pyproject.toml

[project]
name = "warpkit"
description = "A python library for neuroimaging transformations"
readme = "README.md"
requires-python = ">=3.11"
authors = [{ name = "Andrew Van", email = "vanandrew77@gmail.com" }]
keywords = ["neuroimaging"]
classifiers = ["Programming Language :: Python :: 3"]
urls = { github = "https://github.com/vanandrew/warpkit", paper = "https://doi.org/10.1162/IMAG.a.1262" }
# include/romeo/LICENSE is the upstream MIT notice for the ROMEO C++ port; it
# travels with the headers in source distributions and (via PEP 639
# license-files) gets bundled into wheels under *.dist-info/licenses/.
license-files = ["LICENSE", "include/romeo/LICENSE"]
dynamic = ["version"]
dependencies = [
  "nibabel >= 4.0.2",
  "numpy >= 1.23.3",
  "scikit-image >= 0.20.0",
  "scipy >= 1.8.1",
  "transforms3d >= 0.4.1",
  "indexed-gzip >= 1.7.0",
]

[project.scripts]
"wk-medic" = "warpkit.scripts.medic:main"
"wk-unwrap-phase" = "warpkit.scripts.unwrap_phase:main"
"wk-compute-fieldmap" = "warpkit.scripts.compute_fieldmap:main"
"wk-apply-warp" = "warpkit.scripts.apply_warp:main"
"wk-convert-warp" = "warpkit.scripts.convert_warp:main"
"wk-convert-fieldmap" = "warpkit.scripts.convert_fieldmap:main"
"wk-compute-jacobian" = "warpkit.scripts.compute_jacobian:main"

[dependency-groups]
dev = [
  "coverage[toml] >= 5.5",
  "pre-commit >= 3.6.0",
  "pybids >= 0.15.1",
  "pybind11-stubgen>=2.5.5",
  "pytest >= 7.2.2",
]

[build-system]
requires = ["scikit-build-core >= 0.10", "setuptools-scm >= 8.0"]
build-backend = "scikit_build_core.build"

[tool.scikit-build]
# Cap CMake at <4 — scikit-build-core picks up the cmake PyPI wheel, and
# 4.2.3 (latest at time of pin) abort()s with glibc heap corruption
# (`free(): invalid next size (fast)` / `corrupted size vs. prev_size`)
# on manylinux during configure teardown. The crash is reproducible on
# the cibuildwheel matrix across Python 3.11–3.14 and unrelated to our
# CMakeLists. CMake 3.31.x is the most recent 3.x release and works fine.
cmake.version = ">=3.24,<4"
ninja.version = ">=1.11"
# Persistent CMake build dir keyed on wheel tag — survives across `uv sync`
# invocations so ITK FetchContent + object files cache properly. Without this
# scikit-build-core defaults to a per-build temp dir, the same problem the old
# setuptools+cmake-build-extension setup had.
build-dir = "build/{wheel_tag}"
wheel.packages = ["warpkit"]
# Only install our extension component — skips ITK's install rules so we
# don't waste I/O copying static libs we never ship.
install.components = ["extension"]
# Editable installs use a redirect importer pointing at the persistent
# build-dir. rebuild = false because the per-import `cmake --build` path can't
# work here: uv provisions ninja and the build python in an ephemeral isolated
# env, CMake bakes those paths into CMakeCache.txt, then uv tears the env
# down — leaving the cache pointing at a dead ninja. Rebuilds go through
# `uv sync --reinstall-package warpkit`, which gets a fresh build env each
# time and hits the persistent build/{wheel_tag}/ cache for ITK + objects.
editable.mode = "redirect"
editable.rebuild = false
metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"

[tool.setuptools_scm]
fallback_version = "0.0.0"

# ── Ruff (linter + formatter) ────────────────────────────────────────
[tool.ruff]
target-version = "py311" # minimum supported Python version
line-length = 88         # matches Black's default
src = ["warpkit"]        # treat warpkit/ as the source root for import sorting
extend-exclude = ["warpkit/build-tmp*"]

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort (import ordering)
    "N",   # pep8-naming
    "UP",  # pyupgrade (modernize syntax)
    "B",   # flake8-bugbear (common pitfalls)
    "SIM", # flake8-simplify
    "RUF", # Ruff-specific rules
]
ignore = [
    "E501", # line too long (handled by the formatter, not the linter)
]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
docstring-code-format = true # format code blocks inside docstrings

[tool.pyright]
include = ["warpkit"]
exclude = ["**/__pycache__", "warpkit/build-tmp*", "tests/data", ".venv", "**/node_modules", "**/.*"]
venvPath = "."
venv = ".venv"
pythonVersion = "3.11"
# Stubs for the CMake extension live at warpkit/warpkit_cpp.pyi (regenerate with
# `uv run pybind11-stubgen warpkit.warpkit_cpp --output-dir .` after binding changes).

[tool.pytest.ini_options]
testpaths = ["tests"]

[tool.coverage.run]
command_line = "-m pytest"

[tool.coverage.report]
omit = ["tests/*"]

[tool.cibuildwheel]
# Skip musllinux (we ship manylinux only). Free-threaded (cp31Xt-*) builds
# are kept: warps.h guards PyErr_CheckSignals() behind WARPKIT_CHECK_SIGNALS,
# which is a no-op under Py_GIL_DISABLED.
skip = "*musllinux*"
build-frontend = "build"
build-verbosity = 3

[tool.cibuildwheel.linux]
archs = ["auto"]

[tool.cibuildwheel.macos]
archs = ["universal2"]
repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}"
before-build = ["pip install delocate>=0.13.0"]

[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = './.git*,*/.git-meta/*,*.pdf,*.lock,*include/romeo/*,*include/itk/*,*/build/*,*/.venv/*'
check-hidden = true
# ignore-words-list rationale:
#   te,tes    - MR-physics abbreviations (echo time / echo times); see CLAUDE.md
#   nd        - DICOM ImageType flag in BIDS test fixtures
#   datas     - PyInstaller Analysis() parameter name (packaging/pyinstaller/)
#   framei    - loop variable "frame i" in tests/test_distortion.py
#   thirdparty - refers to ITK's ThirdParty/Eigen3 module in CMakeLists.txt comment
ignore-words-list = 'te,tes,nd,datas,framei,thirdparty'