Remove database generation from main function

[brendanreardon]

This pull request and branch is an offshoot of Refactor ini files to be arguments, instead focusing on refactoring the use of the config.ini file instead of both config.ini and colnames.ini. The interpreter version number was increased to 0.7.0 for this pull request.

Additions:

• The databases and preclinical sections of config.ini were refactored into their own ini files, annotation-databases.ini and preclinical-databases.ini, respectively. config.ini and annotation-databases.ini are now required input arguments to moalmanac.py and simplified_input.py, and preclinical-databases.ini is optional.

Revisions:

• moalmanac/datasources/was moved to the root directory of the repository, datasources/.
• The main function within moalmanac/moalmanac.py was updated to accept the config and datasource dictionaries as arguments. As a result of removing config.ini as a global variable, many functions throughout the codebase now require the config ini to be passed as an argument.
• Usage documentation, moalmanac/README.md was updated to reflect the changes to the ini files.
• Reading ini files was moved from config.py to reader.py.
• Several tests in moalmanac/test/datasources_tests.py, moalmanac/test/evaluator_tests.py, moalmanac/test/features_tests.py, and moalmanac/test/investigator_tests.py.

Secondary changes:

• Removed moalmanac/run_deconstructSigs.R and moalmanac/wrapper_deconstructSigs.sh from repository.
• run_example.py was revised to add the date in ISO format to the default output directory

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]

All unit tests pass as well as output regression tests. Documentation updated and all changed files have been reviewed.

[brendanreardon]

Attaching zips of output directory used for output regression test.

• 2024-07-09-refactor-output-dir.zip
• 2024-07-03-main-branch-all-toggles-on.zip