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fix ruff config deprecation warnings
It said: warning: The top-level linter settings are deprecated in favour of their counterparts in the `lint` section. Please update the following options in `pyproject.toml`: - 'dummy-variable-rgx' -> 'lint.dummy-variable-rgx' - 'fixable' -> 'lint.fixable' - 'ignore' -> 'lint.ignore' - 'select' -> 'lint.select' - 'unfixable' -> 'lint.unfixable' - 'isort' -> 'lint.isort' - 'per-file-ignores' -> 'lint.per-file-ignores' Fixed it the same way as in the Python template (NLeSC/python-template@3ce8ff9)
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