pyproject.toml

[build-system]
build-backend = "setuptools.build_meta"
requires = [
    "setuptools>=42",
    "wheel",
    "setuptools_scm[toml]>=3.4",
]

[project]
name = "altocumulus"
description = "Command line utilities for workflows on Terra or Cromwell"
authors = [
    { name = "Bo Li" },
    { name = "Joshua Gould" },
    { name = "Yiming Yang" },
    { email = "cumulus-support@googlegroups.com" },
]
license = { file = "LICENSE" }
readme = { file = "README.rst", content-type = "text/x-rst" }
requires-python = ">=3.9"
dynamic = ["version"]
keywords = ["Terra", "Cromwell"]
classifiers = [# https://pypi.python.org/pypi?%3Aaction=list_classifiers
    "License :: OSI Approved :: BSD License",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Operating System :: MacOS :: MacOS X",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    "firecloud",
    "fsspec",
    "matplotlib",
    "numpy",
    "openpyxl",
    "pandas>=2.1.0",
    "python-dateutil",
    "six",
    "stratocumulus>=0.2.0",
]

[project.scripts]
alto = "alto.__main__:main"

[project.optional-dependencies]
test = [
    'pytest'
]

[project.urls]
Repository = "https://github.com/lilab-bcb/altocumulus"
Documentation = "https://altocumulus.readthedocs.io"

[tool.setuptools]
include-package-data = true
zip-safe = false

[tool.setuptools_scm]

[tool.black]
line-length = 100
include = '\.pyi?$'

[tool.docformatter]
include = '\.pyi?$'

[tool.isort]
profile = 'black'
length_sort_straight = true
line_length = 100
lines_after_imports = 2

[tool.flake8]
max-line-length = 100
include = '\.pyi?$'
ignore = [
    'E731', # Do not assign a lambda expression, use a def
    'E203', # whitespace before ':'
    'W503', # line break before binary operator ==
    'E501', # Line too long (82 > 79 characters)
    'E722', # Do not use bare except, specify exception instead
]