pyproject.toml

[tool.poetry]
name = "aphylogeo"
version = "1.0.0"
description = "A phylogenetic and geographic analysis tool"
authors = ["'Tahiri Lab'"]
license = "MIT"
readme = "README.md"
repository = "https://github.com/tahiri-lab/aPhyloGeo"
include = ["bin/**"]

[tool.poetry.dependencies]
python = ">=3.9.0"
bio = "^1.5.9"
multiprocess = "^0.70.15"
pandas = "^2.1.1"
psutil = "^5.9.5"
pyyaml = "^6.0.1"
pytest = "^7.4.2"
numpy = "^1.26.0"
cython = "^3.0.2"
robinson-foulds = "^1.2"
ete3 = "^3.1.3"
dendropy = "^4.6.1"
textdistance = "^4.6.0"
typer = "^0.13.1"


[tool.poetry.group.dev.dependencies]
pytest = "^7.4.2"

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

[tool.pytest.ini_options]
pythonpath = "aphylogeo/"
testpaths = 'tests/'

[tool.ruff]
line-length = 130
ignore = ["F405"]
fix = true

[tool.black]
--line-length = 130
exclude = '''
(
    tests/testFiles
  | img
  | bin
  | build
  | dist
  | setup.py
  | .venv
)
'''

[tool.isort]
profile = "black"
line_length = 130
multi_line_output = 3
include_trailing_comma = true
force_grid_wrap = 0
use_parentheses = true
ensure_newline_before_comments = true
skip_glob = '''
(
    tests/testFiles
  | img
  | bin
  | build
  | dist
  | setup.py
  | .venv
)
'''