PyCLM/pyproject.toml at main · Harrison-Oatman/PyCLM · GitHub

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[project]
name = "PyCLM"
version = "0.1.0"
description = "Closed-loop feedback control for optogenetic microscopy in Python"
readme = "README.md"
authors = [
    { name = "Harrison-Oatman", email = "ho6729@princeton.edu" }
]
requires-python = ">=3.11"
dependencies = [
    "h5py>=3.14.0",
    "natsort>=8.4.0",
    "notebook>=7.5.1",
    "opencv-python>=4.12.0.88",
    "pandas-stubs==2.3.2.250827",
    "pymmcore-plus==0.13.7",
    "pymmcore==11.2.1.71.0",
    "scikit-image>=0.25.2",
    "tifffile>=2025.9.20",
    "toml>=0.10.2",
]

[optional-dependencies]
cellpose = [
    "cellpose>=4.0.6",
    "torch",
    "torchvision",
]

calibration = [
    "pycromanager>=1.0.2",
]

[dependency-groups]

analysis = [
    "laptrack>=0.17.0",
    "matplotlib>=3.10.6",
    "pandas>=2.3.2",
    "tqdm>=4.67.1",
    "statannotations>=0.7.2",
]

docs = [
    "matplotlib>=3.10.6",
    "myst-parser",
    "nox>=2025.2.9",
    "pytest>=8.4.2",
    "scipy>=1.15.0",
    "sphinx",
    "sphinx-rtd-theme",
]

dev = [
    { include-group = "analysis" },
    { include-group = "docs" },
]
test = [
    "pytest>=8.4.2",
]

[tool.uv.sources]
torch = [
    { index = "pytorch-cu128" },
]
torchvision = [
    { index = "pytorch-cu128" },
]

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

[tool.ruff.lint]
select = [
  "B",
  "I",
  "RUF",
  "PT",
  "UP",
]

[project.scripts]
pyclm = "pyclm.__main__:main"
convert_hdf5s = "pyclm.convert_hdf5s:main"

[project.optional-dependencies]
analysis = [
    "colorcet>=3.1.0",
    "colorstamps>=0.1.3",
    "seaborn>=0.13.2",
]

[build-system]
requires = ["uv_build>=0.8.14,<0.9.0"]
build-backend = "uv_build"