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pyproject.toml
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[build-system]
requires = [
"setuptools>=62",
"wheel",
]
build-backend = "setuptools.build_meta"
[project]
name = "petab"
dynamic = ["version", "readme"]
description = "Parameter estimation tabular data"
requires-python = ">=3.10"
dependencies = [
"numpy>=1.15.1",
"pandas>=1.2.0",
# remove when pandas >= 3, see also
# https://github.com/pandas-dev/pandas/issues/54466
"pyarrow",
"python-libsbml>=5.17.0",
"sympy",
"colorama",
"pyyaml",
"jsonschema",
"antlr4-python3-runtime==4.13.1",
]
license = {text = "MIT License"}
authors = [
{name = "The PEtab developers"},
]
maintainers = [
{name = "Daniel Weindl", email = "[email protected]"},
{name = "Dilan Pathirana", email = "[email protected]"},
{name = "Maren Philipps", email = "[email protected]"},
]
[project.optional-dependencies]
tests = [
"pytest",
"pytest-cov",
"simplesbml",
"scipy",
"pysb",
]
quality = [
"pre-commit",
]
reports = [
# https://github.com/spatialaudio/nbsphinx/issues/641
"Jinja2==3.0.3",
]
combine = [
"python-libcombine>=0.2.6",
]
doc = [
"sphinx>=3.5.3, !=5.1.0",
"sphinxcontrib-napoleon>=0.7",
"sphinx-markdown-tables>=0.0.15",
"sphinx-rtd-theme>=0.5.1",
"m2r2",
"myst-nb>=0.14.0",
# https://github.com/spatialaudio/nbsphinx/issues/687#issuecomment-1339271312
"ipython>=7.21.0, !=8.7.0",
"pysb",
]
vis = [
"matplotlib>=3.6.0",
"seaborn",
"scipy"
]
[project.scripts]
petablint = "petab.petablint:main"
petab_visualize = "petab.v1.visualize.cli:_petab_visualize_main"
[project.urls]
Repository = "https://github.com/PEtab-dev/libpetab-python"
Documentation = "https://petab.readthedocs.io/projects/libpetab-python/"
[tool.setuptools.packages.find]
include = ["petab", "petab.*"]
namespaces = false
[tool.setuptools.package-data]
petab = ["petab/schemas/*", "petab/visualize/templates/*"]
[tool.ruff]
line-length = 79
lint.extend-select = [
"F", # Pyflakes
"I", # isort
"S", # flake8-bandit
"B", # flake8-bugbear
"C4", # flake8-comprehensions
"T20", # flake8-print
"W", # pycodestyle Warnings
"E", # pycodestyle Errors
"UP", # pyupgrade
# TODO: "ANN001", "D", # pydocstyle (PEP 257)
]
lint.extend-ignore = ["F403", "F405", "S101"]
lint.exclude = [
"petab/v1/math/_generated/*", # auto-generated
]
[tool.ruff.lint.pydocstyle]
convention = "pep257"
[tool.ruff.lint.per-file-ignores]
"tests/*" = ["T201"]
[tool.ruff.format]
exclude = [
"petab/math/_generated/*", # auto-generated
]