Apply pre-commit checks to all files and make CI green

[turbaszek]

I applied all pre-commit check by running pre-commit run --all-files to fix the CI. Now contributors will need to care only about files they edit :)

[turbaszek]

@sharanf @Humbedooh - there's a lot of changes but they were automatically done by pre-commit (removing ending whitespaces and adding missing new lines at the end of files)

[Humbedooh]

I've only checked about 10% of the changes, but yeah looks like generic linting.
Can you confirm that there is no functional change?

[turbaszek]

Can you confirm that there is no functional change?

Yes, I only applied auto changes. And using them for last year I'm sure there's no functional change