spOT-NMF/pyproject.toml at main · MorrissyLab/spOT-NMF · GitHub

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[build-system]
requires = ["setuptools>=69", "wheel", "build"]
build-backend = "setuptools.build_meta"

[project]
name = "spot-nmf"
version = "0.1.1"
description = "Optimal Transport-based Matrix Factorization for spatial transcriptomics deconvolution."
readme = "README.md"
requires-python = ">=3.12"
license = { file = "LICENSE" }
authors = [
  { name = "Aly O. Abdelkareem" },
  { name = "Morrissy Lab" }
]
keywords = ["spatial transcriptomics", "single-cell", "omics", "optimal transport", "NMF"]
classifiers = [
  "Development Status :: 3 - Alpha",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Topic :: Scientific/Engineering :: Bio-Informatics"
]

# ---- Core runtime dependencies (important ones only) ----
# Torch is intentionally excluded; users install it per platform (CPU/CUDA).
dependencies = [
  "numpy==1.26.4",
  "scipy==1.16.2",
  "pandas==2.3.3",
  "scikit-learn==1.7.2",
  "matplotlib>=3.7,<3.11",
  "seaborn>=0.12",                     # used by plotting (keep light)
  "anndata==0.9.2",
  "scanpy==1.9.3",
  "igraph>=0.10",                      # aka python-igraph on PyPI as 'igraph'
  "leidenalg>=0.10",
  "networkx>=3.1",
  "umap-learn>=0.5.4",
  "pynndescent>=0.5",
  "statsmodels>=0.14",
  "pygam>=0.9",
  "natsort>=8.4",
  "tqdm>=4.65",
  "progressbar2>=4.4",
  "session-info>=1.0",
  "distinctipy>=1.3.4",
  "rbo==0.1.3",
  "fastcluster==1.2.6",
  "adjustText>=0.8",
  "texttable>=1.7",
  "requests>=2.31",
  "charset-normalizer>=3.3",
  "idna>=3.4",
  "urllib3>=2.0",
  "gprofiler-official==1.0.0"
]

[project.optional-dependencies]
# Let users opt into these.
dev = [
  "pytest>=7.4",
]
docs = [
  "mkdocs>=1.5",
  "mkdocs-material>=9.5",
  "mkdocstrings[python]>=0.24",
]
# Users who want PyTorch can choose their own build (CPU/CUDA).
torch = [
  "torch", "torchvision", "torchaudio"
]

[project.urls]
Homepage = "https://github.com/MorrissyLab/spOT-NMF"
Issues   = "https://github.com/MorrissyLab/spOT-NMF/issues"
Source   = "https://github.com/MorrissyLab/spOT-NMF"

# Console entry point
[project.scripts]
spotnmf = "spotnmf.cli:main"

# Packaging config (flat layout)
[tool.setuptools]
packages = ["spotnmf"]
include-package-data = true
zip-safe = false