[pycodestyle] Handle each cell separately for too-many-newlines-at-end-of-file (W391)

[dylwil3]

Jupyter notebooks are converted into source files by joining with newlines, which confuses the check too-many-newlines-at-end-of-file (W391). This PR introduces logic to apply the check cell-wise (and, in particular, correctly handles empty cells.)

Closes #13763

[dylwil3]

One aesthetic question is whether internal cells should still be allowed to have a single trailing newline (at the moment this is what the fix produces/allows).

[github-actions]

ruff-ecosystem results

Linter (stable)

✅ ecosystem check detected no linter changes.

Linter (preview)

ℹ️ ecosystem check detected linter changes. (+2 -17 violations, +0 -0 fixes in 3 projects; 52 projects unchanged)

PlasmaPy/PlasmaPy (+0 -1 violations, +0 -0 fixes)

ruff check --no-cache --exit-zero --ignore RUF9 --no-fix --output-format concise --preview

- docs/notebooks/dispersion/stix_dispersion.ipynb:cell 34:1:1: W391 [*] Extra newline at end of file

bokeh/bokeh (+2 -5 violations, +0 -0 fixes)

ruff check --no-cache --exit-zero --ignore RUF9 --no-fix --output-format concise --preview --select ALL

+ examples/output/jupyter/push_notebook/Basic Usage.ipynb:cell 14:1:1: W391 [*] Extra newline at end of cell
- examples/output/jupyter/push_notebook/Basic Usage.ipynb:cell 14:1:1: W391 [*] Too many newlines at end of file
- examples/output/jupyter/push_notebook/Continuous Updating.ipynb:cell 8:1:1: W391 [*] Extra newline at end of file
- examples/output/jupyter/push_notebook/Jupyter Interactors.ipynb:cell 8:1:1: W391 [*] Extra newline at end of file
- examples/output/jupyter/push_notebook/Numba Image Example.ipynb:cell 28:1:1: W391 [*] Extra newline at end of file
+ examples/server/api/notebook_embed.ipynb:cell 7:1:1: W391 [*] Extra newline at end of cell
- examples/server/api/notebook_embed.ipynb:cell 7:1:1: W391 [*] Too many newlines at end of file

mlflow/mlflow (+0 -11 violations, +0 -0 fixes)

ruff check --no-cache --exit-zero --ignore RUF9 --no-fix --output-format concise --preview

- docs/source/llms/llm-evaluate/notebooks/question-answering-evaluation.ipynb:cell 29:1:1: W391 [*] Extra newline at end of file
- docs/source/llms/llm-evaluate/notebooks/rag-evaluation.ipynb:cell 19:1:1: W391 [*] Extra newline at end of file
- docs/source/llms/rag/notebooks/retriever-evaluation-tutorial.ipynb:cell 50:1:1: W391 [*] Extra newline at end of file
- docs/source/traditional-ml/hyperparameter-tuning-with-child-runs/notebooks/parent-child-runs.ipynb:cell 15:1:1: W391 [*] Extra newline at end of file
- docs/source/traditional-ml/serving-multiple-models-with-pyfunc/notebooks/MME_Tutorial.ipynb:cell 25:1:1: W391 [*] Extra newline at end of file
- examples/evaluation/qa-evaluation.ipynb:cell 29:1:1: W391 [*] Extra newline at end of file
- examples/evaluation/rag-evaluation.ipynb:cell 16:1:1: W391 [*] Extra newline at end of file
- examples/h2o/random_forest.ipynb:cell 6:1:1: W391 [*] Extra newline at end of file
- examples/llms/RAG/retriever-evaluation-tutorial.ipynb:cell 48:1:1: W391 [*] Extra newline at end of file
- examples/rapids/mlflow_project/notebooks/rapids_mlflow.ipynb:cell 14:1:1: W391 [*] Extra newline at end of file
- examples/sklearn_elasticnet_wine/train.ipynb:cell 6:1:1: W391 [*] Extra newline at end of file

Changes by rule (1 rules affected)

code	total	+ violation	- violation	+ fix	- fix
W391	19	2	17	0	0

[MichaReiser]

One aesthetic question is whether internal cells should still be allowed to have a single trailing newline (at the moment this is what the fix produces/allows).

I think we should and doing so would be consistent with the formatter.

It would be very annoying if you write a cell with a newline at the end, hit save and Ruff fixes away the newline before you had a chance to write the next content.

[MichaReiser]

Thanks