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fix: apply lazy init pattern and pydantic-ai fixes to ReportAgent (#12)
Applies the same fixes as Phase 7 HypothesisAgent: - Lazy initialization via _get_agent() to avoid API key requirement at import - Use output_type instead of result_type (pydantic-ai API) - Use result.output instead of result.data - Fix line length issues in tests - Proper mocking of get_model in tests3139749 -
fix: address CodeRabbit Phase 7 review feedback
- Lazy initialize HypothesisAgent's pydantic-ai Agent to avoid requiring API keys at import time (fixes CI failure) - Add explicit default=None to primary_hypothesis field for Pydantic v2 compliancebc74531 -
feat(phase7): implement Hypothesis Agent for mechanistic reasoning
Add HypothesisAgent that generates Drug → Target → Pathway → Effect hypotheses based on collected evidence. Key features: Models: - MechanismHypothesis: structured hypothesis with confidence scoring - HypothesisAssessment: container for hypotheses with knowledge gaps Utilities: - MMR (Maximal Marginal Relevance) for diverse evidence selection - Sentence-aware truncation for clean text processing Agent: - HypothesisAgent generates 2-4 testable hypotheses per query - Integrated with EmbeddingService for semantic evidence selection Orchestrator: - Refactored MagenticOrchestrator into smaller methods - Added "hypothesizing" event type for UI feedback - Workflow: Search → Hypothesize → Targeted Search → Judge Tests: 53/53 passing, mypy clean, ruff cleanc690006 -
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 -
fix: linting and types for phase 5
1922dbd -
refactor(phase4): address CodeRabbit review
- Pin uv version in Dockerfile and add non-root user - Use OrchestratorConfig for timeout in app.py - Use timezone.utc for timestamps in models.py36983ae -
feat(phase4): Orchestrator and UI complete
25c3a8b -
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(phase2): implement search slice (PubMed, Web, Orchestrator) (#4)
Implemented search tools with strict TDD and scatter-gather pattern. 100% test coverage.499170b
