refactor: apply bandit checks

[kenibrewer]

Description

This PR is intended to be merged after #386 .
It enables the bandit set of linting checks for the repository along with making some of the needed fixes. As my main priority with these changes is to ensure the full set of planned linting checks are in place for new development efforts, some path and line-based ignores have been applied.
In addition, this PR also in a slight decrease in test coverage. However, because none of the replaced assert statements were triggered in previous test cases this is a coverage decrease in form but not function. As such, I propose merging this PR with the improvements already present, and tackle the missing coverage during the planned post-core refactor.

Note: For review purposes this is currently targeting the branch cytomining:ci/update-ruff-to-0.3.4. It will be switched to target main after that branch is merged.

What is the nature of your change?

• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

Checklist

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• I have read the CONTRIBUTING.md guidelines.
• My code follows the style guidelines of this project.
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• I have made corresponding changes to the documentation.
• My changes generate no new warnings.
• New and existing unit tests pass locally with my changes.
• I have added tests that prove my fix is effective or that my feature works.
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[codecov-commenter]

Codecov Report

Attention: Patch coverage is 92.68293% with 9 lines in your changes are missing coverage. Please review.

Project coverage is 94.72%. Comparing base (af5a4ef) to head (071fa1c).
Report is 2 commits behind head on main.

Files	Patch %	Lines
pycytominer/feature_select.py	50.00%	2 Missing ⚠️
pycytominer/operations/variance_threshold.py	50.00%	2 Missing ⚠️
pycytominer/annotate.py	50.00%	1 Missing ⚠️
pycytominer/cyto_utils/collate.py	0.00%	1 Missing ⚠️
pycytominer/normalize.py	50.00%	1 Missing ⚠️
pycytominer/operations/correlation_threshold.py	50.00%	1 Missing ⚠️
pycytominer/operations/transform.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #387      +/-   ##
==========================================
- Coverage   94.96%   94.72%   -0.24%     
==========================================
  Files          56       56              
  Lines        3137     3147      +10     
==========================================
+ Hits         2979     2981       +2     
- Misses        158      166       +8     

Flag	Coverage Δ
unittests	94.72% <92.68%> (-0.24%)	⬇️

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[d33bs]

Good work, glad to see these changes applied! I left a minor comment about the ignore rules / noqa. In addition, if it's not already in place, consider adding an issue (or two) to help address ruff ignores for S108 and S603 at a later point. Generally, I feel these are distinct and important enough to warrant their own issues / PR's (as noqa's may become ignored / invisible on their own).

Please don't hesitate to let me know if you have any questions.