
312
|
+
{},
|
|
313
|
+
) == ["mechanism_or_relation"]
|
|
314
|
+
assert _route_contract_incomplete_fields(
|
|
315
|
+
"object_substitution",
|
|
316
|
+
parent_contract,
|
|
317
|
+
{"scientific_object": {"object_type": "child_object"}},
|
|
318
|
+
) == []
|
|
319
|
+
assert _route_contract_noop_fields(
|
|
320
|
+
"mechanism_replacement",
|
|
321
|
+
parent_contract,
|
|
322
|
+
{"mechanism_or_relation": "parent mechanism"},
|
|
323
|
+
) == ["mechanism_or_relation"]
|
|
324
|
+
assert _route_contract_noop_fields(
|
|
325
|
+
"object_substitution",
|
|
326
|
+
parent_contract,
|
|
327
|
+
{"scientific_object": {"object_type": "parent_object"}},
|
|
328
|
+
) == ["scientific_object"]
|
|
329
|
+
|
|
330
|
+
|
|
331
|
+
def test_materialized_child_preserves_parent_contract_and_marks_missing_route_change() -> None:
|
|
332
|
+
parent = SimpleNamespace(
|
|
333
|
+
title="Parent hypothesis",
|
|
334
|
+
abstract="Parent abstract",
|
|
335
|
+
core_contribution="Parent contribution",
|
|
336
|
+
method="Parent method",
|
|
337
|
+
risks="Parent risks",
|
|
338
|
+
tags=["parent"],
|
|
339
|
+
target_defects=["unexplored_gap"],
|
|
340
|
+
components=[],
|
|
341
|
+
component_explanations={},
|
|
342
|
+
root_domains=["physics"],
|
|
343
|
+
discipline_resolution={},
|
|
344
|
+
paper_graph_context="",
|
|
345
|
+
scientific_intervention={
|
|
346
|
+
"hypothesis_contract": {
|
|
347
|
+
"central_hypothesis": "Parent hypothesis remains available.",
|
|
348
|
+
"mechanism_or_relation": "Parent mechanism must not disappear.",
|
|
349
|
+
"target_gap_ids": ["gap-1"],
|
|
350
|
+
}
|
|
351
|
+
},
|
|
352
|
+
)
|
|
353
|
+
plan = EditPlan(
|
|
354
|
+
skill_name="route-test",
|
|
355
|
+
objective="Refine the mechanism.",
|
|
356
|
+
target_defects=["unexplored_gap"],
|
|
357
|
+
component_edits=[],
|
|
358
|
+
validation=ValidationProtocol(),
|
|
359
|
+
guardrails=[],
|
|
360
|
+
memory_refs=[],
|
|
361
|
+
compile_notes="test plan",
|
|
362
|
+
)
|
|
363
|
+
mcts = SimpleNamespace(
|
|
364
|
+
route_id="mechanism_replacement",
|
|
365
|
+
idea_taste_preset=None,
|
|
366
|
+
_skill_prior_for_prompt=lambda _skill_name: 0.0,
|
|
367
|
+
)
|
|
368
|
+
|
|
369
|
+
child = materialize_child_state(
|
|
370
|
+
mcts,
|
|
371
|
+
parent,
|
|
372
|
+
plan,
|
|
373
|
+
{"claim_scope": "A narrower scope."},
|
|
374
|
+
idea_state_cls=lambda **payload: SimpleNamespace(**payload),
|
|
375
|
+
)
|
|
376
|
+
|
|
377
|
+
contract = child.scientific_intervention["hypothesis_contract"]
|
|
378
|
+
assert contract["central_hypothesis"] == "Parent hypothesis remains available."
|
|
379
|
+
assert contract["mechanism_or_relation"] == "Parent mechanism must not disappear."
|
|
380
|
+
assert contract["claim_scope"] == "A narrower scope."
|
|
381
|
+
assert child.scientific_intervention["route_contract_incomplete_fields"] == [
|
|
382
|
+
"mechanism_or_relation"
|
|
383
|
+
]
|
|
384
|
+
|
|
385
|
+
|
|
386
|
+
def test_materialized_child_marks_parent_mechanism_restatement_as_route_noop() -> None:
|
|
387
|
+
parent = SimpleNamespace(
|
|
388
|
+
title="Parent hypothesis",
|
|
389
|
+
abstract="Parent abstract",
|
|
390
|
+
core_contribution="Parent contribution",
|
|
391
|
+
method="Parent method",
|
|
392
|
+
risks="Parent risks",
|
|
393
|
+
tags=["parent"],
|
|
394
|
+
target_defects=["unexplored_gap"],
|
|
395
|
+
components=[],
|
|
396
|
+
component_explanations={},
|
|
397
|
+
root_domains=["physics"],
|
|
398
|
+
discipline_resolution={},
|
|
399
|
+
paper_graph_context="",
|
|
400
|
+
scientific_intervention={
|
|
401
|
+
"hypothesis_contract": {
|
|
402
|
+
"mechanism_or_relation": "Parent mechanism.",
|
|
403
|
+
"target_gap_ids": ["gap-1"],
|
|
404
|
+
}
|
|
405
|
+
},
|
|
406
|
+
)
|
|
407
|
+
plan = EditPlan(
|
|
408
|
+
skill_name="route-test",
|
|
409
|
+
objective="Replace the mechanism.",
|
|
410
|
+
target_defects=["unexplored_gap"],
|
|
411
|
+
component_edits=[],
|
|
412
|
+
validation=ValidationProtocol(),
|
|
413
|
+
guardrails=[],
|
|
414
|
+
memory_refs=[],
|
|
415
|
+
compile_notes="test plan",
|
|
416
|
+
)
|
|
417
|
+
mcts = SimpleNamespace(
|
|
418
|
+
route_id="mechanism_replacement",
|
|
419
|
+
idea_taste_preset=None,
|
|
420
|
+
_skill_prior_for_prompt=lambda _skill_name: 0.0,
|
|
421
|
+
)
|
|
422
|
+
|
|
423
|
+
child = materialize_child_state(
|
|
424
|
+
mcts,
|
|
425
|
+
parent,
|
|
426
|
+
plan,
|
|
427
|
+
{"mechanism_or_relation": "Parent mechanism."},
|
|
428
|
+
idea_state_cls=lambda **payload: SimpleNamespace(**payload),
|
|
429
|
+
)
|
|
430
|
+
|
|
431
|
+
assert "route_contract_incomplete_fields" not in child.scientific_intervention
|
|
432
|
+
assert child.scientific_intervention["route_contract_noop_fields"] == [
|
|
433
|
+
"mechanism_or_relation"
|
|
434
|
+
]
|
|
435
|
+
assert child.scientific_intervention["route_contract_parent_values"] == {
|
|
436
|
+
"mechanism_or_relation": "Parent mechanism."
|
|
437
|
+
}
|
|
438
|
+
|
|
439
|
+
|
|
440
|
+
def test_profile_priority_defects_are_visible() -> None:
|
|
441
|
+
registry = format_defect_registry("formal_theoretical")
|
|
442
|
+
assert "Profile priority: formal_theoretical" in registry
|
|
443
|
+
assert "missing_assumption [profile-priority]" in registry
|
|
444
|
+
assert "proof_gap [profile-priority]" in registry
|
|
445
|
+
|
|
446
|
+
|
|
447
|
+
def test_profile_priority_defects_drive_skill_overlap() -> None:
|
|
448
|
+
assert "missing_boundary_condition" in profile_skill_defect_tags(
|
|
449
|
+
"clinical_health",
|
|
450
|
+
"alternative-path-contrast",
|
|
451
|
+
)
|
|
452
|
+
assert "proof_gap" in profile_skill_defect_tags(
|
|
453
|
+
"formal_theoretical",
|
|
454
|
+
"theory-transfer-injection",
|
|
455
|
+
)
|
|
456
|
+
|
|
457
|
+
|
|
458
|
+
def test_taste_presets_include_scientific_weights_and_normalize() -> None:
|
|
459
|
+
for mode in ("moonshot_inventor", "bridge_builder", "steady_engineer", "ambitious_realist"):
|
|
460
|
+
preset = get_idea_taste_preset(mode)
|
|
461
|
+
assert preset is not None
|
|
462
|
+
assert set(SCORE_WEIGHT_FIELDS).issubset(preset.weights)
|
|
463
|
+
assert sum(preset.weights[field] for field in SCORE_WEIGHT_FIELDS) == pytest.approx(1.0)
|
|
464
|
+
|
|
465
|
+
|
|
466
|
+
def test_cache_key_changes_with_profile_and_rubric_versions() -> None:
|
|
467
|
+
base = evaluation_prompt_cache_key("candidate")
|
|
468
|
+
other_profile = evaluation_prompt_cache_key("candidate", profile_id="clinical_health")
|
|
469
|
+
other_rubric = evaluation_prompt_cache_key("candidate", rubric_version="scientific_rubric_v2")
|
|
470
|
+
assert base != other_profile
|
|
471
|
+
assert base != other_rubric
|
|
472
|
+
|
|
473
|
+
|
|
474
|
+
def _mcts_module():
|
|
475
|
+
pytest.importorskip("faiss")
|
|
476
|
+
return importlib.import_module("src.agents.idea_agent.agent.mcts")
|
|
477
|
+
|
|
478
|
+
|
|
479
|
+
def test_idea_evaluation_scientific_dimensions_are_backward_compatible() -> None:
|
|
480
|
+
mcts = _mcts_module()
|
|
481
|
+
legacy = mcts.IdeaEvaluation.from_payload(
|
|
482
|
+
{
|
|
483
|
+
"novelty": 4,
|
|
484
|
+
"surprise": 3,
|
|
485
|
+
"feasibility": 4,
|
|
486
|
+
"clarity": 3,
|
|
487
|
+
"impact": 4,
|
|
488
|
+
"risk": 1,
|
|
489
|
+
"conciseness": 3,
|
|
490
|
+
"alignment_score": 4,
|
|
491
|
+
"complexity_penalty": 1,
|
|
492
|
+
"protocol_score": 3,
|
|
493
|
+
}
|
|
494
|
+
)
|
|
495
|
+
assert legacy.explanatory_power == 0
|
|
496
|
+
assert "claim_overreach_penalty" in legacy.to_dict()
|
|
497
|
+
low_overreach = mcts.IdeaEvaluation.from_payload(
|
|
498
|
+
{**legacy.to_dict(), "claim_overreach_penalty": 0}
|
|
499
|
+
)
|
|
500
|
+
high_overreach = mcts.IdeaEvaluation.from_payload(
|
|
501
|
+
{**legacy.to_dict(), "claim_overreach_penalty": 5}
|
|
502
|
+
)
|
|
503
|
+
assert low_overreach.composite > high_overreach.composite
|
|
504
|
+
|
|
505
|
+
|
|
506
|
+
def test_fixed_scientific_candidate_fixtures_do_not_lose_to_benchmark_only_cs() -> None:
|
|
507
|
+
mcts = _mcts_module()
|
|
508
|
+
|
|
509
|
+
common = {
|
|
510
|
+
"surprise": 3,
|
|
511
|
+
"feasibility": 4,
|
|
512
|
+
"clarity": 4,
|
|
513
|
+
"impact": 4,
|
|
514
|
+
"risk": 1,
|
|
515
|
+
"conciseness": 3,
|
|
516
|
+
"alignment_score": 4,
|
|
517
|
+
"complexity_penalty": 1,
|
|
518
|
+
"protocol_score": 4,
|
|
519
|
+
"confidence": 0.9,
|
|
520
|
+
}
|
|
521
|
+
benchmark_only_cs = mcts.IdeaEvaluation.from_payload(
|
|
522
|
+
{
|
|
523
|
+
**common,
|
|
524
|
+
"novelty": 5,
|
|
525
|
+
"feasibility": 5,
|
|
526
|
+
"clarity": 3,
|
|
527
|
+
"impact": 3,
|
|
528
|
+
"protocol_score": 2,
|
|
529
|
+
"explanatory_power": 1,
|
|
530
|
+
"identifiability": 1,
|
|
531
|
+
"boundary_calibration": 1,
|
|
532
|
+
"claim_overreach_penalty": 3,
|
|
533
|
+
},
|
|
534
|
+
profile_id="computational_algorithmic",
|
|
535
|
+
)
|
|
536
|
+
fixture_scores = {}
|
|
537
|
+
for name, (profile_id, values) in {
|
|
538
|
+
"materials_mechanism": ("physical_materials_chemical", (4, 5, 5, 4, 1)),
|
|
539
|
+
"medicine_causal": ("clinical_health", (4, 5, 4, 4, 1)),
|
|
540
|
+
"math_counterexample": ("formal_theoretical", (4, 5, 5, 5, 0)),
|
|
541
|
+
"cs_typical": ("computational_algorithmic", (5, 4, 4, 4, 1)),
|
|
542
|
+
}.items():
|
|
543
|
+
novelty, explanatory, identifiability, boundary, overreach = values
|
|
544
|
+
fixture_scores[name] = mcts.IdeaEvaluation.from_payload(
|
|
545
|
+
{
|
|
546
|
+
**common,
|
|
547
|
+
"novelty": novelty,
|
|
548
|
+
"explanatory_power": explanatory,
|
|
549
|
+
"identifiability": identifiability,
|
|
550
|
+
"boundary_calibration": boundary,
|
|
551
|
+
"claim_overreach_penalty": overreach,
|
|
552
|
+
},
|
|
553
|
+
profile_id=profile_id,
|
|
554
|
+
).composite
|
|
555
|
+
|
|
556
|
+
assert fixture_scores["materials_mechanism"] >= benchmark_only_cs.composite
|
|
557
|
+
assert fixture_scores["medicine_causal"] >= benchmark_only_cs.composite
|
|
558
|
+
assert fixture_scores["math_counterexample"] >= benchmark_only_cs.composite
|
|
559
|
+
assert fixture_scores["cs_typical"] >= benchmark_only_cs.composite
|
|
@@ -0,0 +1,48 @@
|
|
|
1
|
+
from __future__ import annotations
|
|
2
|
+
|
|
3
|
+
import pytest
|
|
4
|
+
|
|
5
|
+
from src.agents.idea_agent.utils.core.response_parsing import (
|
|
6
|
+
JsonObjectResponseError,
|
|
7
|
+
parse_json_object_response,
|
|
8
|
+
)
|
|
9
|
+
from src.agents.idea_agent.utils.workflow.ligagent_utils import LigRuntime
|
|
10
|
+
|
|
11
|
+
|
|
12
|
+
class _CapturingAgent:
|
|
13
|
+
model = "mock-model"
|
|
14
|
+
|
|
15
|
+
def __init__(self) -> None:
|
|
16
|
+
self.request_kwargs: dict = {}
|
|
17
|
+
|
|
18
|
+
def chat(self, prompt: str, **kwargs):
|
|
19
|
+
del prompt
|
|
20
|
+
self.request_kwargs = kwargs
|
|
21
|
+
return '{"status": "ok"}'
|
|
22
|
+
|
|
23
|
+
|
|
24
|
+
def test_strict_json_object_parser_accepts_only_one_top_level_object() -> None:
|
|
25
|
+
assert parse_json_object_response('{"status": "ok"}') == {"status": "ok"}
|
|
26
|
+
|
|
27
|
+
with pytest.raises(JsonObjectResponseError):
|
|
28
|
+
parse_json_object_response('["not", "an object"]')
|
|
29
|
+
with pytest.raises(JsonObjectResponseError):
|
|
30
|
+
parse_json_object_response('Preamble\n["fragment"]\n{"status": "ok"}')
|
|
31
|
+
|
|
32
|
+
|
|
33
|
+
def test_runtime_forwards_json_object_mode_without_leaking_internal_flag() -> None:
|
|
34
|
+
agent = _CapturingAgent()
|
|
35
|
+
runtime = LigRuntime(agent)
|
|
36
|
+
|
|
37
|
+
result = runtime.llm_json(
|
|
38
|
+
session=None,
|
|
39
|
+
stage="advanced_analysis",
|
|
40
|
+
op_name="test",
|
|
41
|
+
prompt="Return an object.",
|
|
42
|
+
require_json_object=True,
|
|
43
|
+
response_format={"type": "json_object"},
|
|
44
|
+
)
|
|
45
|
+
|
|
46
|
+
assert result == {"status": "ok"}
|
|
47
|
+
assert agent.request_kwargs["response_format"] == {"type": "json_object"}
|
|
48
|
+
assert "require_json_object" not in agent.request_kwargs
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
"""Core utilities shared across Idea Agent modules."""
|
|
@@ -0,0 +1,60 @@
|
|
|
1
|
+
"""Helpers for optional ablation-results ingestion into LigAgent runs."""
|
|
2
|
+
|
|
3
|
+
from __future__ import annotations
|
|
4
|
+
|
|
5
|
+
import json
|
|
6
|
+
from pathlib import Path
|
|
7
|
+
from typing import Any, Mapping, Optional
|
|
8
|
+
|
|
9
|
+
|
|
10
|
+
def _resolve_ablation_results_file(raw_path: Any) -> Optional[Path]:
|
|
11
|
+
path_text = str(raw_path).strip() if raw_path is not None else ""
|
|
12
|
+
if not path_text:
|
|
13
|
+
return None
|
|
14
|
+
|
|
15
|
+
path = Path(path_text).expanduser()
|
|
16
|
+
if not path.exists():
|
|
17
|
+
return None
|
|
18
|
+
|
|
19
|
+
if path.is_file():
|
|
20
|
+
return path if path.suffix.lower() == ".json" else None
|
|
21
|
+
|
|
22
|
+
json_files = sorted(
|
|
23
|
+
candidate for candidate in path.iterdir() if candidate.is_file() and candidate.suffix.lower() == ".json"
|
|
24
|
+
)
|
|
25
|
+
if not json_files:
|
|
26
|
+
return None
|
|
27
|
+
if len(json_files) > 1:
|
|
28
|
+
raise ValueError(
|
|
29
|
+
f"Expected exactly one JSON file under ablation_results_path={path}, found {len(json_files)}."
|
|
30
|
+
)
|
|
31
|
+
return json_files[0]
|
|
32
|
+
|
|
33
|
+
|
|
34
|
+
def load_ablation_results_payload(run_inputs: Mapping[str, Any]) -> Any:
|
|
35
|
+
"""Resolve ablation results from an optional JSON directory or JSON file path."""
|
|
36
|
+
resolved_file = _resolve_ablation_results_file(run_inputs.get("ablation_results_path"))
|
|
37
|
+
if resolved_file is None:
|
|
38
|
+
return None
|
|
39
|
+
|
|
40
|
+
with resolved_file.open("r", encoding="utf-8") as f:
|
|
41
|
+
payload = json.load(f)
|
|
42
|
+
return payload if payload else None
|
|
43
|
+
|
|
44
|
+
|
|
45
|
+
def ingest_ablation_results_if_available(
|
|
46
|
+
agent: Any,
|
|
47
|
+
run_inputs: Mapping[str, Any],
|
|
48
|
+
logger: Optional[Any] = None,
|
|
49
|
+
) -> bool:
|
|
50
|
+
"""Inject ablation results when a non-empty payload is available."""
|
|
51
|
+
payload = load_ablation_results_payload(run_inputs)
|
|
52
|
+
if not payload:
|
|
53
|
+
if logger is not None:
|
|
54
|
+
logger.info("[LigAgent] No ablation results provided; skipping ingestion.")
|
|
55
|
+
return False
|
|
56
|
+
|
|
57
|
+
agent.ingest_ablation_results(payload)
|
|
58
|
+
if logger is not None:
|
|
59
|
+
logger.info("[LigAgent] Injected ablation results into artifact state.")
|
|
60
|
+
return True
|