pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel>=0.42"]
build-backend = "setuptools.build_meta"

[project]
name = "krakenparser"
version = "1.1.4"
description = "A collection of scripts designed to process Kraken2 reports and convert them into CSV format."
readme = { file = "README.md", content-type = "text/markdown" }
license = { file = "LICENSE" }
authors = [{ name = "Ilya (Ilia) Popov", email = "ilypopv@gmail.com" }]
requires-python = ">=3.10,<=3.16"
dependencies = [
    "pandas>=2.0.0,<=2.3.3",
    "matplotlib>=3.7.0,<=3.10.8",
    "numpy>=1.24.0,<=2.3.5",
    "seaborn>=0.12.0,<=0.13.2",
    "scipy>=1.9.0,<=1.16.3",
    "typer>=0.12.0,<1",
]

[project.optional-dependencies]
dev = ["pytest>=7.0.0", "pytest-cov>=4.0.0"]

[project.urls]
Homepage = "https://github.com/PopovIILab/KrakenParser"

[project.scripts]
KrakenParser = "krakenparser.krakenparser:entry_point"
krakenparser = "krakenparser.krakenparser:entry_point"

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


[tool.pytest.ini_options]
filterwarnings = [
    "ignore:This figure includes Axes that are not compatible with tight_layout:UserWarning",
    "ignore:Tight layout not applied.*:UserWarning",
    "ignore:Samples with zero total abundance.*:UserWarning",
]
pythonpath = ["."]

[tool.coverage.run]
source = ["krakenparser"]
omit = [
    "krakenparser/krakenparser.py",
    "krakenparser/mpa/transform2mpa.py",
    "krakenparser/mpa/mpa_table.py",
]

[tool.coverage.report]
exclude_lines = ["pragma: no cover", "if __name__ == .__main__.:"]