Add bonds_penalty hyperparam

[andreea-popescu-reef]

Description

reviving #181

Type of Change

• Bug fix (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)
• Documentation update
• Other (please describe):

Breaking Change

N/A

Checklist

• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have run cargo fmt and cargo clippy to ensure my code is formatted and linted correctly
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules

[camfairchild]

Make sure to squash the clippy issues.
Otherwise LGTM, thanks for the contribution!