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refactor: resolve pylint errors and warnings across api and src routers
- Enforced explicit exception chaining (raise from exc) in ask/search/analyze routes - Fixed dynamic method call references pointing to llm_config missing members - Patched missing explicit utf-8 encodings in file handlers via BiomarkerValidator7caf4dc -
chore: codebase audit and fixes (ruff, mypy, pytest)
- Fixed pytest collection hang by adding root conftest.py and testpaths in pytest.ini - Fixed mypy missing keys for GuildState TypedDict definitions - Fixed ruff whitespace formatting and unhandled B904 exceptions - Added skip markers for unmocked LLM API calls in integration tests - Removed redundant debug script logging and trace files9659593
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Fix codebase issues: linting, types, tests, and security.
Nikhil Pravin Pise- Resolved over 3,000 ruff linting violations - Enforced strict type checking with mypy - Fixed infinite loop in pytest suite by migrating obsolete tests - Remediated security warnings flagged by Bandit696f787
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Refactor: Improve code quality, security, and configuration
Nikhil Pravin Pise- Remove redundant sys.path manipulation in agents and services - Enhance CORS configuration with environment-based origin handling - Improve error handling (no internal detail leakage) - Fix environment variable handling in setup scripts (remove extra quotes) - Update gitignore for external tools and course materials - Correct clinical biomarker reference ranges - Add comprehensive production upgrade plan - Improve test configuration (HuggingFace deprecation filters) - Add optional dependencies for evaluation tools - Consolidate path initialization patternsad2e847 -
docs: update all documentation to reflect current codebase state
Nikhil Pravin Pise- Update README.md: correct test count (83 -> 30), fix test commands - Rewrite START_HERE.md as proper onboarding guide - Update QUICKSTART.md and CONTRIBUTING.md test commands - Update api/ docs: Groq/Gemini as default providers (not Ollama) - Update api/ARCHITECTURE.md: multi-provider LLM diagram - Update api/GETTING_STARTED.md: Groq/Gemini prerequisites - Update api/QUICK_REFERENCE.md: fix troubleshooting, commands - Update docs/DEVELOPMENT.md: fix code examples, test commands - Update docs/DEEP_REVIEW.md: add RESOLVED/OPEN status to all findings - Update scripts/README.md: use .venv python paths - Archive stale root-level docs to docs/archive/ - All 30 tests passingaefac4f
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refactor: major repository cleanup and bug fixes
Nikhil Pravin PiseCleanup & Organization: - Removed clutter: deleted archive/ and setup.py - Reorganized scripts: moved PowerShell startup scripts to scripts/ - Created examples/ folder with HTML/JS integration examples - Consolidated docs: archived 13 old implementation notes to docs/archive/ - Rewrote root README.md for clarity and professional appearance Core Bug Fixes: - Fixed Google Gemini embedding API 404 error by switching to HuggingFace local embeddings - Upgraded torch/torchvision to resolve PyTorch compatibility issues - Fixed HuggingFaceEmbeddings import and configuration in pdf_processor.py - Successfully rebuilt FAISS vector store with compatible embeddings (2,609 chunks) Documentation: - Created docs/ARCHITECTURE.md: system design, components, data flow - Created docs/API.md: complete REST API reference with examples - Created docs/DEVELOPMENT.md: extension guide for developers - Created scripts/README.md: utility scripts reference - Created examples/README.md: integration patterns for …6dc9d46