pyproject.toml

[tool.pdm.build]
includes = ["bidcell", "data"]

[tool.pdm.dev-dependencies]
test = [
    "pytest>=7.4.1",
]
dev = [
    "black>=23.7.0",
    "deptry>=0.12.0",
    "flake8>=6.1.0",
    "ipython>=8.15.0",
]
[build-system]
requires = ["pdm-backend"]
build-backend = "pdm.backend"

[project]
name = "bidcell"
version = "1.0.3"
description = "Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data."
authors = [
    {name = "Helen Fu", email = "xiaohang.fu@sydney.edu.au"},
]
dependencies = [
    "pandas>=2.1.0",
    "numpy>=1.24.4",
    "tifffile>=2023.8.30",
    "imgaug>=0.4.0",
    "h5py>=3.9.0",
    "scipy>=1.11.2",
    "matplotlib>=3.7.2",
    "natsort>=8.4.0",
    "cellpose>=2.2.3",
    "scikit-image>=0.21.0",
    "segmentation-models-pytorch>=0.3.3",
    "opencv-python>=4.8.0.76",
    "pillow>=10.0.0",
    "pyyaml>=6.0.1",
    "pydantic>=2.3.0",
    "tqdm>=4.66.1",
]
requires-python = ">=3.9,<3.13"
readme = "README.md"
license = {text = "MIT"}