* 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…
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.
* feat: implement SPEC_10 domain-agnostic refactor
* fix: complete SPEC_10 audit - license + HierarchicalOrchestrator domain
License Fixes:
- LICENSE: Fix copyright "Antibody Training Pipeline ESM" → "DeepBoner Contributors"
- pyproject.toml: Add missing license = "Apache-2.0" field
- README.md: Fix frontmatter license: mit → apache-2.0
Domain Threading Fixes:
- hierarchical.py: Add domain param to __init__ and pass to ResearchTeam
- factory.py: Pass domain to HierarchicalOrchestrator
All 237 tests pass. Domain now properly threaded through all orchestrators.
* test: enhance domain handling in orchestrators and judges
- Updated unit tests for `configure_orchestrator` to include mock mode and free tier scenarios, ensuring the domain is correctly passed to handlers.
- Refactored tests for `JudgeHandler` to mock model retrieval, allowing for domain acceptance without API key requirements.
- Improved `AdvancedOrchestrator` tests to mock API key validation and ensure domain handling i…
* feat: implement SPEC_06 fixes for simple mode synthesis
Implements research-backed architecture changes for Simple mode:
- Diverse evidence selection with lost-in-the-middle mitigation
- Debiased judge prompt (scoring only, no decision making)
- Code-enforced termination criteria (prevents infinite loops)
- Real partial synthesis with drug candidates when max iterations reached
- Unit and integration tests for all new logic
* fix: address CodeRabbit review feedback
- Fix type annotation: recommendation str -> Literal["continue", "synthesize"]
- Add @pytest.mark.unit markers to unit tests
- Add @pytest.mark.integration markers to integration tests
- Simplify early/late evidence assertions using set intersection
- Replace next() with explicit filtering for clearer test diagnostics
- Extract hardcoded thresholds (50, 30) to TERMINATION_CRITERIA
- Fix e2e mock to accept iteration/max_iterations parameters
All 177 tests pass, mypy clean, ruff clean.
* docs: add P3 architectural gap r…
refactor: Organize orchestrators into dedicated package
Claude
e82d9c9
- Create src/orchestrators/ package with proper module structure
- base.py: Shared protocols (SearchHandlerProtocol, JudgeHandlerProtocol)
- simple.py: Basic search-judge loop orchestrator (was orchestrator.py)
- advanced.py: Multi-agent MS Agent Framework orchestrator (was orchestrator_magentic.py)
- hierarchical.py: Sub-iteration middleware orchestrator
- factory.py: Factory pattern for orchestrator creation
- __init__.py: Clean public API with facade pattern
Design principles applied:
- Single Responsibility (SRP): Each file has one clear job
- Interface Segregation (ISP): Protocols in base.py
- Factory Pattern (GoF): Centralized creation logic
- Facade Pattern: Clean public imports via __init__.py
All imports updated across:
- src/app.py, src/agents/
- tests/unit/, tests/e2e/, tests/integration/
- examples/orchestrator_demo/
All 147 tests pass, linting and typecheck clean.
* docs: sync documentation with codebase reality
- Fix test count 127→142+ (index.md)
- Fix OpenAI model gpt-5.1→gpt-5 to match config.py (CLAUDE.md)
- Mark phases 13-14 as COMPLETE (roadmap.md)
- Auto-format 2 test files (ruff)
* docs: add specs for P0 termination fix and P1 E2E testing
SPEC_01: Demo Termination Fix
- Investigate if max_round_count actually works
- Add hard timeout (5 min) for hackathon
- Add round progress indicator
SPEC_02: E2E Testing
- Smoke tests (does it run?)
- Structure tests (is output valid?)
- Quality tests (is output useful?)
- Must pass BEFORE adding new features (OpenAlex, etc.)
* docs: fix spec accuracy (line numbers and test counts)
SPEC_01: Line reference 112 → 110 (actual location of .with_standard_manager)
SPEC_02: Test count 142 → 140 (verified with pytest --collect-only)
Both specs now match codebase exactly per audit verification.
* feat: Implement SPEC_01 (Termination) and SPEC_02 (E2E Tests)
- SPEC_01: Added timeout (300s) and progress…
