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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "obnb"
version = "0.1.1-dev"
description = "A Python toolkit for biological network learning evaluation"
readme = "README.md"
authors = [
{name = "Remy Liu", email = "[email protected]"},
]
license = {text = "MIT"}
requires-python = ">=3.8"
classifiers = [
"Development Status :: 4 - Beta",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python",
"Topic :: Scientific/Engineering :: Artificial Intelligence",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
keywords = [
"Data Processing",
"Gene Classification",
"Machine Learning",
"Network Biology",
"Network Repositories",
]
dependencies = [
"matplotlib",
"mygene",
"ndex2",
"numpy>=1.20.0",
"pyOpenSSL>=23.1.1",
"pyyaml",
"requests",
"scikit-learn>=1.0.0",
"scipy",
"tqdm",
"outdated",
]
[project.urls]
home = "https://github.com/krishnanlab/obnb"
bug-tracker = "https://github.com/krishnanlab/obnb/issues"
[project.optional-dependencies]
dev = [
"bump2version",
"click",
"jinja2",
"parameterized",
"pre-commit",
"pytest",
"pytest-cov",
"pytest-mock",
"pytest-subtests",
"pytest-xdist",
"requests-mock",
"tabulate", # print dataframe as markdown table
"tox",
]
doc = [
"sphinx",
"sphinx-autodoc-typehints",
"sphinx_rtd_theme",
"sphinxcontrib-napoleon",
"yacs",
]
pyroe = [
"pyroe",
"scanpy",
]
ext = [
"grape",
"pecanpy",
"scikit-network",
"networkx",
]
full = ["obnb[pyroe,ext]"]
[tool.setuptools]
license-files = ["LICENSE"]
zip-safe = false
include-package-data = true
[tool.setuptools.packages.find]
where = ["src"]
namespaces = false # disable scanning PEP 420 namespaces
[tool.black]
line-length = 88
[tool.isort]
profile = "black"
line_length = 88
[tool.mypy]
ignore_missing_imports = true
follow_imports = "skip"
exclude = [
"src/obnb/graph/",
]
[[tool.mypy.overrides]]
module = "requests"
ignore_missing_imports = true
[tool.pytest.ini_options]
minversion = "6.0"
required_plugins = [
"pytest-cov",
"pytest-mock",
"pytest-subtests",
"requests-mock",
]
testpaths = [
"test",
]
addopts = [
"--strict-markers",
"-m",
"not longruns and not mediumruns and not ext",
]
markers = [
"longruns",
"mediumruns",
"highmemory",
"ext",
]