morphix/pyproject.toml at main · funkelab/morphix · GitHub

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# https://peps.python.org/pep-0517/
# https://hatch.pypa.io/latest/config/build/
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

# https://peps.python.org/pep-0621/
[project]
name = "morphix"
description = "Trainable Morphogenesis Simulation in JAX"
readme = "README.md"
license = { text = "MIT" }
authors = [
    { name = "Jan Funke", email = "funkej@janelia.hhmi.org" },
    { name = "Morgan Schwartz", email = "schwartzm10@janelia.hhmi.org" },
]
dynamic = ["version"]
dependencies = ["jax", "equinox", "optax", "rich"]

[project.optional-dependencies]
gui = ["pygfx", "pyqt5", "umap-learn", "spatial_graph", "pillow", "ffmpegio"]
dev = ["pre-commit", "pytest", "pytest-cov", "ruff", "twine", "build"]
test = ["pytest", "pytest-cov"]

[project.urls]
homepage = "https://github.com/funkelab/morphix"

[tool.uv.sources]
spatial_graph = { git = "https://github.com/funkelab/spatial_graph", rev = "b56072d71f976e25d9cd70cb84a08caf7214c62f" }

# https://hatch.pypa.io/latest/version/
[tool.hatch.version]
path = "src/morphix/__init__.py"

# https://beta.ruff.rs/docs
[tool.ruff]
target-version = "py310"
src = ["src/morphix"]

[tool.ruff.lint]
select = [
    "F",   # pyflakes
    "E",   # pycodestyle
    "I",   # isort
    "UP",  # pyupgrade
    "RUF", # ruff specific rules
    "D",
]
ignore = [
    "D100", # Missing docstring in public mod
    "D104", # Missing docstring in public package
    "D105", # Missing docstring in magic method
    "D107", # Missing docstring in `__init__`
    "D102", # Missing docstring in public method
]

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["D"]

# https://docs.pytest.org/en/6.2.x/customize.html
[tool.pytest.ini_options]
minversion = "6.0"
testpaths = ["tests"]
filterwarnings = [
    "error:::morphix",
]

# https://coverage.readthedocs.io/en/6.4/config.html
[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "pragma: ${PY_MAJOR_VERSION} no cover",
    "if TYPE_CHECKING:",
    "\\.\\.\\.",
]

[tool.mypy]
files = "src/morphix"
strict = true             # feel free to relax this if it's annoying
allow_untyped_defs = true # TODO: can eventually fill out typing and remove this
# allow_untyped_calls = true    # TODO: can eventually fill out typing and remove this
disallow_any_generics = false
ignore_missing_imports = true

[tool.pyright]
venvPath = "."
venv = ".venv"
pythonVersion = "3.10"