DeepSpot2Cell/pyproject.toml at main · ratschlab/DeepSpot2Cell · GitHub

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[build-system]
requires = ["setuptools>=65", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "deepspot2cell"
version = "0.1.0"
description = "DeepSpot2Cell: Predicting virtual single-cell spatial transcriptomics from H&E histopathology images using spot-level supervision"
authors = [{ name = "Kalin Nonchev" }, { name = "Glib Manaiev" }]
readme = "README.md"
license = "MIT"
requires-python = ">=3.9"
keywords = [
    "spatial-transcriptomics",
    "deep-learning",
    "computational-pathology",
    "digital-pathology",
    "gene-expression",
    "histopathology",
    "single-cell",
    "foundation-models",
    "pytorch",
    "spatial-biology",
    "cell-segmentation",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
]
dependencies = [
    "torch>=2.2.0",
    "torchvision>=0.17.0",
    "torchaudio>=2.2.0",
    "lightning>=2.2.0",
    "torchmetrics>=1.3.0",
    "numpy>=1.23.0",
    "pandas>=1.5.0",
    "scipy>=1.11.0",
    "scikit-learn>=1.2.0",
    "numba>=0.56.0",
    "llvmlite>=0.39.0",
    "anndata>=0.8.0",
    "scanpy>=1.9.0",
    "squidpy>=1.2.0",
    "matplotlib>=3.8.0",
    "tqdm>=4.65.0",
    "h5py>=3.8.0",
    "pyyaml>=6.0",
    "shapely>=2.0",
    "pyvips>=2.2.1",
    "opencv-python>=4.9.0",
    "pillow>=10.0.0",
    "huggingface_hub>=0.23.0",
    "transformers>=4.42.0",
    "timm>=0.9.12",
    "plotnine>=0.12.0",
    "einops>=0.7.0",
    "hest>=0.2.0",
]

[project.optional-dependencies]
dev = ["black", "isort", "nbstripout"]

[project.urls]
Homepage = "https://github.com/ratschlab/DeepSpot2Cell"
Repository = "https://github.com/ratschlab/DeepSpot2Cell"
"Bug Tracker" = "https://github.com/ratschlab/DeepSpot2Cell/issues"
"Preprint" = "https://www.biorxiv.org/content/10.1101/2025.09.23.678121v1"

[tool.setuptools.packages.find]
include = ["deepspot2cell", "deepspot2cell.*"]