villa/spiral-fitting/pyproject.toml at main · ScrollPrize/villa · GitHub

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[project]
name = "spiral"
version = "0.1.0"
description = "Code and helpers to fit a canonical archimedean spiral to deformed scrolls"
requires-python = ">=3.14"
dependencies = [
    "click>=8.4.2",
    "connected-components-3d>=4.0.0",
    "crackle-codec>=0.42.0",
    "einops>=0.8.2",
    "imageio>=2.37.3",
    "kimimaro[all]>=5.8.1; sys_platform != 'linux' or platform_machine != 'x86_64'",
    "kornia>=0.8.3",
    # 2.6.2 shipped no Windows wheel; 2.6.3 restored it.
    "libigl>=2.6.3",
    "matplotlib>=3.11.0",
    "networkx>=3.6.1",
    "numba>=0.67.0; sys_platform == 'linux' and platform_machine == 'x86_64'",
    "numcodecs>=0.16.0",
    "numpy>=2.5.0",
    "opencv-python-headless>=4.13.0.92",
    "pillow>=12.2.0",
    "posix-ipc>=1.3.2; sys_platform != 'win32'",
    "pynrrd>=1.1.3",
    "pyro-ppl>=1.9.1",
    "rustworkx>=0.18.0",
    "s3fs>=2026.6.0",
    "scipy>=1.18.0",
    "tifffile>=2026.6.1",
    "tensorstore>=0.1.80",
    "threadpoolctl>=3.6.0",
    "torch>=2.11,<2.13",
    "torchdiffeq>=0.2.5",
    "tqdm>=4.68.3",
    "trimesh>=4.12.2",
    # Monorepo-only C++ package (resolved via [tool.uv.sources]): surfaces, fibers
    # and point collections are read and written through the object store.
    "vc-object-store",
    "vc-reader",
    # PyTorch ships no triton wheel for Windows; this community build stands in
    # for the triton 3.6 that torch 2.11 pins elsewhere.
    "triton-windows>=3.6,<3.7; sys_platform == 'win32'",
    "vc-delta3d>=0.2.0,<0.3",
    "wandb>=0.28.0",
    "zarr>=3.2.1",
]

[project.optional-dependencies]
# Kimimaro for Linux x86-64 machines without a compatible NVIDIA GPU
# (other platforms install it by default).
cpu = ["kimimaro[all]>=5.8.1"]

[dependency-groups]
dev = ["pytest>=9.1.1"]
# NVIDIA-only GPU backend of extract_surface_tracks.py. Installed by a plain
# `uv sync` (see default-groups). `--no-group cuda` skips it, but torch still comes from
# the cu128 index in [tool.uv.sources]; on ROCm use the README recipe ("Creating the Spiral Python environment").
cuda = [
    "brook-cu12>=0.1.0; sys_platform == 'linux' and platform_machine == 'x86_64'",
    "cucim-cu12>=26.8.0; sys_platform == 'linux' and platform_machine == 'x86_64'",
    "cupy-cuda12x>=14.2.0; sys_platform == 'linux' and platform_machine == 'x86_64'",
]

[tool.uv]
default-groups = ["dev", "cuda"]

[tool.uv.sources]
vc-reader = { path = "../vc_reader", editable = true }
vc-object-store = { path = "../vc_object_store", editable = true }
torch = [
    { index = "pytorch-cu128", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
]

[[tool.uv.index]]
name = "pytorch-cu128"
url = "https://download.pytorch.org/whl/cu128"
explicit = true

[build-system]
requires = [
    "scikit-build-core>=0.10",
    "nanobind>=2.0",
]
build-backend = "scikit_build_core.build"

[tool.scikit-build]
cmake.source-dir = "cpp"
cmake.version = ">=3.22"
wheel.packages = ["vc_spiral"]