diff --git a/.note/code_structure.md b/.note/code_structure.md index 6fb0687..bd226a1 100644 --- a/.note/code_structure.md +++ b/.note/code_structure.md @@ -11,7 +11,6 @@ sim-search/ ├── query/ │ ├── __init__.py │ ├── query_processor.py # Module for processing user queries -│ ├── query_classifier.py # Module for classifying query types │ └── llm_interface.py # Module for interacting with LLM providers ├── execution/ │ ├── __init__.py @@ -22,15 +21,68 @@ sim-search/ │ ├── base_handler.py # Base class for search handlers │ ├── serper_handler.py # Handler for Serper API (Google search) │ ├── scholar_handler.py # Handler for Google Scholar via Serper +│ ├── google_handler.py # Handler for Google search │ └── arxiv_handler.py # Handler for arXiv API ├── ranking/ │ ├── __init__.py -│ ├── jina_reranker.py # Module for reranking documents using Jina AI -│ └── filter_manager.py # Module for filtering documents -├── test_search_execution.py # Test script for search execution -├── test_all_handlers.py # Test script for all search handlers -├── requirements.txt # Project dependencies -└── search_execution_test_results.json # Test results +│ └── jina_reranker.py # Module for reranking documents using Jina AI +├── report/ +│ ├── __init__.py +│ ├── report_generator.py # Module for generating reports +│ ├── report_synthesis.py # Module for synthesizing reports +│ ├── document_processor.py # Module for processing documents +│ ├── document_scraper.py # Module for scraping documents +│ ├── report_detail_levels.py # Module for managing report detail levels +│ └── database/ # Database for storing reports +│ ├── __init__.py +│ └── db_manager.py # Module for managing the database +├── ui/ +│ ├── __init__.py +│ └── gradio_interface.py # Gradio-based web interface +├── utils/ +│ ├── __init__.py +│ ├── jina_similarity.py # Module for computing text similarity +│ └── markdown_segmenter.py # Module for segmenting markdown documents +├── scripts/ +│ └── query_to_report.py # Script for generating reports from queries +├── tests/ +│ ├── __init__.py +│ ├── query/ # Tests for query module +│ │ ├── __init__.py +│ │ ├── test_query_processor.py +│ │ ├── test_query_processor_comprehensive.py +│ │ └── test_llm_interface.py +│ ├── execution/ # Tests for execution module +│ │ ├── __init__.py +│ │ ├── test_search.py +│ │ ├── test_search_execution.py +│ │ └── test_all_handlers.py +│ ├── ranking/ # Tests for ranking module +│ │ ├── __init__.py +│ │ ├── test_reranker.py +│ │ ├── test_similarity.py +│ │ └── test_simple_reranker.py +│ ├── report/ # Tests for report module +│ │ ├── __init__.py +│ │ ├── test_custom_model.py +│ │ └── test_detail_levels.py +│ ├── ui/ # Tests for UI module +│ │ ├── __init__.py +│ │ └── test_ui_search.py +│ ├── integration/ # Integration tests +│ │ ├── __init__.py +│ │ ├── test_ev_query.py +│ │ └── test_query_to_report.py +│ ├── test_document_processor.py +│ ├── test_document_scraper.py +│ └── test_report_synthesis.py +├── examples/ +│ ├── __init__.py +│ ├── data/ # Example data files +│ └── scripts/ # Example scripts +│ └── __init__.py +├── run_ui.py # Script to run the UI +└── requirements.txt # Project dependencies ``` ## Module Details diff --git a/.note/current_focus.md b/.note/current_focus.md index 10733d2..e41df24 100644 --- a/.note/current_focus.md +++ b/.note/current_focus.md @@ -1,52 +1,55 @@ -# Current Focus: Google Gemini Integration, Reference Formatting, and NoneType Error Fixes +# Current Focus: Project Directory Reorganization, Testing, and Embedding Usage ## Active Work -### Google Gemini Integration -- ✅ Fixed the integration of Google Gemini models with LiteLLM -- ✅ Updated message formatting for Gemini models -- ✅ Added proper handling for the 'gemini' provider in environment variables -- ✅ Fixed reference formatting issues with Gemini models -- ✅ Converted LLM interface methods to async to fix runtime errors +### Project Directory Reorganization +- ✅ Reorganized project directory structure for better maintainability +- ✅ Moved utility scripts to the `utils/` directory +- ✅ Organized test files into subdirectories under `tests/` +- ✅ Moved sample data to the `examples/data/` directory +- ✅ Created proper `__init__.py` files for all packages +- ✅ Verified pipeline functionality after reorganization -### Gradio UI Updates -- ✅ Updated the Gradio interface to handle async methods -- ✅ Fixed parameter ordering in the report generation function -- ✅ Improved error handling in the UI +### Embedding Usage Analysis +- ✅ Confirmed that the pipeline uses Jina AI's Embeddings API through the `JinaSimilarity` class +- ✅ Verified that the `JinaReranker` class uses embeddings for document reranking +- ✅ Analyzed how embeddings are integrated into the search and ranking process -### Bug Fixes -- ✅ Fixed NoneType error in report synthesis when chunk titles are None -- ✅ Added defensive null checks throughout document processing and report synthesis -- ✅ Improved chunk counter in map_document_chunks method +### Pipeline Testing +- ✅ Tested the pipeline after reorganization to ensure functionality +- ✅ Verified that the UI works correctly with the new directory structure +- ✅ Confirmed that all imports are working properly with the new structure ## Recent Changes -### Reference Formatting Improvements -- Enhanced the instructions for reference formatting to ensure URLs are included -- Added a recovery mechanism for truncated references -- Improved context preparation to better extract URLs for references -- Added duplicate URL fields in the context to emphasize their importance +### Directory Structure Reorganization +- Created a dedicated `utils/` directory for utility scripts + - Moved `jina_similarity.py` to `utils/` + - Added `__init__.py` to make it a proper Python package +- Organized test files into subdirectories under `tests/` + - Created subdirectories for each module (query, execution, ranking, report, ui, integration) + - Added `__init__.py` files to all test directories +- Created an `examples/` directory with subdirectories for data and scripts + - Moved sample data to `examples/data/` + - Added `__init__.py` files to make them proper Python packages +- Added a dedicated `scripts/` directory for utility scripts + - Moved `query_to_report.py` to `scripts/` -### Async LLM Interface -- Made `generate_completion`, `classify_query`, `enhance_query`, and `generate_search_queries` methods async -- Updated dependent code to properly await these methods -- Fixed runtime errors related to async/await patterns in the QueryProcessor - -### Error Handling Improvements -- Added null checks for chunk titles in report synthesis -- Improved chunk counter in map_document_chunks method -- Added defensive code to ensure all chunks have titles -- Updated document processor to handle None titles with default values +### Pipeline Verification +- Verified that the pipeline functions correctly after reorganization +- Confirmed that the `JinaSimilarity` class in `utils/jina_similarity.py` is properly used for embeddings +- Tested the reranking functionality with the `JinaReranker` class +- Checked that the report generation process works with the new structure ## Next Steps -1. Continue testing with Gemini models to ensure stable operation -2. Consider adding more robust error handling for LLM provider-specific issues -3. Improve the reference formatting further if needed -4. Update documentation to reflect the changes made to the LLM interface -5. Consider adding more unit tests for the async methods -6. Add more comprehensive null checks throughout the codebase -7. Implement better error handling and recovery mechanisms +1. Run comprehensive tests to ensure all functionality works with the new directory structure +2. Update any remaining documentation to reflect the new directory structure +3. Consider moving the remaining test files in the root of the `tests/` directory to appropriate subdirectories +4. Review import statements throughout the codebase to ensure they follow the new structure +5. Add more comprehensive documentation about the directory structure +6. Consider creating a development guide for new contributors +7. Implement automated tests to verify the directory structure remains consistent ### Future Enhancements diff --git a/.note/session_log.md b/.note/session_log.md index 872efb6..eaa80c9 100644 --- a/.note/session_log.md +++ b/.note/session_log.md @@ -644,6 +644,60 @@ Fixed reference formatting issues with Gemini models and updated the codebase to - Fixed the parameter order in the lambda function for async execution - Improved error handling in the UI +## Session: 2025-03-11 + +### Overview + +Reorganized the project directory structure to improve maintainability and clarity, ensuring all components are properly organized into their respective directories. + +### Key Activities + +1. **Directory Structure Reorganization**: + + - Created a dedicated `utils/` directory for utility scripts + - Moved `jina_similarity.py` to `utils/` + - Added `__init__.py` to make it a proper Python package + - Organized test files into subdirectories under `tests/` + - Created subdirectories for each module (query, execution, ranking, report, ui, integration) + - Added `__init__.py` files to all test directories + - Created an `examples/` directory with subdirectories for data and scripts + - Moved sample data to `examples/data/` + - Added `__init__.py` files to make them proper Python packages + - Added a dedicated `scripts/` directory for utility scripts + - Moved `query_to_report.py` to `scripts/` + +2. **Pipeline Verification**: + + - Tested the pipeline after reorganization to ensure functionality + - Verified that the UI works correctly with the new directory structure + - Confirmed that all imports are working properly with the new structure + +3. **Embedding Usage Analysis**: + + - Confirmed that the pipeline uses Jina AI's Embeddings API through the `JinaSimilarity` class + - Verified that the `JinaReranker` class uses embeddings for document reranking + - Analyzed how embeddings are integrated into the search and ranking process + +### Insights + +- A well-organized directory structure significantly improves code maintainability and readability +- Using proper Python package structure with `__init__.py` files ensures clean imports +- Separating tests, utilities, examples, and scripts into dedicated directories makes the codebase more navigable +- The Jina AI embeddings are used throughout the pipeline for semantic similarity and document reranking + +### Challenges + +- Ensuring all import statements are updated correctly after moving files +- Maintaining backward compatibility with existing code +- Verifying that all components still work together after reorganization + +### Next Steps + +1. Run comprehensive tests to ensure all functionality works with the new directory structure +2. Update any remaining documentation to reflect the new directory structure +3. Consider moving the remaining test files in the root of the `tests/` directory to appropriate subdirectories +4. Review import statements throughout the codebase to ensure they follow the new structure + ### Key Insights - Async/await patterns need to be consistently applied throughout the codebase - Reference formatting requires explicit instructions to include URLs