Apply ruff 0.6

[DimitriPapadopoulos]

Exclude docs/notebooks for now, as notebook liniting is a new addition:

• Jupyter notebooks are now linted and formatted by default

Re-enable ruff check, after it had been disabled by #1274.

Not sure how to address this remaining issue:

mriqc/tests/test_parser.py:97:40: PT019 Fixture `_species` without value is injected as parameter, use `@pytest.mark.usefixtures` instead
   |
95 |     ],
96 | )
97 | def test_species_arg(tmp_path, argval, _species):
   |                                        ^^^^^^^^ PT019
98 |     """Check the correct parsing of the species argument."""
99 |     args = MIN_ARGS + ['--species', argval]
   |

[DimitriPapadopoulos]

I'm not certain ruff check --diff and run format --diff do what we think they do. I would expect ruff 0.6.2 to print this residual error, but it doesn't:

mriqc/tests/test_parser.py:97:40: PT019 Fixture `_species` without value is injected as parameter, use `@pytest.mark.usefixtures` instead
   |
95 |     ],
96 | )
97 | def test_species_arg(tmp_path, argval, _species):
   |                                        ^^^^^^^^ PT019
98 |     """Check the correct parsing of the species argument."""
99 |     args = MIN_ARGS + ['--species', argval]
   |

[DimitriPapadopoulos]

Yep, works much better without --diff! I don't understand why it was added by #1274.

[DimitriPapadopoulos]

I don't know enough about fixtures to fix the residual issue PT019.