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pyproject.toml
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[build-system]
requires = ["setuptools>=42", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "SemiBin"
dynamic = ['version']
description = "Metagenomic binning with siamese neural networks"
readme = "README.md"
requires-python = ">=3.8"
authors = [
{ name = "Shaojun Pan" },
{ name = "Luis Pedro Coelho", email = "[email protected]" }
]
license = { text = "MIT" }
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Artificial Intelligence",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
]
dependencies = [
"numpy",
"tqdm",
"pyyaml",
"torch>=1.13", # torch.load() only supports the weights_only argument since 1.13
"python-igraph",
"pandas",
"scikit-learn",
"requests",
"numexpr",
]
urls = { homepage = "https://github.com/BigDataBiology/SemiBin" }
[project.optional-dependencies]
dev = ['pytest', 'hypothesis<=6.112.1']
[project.scripts]
SemiBin = "SemiBin.main:main_no_version"
SemiBin2 = "SemiBin.main:main2"
SemiBin1 = "SemiBin.main:main1"
[tool.setuptools]
packages = ["SemiBin"]
include-package-data = true
zip-safe = false
[tool.setuptools.package-data]
SemiBin = ["*.hmm", "models/*.pt"]
[tool.setuptools.dynamic]
version = {attr = "SemiBin.semibin_version.__version__"}
[tool.pixi.project]
channels = ["conda-forge", "bioconda"]
platforms = ["linux-64"]
[tool.pixi.dependencies]
samtools = ">=1.21,<2"
mmseqs2 = ">=17.b804f,<18"
bedtools = ">=2.31.1,<3"
hmmer = ">=3.4,<4"
fraggenescan = ">=1.32,<2"
prodigal = ">=2.6.3,<3"
[tool.pixi.feature.test]
dependencies = { pytest = "*", hypothesis = "<=6.112.1", "uv" = "*" }
[tool.pixi.feature.py38]
dependencies = { python = "3.8.*" }
[tool.pixi.feature.py39]
dependencies = { python = "3.9.*" }
[tool.pixi.feature.py310]
dependencies = { python = "3.10.*" }
[tool.pixi.feature.py311]
dependencies = { python = "3.11.*" }
[tool.pixi.feature.py312]
dependencies = { python = "3.12.*" }
[tool.pixi.feature.py313]
dependencies = { python = "3.13.*" }
[tool.pixi.environments]
test-py38 = ["py38", "test"]
test-py39 = ["py39", "test"]
test-py310 = ["py310", "test"]
test-py311 = ["py311", "test"]
test-py312 = ["py312", "test"]
test-py313 = ["py313", "test"]