[ci] use `nbqa` or `ruff` to auto-format and lint notebooks?

[jameslamb]

The nbqa project (nbQA-dev/nbQA) understands the Ipython notebook format and knows how to run common Python static analysis and autoformatting tools over them.

For example:

conda create --name deployment-dev \
    python=3.10 \
    nbqa \
    flake8

source activate deployment-dev
nbqa flake8 \
   . \
   --extend-ignore 'E402,E501'

As of this writing, that finds some legitimate correctness and efficiency issues:

source/examples/rapids-1brc-single-node/notebook.ipynb:cell_3:8:17: F541 f-string is missing placeholders
source/examples/rapids-autoscaling-multi-tenant-kubernetes/notebook.ipynb:cell_23:7:5: F401 'dask.distributed.wait' imported but unused
source/examples/rapids-azureml-hpo/notebook.ipynb:cell_7:5:29: F821 undefined name 'os'
source/examples/rapids-azureml-hpo/notebook.ipynb:cell_8:7:10: F821 undefined name 'os'
source/examples/rapids-azureml-hpo/notebook.ipynb:cell_9:1:1: F401 'azure.ai.ml.sweep.MedianStoppingPolicy' imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell_1:3:17: F821 undefined name 'cluster'
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell_2:1:1: F401 'math' imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell_2:2:1: F401 'datetime.datetime' imported but unused
...

It supports a bunch of tools, like this:

nbqa black .
nbqa isort .
nbqa flake8 .

See https://github.com/nbQA-dev/nbQA?tab=readme-ov-file#-examples.

Other nice features of that tool:

• finds all .ipynb recursively in the project (no need to specify specific directories unless you want to)
• can be configured in pyproject.toml

Benefits of this work

• would provide more automated detection (in CI and pre-commit) of issues that otherwise have to be caught by humans
• would make enforcement of team agreements around things like style automatic

[jacobtomlinson]

This would be a great addition! Perhaps we could add this to the pre-commit hooks?

[jameslamb]

If you all are open to it, sure! I'd be happy to contribute that.

I did notice pre-commit is run in CI here: https://github.com/rapidsai/deployment/blob/main/.github/workflows/pre-commit.yml

[jacobtomlinson]

Yes please that would be great!

[bdice]

Feel free to copy from cudf — it uses nbqa in pre-commit.

[jameslamb]

excellent, thanks!

[jameslamb]

Working through these in pieces, but thought it'd be useful to share how much is left to go.

Here's what remains to enable ruff on this project's notebooks.

error: Failed to parse source/examples/xgboost-azure-mnmg-daskcloudprovider/notebook.ipynb:23:6:27: Unexpected token '<'
error: Failed to parse source/examples/rapids-sagemaker-higgs/notebook.ipynb:39:1:5: Unexpected token 'ecr'
source/examples/rapids-1brc-single-node/notebook.ipynb:cell 7:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/rapids-1brc-single-node/notebook.ipynb:cell 10:8:17: F541 [*] f-string without any placeholders
source/examples/rapids-1brc-single-node/notebook.ipynb:cell 12:13:121: E501 Line too long (129 > 120)
source/examples/rapids-autoscaling-multi-tenant-kubernetes/notebook.ipynb:cell 43:2:1: E402 Module level import not at top of cell
source/examples/rapids-autoscaling-multi-tenant-kubernetes/notebook.ipynb:cell 43:3:1: E402 Module level import not at top of cell
source/examples/rapids-autoscaling-multi-tenant-kubernetes/notebook.ipynb:cell 51:6:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/rapids-autoscaling-multi-tenant-kubernetes/notebook.ipynb:cell 51:7:42: F401 [*] `dask.distributed.wait` imported but unused
source/examples/rapids-azureml-hpo/notebook.ipynb:cell 6:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/rapids-azureml-hpo/notebook.ipynb:cell 13:10:1: E722 Do not use bare `except`
source/examples/rapids-azureml-hpo/notebook.ipynb:cell 23:2:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/rapids-azureml-hpo/notebook.ipynb:cell 23:5:29: F821 Undefined name `os`
source/examples/rapids-azureml-hpo/notebook.ipynb:cell 26:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/rapids-azureml-hpo/notebook.ipynb:cell 26:7:10: F821 Undefined name `os`
source/examples/rapids-azureml-hpo/notebook.ipynb:cell 26:17:121: E501 Line too long (158 > 120)
source/examples/rapids-azureml-hpo/notebook.ipynb:cell 26:18:121: E501 Line too long (142 > 120)
source/examples/rapids-azureml-hpo/notebook.ipynb:cell 31:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/rapids-azureml-hpo/notebook.ipynb:cell 31:1:48: F401 [*] `azure.ai.ml.sweep.MedianStoppingPolicy` imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 4:3:17: F821 Undefined name `cluster`
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 7:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 7:1:8: F401 [*] `math` imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 7:2:22: F401 [*] `datetime.datetime` imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 7:4:8: F401 [*] `cudf` imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 7:5:8: F401 [*] `dask` imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 7:13:22: F401 [*] `dateutil.parser` imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 7:14:1: E401 [*] Multiple imports on one line
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 7:14:8: F401 [*] `configparser` imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 7:14:22: F401 [*] `os` imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 7:14:26: F401 [*] `contextlib` imported but unused
source/examples/rapids-ec2-mnmg/notebook.ipynb:cell 27:3:1: F821 Undefined name `cluster`
source/examples/rapids-optuna-hpo/notebook.ipynb:cell 3:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/rapids-optuna-hpo/notebook.ipynb:cell 3:2:8: F401 [*] `cuml` imported but unused
source/examples/rapids-optuna-hpo/notebook.ipynb:cell 3:3:8: F401 [*] `dask_cudf` imported but unused
source/examples/rapids-optuna-hpo/notebook.ipynb:cell 3:4:17: F401 [*] `numpy` imported but unused
source/examples/rapids-optuna-hpo/notebook.ipynb:cell 3:7:8: F401 [*] `dask` imported but unused
source/examples/rapids-optuna-hpo/notebook.ipynb:cell 3:14:44: F401 [*] `dask.distributed.performance_report` imported but unused
source/examples/rapids-optuna-hpo/notebook.ipynb:cell 7:1:8: F811 [*] Redefinition of unused `os` from cell 3, line 6
source/examples/rapids-optuna-hpo/notebook.ipynb:cell 9:1:18: F401 [*] `pandas` imported but unused
source/examples/rapids-sagemaker-higgs/notebook.ipynb:cell 39:1:5: E999 SyntaxError: Unexpected token 'ecr'
source/examples/time-series-forecasting-with-hpo/notebook.ipynb:cell 23:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/time-series-forecasting-with-hpo/notebook.ipynb:cell 23:13:12: UP031 Use format specifiers instead of percent format
source/examples/time-series-forecasting-with-hpo/notebook.ipynb:cell 23:18:9: UP032 [*] Use f-string instead of `format` call
source/examples/time-series-forecasting-with-hpo/notebook.ipynb:cell 90:11:13: E741 Ambiguous variable name: `l`
source/examples/time-series-forecasting-with-hpo/notebook.ipynb:cell 103:12:26: F541 [*] f-string without any placeholders
source/examples/time-series-forecasting-with-hpo/notebook.ipynb:cell 109:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/time-series-forecasting-with-hpo/notebook.ipynb:cell 120:46:5: F841 Local variable `t` is assigned to but never used
source/examples/time-series-forecasting-with-hpo/notebook.ipynb:cell 143:4:9: F841 Local variable `product_weights` is assigned to but never used
source/examples/xgboost-azure-mnmg-daskcloudprovider/notebook.ipynb:cell 23:6:27: E999 SyntaxError: Unexpected token '<'
source/examples/xgboost-azure-mnmg-daskcloudprovider/notebook.ipynb:cell 23:21:121: E501 Line too long (123 > 120)
source/examples/xgboost-azure-mnmg-daskcloudprovider/notebook.ipynb:cell 30:1:121: E501 Line too long (146 > 120)
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 4:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 4:2:18: F401 [*] `time.time` imported but unused
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 4:5:18: F401 [*] `pandas` imported but unused
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 4:7:8: F401 [*] `cupy` imported but unused
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 4:8:8: F401 [*] `cudf` imported but unused
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 4:9:8: F401 [*] `dask` imported but unused
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 4:10:26: F401 [*] `dask.dataframe` imported but unused
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 8:14:121: E501 Line too long (128 > 120)
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 12:4:4: F821 Undefined name `spark`
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 12:10:12: F821 Undefined name `spark`
source/examples/xgboost-dask-databricks/notebook.ipynb:cell 13:1:9: F821 Undefined name `spark`
source/examples/xgboost-gpu-hpo-job-parallel-k8s/notebook.ipynb:cell 20:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/xgboost-gpu-hpo-job-parallel-ngc/notebook.ipynb:cell 14:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/xgboost-randomforest-gpu-hpo-dask/notebook.ipynb:cell 3:1:1: I001 [*] Import block is un-sorted or un-formatted
source/examples/xgboost-randomforest-gpu-hpo-dask/notebook.ipynb:cell 3:4:8: F401 [*] `cuml` imported but unused
source/examples/xgboost-randomforest-gpu-hpo-dask/notebook.ipynb:cell 3:10:38: F401 [*] `dask.distributed.wait` imported but unused
source/examples/xgboost-randomforest-gpu-hpo-dask/notebook.ipynb:cell 3:13:21: F401 [*] `sklearn.datasets` imported but unused
source/examples/xgboost-randomforest-gpu-hpo-dask/notebook.ipynb:cell 3:21:8: F401 [*] `gzip` imported but unused
source/examples/xgboost-randomforest-gpu-hpo-dask/notebook.ipynb:cell 11:1:8: F811 [*] Redefinition of unused `time` from cell 3, line 1
source/examples/xgboost-randomforest-gpu-hpo-dask/notebook.ipynb:cell 19:27:9: UP032 [*] Use f-string instead of `format` call
source/examples/xgboost-randomforest-gpu-hpo-dask/notebook.ipynb:cell 20:8:11: UP032 [*] Use f-string instead of `format` call
Found 70 errors.

Got those by modifying the ruff hook like this in .pre-commit-config.yaml.

- id: ruff
  types_or: [jupyter, python]

[jameslamb]

🎉 woo! Thanks for all the reviews @jacobtomlinson