Task: Refactor Logging and Debug Output Implementation

[nlebovits]

Describe the task

Refactor the inconsistent logging and debugging statements throughout the data/src pipeline to create a unified, configurable, and efficient logging system. Currently, a mix of logging calls and print statements are scattered across the codebase with inconsistent implementation, making terminal output verbose and difficult to manage during pipeline execution. While config.py contains some logging configuration functionality, it is not properly integrated throughout the pipeline. This task involves consolidating all output statements into a standardized logging system that is both parsimonious for normal operation and helpful for debugging, with particular attention to managing verbose geometry debugging output.

Acceptance Criteria

• Audit all logging, print, and debug statements in data/src directory and subdirectories
• Replace all print statements with appropriate logging calls using standard log levels
• Implement consistent logging configuration that properly utilizes the existing config.py logging functionality
• Remove or properly gate verbose debug output that clutters terminal during normal pipeline execution
• Verify that logging performance does not negatively impact pipeline execution time
• Update relevant documentation to reflect the new logging patterns, configuration options, and best practices

Additional context

• Preserve existing config.py logging functionality where possible, but refactor as needed for consistency
• Pay special attention to geometry processing modules where debug output can become extremely verbose
• Consider both development and production use cases when designing the logging system
• Ensure the solution is maintainable and follows Python logging best practices