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pyproject.toml
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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "biolearn"
description = "Machine learning for biomarkers computing"
long_description = { file = "README.rst" }
authors = [{ name = "Biolearn developers" }]
maintainers = [{ name = "Martin Perez-Guevara", email = "[email protected]" }]
readme = "README.rst"
license = { text = "new BSD" }
requires-python = ">=3.10"
dependencies = [
"numpy>=1.19.0",
"pandas>=2.1.0",
"requests",
"appdirs",
"pyyaml",
"scipy",
"cvxpy"
]
keywords = ["biomarker"]
classifiers = [
"Intended Audience :: Science/Research",
"Intended Audience :: Developers",
"License :: OSI Approved",
"Programming Language :: C",
"Programming Language :: Python",
"Topic :: Software Development",
"Topic :: Scientific/Engineering",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
]
dynamic = ["version"]
[project.optional-dependencies]
# For running unit and docstring tests
test = [
"coverage",
"pytest>=6.0.0",
"pytest-cov",
]
# Necessary req to use biolearn's plotting module
plotting = ["matplotlib>=3.3.0", "seaborn>=0.13.0"]
# Examples external dependencies
examples = ["lifelines"]
# Requirements necessary for building the documentation
doc = [
"biolearn[plotting,examples]",
"coverage",
"flake8",
"flake8-docstrings",
"black",
"furo",
"memory_profiler", # measuring memory during docs building
"myst-parser",
"numpydoc",
"sphinx",
"sphinx-copybutton",
"sphinx-design",
"sphinx-gallery",
"sphinxcontrib-bibtex",
"sphinxext-opengraph",
]
# A combination of dependencies useful for developers
dev = [
"biolearn[test,plotting,examples,doc]",
"jupyterlab",
"scikit-learn",
"torch",
"torchvision"
]
[tool.hatch.build.targets.wheel]
packages = ["biolearn"]
[tool.hatch.version]
source = "vcs"
[tool.hatch.build.hooks.vcs]
version-file = "biolearn/_version.py"
[tool.black]
line-length = 79
extend-include = """
(
examples/.*py
)
"""
extend-exclude = """
(
doc
)
"""
[tool.isort]
profile = "black"
line_length = 79
skip_gitignore = true
combine_as_imports = true