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feat: SPEC_01 (Termination) + SPEC_02 (E2E Tests) implementation (#66)
Unverified signature* docs: sync documentation with codebase reality - Fix test count 127→142+ (index.md) - Fix OpenAI model gpt-5.1→gpt-5 to match config.py (CLAUDE.md) - Mark phases 13-14 as COMPLETE (roadmap.md) - Auto-format 2 test files (ruff) * docs: add specs for P0 termination fix and P1 E2E testing SPEC_01: Demo Termination Fix - Investigate if max_round_count actually works - Add hard timeout (5 min) for hackathon - Add round progress indicator SPEC_02: E2E Testing - Smoke tests (does it run?) - Structure tests (is output valid?) - Quality tests (is output useful?) - Must pass BEFORE adding new features (OpenAlex, etc.) * docs: fix spec accuracy (line numbers and test counts) SPEC_01: Line reference 112 → 110 (actual location of .with_standard_manager) SPEC_02: Test count 142 → 140 (verified with pytest --collect-only) Both specs now match codebase exactly per audit verification. * feat: Implement SPEC_01 (Termination) and SPEC_02 (E2E Tests) - SPEC_01: Added timeout (300s) and progress…0257d2f -
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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docs: address CodeRabbit feedback for Phase 12 PR
- Add `text` fence language to architecture diagrams (MD040) - Update roadmap directory structure (remove websearch, add clinicaltrials/biorxiv) - Mark Phase 12 as COMPLETE in roadmap - Rename test_mcp_server.py to test_mcp_tools_live.py for clarity - Update hackathon requirements with MCP implementation status - Fix async pattern in Modal integration docf9cb2b7 -
docs: add Phase 14 Demo Video & Hackathon Submission specification
- Created documentation for the demo video and hackathon submission process, outlining goals, requirements, and deadlines. - Included detailed specifications for the demo video format, content, and recommended tools. - Established a checklist for submission requirements, including social media posts and HuggingFace Space configuration. - Summarized prize eligibility and potential awards based on completed phases. Files added: - docs/implementation/14_phase_demo_submission.mde16b9e6
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feat(docs): update implementation roadmap and add specs for Phases 9-11
- Updated the implementation roadmap to reflect the completion of Phases 1-8. - Added detailed specifications for Phase 9: Remove DuckDuckGo, Phase 10: ClinicalTrials.gov Integration, and Phase 11: bioRxiv Preprint Integration. - Enhanced the status section to indicate the completion of Phases 1-8 and readiness for Phases 9-11.3fcd8e7 -
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 -
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 -
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 -
fix: markdown lint warnings in roadmap.md
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fix: add bash language identifier to code block (CodeRabbit)
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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: 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