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pyproject.toml
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pyproject.toml
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# pyproject.toml
# Metadata
[build-system]
requires = ["setuptools>=61.0.0", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "multidms"
version = "1.1.0"
description = "Joint modeling of multiple deep mutational scanning experiments."
readme = "README.md"
authors = [
{ name = "Jared Galloway", email= "[email protected]" },
{ name = "Hugh Haddox", email = "[email protected]" }
]
license = { file = "LICENSE" }
classifiers = [
"License :: OSI Approved :: MIT License",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
]
keywords = [
"multidms",
"generalized lasso",
"deep",
"mutational",
"scanning",
"dms",
"bloom",
"matsen"
]
# Software Dependencies
requires-python = ">=3.9"
dependencies = [
"polyclonal",
"jax[cpu]>=0.4.29",
"jaxopt",
"typing_extensions",
"numpy<=1.26.0",
"pandas>=2.2.0",
"binarymap",
"altair==5.1.2", # pandas convert_dtypes bug
"matplotlib",
"seaborn",
"scipy",
"pylops",
"pyproximal",
"tqdm",
"pandarallel",
]
[project.optional-dependencies]
dev = [
"pytest",
"pytest-pep8",
"ruff~=0.0.289",
"black~=23.3.0",
"notebook",
# "sphinx",
"sphinx==6.2.1",
"sphinx-autoapi==3.0.0",
"nbsphinx",
"nbsphinx_link",
"bumpver",
"sphinxcontrib-bibtex",
"dms_variants",
"ipywidgets"
]
[tool.ruff]
select = [
"E", # pycodestyle
"F", # pyflakes
"UP", # pyupgrade
"D", # pydocstyle
]
line-length = 89
extend-exclude = [
"build",
"dist",
"docs/*",
"notebooks/.*",
"notebooks",
"optimization_benchmarks",
".*",
]
ignore = [
"D203",
"D205",
"D212",
"D213",
"D400",
"D415",
"D416",
"D401"
]
# Poetry
[tool.poetry]
readme = "README.rst"
[project.urls]
# documentation = "https://matsengrp.github.io/multidms/"
repository = "https://github.com/matsengrp/multidms"
[tool.setuptools]
packages = ["multidms"]
[tool.bumpver]
current_version = "1.1.0"
version_pattern = "MAJOR.MINOR.PATCH"
commit_message = "bump version {old_version} -> {new_version}"
commit = true
tag = true
push = false
[tool.bumpver.file_patterns]
"pyproject.toml" = [
'current_version = "{version}"', 'version = "{version}"'
]
"multidms/__init__.py" = ["{version}"]
"docs/conf.py" = ['release = "{version}"']