pyproject.toml

[tool.poetry]
name = "usefulgnom"
version = "0.1.0"
description = "Viral Genomic Utilities"
authors = ["Gordon Julian Koehn <gordon.koehn@dbsse.ethz.ch>"]
readme = "README.md"
packages = [{include = "usefulgnom", from = "src"}]

[tool.poetry.dependencies]
python = "^3.11.2"
pandas = "^2.2.2"
matplotlib = "^3.9.2"
seaborn = "^0.13.2"
pandas-stubs = "^2.2.2.240807"
click = "^8.1.7"
# Pinned as later snakemake version fail to unit test generation
snakemake = "8.18.1" 

[tool.poetry.group.dev.dependencies]
pytest = "^7.2.1"
ruff = "^0.0.253"
black = "^24.8.0"
pytest-cov = "^4.0.0"
pytest-xdist = "^3.2.0"
pre-commit = "^3.1.0"
interrogate = "^1.5.0"
pyright = "^1.1.309"
mkdocs-material = "^9.1.6"
mkdocstrings = {extras = ["python"], version = "^0.21.2"}
mkdocs-gen-files = "^0.4.0"
mkdocs-literate-nav = "^0.6.0"
setuptools = "^74.1.2"
snakefmt = "^0.10.2"

[tool.coverage.report]
fail_under = 85.0

[tool.interrogate]
ignore-init-method = false
ignore-init-module = false
ignore-magic = true
ignore-semiprivate = true
ignore-private = true
ignore-property-decorators = false
ignore-module = false
fail-under = 95
exclude = ["setup.py", "docs", "build"]
ignore-regex = ["^get$", "^mock_.*", ".*BaseClass.*"]
verbose = 2
quiet = false
whitelist-regex = []
color = true

[tool.pyright]
include = ["src"]
exclude = ["**/node_modules",
    "**/__pycache__",
    "src/experimental",
    "src/typestubs"
]

[tool.snakefmt]
line_length = 88
include = '\.smk$|^Snakefile'


[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"