Update Python friends packages - black, flake8, pylint, pytest

The MR updates:

• astroid-3.3.2(2.15.8)
• autopep8-2.3.1(1.4.4)
• black-24.8.0(23.3.0)
• flake8-7.1.1(7.0.0)
• flake8_bugbear-24.8.19(24.2.6)
• pre_commit-3.8.0(3.3.1)
• pycodestyle-2.12.1(2.11.1)
• pylint-3.2.6(2.17.4)
• pytest-8.3.2(8.0.0)

And remove tomli/toml, typing_extenstions from some of them which started to used it from Python >= 3-11.