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pyproject.toml
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[tool.poetry]
authors = [
"Kaiyuan Zhu <[email protected]>",
"Matt Jones <[email protected]>",
"Jens Luebeck <[email protected]>",
"Suhas Rao <[email protected]>"
]
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"Natural Language :: English",
"Programming Language :: Python :: 3 :: Only", # Specify Python 3 only
"Operating System :: MacOS :: MacOS X",
"Operating System :: Microsoft :: Windows",
"Operating System :: POSIX :: Linux",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
description = "Amplicon reconstruction from long-read data"
homepage = "https://github.com/AmpliconSuite/CoRAL"
license = "MIT"
name = "CoRAL"
readme = 'README.md'
repository = "https://github.com/AmpliconSuite/CoRAL"
version = "2.0.0"
packages = [{ include = "coral" }]
[tool.poetry.dependencies]
cvxopt = "*"
cnvkit = "*"
intervaltree = "*"
matplotlib = "*"
pandas = { version = "*", python = ">=3.7,<4.0" }
pysam = { version = ">0.1.7" }
pytest = { version = ">=4.4", optional = true }
python = ">=3.10,<4.0"
numpy = "==2.0.2"
numba = "==0.60.0"
llvmlite = "==0.43.0"
pomegranate = "==1.1.0"
scanpydoc = { version = ">=0.5", optional = true }
typing-extensions = ">=3.7.4"
typing_extensions = { version = "*", python = "<3.9", optional = true }
click = "^8.1.7"
mypy = "^1.11.2"
pydantic = "^2.9.2"
pyomo = "^6.8.0"
ruff = "^0.6.9"
highspy = "^1.7.2"
pyranges = "^0.1.2"
seaborn = "^0.13.2"
typer = "^0.12.5"
[build-system]
build-backend = "poetry.core.masonry.api"
requires = [
"setuptools",
"poetry-core>=1.0.7",
"Cython",
"pip>=22.0.0",
"pyproject-hooks==1.0.0",
]
[tool.poetry.extras]
dev = ["black", "pytest", "flake8", "codecov", "jupyter", "pre-commit", "isort"]
docs = [
"sphinx",
"scanpydoc",
"nbsphinx",
"nbsphinx-link",
"ipython",
"pydata-sphinx-theme",
"typing_extensions",
"sphinx-autodoc-typehints",
"sphinx_gallery",
]
[tool.poetry.scripts]
coral = "coral.cli:coral_app"
[tool.ruff]
lint.select = ["ALL"]
lint.ignore = [
"E501",
"D", # Docstrings
"COM812", # Trailing comma
"PLR2004", # "magic" value in comparison rather than constant
"G004", # f-strings
"UP006", # Use primitive types rather than `typing` equivalents (only allowed py3.12+)
"FBT002", # Boolean default positional arg
"PLR0913", # > 5 args in function signature
"T201", # No prints
"TRY003", # Long messages outside exception class
"EM102", # f-string in exception
]
lint.extend-select = ["I"]
line-length = 80
lint.pycodestyle.max-doc-length = 80
[tool.mypy]
enable_error_code = "possibly-undefined"
disable_error_code = "import-untyped"
# strict = true