chore: Refactored dependencies management and fixed linters configurations

[svdimchenko]

I've implemented the following optimisations and fixes:

• generalised dependencies in pyproject.toml (before there was extra dev-requirements.txt file)
• enabled mypy check (it was somehow disabled at all) Found 408 errors in 74 files (checked 149 source files)
• enabled black (seems it was disabled as well)
• bumped pre-commit hooks to the latest versions

TODO: the following flags shoould be removed and corresponding code fixed: --strict (to enable) --allow-untyped-defs (to remove) --allow-untyped-call (to remove)