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feat: Complete Phase 9 Source Cleanup (Remove WebTool) (#14)
* feat: complete Phase 9 source cleanup - Removed WebTool (src/tools/websearch.py) and related tests - Updated SearchHandler and models to support only PubMed - Refactored all examples and tests to remove web search dependencies - Added verification tests to ensure no WebTool references remain - Fixed all unit tests to align with strict 'pubmed' source typing * fix: address CodeRabbit review feedback - Deduplicate tenacity dependency in pyproject.toml - Remove 'and web' from search agent description - Normalize Citation source to 'pubmed' in search agent - Update app.py markdown to remove web search references - Update embeddings demo with realistic PubMed URL/author - Enhance SearchHandler tests to verify multi-tool aggregation * refactor: replace mock data with real PubMed data in embeddings demo * fix: address CodeRabbit review feedback - Fix nested test_search_handler_pubmed_only (was inside another test, never ran) - Improve test_no_webtool_references to catch `from src.tool…cd004e1
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feat(examples): add Phase 6-8 demos for full stack demonstration
- Add embeddings_demo: semantic search & deduplication (no API keys) - Add hypothesis_demo: mechanistic reasoning (requires LLM) - Add full_stack_demo: complete pipeline with mock and real modes - Update examples README with comprehensive documentation Examples demonstrate: - Text embedding with sentence-transformers - ChromaDB vector storage and similarity search - Semantic deduplication by meaning - Drug -> Target -> Pathway -> Effect hypothesis generation - Structured scientific report generation0efdc2f