stwhite
/
ira
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Update memory bank to reflect project directory reorganization

This commit is contained in:
Steve White 2025-03-11 15:30:35 -05:00
parent 7f440286bc
commit 7744249d65
3 changed files with 153 additions and 44 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

66
.note/code_structure.md
View File

@ -11,7 +11,6 @@ sim-search/
├── query/ ├── query/
│ ├── __init__.py │ ├── __init__.py
│ ├── query_processor.py # Module for processing user queries │ ├── 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 │ └── llm_interface.py # Module for interacting with LLM providers
├── execution/ ├── execution/
│ ├── __init__.py │ ├── __init__.py
@ -22,15 +21,68 @@ sim-search/
│ ├── base_handler.py # Base class for search handlers │ ├── base_handler.py # Base class for search handlers
│ ├── serper_handler.py # Handler for Serper API (Google search) │ ├── serper_handler.py # Handler for Serper API (Google search)
│ ├── scholar_handler.py # Handler for Google Scholar via Serper │ ├── scholar_handler.py # Handler for Google Scholar via Serper
│ ├── google_handler.py # Handler for Google search
│ └── arxiv_handler.py # Handler for arXiv API │ └── arxiv_handler.py # Handler for arXiv API
├── ranking/ ├── ranking/
│ ├── __init__.py │ ├── __init__.py
│ ├── jina_reranker.py # Module for reranking documents using Jina AI │ └── jina_reranker.py # Module for reranking documents using Jina AI
│ └── filter_manager.py # Module for filtering documents ├── report/
├── test_search_execution.py # Test script for search execution │ ├── __init__.py
├── test_all_handlers.py # Test script for all search handlers │ ├── report_generator.py # Module for generating reports
├── requirements.txt # Project dependencies │ ├── report_synthesis.py # Module for synthesizing reports
└── search_execution_test_results.json # Test results │ ├── 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 ## Module Details

77
.note/current_focus.md
View File

@ -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 ## Active Work
### Google Gemini Integration ### Project Directory Reorganization
- ✅ Fixed the integration of Google Gemini models with LiteLLM - ✅ Reorganized project directory structure for better maintainability
- ✅ Updated message formatting for Gemini models - ✅ Moved utility scripts to the `utils/` directory
- ✅ Added proper handling for the 'gemini' provider in environment variables - ✅ Organized test files into subdirectories under `tests/`
- ✅ Fixed reference formatting issues with Gemini models - ✅ Moved sample data to the `examples/data/` directory
- ✅ Converted LLM interface methods to async to fix runtime errors - ✅ Created proper `__init__.py` files for all packages
- ✅ Verified pipeline functionality after reorganization
### Gradio UI Updates ### Embedding Usage Analysis
- ✅ Updated the Gradio interface to handle async methods - ✅ Confirmed that the pipeline uses Jina AI's Embeddings API through the `JinaSimilarity` class
- ✅ Fixed parameter ordering in the report generation function - ✅ Verified that the `JinaReranker` class uses embeddings for document reranking
- ✅ Improved error handling in the UI - ✅ Analyzed how embeddings are integrated into the search and ranking process
### Bug Fixes ### Pipeline Testing
- ✅ Fixed NoneType error in report synthesis when chunk titles are None - ✅ Tested the pipeline after reorganization to ensure functionality
- ✅ Added defensive null checks throughout document processing and report synthesis - ✅ Verified that the UI works correctly with the new directory structure
- ✅ Improved chunk counter in map_document_chunks method - ✅ Confirmed that all imports are working properly with the new structure
## Recent Changes ## Recent Changes
### Reference Formatting Improvements ### Directory Structure Reorganization
- Enhanced the instructions for reference formatting to ensure URLs are included - Created a dedicated `utils/` directory for utility scripts
- Added a recovery mechanism for truncated references - Moved `jina_similarity.py` to `utils/`
- Improved context preparation to better extract URLs for references - Added `__init__.py` to make it a proper Python package
- Added duplicate URL fields in the context to emphasize their importance - 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 ### Pipeline Verification
- Made `generate_completion`, `classify_query`, `enhance_query`, and `generate_search_queries` methods async - Verified that the pipeline functions correctly after reorganization
- Updated dependent code to properly await these methods - Confirmed that the `JinaSimilarity` class in `utils/jina_similarity.py` is properly used for embeddings
- Fixed runtime errors related to async/await patterns in the QueryProcessor - Tested the reranking functionality with the `JinaReranker` class
- Checked that the report generation process works with the new structure
### 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
## Next Steps ## Next Steps
1. Continue testing with Gemini models to ensure stable operation 1. Run comprehensive tests to ensure all functionality works with the new directory structure
2. Consider adding more robust error handling for LLM provider-specific issues 2. Update any remaining documentation to reflect the new directory structure
3. Improve the reference formatting further if needed 3. Consider moving the remaining test files in the root of the `tests/` directory to appropriate subdirectories
4. Update documentation to reflect the changes made to the LLM interface 4. Review import statements throughout the codebase to ensure they follow the new structure
5. Consider adding more unit tests for the async methods 5. Add more comprehensive documentation about the directory structure
6. Add more comprehensive null checks throughout the codebase 6. Consider creating a development guide for new contributors
7. Implement better error handling and recovery mechanisms 7. Implement automated tests to verify the directory structure remains consistent
### Future Enhancements ### Future Enhancements

54
.note/session_log.md
View File

@ -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 - Fixed the parameter order in the lambda function for async execution
- Improved error handling in the UI - 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 ### Key Insights
- Async/await patterns need to be consistently applied throughout the codebase - Async/await patterns need to be consistently applied throughout the codebase
- Reference formatting requires explicit instructions to include URLs - Reference formatting requires explicit instructions to include URLs