pyproject.toml

[tool.poetry]
name = "picea"
version = "0.0.31"
description = "A lightweight python library for working with trees and biological sequence collections"
authors = ["Rens Holmer"]
readme = "README.md"
license = "MIT"
classifiers = [
    'Development Status :: 3 - Alpha',
    'Natural Language :: English',
    'Operating System :: MacOS',
    'Operating System :: Microsoft :: Windows',
    'Operating System :: POSIX',
    'Operating System :: Unix',
    'Intended Audience :: Developers',
    'Intended Audience :: Science/Research',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
    'Topic :: Utilities',
]
repository = 'https://github.com/holmrenser/picea'

[tool.poetry.dependencies]
python = ">=3.10, <3.13"
numpy = "1.26"
matplotlib = "^3.9.0"


[tool.poetry.group.dev.dependencies]
pytest = "^8.2.1"
black = "^24.4.2"
coverage = { extras = ["toml"], version = "^7.5.3" }
coveralls = "^4.0.1"
mkdocs = "^1.6.0"
mkapi = "^2.1.0"
mkdocs-material = "^9.5.25"
mkdocs-jupyter = "^0.24.7"
mkdocstrings = "^0.25.1"
jupyter = "^1.0.0"
ipykernel = "^6.29.4"
scipy = "^1.13.1"
scikit-learn = "^1.5.0"
mkdocstrings-python = "^1.10.3"
jupytext = "^1.16.2"
jupyterlab = "^4.2.1"
ruff = "^0.4.5"

[tool.pytest.ini_options]
minversion = "7.0"
addopts = "--verbose --doctest-modules"
testpaths = ["picea", "tests"]
python_classes = "*Tests"
python_functions = "test*"
python_files = "*tests.py"

[tool.coverage.run]
branch = true
command_line = "-m pytest"

[tool.coverage.report]
omit = ["tests/*", "*__init__.py"]

[tool.black]
line-length = 120

[tool.ruff]
line-length = 120
exclude = ['docs/*']
lint.select = [
    "E", # pycodestyle errors (settings from FastAPI, thanks, @tiangolo!)
    "W", # pycodestyle warnings
    "F", # pyflakes
    "I", # isort
    "C", # flake8-comprehensions
    "B", # flake8-bugbear
]
lint.ignore = [
    "E501", # line too long, handled by black
    "C901", # too complex
    "C408", # allow explicit `dict` and `list` calls
    "B028", # don't want to always specify stacklevel for warnings
]