Update to snakebids v0.12.x

[kaitj]

Proposed changes

DO NOT MERGE - This is currently a draft PR for testing snakebids v0.12.x

This PR makes changes for upgrading to snakebids v0.12.x, removing unnecessary config options and refactoring the run.py. as needed.

Types of changes

What types of changes does your code introduce? Put an x in the boxes that apply

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Other (if none of the other choices apply)

Checklist

Put an x in the boxes that apply. You can also fill these out after creating the PR. If you are unsure about any of the choices, don't hesitate to ask!

• Changes have been tested to ensure that fix is effective or that a feature works.
• Changes pass the unit tests
• Code has been run through the poe quality task
• I have included necessary documentation or comments (as necessary)
• Any dependent changes have been merged and published

Notes

All PRs will undergo the unit testing before being reviewed. You may be requested to explain or make additional changes before the PR is accepted.

[kaitj]

Closing as this was for testing purposes.