pyproject.toml

[build-system]
requires = ["setuptools", "setuptools-scm", "wheel", "toml"]
build-backend = "setuptools.build_meta"

[tool.distutils.bdist_wheel]
universal = "true"

[tool.setuptools_scm]

[project]
name = "proxbias"
authors = [
	{ name = "Recursion Pharmaceuticals", email = "devs@recursionpharma.com" },
]
readme = "README.md"
classifiers = [
	"Operating System :: OS Independent",
	"Programming Language :: Python",
	"Programming Language :: Python :: 3",
]
keywords = ["proxbias"]
requires-python = ">=3.8"
dynamic = ["version"]

dependencies = [
	"efaar-benchmarking >= 0.1.0",
	"fastparquet",
	"importlib_resources",
	"infercnvpy",
	"numpy",
	"pandas",
	"pyarrow",
	"s3fs",
	"s3fs",
	"scanpy",
	"scikit-image",
	"scikit-learn",
	"scipy",
	"seaborn",
	"statsmodels",
	"tqdm",
	"wget",
]

[project.optional-dependencies]
dev = [
	"bandit",
	"black[jupyter]",
	"coverage",
	"flake8",
	"ipython; python_version > '3.8'",
	"ipython<8.13.0; python_version <= '3.8'",
	"isort",
	"mypy",
	"pip-tools",
	"pre-commit",
	"pytest",
	"pytest-cov",
	"pyupgrade",
	"radon",
	"types-pkg_resources",
	"tox",
	"validate-pyproject[all]",
]

[tool.pytest.ini_options]
addopts = [
	"--ignore",
	"setup.py",
	"--ignore",
	"run_test.py",
	"--tb",
	"native",
	"--strict-markers",
	"--durations=20",
	"--cov-report",
	"term-missing",
	"--cov=proxbias",
]
testpaths = ["tests"]
env = ["PYTHONHASHSEED=0"]

[tool.mypy]
files = "proxbias"
python_version = "3.9"
ignore_missing_imports = true
show_error_codes = true
# strict = true
allow_untyped_calls = true
plugins = "numpy.typing.mypy_plugin"

[tool.isort]
profile = "black"
py_version = "auto"
line_length = 120

[tool.bandit]
exclude = "tests"

[tool.black]
line-length = 120
target-version = ["py39"]

[tool.setuptools]
packages = ["proxbias"]