MAINT: silence ruff deprecation warning

[lucascolley]

warning: The top-level linter settings are deprecated in favour of their counterparts in the `lint` section. Please update the following options in `tools/lint.toml`:
  - 'dummy-variable-rgx' -> 'lint.dummy-variable-rgx'
  - 'ignore' -> 'lint.ignore'
  - 'select' -> 'lint.select'
  - 'mccabe' -> 'lint.mccabe'
  - 'pydocstyle' -> 'lint.pydocstyle'
  - 'per-file-ignores' -> 'lint.per-file-ignores'

Silences the deprecation warning and slightly restructures the file to follow the ruff docs.

[j-bowhay]

Thanks @lucascolley