Fix device allocation in sample.py / simplify sequence generation

[ssenan]

• Resolves Sample generation fails to run #159
• Adds accelerate to sample.py for easy device allocation during sample generation
• Adds save_timesteps and save_dataframe flags to more easily specify how many samples to generate
• Removes some old depedencies from environment.yml and pyproject.toml that are currently unused and updates them to allow for torch>=2.0.0

[codecov]

Codecov Report

Merging #160 (133c2a8) into main (a16a94f) will decrease coverage by 0.07%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##             main     #160      +/-   ##
==========================================
- Coverage   11.39%   11.32%   -0.07%     
==========================================
  Files          13       13              
  Lines         825      830       +5     
  Branches       89       91       +2     
==========================================
  Hits           94       94              
- Misses        730      735       +5     
  Partials        1        1              

Impacted Files	Coverage Δ
src/dnadiffusion/metrics/metrics.py	0.00% <0.00%> (ø)
src/dnadiffusion/utils/sample_util.py	0.00% <0.00%> (ø)

[cameronraysmith]

This should be a separate issue, but we should just make a top-level data/ folder or specify an external source rather than keeping these in a src/ subfolder.