🎉 Major Release - Dependency Removal & Codebase Modernization
This release represents a substantial modernization of the timecorr package, removing external dependencies, improving code quality, and enhancing documentation.
🔥 Breaking Changes
- Removed brainconn dependency: Implemented core graph theory functions directly (eigenvector centrality, PageRank, node strength) to eliminate external dependency issues
- Cleaned up public API: Removed non-existent functions from API documentation that were causing import errors
✨ New Features
- GitHub Actions CI/CD: Added automated testing on Python 3.8-3.11 for all pushes and pull requests
- Enhanced documentation: All user-facing functions now have comprehensive NumPy-style docstrings with examples
- Direct graph theory implementation: Native implementations of
eigenvector_centrality_und(),pagerank_centrality(), andstrengths_und()
🛠️ Improvements
- Code formatting: Applied black and isort across entire codebase for consistent style
- Import organization: Cleaned up import statements throughout the project
- Documentation cleanup: Removed build artifacts and redundant files from docs/ directory
- Tutorial enhancements: Fixed and verified all tutorial notebooks and examples
- Test coverage: Maintained 100% test coverage with 132 passing tests
🐛 Bug Fixes
- Fixed kernel parameter errors in Mexican Hat weights (changed 'var' to 'sigma')
- Fixed reshape errors in applications tutorial
- Resolved deprecation warnings by replacing
np.math.piwithmath.pi - Fixed PCA dimension errors by limiting to number of samples
- Fixed padding logic for different array dimensions and list inputs
📚 Documentation
- API Documentation: Updated to reflect only existing functions, removed references to non-existent ones
- Enhanced docstrings: Added comprehensive documentation for all major user-facing functions
- Tutorial improvements: Fixed and verified all Jupyter notebooks and Python examples
- README updates: Enhanced with working examples and current API information
🧹 Cleanup
- Removed outdated files: Cleaned up PNG files, temporary scripts, and build artifacts
- Docker removal: Removed outdated Docker setup with broken notebook
- File organization: Streamlined repository structure removing unnecessary files
🔧 Development
- Modern workflow: Transitioned from nose to pytest for testing
- Linting: Applied comprehensive code formatting and style improvements
- CI/CD: Automated testing pipeline for continuous integration
📦 Dependencies
- Removed: brainconn (replaced with native implementations)
- Updated: All dependencies to supported versions
- Simplified: Reduced external dependency footprint
🧪 Testing
- 132 tests passing: Complete test suite with comprehensive coverage
- Cross-platform: Verified on multiple Python versions (3.8-3.11)
- Automated: GitHub Actions ensures tests run on every change
See CHANGELOG.md for detailed changes.