This commit completes the transition of DeepBoner to a dedicated Sexual Health Research Agent by removing all references to "general" and "drug repurposing" domains. Key changes include:
- Updated domain defaults to exclusively use "sexual_health".
- Replaced all example queries and documentation to reflect a focus on sexual health topics.
- Removed any lingering references to non-sexual health concepts in code and tests.
- Ensured all tests are aligned with the new domain focus, passing successfully.
This change reinforces the project's identity and simplifies the codebase, enhancing clarity and usability for users focused on sexual health research.
Closes #89.
Enhanced test files by adding type annotations to test functions and fixtures for better clarity and type checking. Cleaned up import statements and ensured consistent formatting across test cases.
fix: address CodeRabbit review feedback for Phase 13
* 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…
- Added EmbeddingService with ChromaDB and SentenceTransformers
- Updated SearchAgent to support semantic deduplication and search
- Updated MagenticOrchestrator to use embeddings if available
- Added 100% async-safe implementation with run_in_executor
- Added comprehensive unit tests
