CI: Speed up Python 3.13 tests — resolve numpy 2.x pre-built wheels

[MarcelRosier]

Summary

Resolves #160.

Problem

Python 3.13 CI install step takes ~2m50s (vs ~1s for 3.9–3.12) because numpy 1.26.4 has no cp313 pre-built wheel, forcing uv sync to compile numpy from source.

Fix

• Add numpy>=2.1; python_version>='3.13' constraint — uv now resolves numpy 2.5.1 with cp313 manylinux wheels for Python 3.13, while keeping numpy 1.26.4 for 3.9–3.12.
• Constrain brainles_preprocessing optional dep to < 3.13 since it pins numpy<2.0.

Compatibility

No code changes needed — the only numpy usage is np.count_nonzero() in brats/core/docker.py:348 and np.ones()/np.zeros() in tests, all fully compatible with numpy 2.x.

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Important: This PR is based on #158 and #159. Please review and merge those first.

[Copilot]

Pull request overview

Updates dependency constraints and CI tooling to avoid building numpy from source on Python 3.13 (by resolving to a numpy 2.x wheel), alongside the broader uv/hatch migration and CI hardening changes referenced in the PR description.

Changes:

• Add a Python 3.13-specific numpy constraint (>=2.1) and restrict the preprocessing extra to <3.13 due to its numpy<2.0 pin.
• Migrate packaging metadata/build backend to hatchling/hatch-vcs and move dev/docs deps into PEP 735 dependency groups.
• Update CI/RTD configuration to use uv, SHA-pin GitHub Actions, add Dependabot, and remove the autoformat workflow.

Reviewed changes

Copilot reviewed 8 out of 11 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
pyproject.toml	Add numpy 3.13 marker constraint; switch build backend to hatch; define dependency groups and optional dependency marker.
CONTRIBUTING.md	Update contributor setup commands from Poetry to uv.
.readthedocs.yaml	Switch RTD installation to use uv sync with the docs group.
.gitignore	Ignore hatch-vcs generated brats/_version.py.
.github/workflows/tests.yml	Use setup-uv and uv sync --frozen; SHA-pin checkout/codecov actions.
.github/workflows/ruff.yml	SHA-pin checkout action.
.github/workflows/release.yml	SHA-pin checkout/setup-python and fetch full history (needed for VCS versioning).
.github/workflows/autoformat.yml	Remove the comment-triggered autoformat workflow.
.github/dependabot.yml	Add Dependabot configuration for GitHub Actions updates.

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[Copilot]

Pull request overview

Copilot reviewed 8 out of 11 changed files in this pull request and generated no new comments.

[MarcelRosier]

Blocking: The < 3.13 constraint on brainles_preprocessing is a workaround until BrainLesion/preprocessing#187 (relaxing numpy<2.0) is merged and released.

Once a new brainles_preprocessing version lands on PyPI with numpy 2.x support, we should:

1. Bump brainles_preprocessing minimum version to that release
2. Remove the python_version < '3.13' marker from the preprocessing optional dep
3. Re-run uv lock

Update: resolved

[Copilot]

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[Copilot]

Pull request overview

Copilot reviewed 6 out of 7 changed files in this pull request and generated no new comments.

Suppressed comments (2)

pyproject.toml:49

• The numpy constraints overlap for Python >=3.13 (both this line and the >=2.1 line apply). It’s clearer (and avoids accidentally allowing numpy 2.x on 3.10–3.12 if other deps start supporting it) to make the markers mutually exclusive and explicitly cap numpy<2 for <3.13, matching the stated intent of keeping numpy 1.26.x on 3.9–3.12.

  "numpy>=1.21.0; python_version<='3.9'",
  "numpy>=2.1; python_version>='3.13'",
  "numpy>=1.26.0; python_version>='3.10'",

pyproject.toml:53

• PR description says the preprocessing extra is constrained to Python <3.13 due to an upstream numpy<2 pin, but this optional dependency still allows 3.13+. Also, uv.lock now resolves brainles-preprocessing with numpy 2.3.5 for Python >=3.13, so the rationale in the PR description may be outdated. Either update the PR description to reflect the new upstream compatibility, or add an explicit < '3.13' marker here if you still want to restrict the extra.

preprocessing = ["brainles_preprocessing>=0.6.13; python_version >= '3.10'"]