Fix broken code quality checks in CI

[brews]

Changes so code quality checks are done with ruff check . instead of flake8.

Close #106.

[brews]

CI is going to start failing this PR because the codequality check is now going to ID new issues with our codebase. So it's actually working. We should deal with these issues in another PR, or actually it looks like we can just do ruff check . --fix here, too.

[brews]

Tagging @kemccusker (if you're available) and @JMGilbert on this for review because you'll likely see this in CI code quality checks in other PRs once it merges. So, heads up.

If you want, I can fix the issues it's flagging here now. Or we can deal with this in a later PR. 👍

[codecov]

Codecov Report

Merging #107 (7d1168a) into main (b9a7696) will decrease coverage by 0.02%.
The diff coverage is 44.44%.

@@            Coverage Diff             @@
##             main     #107      +/-   ##
==========================================
- Coverage   70.34%   70.33%   -0.02%     
==========================================
  Files          17       17              
  Lines        1878     1847      -31     
==========================================
- Hits         1321     1299      -22     
+ Misses        557      548       -9     

Impacted Files	Coverage Δ
src/dscim/__init__.py	39.44% <ø> (-0.56%)	⬇️
src/dscim/menu/baseline.py	77.77% <ø> (-2.23%)	⬇️
src/dscim/menu/risk_aversion.py	97.29% <ø> (-0.08%)	⬇️
src/dscim/menu/simple_storage.py	93.03% <ø> (-0.05%)	⬇️
src/dscim/preprocessing/input_damages.py	88.68% <ø> (-0.05%)	⬇️
src/dscim/preprocessing/midprocessing.py	0.00% <ø> (ø)
src/dscim/utils/generate_yaml.py	0.00% <ø> (ø)
src/dscim/utils/menu_runs.py	0.00% <0.00%> (ø)
src/dscim/utils/plotting_utils.py	0.00% <0.00%> (ø)
src/dscim/utils/rff.py	92.02% <ø> (-0.13%)	⬇️
... and 4 more

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

[JMGilbert]

Tagging @kemccusker (if you're available) and @JMGilbert on this for review because you'll likely see this in CI code quality checks in other PRs once it merges. So, heads up.

If you want, I can fix the issues it's flagging here now. Or we can deal with this in a later PR. 👍

Seems like most of the fixes should be pretty benign (just removing unnecessary imports), so as long as this code quality package does everything we want it to do I'm happy with this update.

[brews]

Thanks, @JMGilbert. Appreciate the input. I'll commit the ruff check fixes here and then merge this PR.