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fix: update remaining bioRxiv references to Europe PMC in examples
- examples/orchestrator_demo/run_agent.py: Update comments (3 places) - examples/README.md: Update documentation (4 places) All examples now consistently reference Europe PMC instead of bioRxiv.1515e72 -
fix: update references to Europe PMC in examples and documentation
Replaced mentions of bioRxiv with Europe PMC in the full stack and hypothesis demo scripts to reflect the current data sources. Updated the pyproject.toml to exclude specific directories from mypy checks using regex patterns for better clarity.9d21bf8 -
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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docs: update demos to use all 3 search sources
- Remove stale DuckDuckGo references from README - Update all demos to use PubMed + ClinicalTrials + bioRxiv - Update docstrings and summary messages - All 76 tests passing Files updated: - examples/README.md - examples/full_stack_demo/run_full.py - examples/hypothesis_demo/run_hypothesis.py - examples/orchestrator_demo/run_agent.py - examples/orchestrator_demo/run_magentic.py8625ded -
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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refactor(examples): apply CodeRabbit feedback (validations, complexity, formatting)
cd11dad -
refactor(examples): purge all mocks - real API calls only
NO MOCKS. NO FAKE DATA. REAL SCIENCE. Changes: - hypothesis_demo: Now does REAL search before hypothesis generation - full_stack_demo: Removed run_mock_demo(), create_mock_*() functions - orchestrator_demo: Removed --mock flag and MockJudgeHandler - README: Updated to reflect "Real or Nothing" philosophy All examples now require API keys and make real API calls. Mocks belong in tests/unit/, not in demos.cfb473d -
fix: linting and types for phase 5
1922dbd -
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