viral-ngs/pyproject.toml at main · broadinstitute/viral-ngs · GitHub

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[build-system]
requires = ["setuptools>=61.0", "setuptools-scm"]
build-backend = "setuptools.build_meta"

[project]
name = "viral-ngs"
dynamic = ["version"]
description = "Consolidated tools for viral NGS data analysis"
readme = "README.md"
license = "MIT"
requires-python = ">=3.10"
authors = [
    { name = "Broad Institute Viral Genomics", email = "viral-ngs@broadinstitute.org" }
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS :: MacOS X",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
keywords = ["bioinformatics", "genomics", "viral", "ngs", "sequencing"]
# Python dependencies for pip-based installs
# Note: For Docker-based usage, all deps (including bioinformatics tools) are
# installed via conda. See docker/requirements/core.txt
dependencies = [
    "arrow>=0.12.1",
    "biopython>=1.72",
    "jinja2>=2.11.3",
    "lz4>=2.2.1",
    "matplotlib>=2.2.4",
    "pandas>=2.0.0",
    "psutil>=6.1.0",
    "pybedtools>=0.7.10",
    "pysam>=0.23.0",
    "pyyaml>=6.0",
    "scipy>=1.10.0",
    "seaborn>=0.12.0",
    "zstandard>=0.23.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-xdist",
    "pytest-cov",
]

[project.scripts]
# Command-line entry points for viral-ngs tools
# Core commands
illumina = "viral_ngs.illumina:main"
read_utils = "viral_ngs.read_utils:main"
reports = "viral_ngs.reports:main"
file_utils = "viral_ngs.file_utils:main"
broad_utils = "viral_ngs.broad_utils:main"
# Assembly commands
assembly = "viral_ngs.assembly:main"
# Classification commands
metagenomics = "viral_ngs.metagenomics:main"
taxon_filter = "viral_ngs.taxon_filter:main"
kmer_utils = "viral_ngs.kmer_utils:main"
# Phylogenetics commands
interhost = "viral_ngs.interhost:main"
intrahost = "viral_ngs.intrahost:main"
ncbi = "viral_ngs.ncbi:main"

[project.urls]
Homepage = "https://github.com/broadinstitute/viral-ngs"
Repository = "https://github.com/broadinstitute/viral-ngs"
Issues = "https://github.com/broadinstitute/viral-ngs/issues"

[tool.setuptools_scm]

[tool.setuptools.packages.find]
where = ["src"]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
addopts = "-v --tb=short"
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
]