rctd-py/pyproject.toml at main · p-gueguen/rctd-py · GitHub

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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

[project]
name = "rctd-py"
dynamic = ["version"]
description = "GPU-accelerated Robust Cell Type Decomposition (RCTD) for spatial transcriptomics using PyTorch"
readme = "README.md"
license = "GPL-3.0-or-later"
requires-python = ">=3.10"
authors = [{ name = "Paul Gueguen" }]
keywords = ["spatial-transcriptomics", "deconvolution", "single-cell", "PyTorch", "GPU"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
]
dependencies = [
    "torch>=2.0",
    "numpy>=1.24",
    "scipy>=1.10",
    "anndata>=0.10",
    "click>=8.0",
]

[project.optional-dependencies]
dev = ["pytest>=7.0", "pytest-cov", "ruff", "pandas>=1.5"]

[project.urls]
Homepage = "https://github.com/p-gueguen/rctd-py"
Repository = "https://github.com/p-gueguen/rctd-py"
Issues = "https://github.com/p-gueguen/rctd-py/issues"

[project.scripts]
rctd = "rctd.cli:main"

[tool.hatch.version]
source = "vcs"

[tool.hatch.build.hooks.vcs]
version-file = "src/rctd/_version.py"

[tool.hatch.build.targets.wheel]
packages = ["src/rctd"]
exclude = ["src/rctd/data/q_matrices.npz"]

[tool.hatch.build.targets.sdist]
exclude = ["src/rctd/data/q_matrices.npz", "data/", "benchmarks/", "docs/", "scripts/", "examples/", ".github/", "*.log", "*.err"]

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "-m 'not performance'"
markers = [
    "slow: R concordance tests (downloads vignette data from GitHub)",
    "performance: Runtime and memory regression tests",
]

[tool.ruff]
line-length = 100
target-version = "py310"
extend-exclude = ["src/rctd/_version.py"]

[tool.ruff.lint]
select = ["E", "F", "I", "W"]
ignore = ["E741"]