Merge pull request #30 from The-Obstacle-Is-The-Way/chore/env-cleanup-model-upgrade

Merge pull request #29 from The-Obstacle-Is-The-Way/claude/debug-gradio-mock-data-01MDfoUPcbfZ7FLootfhe8zs

fix: address CodeRabbit review feedback

chore: clean up env config and upgrade model defaults

fix: use config settings for model names instead of hardcoded values

feat: add demo mode warnings and BYOK (Bring Your Own Key) support

Merge pull request #28 from The-Obstacle-Is-The-Way/fix/gradio-upgrade-cleanup

fix: upgrade Gradio to 5.32.0+ for MCP server support

fix: remove duplicate typer dependency per CodeRabbit review

feat: add smoke tests and fix Gradio 6.x compatibility

fix: Gradio examples format for additional_inputs

chore: update README to specify Python version as 3.11 (#26)

fix: update requirements.txt for HuggingFace Spaces build

chore: include coverage in make check for better DevEx

chore: improve DevEx and clean up obsolete docs (#25)

Merge pull request #24 from The-Obstacle-Is-The-Way/fix/research-report-references-default

style: add pytest.mark.unit to test_models (CodeRabbit)

fix: make ResearchReport.references optional with default

Merge pull request #22 from The-Obstacle-Is-The-Way/feat/phase14-demo-submission

docs: add Josephrp to team contributors

docs: update README for Phase 14 submission

Merge pull request #21 from The-Obstacle-Is-The-Way/feat/phase13-modal-integration

Merge branch 'main' into feat/phase13-modal-integration

docs: sync AI agent context files and fix final nitpicks

refactor: address CodeRabbit nitpick suggestions

fix: address CodeRabbit review feedback for Phase 13

docs: add AI agent context files for team collaboration

docs: add AI agent context files for team collaboration

fix: wire analyze_hypothesis MCP tool into Gradio app

feat: implement phase 13 modal pipeline integration

Merge pull request #20 from The-Obstacle-Is-The-Way/feat/phase12-mcp-server

docs: address CodeRabbit feedback for Phase 12 PR

docs: update MCP server integration documentation and status

feat: enhance Gradio UI with MCP server support and new tool interfaces

feat: add MCP tool wrappers for biomedical search tools

chore: update Gradio dependency to include MCP extras and version bump

docs: enhance Phase 13 Modal integration documentation

docs: add Phase 14 Demo Video & Hackathon Submission specification

docs: add Phase 12 MCP Server Integration specification

docs: add comprehensive hackathon documentation and integration plans

docs: update demos to use all 3 search sources

feat: Phase 11 bioRxiv Preprint Integration (#19)

Merge pull request #16 from The-Obstacle-Is-The-Way/feat/mario-integration

refactor: centralize embedding configuration in Settings

refactor: address final CodeRabbit feedback

fix(rag): address remaining CodeRabbit feedback

refactor: address CodeRabbit review feedback for Mario integration

fix(rag): use get_content() for BaseNode compatibility

fix(rag): apply lazy imports and use centralized config

feat: Integrate Mario's Modal code execution + LlamaIndex RAG