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refactor(tools): replace BioRxiv with Europe PMC (Phase 01)
Replaced broken BioRxivTool with EuropePMCTool which supports keyword search. Updated all agents, MCP tools, and examples to use the new tool. Deleted legacy BioRxiv implementation.2f8ae1f -
fix: exclude reference_repos from mypy and cleanup
- Add mypy exclude for reference_repos/ and examples/ to prevent scanning of local reference code that isn't part of the project - Fix string concatenation in orchestrator_magentic.py - Fix formatting in examples (spaces around operators) - Remove resolved bug documentation (001, 002, 003)0a480cb
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feat: Phase 11 bioRxiv Preprint Integration (#19)
Unverified signature* feat: Implement Phase 11 (bioRxiv Preprint Integration) * chore: add .mypy_cache to .gitignore * fix: address CodeRabbit review feedback for bioRxiv tool - Catch httpx.RequestError for network failures (major issue) - Use SourceName type alias in Citation model (DRY) - Only add '...' suffix when abstract is truncated - Add test for network error handlinge67c99f -
refactor: address CodeRabbit nitpicks for Phase 10
- Centralize SourceName type alias in models.py - Update search_handler.py to use SourceName (reduces cast brittleness) - Update app.py intro text to mention ClinicalTrials.gov - Update run_search.py docstring for multi-source search - DRY test setup with mock_requests_get fixture - Speed up error test by patching tenacity retry stop condition1bc9785 -
feat: Implement Phase 10 (ClinicalTrials.gov) with requests
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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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fix(phase2): address CodeRabbit review feedback + add examples
CodeRabbit fixes: - Fix deprecated asyncio.get_event_loop() → get_running_loop() - Remove dead flatten() function from search_handler.py - Remove redundant getattr() in pubmed.py - Add truncation rationale comments New: - Add examples/search_demo/ with run_search.py demo script - Add examples/README.md32e3b61