cellbin2/pyproject.toml at main · STOmics/cellbin2 · GitHub

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[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "cellbin2"
# Parse version number
dynamic = ["version"]
description = "A framework for generating single-cell gene expression data"
authors = [
    { name = "cell bin research group", email = "bgi@genomics.cn" }
]
dependencies = [
    "numpy==1.23.5",
    "h5py==3.8.0",
    "objtyping",
    "pydantic",
    "opencv-python==4.8.0.76",
    "imagecodecs==2023.3.16",
    "aenum",
    "tqdm==4.65.0",
    "tifffile==2023.2.3",
    "scipy",
    "scikit-image==0.21.0",
    "numba==0.56.4",
    "onnxruntime-gpu==1.15.1",
    "scikit-learn==1.3.0",
    "imreg_dft==2.0.0",
    "prettytable==3.11.0",
    "PyYAML",
    "matplotlib==3.7.1",
    "requests",
    "pandas==1.5.3",
    "pyvips-binary",  # if pip install pyvips error, comment it and use conda install instead. (conda install conda-forge/label/main::pyvips==2.2.3)
    "pyvips",  # if pip install pyvips error, comment it and use conda install instead. (conda install conda-forge/label/main::pyvips==2.2.3)
    "rasterio",
    "shapely",
    "geopandas"
]
requires-python = ">=3.8"

[tool.setuptools]
include-package-data = true

[tool.setuptools.dynamic]
version = { attr = "cellbin2.__version__"}

[tool.setuptools.package-data]
"cellbin2.utils" = ["*.so", "*.pyd"]

[tool.setuptools.packages.find]
where = ["."]

[project.optional-dependencies]
cp = ['cellpose==3.0.11', 'patchify==0.2.3']
rs = [
    'gefpy==1.2.6',  # generate cellbin matrix
    'mapbox_earcut'
]
rp = [
    'fastcluster==1.2.6',
    'stereopy==1.6.0', # research report
    'beautifulsoup4',
    'csscompressor',
    'jsmin'
]