Update ruff config and pre-commit

[TimMonko]

• ruff check with new config
• update ruff config
• update precommit

[codecov]

Codecov Report

❌ Patch coverage is 80.62016% with 25 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/ndevio/widgets/_utilities_container.py	72.72%	15 Missing ⚠️
src/ndevio/widgets/_plugin_install_widget.py	63.63%	4 Missing ⚠️
src/ndevio/_bioio_plugin_utils.py	75.00%	3 Missing ⚠️
src/ndevio/__init__.py	66.66%	1 Missing ⚠️
src/ndevio/_plugin_manager.py	85.71%	1 Missing ⚠️
src/ndevio/helpers.py	93.33%	1 Missing ⚠️

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