resynth 0.1.0__tar.gz

resynth-0.1.0/.env.example

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+# OpenAI API Key (for embeddings and chat completion)
+OPENAI_API_KEY=your_openai_api_key_here
+
+# Alternative: Hugging Face model for embeddings
+HUGGINGFACE_MODEL_NAME=sentence-transformers/all-MiniLM-L6-v2
+
+# Vector database settings
+CHROMA_PERSIST_DIRECTORY=./chroma_db
+CHROMA_COLLECTION_NAME=research_papers
+
+# Paper fetching settings
+MAX_PAPERS_PER_QUERY=10
+PAPER_DOWNLOAD_DIR=./papers
+
+# API settings
+API_HOST=0.0.0.0
+API_PORT=8000
+
+# Chunking settings
+CHUNK_SIZE=1000
+CHUNK_OVERLAP=200
+
+# Retrieval settings
+TOP_K_RETRIEVAL=5
+SIMILARITY_THRESHOLD=0.7

resynth-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+- Initial release of ReSynth research paper synthesis agent
+- Paper fetching from arXiv and PubMed
+- Intelligent text chunking and preprocessing
+- Vector embeddings with ChromaDB storage
+- Query processing and retrieval system
+- AI-powered answer synthesis with citations
+- Multiple citation styles (APA, MLA, numeric, author-date)
+- Web interface with Streamlit
+- REST API with FastAPI
+- Command-line interface
+- Comprehensive test suite
+- Documentation and examples
+
+### Features
+- **Paper Fetching**: Search and download papers from arXiv and PubMed
+- **Text Processing**: Advanced chunking, cleaning, and preprocessing
+- **Vector Storage**: Efficient storage and retrieval with ChromaDB
+- **Query System**: Intelligent query processing with expansion
+- **Answer Synthesis**: AI-powered answers with proper citations
+- **Multiple Interfaces**: Web UI, API, and CLI
+- **Citation Management**: Automatic citation generation in multiple styles
+- **Quality Metrics**: Retrieval quality validation and confidence scoring
+
+## [0.1.0] - 2024-02-14
+
+### Added
+- Initial release
+- Core functionality for research paper synthesis
+- Support for arXiv and PubMed paper fetching
+- Semantic text chunking
+- Vector embeddings and storage
+- Query processing and retrieval
+- Answer synthesis with citations
+- Web interface, API, and CLI
+- Comprehensive documentation
+
+### Technical Details
+- Python 3.8+ support
+- Integration with OpenAI and Hugging Face models
+- ChromaDB for vector storage
+- FastAPI for REST API
+- Streamlit for web interface
+- Comprehensive test coverage
+- Modern packaging with pyproject.toml

resynth-0.1.0/CONTRIBUTING.md

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+# Contributing to ReSynth
+
+Thank you for your interest in contributing to ReSynth! This document provides guidelines for contributors.
+
+## Getting Started
+
+### Prerequisites
+
+- Python 3.8 or higher
+- Git
+- Basic knowledge of Python development
+
+### Development Setup
+
+1. **Fork the repository**
+   ```bash
+   # Fork on GitHub, then clone your fork
+   git clone https://github.com/your-username/resynth.git
+   cd resynth
+   ```
+
+2. **Set up development environment**
+   ```bash
+   # Install development dependencies
+   make dev-install
+   
+   # Set up pre-commit hooks
+   pre-commit install
+   ```
+
+3. **Create a virtual environment**
+   ```bash
+   python -m venv venv
+   source venv/bin/activate  # On Windows: venv\Scripts\activate
+   ```
+
+## Development Workflow
+
+### 1. Create a Branch
+
+```bash
+git checkout -b feature/your-feature-name
+# or
+git checkout -b fix/issue-number
+```
+
+### 2. Make Changes
+
+- Follow the existing code style
+- Add tests for new functionality
+- Update documentation as needed
+- Ensure all tests pass
+
+### 3. Code Quality
+
+Run the following checks before committing:
+
+```bash
+# Format code
+make format
+
+# Run linting
+make lint
+
+# Run tests
+make test
+```
+
+### 4. Commit Changes
+
+Use clear, descriptive commit messages:
+
+```
+feat: add support for new paper source
+fix: resolve chunking issue with large papers
+docs: update API documentation
+test: add integration tests for retrieval system
+```
+
+### 5. Submit Pull Request
+
+- Push your branch to your fork
+- Create a pull request with a clear description
+- Link any relevant issues
+- Wait for code review
+
+## Code Style
+
+### Python Style
+
+We use:
+- **Black** for code formatting
+- **isort** for import sorting
+- **flake8** for linting
+- **mypy** for type checking
+
+### Documentation
+
+- Use docstrings for all public functions and classes
+- Follow the Google style for docstrings
+- Update README.md for user-facing changes
+- Add inline comments for complex logic
+
+### Testing
+
+- Write unit tests for new functionality
+- Add integration tests for major features
+- Maintain test coverage above 80%
+- Use descriptive test names
+
+## Project Structure
+
+```
+resynth/
+├── src/resynth/           # Main package
+│   ├── fetchers/          # Paper fetching modules
+│   ├── processors/        # Text processing
+│   ├── embeddings/        # Vector embeddings
+│   ├── retrieval/         # Query processing
+│   └── synthesis/         # Answer generation
+├── tests/                 # Test suite
+├── docs/                  # Documentation
+├── examples/              # Usage examples
+└── scripts/              # Utility scripts
+```
+
+## Adding Features
+
+### New Paper Sources
+
+1. Create a new fetcher in `src/resynth/fetchers/`
+2. Inherit from `BaseFetcher`
+3. Implement required methods
+4. Add tests
+5. Update documentation
+
+### New Citation Styles
+
+1. Add formatting methods to `CitationFormatter`
+2. Update citation style options
+3. Add tests for new style
+4. Update documentation
+
+### New Embedding Models
+
+1. Update `EmbeddingManager` to support new model
+2. Add configuration options
+3. Add tests
+4. Update documentation
+
+## Reporting Issues
+
+### Bug Reports
+
+- Use the GitHub issue tracker
+- Provide clear reproduction steps
+- Include environment details
+- Add relevant logs or error messages
+
+### Feature Requests
+
+- Describe the use case
+- Explain why it's needed
+- Suggest implementation approach
+- Consider potential edge cases
+
+## Review Process
+
+### What We Look For
+
+- Code quality and style
+- Test coverage
+- Documentation
+- Performance impact
+- Security considerations
+- Backward compatibility
+
+### Review Guidelines
+
+- Be constructive and respectful
+- Focus on the code, not the person
+- Provide specific suggestions
+- Ask questions for clarity
+
+## Release Process
+
+### Version Management
+
+- Follow semantic versioning
+- Update version in `src/resynth/__init__.py`
+- Update `CHANGELOG.md`
+- Tag releases on GitHub
+
+### Publishing
+
+1. Update version and changelog
+2. Run full test suite
+3. Build package
+4. Test installation
+5. Publish to PyPI
+
+## Community Guidelines
+
+### Code of Conduct
+
+- Be respectful and inclusive
+- Welcome newcomers
+- Focus on what's best for the community
+- Show empathy towards other community members
+
+### Getting Help
+
+- Check documentation first
+- Search existing issues
+- Ask questions in discussions
+- Join community channels
+
+## Recognition
+
+Contributors are recognized in:
+- README.md contributors section
+- Release notes
+- GitHub contributors list
+
+Thank you for contributing to ReSynth! 🚀

resynth-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 ReSynth Team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

resynth-0.1.0/MANIFEST.in

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+# Include additional files in the distribution
+
+# Documentation
+include README.md
+include CHANGELOG.md
+include CONTRIBUTING.md
+include LICENSE
+include MANIFEST.in
+
+# Configuration files
+include pyproject.toml
+include requirements.txt
+include .env.example
+include Makefile
+
+# Source files
+recursive-include src *.py
+recursive-include src *.yaml
+recursive-include src *.yml
+recursive-include src *.json
+recursive-include src *.txt
+recursive-include src *.md
+
+# Test files
+recursive-include tests *.py
+recursive-include tests *.yaml
+recursive-include tests *.json
+
+# Static files (if any)
+recursive-include src *.css
+recursive-include src *.js
+recursive-include src *.html
+recursive-include src *.png
+recursive-include src *.jpg
+recursive-include src *.gif
+recursive-include src *.ico
+
+# Templates (if any)
+recursive-include src *.html
+recursive-include src *.jinja2
+
+# Exclude development files
+global-exclude *.pyc
+global-exclude *.pyo
+global-exclude *.pyd
+global-exclude __pycache__
+global-exclude .git*
+global-exclude .DS_Store
+global-exclude *.so
+global-exclude .coverage
+global-exclude .pytest_cache
+global-exclude .mypy_cache
+global-exclude .tox
+global-exclude build
+global-exclude dist
+global-exclude *.egg-info
+
+# Exclude environment files
+exclude .env
+exclude .venv
+exclude venv/
+exclude env/
+exclude ENV/
+
+# Exclude IDE files
+exclude .vscode/
+exclude .idea/
+exclude *.swp
+exclude *.swo
+
+# Exclude OS files
+exclude Thumbs.db
+exclude *.log

resynth-0.1.0/Makefile

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+# Makefile for ReSynth
+
+.PHONY: help install dev-install test lint format clean run-api run-cli run-web
+
+# Default target
+help:
+	@echo "ReSynth - Research Paper Synthesis Agent"
+	@echo ""
+	@echo "Available commands:"
+	@echo "  install      Install dependencies"
+	@echo "  dev-install  Install development dependencies"
+	@echo "  test         Run tests"
+	@echo "  lint         Run linting"
+	@echo "  format       Format code"
+	@echo "  clean        Clean temporary files"
+	@echo "  run-api      Run API server"
+	@echo "  run-cli      Run CLI example"
+	@echo "  run-web      Run web interface"
+	@echo ""
+
+# Installation
+install:
+	pip install -r requirements.txt
+	python -m spacy download en_core_web_sm
+
+dev-install: install
+	pip install -e ".[dev]"
+
+# Testing
+test:
+	python -m pytest tests/ -v --cov=src --cov-report=html --cov-report=term
+
+test-quick:
+	python -m pytest tests/ -v --tb=short
+
+# Code quality
+lint:
+	flake8 src/ tests/ main.py cli.py app.py
+	mypy src/ --ignore-missing-imports
+
+format:
+	black src/ tests/ main.py cli.py app.py setup.py
+	isort src/ tests/ main.py cli.py app.py setup.py
+
+# Cleaning
+clean:
+	find . -type f -name "*.pyc" -delete
+	find . -type d -name "__pycache__" -delete
+	find . -type d -name "*.egg-info" -exec rm -rf {} +
+	rm -rf build/
+	rm -rf dist/
+	rm -rf .coverage
+	rm -rf htmlcov/
+	rm -rf .pytest_cache/
+	rm -rf .mypy_cache/
+
+# Running the application
+run-api:
+	python main.py
+
+run-cli:
+	python cli.py --search "machine learning interpretability" --max-papers 3
+
+run-web:
+	streamlit run app.py
+
+# Development helpers
+setup-env:
+	cp .env.example .env
+	@echo "Please edit .env file with your API keys"
+
+check-deps:
+	pip check
+	pip list | grep -E "(fastapi|streamlit|chromadb|sentence-transformers|arxiv|openai)"
+
+# Documentation
+docs:
+	@echo "Documentation is available in README.md"
+	@echo "API docs: http://localhost:8000/docs (when API server is running)"
+
+# Quick start
+quickstart: install
+	@echo "Setting up quick start example..."
+	python cli.py --search "transformer architectures" --max-papers 2 --no-content
+	@echo "Now you can query with:"
+	@echo "python cli.py --query 'What are attention mechanisms in transformers?'"