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Commit History
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fix: complete audit fixes for documentation accuracy
Code Changes: - Remove DeepCriticalError backwards-compat alias (src/utils/exceptions.py) Documentation Accuracy Fixes: - Update CLAUDE.md, AGENTS.md, GEMINI.md: "Phases 1-13" → "Phases 1-14" - Replace 11_phase_biorxiv.md with 11_phase_europepmc.md (actual implementation) - Fix all bioRxiv → Europe PMC references in: - workflow-diagrams.md (mermaid diagrams) - 05_phase_magentic.md (code examples) - 04_phase_ui.md (imports) - roadmap.md (directory tree, phase list) - index.md (links) All 127 tests still pass. Documentation now accurately reflects codebase.e720905
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rebrand: DeepCritical → DeepBoner (sexual health research agent)
🍆 AI-Native Sexual Health Research Agent - Package renamed: deepcritical → deepboner - New focus: sexual wellness, ED, hormone therapy, libido, reproductive health - Exception class: DeepCriticalError → DeepBonerError (with backwards compat) - UI examples updated for sexual health queries - Modal app renamed: deepboner-code-execution - Fixed pre-existing mypy issue (Modal API: uv_pip_install → pip_install) 46 files updated across: - Core: pyproject.toml, README.md, CLAUDE.md, AGENTS.md, GEMINI.md - Source: app.py, mcp_tools.py, exceptions.py, code_execution.py - Docs: ~25 markdown files - Examples: 8 demo scripts - Tests: exception tests updated All tests passing (102 passed, 6 skipped)5d12635
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fix: address CodeRabbit feedback and P0 blockers
Code Fixes (HIGH priority): - Add API key/provider validation to prevent silent auth failures - Fix hardcoded manager model in orchestrator_magentic.py (now uses settings.openai_model) - Add bounds checking to JSON extraction in judges.py (prevents IndexError) - Fix fragile test assertion in test_judges_hf.py Code Quality (MEDIUM priority): - Add explicit type annotation for models_to_try: list[str] - Fix structured logging (f-string → structured params) - Align fallback query count (3 queries) between handlers Test Improvements: - Add @pytest.mark.unit decorator to TestHFInferenceJudgeHandler Documentation Sync: - Update Phase 3 docs to match actual implementation: - __init__ signature (simplified, no inline imports) - _extract_json (string split with bounds checking) - _call_with_retry (tenacity decorator, asyncio.get_running_loop()) - assess method (simplified model loop) - Update Phase 4 docs with ChatInterface additional_inputs for BYOK All 104 tests pass.f985224 -
feat: implement HFInferenceJudgeHandler for free-tier AI analysis
Replace MockJudgeHandler with real AI analysis using HuggingFace Inference API: - Add HFInferenceJudgeHandler with chat_completion API - Model fallback chain: Llama 3.1 → Mistral → Zephyr (ungated) - Robust JSON extraction (handles markdown blocks, nested braces) - Tenacity retry with exponential backoff for rate limits - Fix app.py to use HF Inference when no paid API keys present Priority: User API key → Env API key → HF Inference (free) Hackathon judges now get real AI analysis without needing API keys. Set HF_TOKEN as Space secret for best model (Llama 3.1).7fab6d4
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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: 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: 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: 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