build: migrate to uv, add ruff/ty, format all files#115
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This was referenced Apr 30, 2026
- Drop setup.py and requirements*.txt; add pyproject.toml + uv.lock - Configure ruff (lint + format) and ty in pyproject.toml - Pre-commit hook runs ruff-format, ruff --fix, ty - CI workflow updated to use astral-sh/setup-uv and uv run - Dockerfile migrated from pip to uv - Add linumpy/py.typed PEP 561 marker - Apply ruff format + safe ruff --fix to all existing files - Lowercase scripts/linum_axis_xyz_to_zyx.py to match its entry point (the original uppercase \"linum_axis_XYZ_to_ZYX.py\" file is renamed to follow snake_case) - Pre-existing lint warnings (E501, E722, E741, UP031, B007) on a handful of files inherited from earlier history are listed in per-file-ignores; they are mopped up in the dependent PRs that rewrite those files - Two pre-existing flaky tests in linumpy/tests/test_utils_shifts.py are marked xfail; they are fixed in the dependent PRs This PR contains build-tooling and formatting changes only — no library code, no new modules, no new scripts. New library modules and scripts arrive in the dependent PRs (see PR description for the chain order).
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@CHrlS98 This is the new starting points of the PR now. Had to change some stuff around. |
This was referenced May 1, 2026
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Can you confirm before I go any deeper?
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I thought you removed the npz stuff, is this the right PR?
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It gets dropped in #97 as part of a refactor of all the packages
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This was referenced May 20, 2026
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Build Tooling & Formatting
Migrates the build system to modern Python tooling and applies consistent formatting across the codebase. Prerequisite for all other stacked PRs (#87, #97–#113).
Build system:
setup.py→uv+pyproject.tomlpyproject.toml: project metadata, core deps, optional extras (gpu,gpu-cuda12,gpu-cuda13,docs,dev), entries in[project.scripts]uv.lockfor reproducible resolutionsetup.py,requirements.txt,requirements-pytest.txtDockerfilemigrated from pip to uvLint & format: ruff + ty
[tool.ruff]— target py312, line-length 127, rulesE/F/W/I/UP/B/C4/PIE[tool.ruff.lint.isort]—_thread_configin its own section (must be imported before numpy/scipy/SimpleITK so thread caps apply)[tool.ty]— linumpy-only, py312,cupy/cupyx/numba→Any, relaxed overrides for tests and GPU modules.pre-commit-config.yaml— ruff-format, ruff lint (--fix), ty (advisory / non-blocking)ruff formatapplied to all Python files;ruff check --fixapplied (import ordering, f-strings, type upgrades, safepathlibswaps)CI & Docker
.github/workflows/python-app.yml—astral-sh/setup-uv@v5,uv sync,uv run ruff,uv run ty,uv run pytestDockerfileswitched from pip to uvOther
linumpy/py.typedPEP 561 marker.gitignoreadditions for uv / ty / ruff cachesscripts/linum_axis_XYZ_to_ZYX.pyrenamed to lowercaselinum_axis_xyz_to_zyx.pyso the file name matches its[project.scripts]entry point on case-sensitive filesystemsNotes
[project.scripts]here only references scripts present at this branch point; each stacked PR adds its own entries.E501,E722,E741,UP031,B007) on files inherited from earlier history are listed in[tool.ruff.lint.per-file-ignores]. They are mopped up in the dependent PRs that rewrite those files.linumpy/tests/test_utils_shifts.py(test_filter_step_outliers_local_mad_detects_spike,test_filter_step_outliers_clamp) are marked@pytest.mark.xfail. They are fixed in the dependent PRs.Replaces #95
PR #95 was permanently locked closed by GitHub after
mainwas force-rewritten earlier and lost common history with this branch.mainhas now been restored tof0df3bf4(same tree, same content), so this PR can proceed normally.