2024 10 23 bug changes

[brendanreardon]

This pull request contains bug fixes to bugs observed within release 0.7.1. The patch version of this code base was increased, now 0.7.2.

Bug fixes:

• moalmanac.py would attempt to access the value "preclinical" in the preclinical_db_paths dictionary, even if no .ini file was provided using the --preclinical-dbs argument.

Revisions:

• Patch number for this code base was increased to 0.7.2.
• The section headers for both annotation-databases.ini and preclinical-databases.ini were named to paths.
• Added documentation to the logging section of config.ini to reference the logging module documentation on docs.python.org.
• run_example.py and moalmanac.py were both refactored with the order of how config_ini, dbs, and preclinical_dbs are set up before executing the main function. Instead of defining paths all at once and then importing each of them, each is processed on its own before moving to the next.
• Minor PEP8 changes to logger.py and moalmanac.py, involving new line breaks or spacing.

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

[brendanreardon]

Bugs observed,

• Failing at report generation if run directly from moalmanac.py if no input data is provided
• Failing if preclinical-dbs is not provided and run directly from moalmanac.py