Refinements made to the logging outputs as mentioned in issue #89:

[harryswift01]

Summary

This PR standardizes logging behavior across CodeEntropy, ensuring consistency in log level handling, including logging from MDAnalysis. It also improves maintainability by enforcing proper configuration in the logger update logic.

Changes

Align log file level with logger configuration

• Updated the program.log file handler to dynamically reflect the log_level provided during initialization.
• Prevents defaulting to verbose logging unless explicitly requested.

Match MDAnalysis logging level with application log level

• Applied the main log level to the MDAnalysis logger during configuration.
• Helps ensure third-party logging is consistent with CodeEntropy verbosity.

Enforce logger and handler level updates in update_logging_level

• Improved the update_logging_level method to update both logger levels and their attached handlers.
• Guarantees runtime log level changes are respected uniformly.

Impact

• Logging configuration is now more reliable and consistent across CodeEntropy.
• Cleaner .log files by avoiding unnecessary verbosity.
• Easier debugging and log filtering for both internal and third-party modules.
• Better separation of error, debug, and standard output streams in production environments.

[jimboid]

Looks good