MetaPanG/pyproject.toml at main · labgem/MetaPanG · GitHub

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[project]
name = "metapang"
license = "CECILL-C"
license-files = ["LICENSE"]
description = "MetaPanG"
readme = "README.md"
dynamic = ['version']
authors = [
    { name = "Téo Lemane", email = "teo.lemane@genoscope.cns.fr" }
]
keywords = ["Pangenomics", "Comparative Genomics", "Bioinformatics", "Prokaryote"]

classifiers = [
    "Development Status :: 3 - Alpha",
    "Envrionment :: Console",
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Bio-Informatics"
]

requires-python = ">=3.11"
dependencies = [
    "click>=8.1.8",
    "loguru>=0.7.3",
    "ppanggolin>=2.3.1",
    "pyfastx>=2.2.0",
    "pygithub>=2.6.1",
    "rich>=13.9.4",
    "rich-click>=1.8.6",
    "semver>=3.0.4",
    "sourmash>=4.9.4",
    "tables>=3.10.1",
    "msgspec>=0.19.0",
    "tomli-w>=1.2.0",
    "jsonschema>=4.24.0",
    "gb-io>=0.3.6",
    "httpx>=0.28.1",
    "scipy>=1.15.3",
    "numpy>=1.26.0",
    "pandas>=2.2.0",
]

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

[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"

[tool.setuptools]
packages = [
    "metapang",
    "metapang.core",
    "metapang.core.index",
    "metapang.core.profile",
    "metapang.pg",
    "metapang.app",
    "metapang.app.tools",
    "metapang.app.index",
    "metapang.app.configure",
    "metapang.app.search",
    "metapang.app.profile",
    "metapang.report",
    "metapang.utils",
]

[tool.setuptools.dynamic]
version = { attr = "metapang.__version__" }

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = ["-v", "--tb=short", "--import-mode=importlib"]
enable_assertion_pass_hook = true
markers = [
    "integration: end-to-end tests",
]

[tool.ruff]
line-length = 88
target-version = "py311"

[tool.ruff.lint]
select = ["E4", "E7", "E9", "F", "W", "I", "UP", "B"]
ignore = ["UP042"]

[tool.pyright]
include = ["metapang"]
pythonVersion = "3.11"
typeCheckingMode = "basic"

[dependency-groups]
dev = [
    "pre-commit>=4.1.0",
    "ruff>=0.16",
    "pytest",
    "ipython",
    "viztracer>=1.1.1",
]
doc = [
    "sphinx>=8.1.3",
    "furo>=2024.8.6",
    "myst-parser>=4.0.1",
    "sphinx-copybutton>=0.5.2",
]