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/swarm/team_lifecycle.py +910 -0
- src/harness/src/openharness/swarm/types.py +398 -0
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- src/harness/src/openharness/tasks/local_agent_task.py +28 -0
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- src/harness/src/openharness/themes/loader.py +55 -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
- src/memory/api/faiss_memory_system_api.py +228 -0
- src/memory/api/slot_process_api.py +827 -0
- src/memory/api/symbolic_memory_system_api.py +572 -0
- src/memory/memory_system/__init__.py +48 -0
- src/memory/memory_system/component_taxonomy.py +430 -0
- src/memory/memory_system/llm.py +437 -0
- src/memory/memory_system/models.py +168 -0
- src/memory/memory_system/user_prompt.py +418 -0
- src/memory/memory_system/utils.py +282 -0
- src/memory/memory_system/vectorstore.py +311 -0
- src/memory/memory_system/working_slot.py +99 -0
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- src/pipeline/discipline_taxonomy.py +916 -0
- src/pipeline/evidence_coverage_ledger.py +1150 -0
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- src/pipeline/retrieval_lanes.py +889 -0
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- 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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"""End-to-end, design-only Research Plan TeX/PDF rendering orchestration."""
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engine = resolve_executable(
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explicit=latex_engine,
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environment_variable="SCIENCE_LATEX_ENGINE",
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configured=settings.get("engine"),
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fallback="pdflatex",
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label="LaTeX engine",
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environment_variable="SCIENCE_BIBTEX",
|
|
104
|
+
configured=settings.get("bibtex"),
|
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105
|
+
fallback="bibtex",
|
|
106
|
+
label="BibTeX engine",
|
|
107
|
+
)
|
|
108
|
+
except LatexCompilerError as error:
|
|
109
|
+
raise AuthorRenderingError("latex_compile", str(error), paths=paths) from error
|
|
110
|
+
try:
|
|
111
|
+
compile_result = compile_latex_project(
|
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+
tex.project_dir,
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|
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|
+
main_tex=tex.main_tex,
|
|
114
|
+
latex_engine=engine,
|
|
115
|
+
bibtex=bibtex_engine,
|
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116
|
+
run_bibtex=bool(tex.bibliography.emitted_keys),
|
|
117
|
+
timeout_seconds=max(1, int(compile_timeout_seconds)),
|
|
118
|
+
staged_pdf_path=paths.staged_pdf,
|
|
119
|
+
logger=logger,
|
|
120
|
+
)
|
|
121
|
+
except LatexCompilerError as error:
|
|
122
|
+
writer.discard_staged_pdf(paths)
|
|
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|
+
raise AuthorRenderingError("latex_compile", str(error), paths=paths) from error
|
|
124
|
+
try:
|
|
125
|
+
writer.publish_compile_diagnostics(paths, report=compile_result.report, log_text=compile_result.log_text)
|
|
126
|
+
except RenderArtifactError as error:
|
|
127
|
+
writer.discard_staged_pdf(paths)
|
|
128
|
+
raise AuthorRenderingError("artifacts", str(error), paths=paths) from error
|
|
129
|
+
if not compile_result.success:
|
|
130
|
+
writer.discard_staged_pdf(paths)
|
|
131
|
+
raise AuthorRenderingError(
|
|
132
|
+
"latex_compile",
|
|
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|
+
"LaTeX compilation failed; retained compile log and structured diagnostics",
|
|
134
|
+
paths=paths,
|
|
135
|
+
)
|
|
136
|
+
try:
|
|
137
|
+
renderer = resolve_executable(
|
|
138
|
+
explicit=pdf_renderer,
|
|
139
|
+
environment_variable="SCIENCE_PDF_RENDERER",
|
|
140
|
+
configured=settings.get("pdf_renderer"),
|
|
141
|
+
fallback="pdftoppm",
|
|
142
|
+
label="PDF renderer",
|
|
143
|
+
)
|
|
144
|
+
validation = validate_pdf(
|
|
145
|
+
paths.staged_pdf,
|
|
146
|
+
renderer=renderer,
|
|
147
|
+
timeout_seconds=max(1, int(settings.get("pdf_validation_timeout_seconds") or 60)),
|
|
148
|
+
logger=logger,
|
|
149
|
+
)
|
|
150
|
+
writer.publish_pdf_validation(paths, validation.report)
|
|
151
|
+
except (PdfValidationError, LatexCompilerError, RenderArtifactError) as error:
|
|
152
|
+
if isinstance(error, PdfValidationError) and error.report is not None:
|
|
153
|
+
try:
|
|
154
|
+
writer.publish_pdf_validation(paths, error.report)
|
|
155
|
+
except RenderArtifactError:
|
|
156
|
+
pass
|
|
157
|
+
writer.discard_staged_pdf(paths)
|
|
158
|
+
raise AuthorRenderingError("pdf_validation", str(error), paths=paths) from error
|
|
159
|
+
try:
|
|
160
|
+
writer.publish_validated_pdf(paths)
|
|
161
|
+
except RenderArtifactError as error:
|
|
162
|
+
raise AuthorRenderingError("artifacts", str(error), paths=paths) from error
|
|
163
|
+
return AuthorRenderingResult(artifacts=paths, tex=tex, pdf_validation=validation)
|
|
164
|
+
|
|
165
|
+
|
|
166
|
+
__all__ = ["AuthorRenderingError", "AuthorRenderingResult", "render_research_plan_document"]
|
|
@@ -0,0 +1,187 @@
|
|
|
1
|
+
"""Atomic, non-overwriting publication of Author TeX/PDF render artifacts."""
|
|
2
|
+
|
|
3
|
+
from __future__ import annotations
|
|
4
|
+
|
|
5
|
+
from dataclasses import dataclass
|
|
6
|
+
import json
|
|
7
|
+
import os
|
|
8
|
+
from pathlib import Path
|
|
9
|
+
import tempfile
|
|
10
|
+
from typing import Any, Mapping
|
|
11
|
+
|
|
12
|
+
from .tex_renderer import TexRenderResult
|
|
13
|
+
|
|
14
|
+
|
|
15
|
+
class RenderArtifactError(RuntimeError):
|
|
16
|
+
"""Raised when a render artifact cannot be allocated or published safely."""
|
|
17
|
+
|
|
18
|
+
|
|
19
|
+
@dataclass(frozen=True)
|
|
20
|
+
class AuthorRenderArtifactPaths:
|
|
21
|
+
timestamp: str
|
|
22
|
+
preparation_collision_index: int
|
|
23
|
+
render_collision_index: int
|
|
24
|
+
project_dir: Path
|
|
25
|
+
tex: Path
|
|
26
|
+
bibtex: Path
|
|
27
|
+
bibliography_needs_completion: Path
|
|
28
|
+
render_manifest: Path
|
|
29
|
+
compile_log: Path
|
|
30
|
+
compile_json: Path
|
|
31
|
+
pdf_validation_json: Path
|
|
32
|
+
pdf: Path
|
|
33
|
+
staged_pdf: Path
|
|
34
|
+
|
|
35
|
+
def as_dict(self) -> dict[str, str | int]:
|
|
36
|
+
return {
|
|
37
|
+
"timestamp": self.timestamp,
|
|
38
|
+
"preparation_collision_index": self.preparation_collision_index,
|
|
39
|
+
"render_collision_index": self.render_collision_index,
|
|
40
|
+
"project_dir": str(self.project_dir),
|
|
41
|
+
"tex": str(self.tex),
|
|
42
|
+
"bibtex": str(self.bibtex),
|
|
43
|
+
"bibliography_needs_completion": str(self.bibliography_needs_completion),
|
|
44
|
+
"render_manifest": str(self.render_manifest),
|
|
45
|
+
"compile_log": str(self.compile_log),
|
|
46
|
+
"compile_json": str(self.compile_json),
|
|
47
|
+
"pdf_validation_json": str(self.pdf_validation_json),
|
|
48
|
+
"pdf": str(self.pdf),
|
|
49
|
+
}
|
|
50
|
+
|
|
51
|
+
|
|
52
|
+
def _json_text(payload: object) -> str:
|
|
53
|
+
return json.dumps(payload, ensure_ascii=False, sort_keys=True, indent=2, allow_nan=False) + "\n"
|
|
54
|
+
|
|
55
|
+
|
|
56
|
+
def _write_bytes_without_overwrite(path: Path, content: bytes) -> None:
|
|
57
|
+
temporary: Path | None = None
|
|
58
|
+
try:
|
|
59
|
+
path.parent.mkdir(parents=True, exist_ok=True)
|
|
60
|
+
descriptor, raw_path = tempfile.mkstemp(prefix=f".{path.name}.", suffix=".tmp", dir=path.parent)
|
|
61
|
+
temporary = Path(raw_path)
|
|
62
|
+
with os.fdopen(descriptor, "wb") as handle:
|
|
63
|
+
handle.write(content)
|
|
64
|
+
handle.flush()
|
|
65
|
+
os.fsync(handle.fileno())
|
|
66
|
+
try:
|
|
67
|
+
os.link(temporary, path)
|
|
68
|
+
except FileExistsError as error:
|
|
69
|
+
raise RenderArtifactError(f"artifact target already exists: {path}") from error
|
|
70
|
+
except OSError:
|
|
71
|
+
descriptor = os.open(path, os.O_WRONLY | os.O_CREAT | os.O_EXCL)
|
|
72
|
+
with os.fdopen(descriptor, "wb") as handle, temporary.open("rb") as source:
|
|
73
|
+
handle.write(source.read())
|
|
74
|
+
handle.flush()
|
|
75
|
+
os.fsync(handle.fileno())
|
|
76
|
+
except OSError as error:
|
|
77
|
+
raise RenderArtifactError(f"cannot publish artifact '{path.name}': {error}") from error
|
|
78
|
+
finally:
|
|
79
|
+
if temporary is not None:
|
|
80
|
+
temporary.unlink(missing_ok=True)
|
|
81
|
+
|
|
82
|
+
|
|
83
|
+
def _write_text_without_overwrite(path: Path, content: str) -> None:
|
|
84
|
+
_write_bytes_without_overwrite(path, content.encode("utf-8"))
|
|
85
|
+
|
|
86
|
+
|
|
87
|
+
class AuthorRenderArtifactWriter:
|
|
88
|
+
"""Reserve one timestamped artifact family and publish it without overwrites."""
|
|
89
|
+
|
|
90
|
+
def __init__(self, output_dir: str | Path) -> None:
|
|
91
|
+
self.output_dir = Path(output_dir).expanduser().resolve()
|
|
92
|
+
|
|
93
|
+
def allocate(
|
|
94
|
+
self,
|
|
95
|
+
*,
|
|
96
|
+
timestamp: str,
|
|
97
|
+
preparation_collision_index: int,
|
|
98
|
+
) -> AuthorRenderArtifactPaths:
|
|
99
|
+
try:
|
|
100
|
+
self.output_dir.mkdir(parents=True, exist_ok=True)
|
|
101
|
+
except OSError as error:
|
|
102
|
+
raise RenderArtifactError(f"cannot create Author render output directory: {error}") from error
|
|
103
|
+
preparation_suffix = "" if preparation_collision_index == 0 else f"_{preparation_collision_index}"
|
|
104
|
+
for render_collision_index in range(1000):
|
|
105
|
+
render_suffix = "" if render_collision_index == 0 else f"_render{render_collision_index}"
|
|
106
|
+
stem = f"research_plan_{timestamp}{preparation_suffix}{render_suffix}"
|
|
107
|
+
paths = AuthorRenderArtifactPaths(
|
|
108
|
+
timestamp=timestamp,
|
|
109
|
+
preparation_collision_index=preparation_collision_index,
|
|
110
|
+
render_collision_index=render_collision_index,
|
|
111
|
+
project_dir=self.output_dir / f"{stem}_project",
|
|
112
|
+
tex=self.output_dir / f"{stem}.tex",
|
|
113
|
+
bibtex=self.output_dir / f"references_{timestamp}{preparation_suffix}{render_suffix}.bib",
|
|
114
|
+
bibliography_needs_completion=self.output_dir
|
|
115
|
+
/ f"bibliography_needs_completion_{timestamp}{preparation_suffix}{render_suffix}.json",
|
|
116
|
+
render_manifest=self.output_dir / f"research_plan_render_{timestamp}{preparation_suffix}{render_suffix}.json",
|
|
117
|
+
compile_log=self.output_dir / f"compile_{timestamp}{preparation_suffix}{render_suffix}.log",
|
|
118
|
+
compile_json=self.output_dir / f"compile_{timestamp}{preparation_suffix}{render_suffix}.json",
|
|
119
|
+
pdf_validation_json=self.output_dir / f"pdf_validation_{timestamp}{preparation_suffix}{render_suffix}.json",
|
|
120
|
+
pdf=self.output_dir / f"{stem}.pdf",
|
|
121
|
+
staged_pdf=self.output_dir / f".{stem}.pdf.staging",
|
|
122
|
+
)
|
|
123
|
+
targets = [
|
|
124
|
+
paths.project_dir,
|
|
125
|
+
paths.tex,
|
|
126
|
+
paths.bibtex,
|
|
127
|
+
paths.bibliography_needs_completion,
|
|
128
|
+
paths.render_manifest,
|
|
129
|
+
paths.compile_log,
|
|
130
|
+
paths.compile_json,
|
|
131
|
+
paths.pdf_validation_json,
|
|
132
|
+
paths.pdf,
|
|
133
|
+
paths.staged_pdf,
|
|
134
|
+
]
|
|
135
|
+
if not any(target.exists() for target in targets):
|
|
136
|
+
return paths
|
|
137
|
+
raise RenderArtifactError(f"could not allocate an unused render artifact family for timestamp '{timestamp}'")
|
|
138
|
+
|
|
139
|
+
def publish_sources(self, rendered: TexRenderResult, paths: AuthorRenderArtifactPaths) -> None:
|
|
140
|
+
if rendered.project_dir.resolve() != paths.project_dir.resolve():
|
|
141
|
+
raise RenderArtifactError("rendered TeX project does not match its allocated artifact directory")
|
|
142
|
+
try:
|
|
143
|
+
_write_bytes_without_overwrite(paths.tex, rendered.main_tex.read_bytes())
|
|
144
|
+
_write_bytes_without_overwrite(paths.bibtex, rendered.bibtex.read_bytes())
|
|
145
|
+
_write_text_without_overwrite(
|
|
146
|
+
paths.bibliography_needs_completion,
|
|
147
|
+
_json_text(
|
|
148
|
+
{
|
|
149
|
+
"schema_version": "research_plan_author_bibliography_completion_v1",
|
|
150
|
+
"needs_completion": list(rendered.bibliography.needs_completion),
|
|
151
|
+
}
|
|
152
|
+
),
|
|
153
|
+
)
|
|
154
|
+
_write_text_without_overwrite(paths.render_manifest, _json_text(rendered.as_dict()))
|
|
155
|
+
except OSError as error:
|
|
156
|
+
raise RenderArtifactError(f"cannot publish generated TeX/BibTeX sources: {error}") from error
|
|
157
|
+
|
|
158
|
+
def publish_compile_diagnostics(
|
|
159
|
+
self,
|
|
160
|
+
paths: AuthorRenderArtifactPaths,
|
|
161
|
+
*,
|
|
162
|
+
report: Mapping[str, Any],
|
|
163
|
+
log_text: str,
|
|
164
|
+
) -> None:
|
|
165
|
+
_write_text_without_overwrite(paths.compile_log, str(log_text))
|
|
166
|
+
_write_text_without_overwrite(paths.compile_json, _json_text(dict(report)))
|
|
167
|
+
|
|
168
|
+
def publish_pdf_validation(self, paths: AuthorRenderArtifactPaths, report: Mapping[str, Any]) -> None:
|
|
169
|
+
_write_text_without_overwrite(paths.pdf_validation_json, _json_text(dict(report)))
|
|
170
|
+
|
|
171
|
+
def publish_validated_pdf(self, paths: AuthorRenderArtifactPaths) -> None:
|
|
172
|
+
if not paths.staged_pdf.is_file():
|
|
173
|
+
raise RenderArtifactError("validated PDF staging file does not exist")
|
|
174
|
+
try:
|
|
175
|
+
_write_bytes_without_overwrite(paths.pdf, paths.staged_pdf.read_bytes())
|
|
176
|
+
finally:
|
|
177
|
+
paths.staged_pdf.unlink(missing_ok=True)
|
|
178
|
+
|
|
179
|
+
def discard_staged_pdf(self, paths: AuthorRenderArtifactPaths) -> None:
|
|
180
|
+
paths.staged_pdf.unlink(missing_ok=True)
|
|
181
|
+
|
|
182
|
+
|
|
183
|
+
__all__ = [
|
|
184
|
+
"AuthorRenderArtifactPaths",
|
|
185
|
+
"AuthorRenderArtifactWriter",
|
|
186
|
+
"RenderArtifactError",
|
|
187
|
+
]
|