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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: pydantic-ai v1 compatibility and Anthropic model update
- Use result.output instead of deprecated result.data (pydantic-ai v1) - Update Anthropic model to claude-sonnet-4-5 - Remove redundant cast in judges.py - Add orchestrator_demo example for end-to-end testing - Fix NCBI_API_KEY placeholder handling in pubmed.py - Update tests to use .output instead of .data4732667 -
feat(phase1): Foundation & Tooling complete
* feat: initialize deepcritical project structure with core configuration and main functionality - Added initial project files including `.python-version`, `pyproject.toml`, and main application logic in `main.py`. - Implemented application configuration using Pydantic in `src/utils/config.py` with environment variable support. - Created directory structure for source code and tests, including placeholders for agents, prompts, tools, and utilities. - Added unit tests for configuration loading and validation in `tests/unit/utils/test_config.py`. Review Score: 100/100 (Ironclad Gucci Banger Edition) * feat(phase1): complete foundation with Python 3.11, tests, and tooling - Fix Python version to 3.11 for HuggingFace Spaces compatibility - Add config.py with pydantic-settings for typed configuration - Add exceptions.py with custom exception hierarchy - Add conftest.py with test fixtures (sample_evidence deferred to Phase 2) - Add .env.example and .pre-commit-config.yaml - Remove refere…069f0a0
