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pyproject.toml
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110 lines (103 loc) · 2.8 KB
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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"
[project]
name = "bioconvert"
version = "1.2.0"
description = "convert between bioinformatics formats"
readme = {file = "README.rst", content-type = "text/x-rst"}
license = {text = "GPLv3"}
authors = [
]
maintainers = [
]
keywords = ["NGS", "bam2bed", "fastq2fasta", "bam2sam", "conversion"]
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Software Development :: Libraries :: Python Modules",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Information Analysis",
]
requires-python = ">=3.9"
dependencies = [
"easydev",
"biosniff",
"colorlog",
"click",
"rich-click",
"cython",
"deeptools",
"pandas",
"pod5",
"biopython>=1.70",
"mappy",
"matplotlib",
"networkx",
"pyyaml",
"pysam",
"openpyxl>=3.1.5",
"pyexcel",
"pyexcel-ods3",
"pyexcel-xls",
"pyexcel-xlsx",
"psutil",
"xlrd>2",
"pyBigWig",
"py2bit",
"statsmodels",
"tqdm",
"hic2cool",
"HiCLift",
]
[project.optional-dependencies]
testing = [
"pytest",
"pytest-cov",
"pytest-env",
"pytest-xdist",
"pytest-mock",
"pytest-timeout",
"pytest-runner",
"pytest-rerunfailures",
"mock",
"coveralls",
]
doc = [
"pillow",
"sphinx",
"sphinx_rtd_theme",
"sphinx_gallery",
"numpydoc",
"pygraphviz",
]
[project.urls]
Homepage = "https://github.com/bioconvert/bioconvert"
"Bug Tracker" = "https://github.com/bioconvert/bioconvert/issues"
Download = "https://github.com/bioconvert/bioconvert"
[project.scripts]
bioconvert = "bioconvert.scripts.converter:main"
bioconvert_init = "bioconvert.scripts.init_convert:main"
bioconvert_stats = "bioconvert.scripts.stats:main"
[tool.setuptools.packages.find]
where = ["."]
[tool.setuptools.package-data]
"*" = ["*.csv", "*.sh"]
"bioconvert.data" = ["*"]
"bioconvert.misc" = ["*"]
[tool.pytest.ini_options]
addopts = "--durations=10 --verbose -n 1 --cov bioconvert --cov-report term-missing --maxfail=2"
markers = [
"slow: marks tests as slow (deselect with '-m \"not slow\"')",
"flaky: marks tests as flaky (deselect with '-m \"not flaky\"')",
]