Pre-commit tools and black update

[peterjc]

• I hereby agree to dual licence this and any previous contributions under both
  the Biopython License Agreement AND the BSD 3-Clause License.

• I have read the CONTRIBUTING.rst file, have run pre-commit
  locally, and understand that continuous integration checks will be used to
  confirm the Biopython unit tests and style checks pass with these changes.

• I have added my name to the alphabetical contributors listings in the files
  NEWS.rst and CONTRIB.rst as part of this pull request, am listed
  already, or do not wish to be listed. (This acknowledgement is optional.)

Some minor housekeeping with the style checking.

[peterjc]

Cross reference PyCQA/flake8#1922 for E704 false positives [fixed link]

[JoaoRodrigues]

Not necessarily related to this PR, but should we have a look at all the linters/rules we use and maybe standardize them? Right now in our CI workflows I see:

• Our CI runs pre-commit
• We have a separate pre-commit.ci service

In the CI workflow, we have:

• flake8
• black
• ruff
• etc.

Could we maybe consider dropping black and flake for ruff alone? Will that make a big difference in style, whereas it might simplify our CI quite a bit?

For instance, these specific flake8 plugins have native support in ruff:

• flake8-blind-except: https://docs.astral.sh/ruff/rules/#flake8-blind-except-ble
• flake8-bugbear: https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
• flake8-comprehensions: https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
• flake8-implicit-str-concat-isc: https://docs.astral.sh/ruff/rules/#flake8-implicit-str-concat-isc
• pydocstyle: https://docs.astral.sh/ruff/rules/#pydocstyle-d

We can also replace black by ruff, since it does the same formatting job.

The only thing we cannot use ruff for are the docs/rst.

[peterjc]

I've been moving some my own stuff to ruff in favour of flake8 and black, but it doesn't cover everything we're using. Dropping pydocstyle on this PR is a step in that direction, happy to take that further 👍

[JoaoRodrigues]

👍 👍 Are there any rules you're following when dropping the linters? Like, run with ruff only, then run the old linters to see if it missed anything?

[peterjc]

You have to enable non-default ruff checks, which ought to be fine if we're already using the original it was based on (e.g. flake8-bugbear), but occasionally there are differences.

I'm hoping once ruff adds array formatting we can use it in place off black.

[peterjc]

@JoaoRodrigues was that an implicit PR approval?

[JoaoRodrigues]

Yes! Sorry, I didn't think you'd be waiting for my approval!