ENH: Use logging in project classes. BUG: Fixed tests.

[aylward]

Add Logging Infrastructure and CI/CD Workflows

Summary

This PR integrates a comprehensive logging system throughout the PhysioMotion4D codebase and establishes GitHub Actions workflows for continuous integration and testing.

Changes

🔧 Infrastructure

• CI/CD: Added GitHub Actions workflows for automated testing
  • Standard test workflow (.github/workflows/test.yml)
  • Slow test workflow (.github/workflows/test-slow.yml)
  • Comprehensive documentation (.github/workflows/README.md)

📝 Logging Integration

• Implemented logging throughout all major modules:
  • Registration modules (register_images_ants.py, register_images_icon.py, register_time_series_images.py, register_model_to_model_*.py)
  • Segmentation modules (segment_chest_*.py)
  • Conversion utilities (convert_*.py)
  • Image and transform tools (image_tools.py, transform_tools.py)
  • USD tools (usd_tools.py, usd_anatomy_tools.py)
  • Workflow modules (heart_gated_ct_to_usd_workflow.py)

✨ Enhancements

• Transform Tools: Significantly enhanced transform_tools.py with improved functionality (+83 lines)
• ANTs Registration: Expanded register_images_ants.py with better logging and error handling (+197 lines)

🧪 Testing

• Updated test files to work with new logging system
• Fixed issues in multiple test modules
• Improved test coverage and reliability

📦 Configuration

• Updated pyproject.toml with new dependencies and configuration
• Modified .gitignore for better file management

Statistics

• 32 files changed
• 1,295 insertions(+), 356 deletions(-)

Testing Notes

All major functionality has been tested and verified. The logging system provides better visibility into processing pipelines and aids in debugging.