ENH: Refactor code linter and formatter dependencies

[jhlegarreta]

Refactor code linter and formatter dependencies:

• Remove black, flake8 and isort dependencies from pyproject.toml: the role has been taken over by ruff in commit 81b3690.
• Transfer the black and isort rules left behind to ruff in pyproject.toml
• Remove black, flake8 and isort from the pre-commit config file and use ruff instead.

[jhlegarreta]

A few comments:

• There seems to be a contradiction between the use of skip-string-normalization = true in
  https://github.com/nipreps/eddymotion/blob/main/pyproject.toml#L118
  and inline-quotes = "double" in
  https://github.com/nipreps/eddymotion/blob/main/pyproject.toml#L155

  according to:
  Add "preserve" quote-style to mimic Black's skip-string-normalization astral-sh/ruff#8822

  skip-string-normalization = true is quote-style=preserve ruff, but inline-quotes = "double" enforces particular style.

• Looks like this adding ruff's import sorting:
  https://github.com/nipreps/eddymotion/pull/144/files#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711R135

  slightly changes isort's vs ruff's import sorting:
  https://github.com/nipreps/eddymotion/actions/runs/8458933073/job/23174220049?pr=144#step:4:14

  Their rules are known to be different:
  https://docs.astral.sh/ruff/faq/#how-does-ruffs-import-sorting-compare-to-isort

  Do we want I001 to be excluded?

• On a related note, before the cleanup proposed by this PR I was getting an error related to isort locally:

  [INFO] Installing environment for https://github.com/timothycrosley/isort.
  [INFO] Once installed this environment will be reused.
  [INFO] This may take a few minutes...
  (...)
    × Preparing metadata (pyproject.toml) did not run successfully.
    │ exit code: 1
     ╰─> [14 lines of output]
          Traceback (most recent call last):
  (...)
              raise RuntimeError("The Poetry configuration is invalid:\n" + message)
          RuntimeError: The Poetry configuration is invalid:
            - data.extras.pipfile_deprecated_finder[2] must match pattern ^[a-zA-Z-_.0-9]+$
  
        [end of output]
  
   note: This error originates from a subprocess, and is likely not a problem with pip.
  error: metadata-generation-failed
  

  which turns out to be related to the specific isort version that is being used. Removing isort fixes it, as ruff has taken over.

[jhlegarreta]

Also, we may want to add the --fix option and ruff format in here:

eddymotion/.github/workflows/contrib.yml

Line 23 in d23dcf0

run: pipx run ruff check

so that it tells us how it would fix the code, instead of trying to discover it by ourselves.

[oesteban]

Also, we may want to add the --fix option and ruff format in here:

eddymotion/.github/workflows/contrib.yml

Line 23 in d23dcf0

run: pipx run ruff check

so that it tells us how it would fix the code, instead of trying to discover it by ourselves.

I don't think we would see how to fix the code unless we do a git diff right after, but I'm happy to do that.

[oesteban]

Oh, I see, this is not the github action, it's pre-commit.

I personally would prefer to avoid pre-commit. But it is not a hill I intend to die on.

[jhlegarreta]

Oh, yes, looks like meant more a diff-like thing than a fix for GHA, and the pre-commit config is probably only checking the modified files, and thus we are not seeing locally what the GHA is reporting.

I fixed the issues in the last push-force. In a separate PR I will bring the ruff formater changes to the whole code (only a few changes are reported).

[oesteban]

Outstanding work - thanks!