replace black formatter with ruff

[ssenan]

• Resolves use ruff instead of black for code formatting #245
• Also removes some unused libraries from the pyproject.toml

[codecov]

Codecov Report

Merging #247 (a9c525b) into main (6e9e327) will decrease coverage by 0.11%.
The diff coverage is 20.00%.

@@            Coverage Diff             @@
##             main     #247      +/-   ##
==========================================
- Coverage   37.11%   37.00%   -0.11%     
==========================================
  Files          23       23              
  Lines        1482     1481       -1     
  Branches      202      202              
==========================================
- Hits          550      548       -2     
- Misses        924      925       +1     
  Partials        8        8              

Files	Coverage Δ
src/dnadiffusion/data/dataloader.py	28.00% <100.00%> (ø)
src/dnadiffusion/data/preprocessing.py	38.61% <ø> (-0.61%)	⬇️
src/dnadiffusion/metrics/motif_composition.py	38.09% <100.00%> (-1.44%)	⬇️
src/dnadiffusion/utils/data_util.py	49.66% <ø> (ø)
src/dnadiffusion/utils/sample_util.py	43.85% <ø> (ø)
src/dnadiffusion/utils/train_util.py	0.00% <0.00%> (ø)
src/dnadiffusion/models/unet.py	0.00% <0.00%> (ø)
src/dnadiffusion/models/layers.py	0.00% <0.00%> (ø)