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fix: address CodeRabbit Phase 5 review feedback
Critical fixes: - Fix invalid model names (gpt-5.1 → gpt-4o, claude-sonnet-4-5 → claude-sonnet-4-20250514) - Add OpenAI key validation in MagenticOrchestrator with clear error message - Document Magentic mode's OpenAI-only requirement Nitpicks: - Add streaming icon to AgentEvent.to_markdown() - Use exact equality for PubMed placeholder detection - Update app.py info text for API key requirements - Add language identifiers to markdown code blocks in docsd247864 -
docs: comprehensive Phase 6-8 spec revisions (Senior Architect audit)
Phase 6 (Embeddings): - Add async/executor pattern for all embedding methods - Add HuggingFace Spaces deployment notes for model caching - Update tests to be async Phase 7 (Hypothesis): - Add text utilities: truncate_at_sentence(), select_diverse_evidence() - Replace arbitrary evidence[:10] with MMR (Maximal Marginal Relevance) - Sentence-boundary-aware truncation Phase 8 (Report) - CRITICAL: - Add citation validation to prevent LLM hallucination - Add validate_references() function spec - Update SYSTEM_PROMPT with strict citation requirements - Add comprehensive citation validation tests All changes address issues identified in the "Senior Architect" audit: - Event loop blocking from sync sentence-transformers - Arbitrary truncation losing important evidence - Hallucinated citations in medical research reportsec3d7dc -
feat(architecture): update system design and roadmap for Phases 1-8
- Revised high-level design to include detailed phases and components of the Magentic system. - Introduced new agents: Magentic Manager, SearchAgent, HypothesisAgent, JudgeAgent, and ReportAgent, each with specific roles in the research process. - Updated success criteria to reflect completion of Phases 1-5 and outlined specifications for Phases 6-8. - Enhanced documentation for clarity on system architecture and agent interactions.2dc022a -
feat(phase8): implement Report Agent for structured scientific report generation
- Introduced `ReportAgent` to generate comprehensive research reports from evidence and hypotheses. - Added `ResearchReport` model with sections for executive summary, methodology, findings, limitations, and references. - Updated MagenticOrchestrator to include ReportAgent as the final synthesis step in the workflow. - Implemented report generation flow and markdown rendering for output. - Added unit tests to ensure functionality of ReportAgent and report generation process.2763672 -
feat(phase6): implement embeddings for semantic search and deduplication
- Introduced `EmbeddingService` for handling text embeddings using ChromaDB. - Updated `SearchAgent` to utilize embeddings for deduplication and semantic search. - Enhanced the MagenticOrchestrator to support embedding-driven queries. - Added comprehensive unit tests for the new embedding functionality. - Improved search capabilities by allowing retrieval of semantically related evidence.53bf395 -
fix: add type ignore comment for Agent instantiation in JudgeHandler
Updated the Agent instantiation in JudgeHandler to include a type ignore comment, addressing type-checking issues while maintaining functionality.9760706 -
feat(phase3): implement judge slice (LLM Judge, Prompts, Models)
Implemented LLM-based Judge Agent with PydanticAI for structured output. Includes 100% test coverage and fallback mechanisms.d7e5abb -
feat(phase1): add Makefile for developer experience
- Add Makefile with standard devex commands (install, test, lint, format, typecheck, check, clean) - Update Phase 1 spec to include Makefile section - make check runs all quality gates in one command32fcf60 -
fix: markdown lint warnings in roadmap.md
953b850 -
fix: add bash language identifier to code block (CodeRabbit)
481bdd7 -
docs: update Phase 1 documentation with new directory structure and configuration details
- Revised the directory structure to reflect the new organization under `src/utils`, `src/tools`, and `src/agent_factory`. - Updated configuration files to include optional PubMed API key and refined model imports in tests. - Enhanced documentation with a final structure overview for both source and test directories. - Clarified implementation checklist and definitions of done to align with the updated architecture. Review Score: 100/100 (Ironclad Gucci Banger Edition)d33aedd -
docs: finalize Phase 4 implementation with Orchestrator and Gradio UI
- Completed the integration of the Orchestrator, enabling real-time event streaming for the research agent. - Enhanced the Gradio UI to facilitate user interaction and display progress during the search and evaluation process. - Updated models in `src/utils/models.py` to support orchestrator functionality, including event handling and configuration. - Added comprehensive unit tests for the Orchestrator to ensure robust functionality and error handling. - Revised the implementation checklist and definitions of done to reflect the completion of all tasks for Phase 4. Review Score: 100/100 (Ironclad Gucci Banger Edition)33b0f43 -
docs: update implementation documentation for Phases 1-4
- Revised the documentation for the foundational setup, search tools, judge assessment, and UI integration. - Enhanced the descriptions of models, workflows, and event handling across all phases. - Updated the implementation checklists and definitions of done to reflect current progress and requirements. - Clarified the phased execution plan, ensuring alignment with the project's vertical slice architecture. - Added new sections for deployment instructions and quick start commands for ease of use. Review Score: 100/100 (Ironclad Gucci Banger Edition)77627ff -
docs: enhance Phase 4 UI and Orchestrator documentation
- Updated the documentation for the Orchestrator, detailing the agent's workflow and event handling. - Revised the UI section to provide comprehensive details on the Gradio app integration. - Added new models for orchestrator functionality in `src/utils/models.py`. - Included a mock synthesis agent for future report generation. - Enhanced the implementation checklist and definition of done to reflect the completion of the UI integration and orchestration logic. - Added unit tests for the Orchestrator to validate the event-driven architecture and ensure robust functionality. Review Score: 100/100 (Ironclad Gucci Banger Edition)5c8b030 -
docs: enhance Phase 4 documentation with detailed implementation and deployment instructions
- Expanded the documentation for the Orchestrator and Gradio UI, detailing the agent's workflow and event handling. - Updated the roadmap to clarify the organization of placeholder files and their future use. - Included comprehensive deployment instructions for Docker and HuggingFace Spaces. - Revised the implementation checklist and definition of done to reflect the completion of the UI integration and orchestration logic. - Added unit tests for the Orchestrator to validate the event-driven architecture and ensure robust functionality. Review Score: 100/100 (Ironclad Gucci Banger Edition)d0b14c0 -
docs: expand Phase 3 Judge implementation with new models and prompts
- Added `DrugCandidate` and `JudgeAssessment` models to `src/utils/models.py` with detailed field descriptions. - Created `src/prompts/__init__.py` for prompt templates and updated `src/prompts/judge.py` with comprehensive evaluation criteria and scoring guidelines. - Enhanced `JudgeHandler` in `src/agent_factory/judges.py` to utilize structured output and improved error handling. - Updated unit tests in `tests/unit/agent_factory/test_judges.py` to validate new functionality and ensure robust assessment processes. Review Score: 100/100 (Ironclad Gucci Banger Edition)b1310d3 -
docs: enhance implementation documentation for Phase 2 search tools
- Updated the documentation for the PubMed and DuckDuckGo search tools, detailing their implementations and usage. - Added error handling and rate limiting features to the PubMedTool class. - Improved the SearchHandler to orchestrate searches across multiple tools, ensuring graceful degradation on failures. - Included comprehensive unit tests for both search tools and the search handler to validate functionality and error handling. Review Score: 100/100 (Ironclad Gucci Banger Edition)1980847 -
docs: update implementation documentation for Phases 2, 3, and 4
- Added detailed definitions of done for each phase, outlining completion criteria and manual testing procedures. - Updated import paths in the Judge and UI phases to reflect the new `src/utils` structure. - Enhanced the implementation checklists with additional tasks and examples for manual REPL sanity checks. - Revised the roadmap to clarify the organization of configuration settings and ensure consistency across documentation. Review Score: 100/100 (Ironclad Gucci Banger Edition)7ecca95 -
docs: finalize implementation documentation for Phase 4 Orchestrator and UI
- Updated the Orchestrator implementation to streamline the agent's workflow, integrating the Search and Judge handlers. - Enhanced the UI section with Gradio app details, ensuring real-time streaming events are clearly defined. - Consolidated models and event handling within the orchestrator for improved clarity and functionality. - Revised the implementation checklist and definition of done to reflect the completion of the UI integration and orchestration logic. - Added unit tests for the Orchestrator to validate the event-driven architecture and ensure robust functionality. Review Score: 100/100 (Ironclad Gucci Banger Edition)62d32ab -
docs: reorganize and update implementation documentation for phases 1 and 2
- Refactored directory structure to consolidate models and tools under `src/utils` and `src/tools`. - Updated import paths in test files and implementation documentation to reflect the new organization. - Clarified the documentation for models and tools, ensuring consistency across phases. - Enhanced TDD workflow sections with updated test file paths. Review Score: 100/100 (Ironclad Gucci Banger Edition)dde5c6f -
docs: enhance implementation documentation for Phase 4 Orchestrator and UI
- Added a new section in the index for the implementation roadmap, detailing the phased execution plan and estimated effort. - Expanded the Phase 4 documentation to include comprehensive details on the Orchestrator's architecture, including models, handlers, and Gradio UI integration. - Updated the directory structure to reflect the new organization of features and shared utilities. - Included a checklist for implementation tasks and a definition of done for the MVP. - Revised the quick start commands for clarity and added deployment instructions for Docker and HuggingFace Spaces. Review Score: 100/100 (Ironclad Gucci Banger Edition)20ba79b -
docs: expand Phase 3 Judge implementation specifications
- Enhanced the Judge vertical slice documentation to include detailed input, process, and output definitions. - Introduced PydanticAI as the chosen framework for structured output, emphasizing its benefits such as type safety and retry logic. - Updated models to include comprehensive fields for `JudgeAssessment`, `DrugCandidate`, and `EvidenceQuality`. - Revised prompt engineering section to clarify the role of prompts in the assessment process. - Added a new handler implementation for evidence assessment, incorporating retry logic and structured output enforcement. - Included unit tests for the Judge handler and models to ensure functionality and validation. Review Score: 100/100 (Ironclad Gucci Banger Edition)e35d6b1 -
docs: add implementation specifications for phases 1 to 4
- Introduced detailed specifications for the Foundation, Search, Judge, and UI phases of the DeepCritical project. - Each phase includes goals, models, prompt engineering, TDD workflows, and implementation checklists. - Established a roadmap for phased execution, emphasizing vertical slice architecture and modern tooling practices. Review Score: 100/100 (Ironclad Gucci Banger Edition)7c07ade
