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pyproject.toml
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pyproject.toml
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[project]
name = "sc2ts"
description = "Infer ARGs for SARS-Cov2 in tskit format"
readme = "README.md"
license = {file = "LICENSE"}
authors = [
{name = "Jerome Kelleher", email = "[email protected]"},
]
requires-python = ">=3.9"
dependencies = [
# "tsinfer==0.3.3", # https://github.com/jeromekelleher/sc2ts/issues/201
# FIXME
"tsinfer @ git+https://github.com/jeromekelleher/tsinfer.git@experimental-hmm",
"pyfaidx",
# FIXME - reinstate when 0.5.9 is released
# "tskit>=0.5.9",
"tskit @ git+https://github.com/tskit-dev/tskit.git@main#subdirectory=python",
"tszip",
"pandas",
"numba",
"tqdm",
"scipy",
"click",
"zarr<2.18",
"humanize",
"resource",
"biotite",
]
dynamic = ["version"]
[project.scripts]
sc2ts = "sc2ts.cli:cli"
[project.optional-dependencies]
dev = [
"msprime",
"pytest",
"pytest-coverage",
]
analysis = [
"matplotlib",
"scikit-learn",
"pandas",
"IPython",
"networkx",
]
[build-system]
requires = [
"setuptools>=42",
"setuptools_scm",
"wheel",
]
build-backend = "setuptools.build_meta"
[tool.setuptools]
packages = ["sc2ts"]
[tool.setuptools_scm]
write_to = "sc2ts/_version.py"