MAINT: Add ruff for linting

[arokem]

Replaces #113

[Copilot]

Pull request overview

This PR modernizes the project's linting infrastructure by replacing flake8 with ruff, a faster Python linter written in Rust. It also updates build system dependencies and adds pre-commit hooks for automated code quality checks.

Key changes:

• Migration from flake8 to ruff for linting with custom rule configuration
• Updated build system requirements (setuptools>=64, setuptools_scm>=8)
• Addition of pre-commit configuration with ruff and codespell hooks

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 4 comments.

File	Description
setup.cfg	Updated build dependencies and added ruff to dev dependencies
pyproject.toml	Added ruff configuration, updated build-system requirements, and modified pytest config section
.pre-commit-config.yaml	Added new pre-commit configuration with ruff linting/formatting and codespell
.github/workflows/test.yml	Replaced flake8 command with ruff check in CI workflow

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[Copilot]

The dev dependencies still include flake8 (line 65) even though it's being replaced by ruff. Since the linting command in the CI workflow is being changed to use ruff, flake8 should be removed from the dependencies to avoid confusion and reduce unnecessary dependencies.

[arokem]

@copilot open a new pull request to apply changes based on this feedback

[arokem]

I believe this is ready for a review and merge, but no rush. It's a very large number of lines of code change, but it's almost exclusively changes in formatting or typos. The only substantive change is here:

pyAFQ/AFQ/tractography/utils.py

Lines 17 to 46 in d4b7044

	def _is_int(val):
	if isinstance(val, np.ndarray):
	return False
	if isinstance(val, int):
	return True
	elif isinstance(val, float):
	if val.is_integer():
	return True
	else:
	raise ValueError(f"n_seeds is set to {val}, which is not an integer")
	def gen_seeds(
	seed_mask,
	seed_threshold,
	n_seeds,
	thresholds_as_percentages,
	random_seeds,
	rng_seed,
	affine,
	):
	"""
	Generate seeds for tracking. For parameters, see
	:func:`AFQ.tractography.tractography.track`.
	"""
	logger.info("Generating Seeds...")
	if _is_int(n_seeds):
	# If it's float type, cast to integer:
	if isinstance(n_seeds, float):
	n_seeds = int(n_seeds)

, with relevant tests here:

pyAFQ/AFQ/tests/test_tractography.py

Lines 28 to 32 in d4b7044

	def test_is_int():
	npt.assert_(_is_int(5))
	npt.assert_(_is_int(5.0))
	npt.assert_(not _is_int(np.array([1, 2, 3])))
	npt.assert_raises(ValueError, _is_int, 5.5)

. This change protects against cases where n_seeds input is provided as a float (with integer value), which otherwise raises an error later on. I saw this error show up on my laptop, even though doesn't show up on the CI, so this might be platform specific. BTW: I upgraded my latpop's OS to the most recent and now I am getting segfaults on our test suite 😅

[36000]

This pull request looks great! I am super excited for this more clean organization for pyAFQ's codebase. Merging