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fix(SPEC_11): address CodeRabbit review feedback (#92)
Unverified signature* fix(SPEC_11): address CodeRabbit review feedback - Update run_full.py docstring to reference sexual health pipeline (not drug repurposing) - Update run_full.py help text to use sexual health query example - Fix app.py domain display to show "Sexual Health" (not "Sexual_Health") - Update test_nodes.py mock data to use sexual health terms (Testosterone, Androgen Receptor) - Add @pytest.mark.unit markers to test_judges.py test classes - Add specific assertion for next_search_queries in test_judges.py - Add missing @pytest.mark.asyncio marker to test_mcp_tools.py - Update test_mcp_tools.py and test_clinicaltrials.py to use sexual health queries - Fix SPEC_12 markdown bare code fence (MD040) * fix(SPEC_11): comprehensive domain alignment audit Second pass of CodeRabbit review fixes - found additional domain mismatches: - examples/search_demo/run_search.py: Update docstring from "drug repurposing" to "sexual health" - examples/orchestrator_demo/run_agent.py: Update help text from "metf…89f1173 -
feat(SPEC_11): finalize transition to Sexual Health Research Specialist
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.fa696e8
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rebrand: DeepCritical → DeepBoner (sexual health research agent)
🍆 AI-Native Sexual Health Research Agent - Package renamed: deepcritical → deepboner - New focus: sexual wellness, ED, hormone therapy, libido, reproductive health - Exception class: DeepCriticalError → DeepBonerError (with backwards compat) - UI examples updated for sexual health queries - Modal app renamed: deepboner-code-execution - Fixed pre-existing mypy issue (Modal API: uv_pip_install → pip_install) 46 files updated across: - Core: pyproject.toml, README.md, CLAUDE.md, AGENTS.md, GEMINI.md - Source: app.py, mcp_tools.py, exceptions.py, code_execution.py - Docs: ~25 markdown files - Examples: 8 demo scripts - Tests: exception tests updated All tests passing (102 passed, 6 skipped)5d12635
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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)
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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 -
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