pyproject.toml

[build-system] # Require setuptool version due to https://github.com/pypa/setuptools/issues/2938
requires = ["setuptools>=61.0.0", "wheel"]

[project]
name = "fenics-smart"
version = "2.2.3"
description = "Spatial Modeling Algorithms for Reactions and Transport (SMART) is a high-performance finite-element-based simulation package for model specification and numerical simulation of spatially-varying reaction-transport processes in biological cells."
authors = [{ name = "Justin Laughlin", email = "justinglaughlin@gmail.com" }]
license = { file = "LICENSE" }
readme = "README.md"
requires-python = ">=3.8"
dependencies = [
    "numpy>=1.16.0, <2.0",
    "pandas",
    "Pint",
    "scipy>=1.1.0",
    "sympy",
    "cached-property",
    "tabulate",
    "termcolor",
]


[project.urls]
homepage = "https://rangamanilabucsd.github.io/smart"
repository = "https://github.com/RangamaniLabUCSD/smart"

[tool.setuptools]
packages = ["smart"]


[project.optional-dependencies]
test = ["pytest", "pytest-cov"]
# Astroid is pinned due to: https://github.com/readthedocs/sphinx-autoapi/issues/407
# which causes https://github.com/executablebooks/jupyter-book/issues/2063
docs = ["jupyter-book==0.15.1", "sphinx-autoapi==2.0.1", "astroid<3"]
examples = ["meshio", "gmsh", "matplotlib", "jupyter", "jupyterlab"]
pyvista = ["pyvista[all]>=0.43.0", "trame-vuetify", "ipywidgets",]

all = [
    "fenics-smart[examples]",
    "fenics-smart[test]",
    "fenics-smart[docs]",
    "fenics-smart[pyvista]",
]


[tool.pytest.ini_options]
addopts = [
    "--cov=smart",
    "--cov-report=html",
    "--cov-report=term-missing",
    "-v",
]

testpaths = ["tests"]


[tool.black]
#line-length = 79


[tool.ruff]
# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
select = ["E", "F"]
ignore = []

# Allow autofix for all enabled rules (when `--fix`) is provided.
fixable = ["A", "B", "C", "D", "E", "F"]
unfixable = []

# Exclude a variety of commonly ignored directories.
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
]

# Same as Black.
line-length = 100

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

# Assume Python 3.10.
target-version = "py310"

[tool.ruff.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 10