## Problem
After report synthesis, extra "JUDGING: ManagerAgent" and "PROGRESS: Step 11"
events appeared in the UI, confusing users. Root cause: we were treating
`ExecutorCompletedEvent` as a UI event when it's actually internal framework
bookkeeping (auto-emitted by MS Agent Framework for every executor).
## Solution
1. **Silence ExecutorCompletedEvent**: Remove UI event emission, keep only
internal state tracking (reporter_ran flag)
2. **Add metadata filtering**: Filter out `task_ledger` and `instruction`
messages from AgentRunUpdateEvent stream
3. **Remove dead code**: Delete unused `_handle_completion_event` and
`_get_event_type_for_agent` methods
## Changes
- src/orchestrators/advanced.py: Silence completion events, add metadata filter
- tests/unit/test_orchestrator_noise.py: New regression tests
- tests/unit/orchestrators/test_accumulator_pattern.py: Update expectations
- docs/bugs/P2_EXECUTOR_COMPLETED_EVENT_UI_NOISE.md: Full bug documentation
## Validation
- Senior …
* fix(deps): Upgrade agent-framework-core to 1.0.0b251204 (SPEC-18)
Breaking API changes in upstream require event class migration:
- MagenticAgentDeltaEvent → AgentRunUpdateEvent
- MagenticAgentMessageEvent → ExecutorCompletedEvent
- MagenticFinalResultEvent → (removed, use WorkflowOutputEvent)
Upstream fixed the repr bug we worked around in SPEC-17.
Keep Accumulator Pattern as safety net for now.
Closes P0: HuggingFace Spaces deployment blocked
* docs: Add SPEC-18 documentation and fix test docstring
- Add docs/specs/SPEC_18_AGENT_FRAMEWORK_UPGRADE.md with full migration guide
- Update test_accumulator_pattern.py docstring to reference new event classes
Part of SPEC-18: Agent Framework Core Upgrade
* refactor: Address CodeRabbit review feedback
- Use defensive getattr for event.data.text (consistency)
- Remove redundant isinstance check in _handle_final_event
- Update sync dates in requirements.txt and workflow-diagrams.md
- Add language specifier to SPEC-18 code block
Note:…
- Extract magic number 45 to class constant _EST_SECONDS_PER_ROUND (advanced.py)
- Add @pytest.mark.unit to test_advanced_p2_dead_zones.py
- Remove debug print statements from test
- Add pytestmark = pytest.mark.unit to test_magentic_judge_termination.py
- Fix import ordering (stdlib before third-party)
- Add fallback p=0.15 for progress events without iteration (app.py)
- Refactor max_iters lookup with getattr chains to reduce statement count
- Fix SPEC_16 markdown: list spacing (1. vs 1. ) and code block languages
All 327 tests pass.
1. Add @pytest.mark.unit to test class for proper categorization
2. Handle user_task before text extraction (edge case fix)
3. Improve truncation tests to actually detect regression:
- Test sentence boundary truncation with proper position
- Test word boundary fallback separately
4. Remove unused imports
Co-authored-by: CodeRabbit AI <coderabbit@users.noreply.github.com>
Problem: Advanced orchestrator exposed raw internal framework events
from agent-framework-core to users:
- `Manager (task_ledger): We are working to address...` (truncated)
- `Manager (instruction): Conduct targeted searches...` (truncated)
- All mapped to type="judging" regardless of actual purpose
Solution:
1. Filter internal events: `task_ledger` and `instruction` now hidden
2. Transform: `user_task` → type="progress" with friendly message
3. Smart truncation: Cut at sentence/word boundaries, not mid-word
Tests: tests/unit/orchestrators/test_advanced_events.py (4 tests)
Closes #106
- Added a new synthesis method in the JudgeHandler to utilize free HuggingFace Inference for narrative generation in Free Tier mode.
- Updated the Orchestrator to check for the judge's synthesis method, ensuring consistent behavior across judging and synthesis.
- Enhanced integration and unit tests to verify the correct usage of the new synthesis method and fallback mechanisms.
- Documented the bug related to synthesis incorrectly using server-side API keys, outlining the root cause and potential fixes.
This change addresses user confusion and improves the Free Tier experience by ensuring expected functionality without requiring an API key.
fix: P0 provider mismatch and code quality audit fixes (#102)
* 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…
