Upgrade dependencies

[lkct]

• Updated pyproject.toml:
  • Python 3.12 added to support list -- should be automatically compatible given dependencies available in 3.12.
  • Dependency versions:
    • torch fixed to ~=2.1.0. we should manually upgrade.
    • mypy fixed to ==1.6.1. minor version also affects typing, so we need exact version.
    • pylint fixed to ~=3.0.0. we should manually upgrade when need to (e.g. bugfixes).
    • pydocstyle fixed to ~=6.3.0. this does not upgrade much and 6.3.0 should be enough.
  • Linting rules:
    • isort target updated to 3.8. previously it's 3.9, which was a typo.
    • pylint updated according to API change, enabled new prefer-typing-namedtuple.
    • mypy sorted according to docs. enabled new possibly-undefined.
• Updated code:
  • PR Fix mypy errors #128 partially reverted -- removed the temp fix for mypy 1.5 upstream bug.
  • Fixed other bugs arising from the version change.
  • Fixed some cyclic import -- previously inconsistent on CI and local.