Shutdown logging

[brendanreardon]

This pull request updates the interpreter to version 0.7.4. We added a new script to run regression tests, run_4x_for_output_regression_test.py, that will run the interpreter 4 times based on passing and not passing inputs and different configuration settings.

We also discovered that the logger was writing to the same log when multiple instantiations of the main function were called within the same Python process. So, we revised moalmanac/logger.py to create a separate log for each call of the main function, which is the intended behavior.

Additions:

• An added function to moalmanac/logger.py to shutdown the logger, and added this to the main function of moalmanac/moalmanac.py.
• A new script run_4x_for_output_regression_test.py to run the run_example.py four times:
  • with toggle-able settings from the function_toggle section of moalmanac/config.in enabled, and example genomic data from example_data/
  • with toggle-able settings from the function_toggle section of moalmanac/config.in enabled, and no input genomic data
  • with toggle-able settings from the function_toggle section of moalmanac/config.in disabled, and example genomic data from example_data/
  • with toggle-able settings from the function_toggle section of moalmanac/config.in disabled, and no input genomic data

Revisions:

• Removed existing handlers for logging within the setup function of moalmanac/logger.py. This allows separate logs to be created if the main function is being called in series within a single python process.

Pre-pull request check list,

• Relevant documentation has been updated
• All unit tests pass
• All outputs pre- and post- changes match by md5 hash
• All files changed have been reviewed
• Docker pushed

[brendanreardon]

All outputs pre- and post- changes match by md5 hash.
Archive.zip

[brendanreardon]

• All files have been reviewed
• No documentation updates required
• All 133 unit tests pass

[brendanreardon]

Docker pushed to 0.7.5_v.2024-10-03.