Require isort on all Python files.

[trivialfis]

After initial refactoring of tests, the required amount of changes for running isort is significantly smaller. Let's require it on the CI from now on.

All changes in this PR except for the linter script are made by isort.

[hcho3]

Doesn't black run isort internally?

[trivialfis]

No, they are different linters.

[trivialfis]

isort --profile=black ..

But we have this option to make them work together.

[trivialfis]

Just a brief note on why are we doing all these refactorings.

• Init estimation for regression. #8272 requires changes to PySpark tests since many of them are written with hardcoded expected results.
• But pyspark and dask tests are conflicting with each other for unknown reasons in new PRs so we split them up into test_distributed.
• Then PySpark tests use the python unittest module, which conflicts with pytest utilities like skipif and fixtures. As a result, we need to clean up the PySpark tests to transition to pytest.

Lastly, having linters and a type checker can help us better maintain these growing Python scripts. This PR makes isort a requirement, but black is still optional for most of the scripts.