bump ruff to 0.9.10 and reformat files as necessary

[pstjohn]

Bumps the ruff version we use to format files. Ruff now will check and format jupyter notebooks, which means we need a couple small edits.

The ruff vscode extension has deprecrated the old ruff-lsp, so the old version is giving me a warning every time I open the container.

[nvdreidenbach]

moco changes lgtm

[codecov-commenter]

Codecov Report

❌ Patch coverage is 72.22222% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.14%. Comparing base (5f22e86) to head (66e0ef3).
⚠️ Report is 494 commits behind head on main.

Files with missing lines	Patch %	Lines
...c/bionemo/geneformer/data/singlecell/datamodule.py	33.33%	2 Missing ⚠️
...ages/bionemo-fw/src/bionemo/fw/dependency_graph.py	0.00%	1 Missing ⚠️
...bionemo-llm/src/bionemo/llm/model/biobert/model.py	0.00%	1 Missing ⚠️
...datamodule/src/bionemo/webdatamodule/datamodule.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #751   +/-   ##
=======================================
  Coverage   84.14%   84.14%           
=======================================
  Files         128      128           
  Lines        8036     8036           
=======================================
  Hits         6762     6762           
  Misses       1274     1274           

Files with missing lines	Coverage Δ
...ackages/bionemo-core/src/bionemo/core/data/load.py	81.02% <ø> (ø)
...-core/src/bionemo/core/data/multi_epoch_dataset.py	92.50% <ø> (ø)
...ages/bionemo-core/src/bionemo/core/model/config.py	85.71% <ø> (ø)
...ages/bionemo-core/src/bionemo/core/utils/dtypes.py	88.46% <ø> (ø)
...ionemo-core/src/bionemo/core/utils/random_utils.py	100.00% <ø> (ø)
...s/bionemo-esm2/src/bionemo/esm2/data/datamodule.py	95.16% <100.00%> (ø)
...s/bionemo-esm2/src/bionemo/esm2/model/embedding.py	78.57% <ø> (ø)
...esm2/src/bionemo/esm2/model/finetune/datamodule.py	95.52% <100.00%> (ø)
...onemo-esm2/src/bionemo/esm2/model/finetune/loss.py	94.59% <ø> (ø)
.../src/bionemo/esm2/model/finetune/sequence_model.py	95.16% <ø> (ø)
... and 30 more

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