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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "pyvcell"
version = "0.0.1"
description = "This is the python wrapper for vcell modeling and simulation"
authors = ["Jim Schaff <[email protected]>"]
repository = "https://github.com/virtualcell/pyvcell"
documentation = "https://virtualcell.github.io/pyvcell/"
readme = "README.md"
packages = [
{include = "pyvcell"}
]
[tool.poetry.dependencies]
python = ">=3.10,<4.0"
numexpr = "^2.10.0"
zarr = "^2.17.2"
h5py = "^3.11.0"
numpy = "^1.26.4"
orjson = "^3.10.3"
vtk = "^9.3.1"
pyvcell-fvsolver = "^0.0.4"
typer = "^0.12.3"
[tool.poetry.group.dev.dependencies]
pytest = "^7.2.0"
pytest-cov = "^4.0.0"
deptry = "^0.16.2"
mypy = "^1.5.1"
pre-commit = "^3.8.0"
tox = "^4.11.1"
h5py-stubs = "^0.1.1"
[tool.poetry.group.docs.dependencies]
mkdocs = "^1.4.2"
mkdocs-material = "^9.2.7"
mkdocstrings = {extras = ["python"], version = "^0.23.0"}
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.mypy]
files = ["pyvcell"]
disallow_untyped_defs = "True"
disallow_any_unimported = "True"
no_implicit_optional = "True"
check_untyped_defs = "True"
warn_return_any = "True"
warn_unused_ignores = "True"
show_error_codes = "True"
[tool.pytest.ini_options]
testpaths = ["tests"]
[tool.ruff]
target-version = "py39"
line-length = 120
fix = true
select = [
# flake8-2020
"YTT",
# flake8-bandit
"S",
# flake8-bugbear
"B",
# flake8-builtins
"A",
# flake8-comprehensions
"C4",
# flake8-debugger
"T10",
# flake8-simplify
"SIM",
# isort
"I",
# mccabe
"C90",
# pycodestyle
"E", "W",
# pyflakes
"F",
# pygrep-hooks
"PGH",
# pyupgrade
"UP",
# ruff
"RUF",
# tryceratops
"TRY",
]
ignore = [
# LineTooLong
"E501",
# DoNotAssignLambda
"E731",
# avoid specifiying long messages outside the exception class
"TRY003",
# avoid functions which are too complex
"C901",
# avoid uses of Uses of `tarfile.extractall()
"S202",
# B008 Do not perform function call `typer.Argument` in argument defaults
"B008",
]
[tool.ruff.format]
preview = true
[tool.coverage.report]
skip_empty = true
[tool.coverage.run]
branch = true
source = ["pyvcell"]
[tool.ruff.per-file-ignores]
"tests/*" = ["S101"]