pyproject.toml

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

# [tool.hatch.metadata]
# this allows dependencies to be specified with a url
# allow-direct-references = true

[project]
name = "bdms-sim"
authors = [
  { name="William DeWitt", email="wsdewitt@uw.edu" },
  { name="Michael Celentano", email="mcelentano@berkeley.edu" },
  { name="Thanasi Bakis", email="abakis@uci.edu" },
  { name="Duncan Ralph", email="dkralph@gmail.com" },
  { name="Sebastian Prillo", email="sprillo@berkeley.edu" },
  { name="Frederick Matsen", email="ematsen@gmail.com" },
  { name="Yun Song", email="yss@berkeley.edu" },
  { name="Volodymyr Minin", email="yss@berkeley.edu" },
]
description = "Tree simulator for birth-death-mutation-sampling (BDMS) processes"
readme = "README.md"
requires-python = ">=3.11"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
dynamic = ["version"]
dependencies = [
  "matplotlib",
  "numpy",
  "scipy",
  "ete3",
  "pyqt5",
]

[project.urls]
"Homepage" = "https://github.com/dewitt-lab/BDMS"
"Bug Tracker" = "https://github.com/dewitt-lab/BDMS/issues"
"Documentation" = "https://dewitt-lab.github.io/BDMS"

# NOTE: dev dependencies are handled by hatch
# [project.optional-dependencies]
# dev = [
# ]

[tool.hatch.build.targets.wheel]
packages = ["bdms"]

[tool.hatch.version]
path = "bdms/__init__.py"

# this puts hatch envs in a .hatch directory, so vscode can find them


# instead of using hatch envs, we put everything
# in the project dev env for vscode intellesense
[tool.hatch.envs.default]
path = ".hatch"
extra-dependencies = [
  # default
  "hatch",
  "jupyter",
  "seaborn",

  # style
  "flake8",
  "black[jupyter]",
  "docformatter",
  "pyright",

  # test
  "pytest",
  "nbval",

  # docs
  "sphinx",
  "sphinx-autodoc-typehints",
  "sphinx-copybutton",
  "sphinx-autoapi",
  "furo",
  "myst-nb",
  "pandoc",
]

[tool.hatch.envs.default.scripts]
tests = [
	"pytest",
	"pytest --doctest-modules",
	"pytest --nbval docs/notebooks",
]
docs = [
  "make -C docs html",
]
lint = [
  "flake8 .",
  "black --check .",
  "docformatter --black --check **/*.py",
  "pyright bdms/*.py",
]
format = [
  "black .",
  "docformatter --black --in-place **/*.py",
]