pyproject.toml

[build-system]
requires = ["setuptools>=64", "setuptools-scm>=8"]
build-backend = "setuptools.build_meta"

[project]
name = "petab_select"
dynamic = ["version"]
maintainers = [
    {name = "Dilan Pathirana", email = "dilan.pathirana@uni-bonn.de"},
]
authors = [
    {name = "The PEtab Select developers"},
]
description = "PEtab Select: an extension to PEtab for model selection."
readme = "README.md"
requires-python = ">=3.10"
license = {text = "BSD-3-Clause"}
dependencies = [
    # TODO minimum versions
    "more-itertools",
    "numpy",
    "pandas",
    "petab",
    "pyyaml",
    "click",
    "dill",
]
[project.optional-dependencies]
plot = [
    "matplotlib>=2.2.3",
    "upsetplot",
    "toposort",
    "networkx",
]
test = [
    "pytest >= 5.4.3",
    "pytest-cov >= 2.10.0",
    "amici >= 0.11.25",
    "fides >= 0.7.5",
    "pypesto > 0.2.13",
    "tox >= 3.12.4",
]
doc = [
    "sphinx>=8.1.3",
    "sphinxcontrib-napoleon>=0.7",
    "sphinx-markdown-tables>=0.0.15",
    "sphinx-rtd-theme>=0.5.1",
    "recommonmark>=0.7.1",
    # pin until ubuntu comes with newer pandoc:
    # /home/docs/checkouts/readthedocs.org/user_builds/petab-select/envs/63/lib/python3.11/site-packages/nbsphinx/__init__.py:1058: RuntimeWarning: You are using an unsupported version of pandoc (2.9.2.1).
    # Your version must be at least (2.14.2) but less than (4.0.0).
    "nbsphinx>=0.9.5",
    "pandoc>=2.4",
    "nbconvert>=7.16.4",
    "ipython>=7.21.0",
    "readthedocs-sphinx-ext>=2.2.5",
    "sphinx-autodoc-typehints",
]

[project.scripts]
petab_select = "petab_select.cli:cli"

[tool.setuptools_scm]

[tool.ruff]
line-length = 79
exclude = ["amici_models"]
extend-include = ["*.ipynb"]
lint.ignore = [
    # FIXME: we should be able to remove move of those
    "D103", # Missing docstring in public function
    "S101", # Use of assert detected
    "E501", # Line too long
    "F403", # star import
    "T201", # print statement
    "S301", # pickle module used
    "S102", # Use of exec detected
    "S307", # Use of possibly insecure function
    "B006",
    "E722",
    "B904",
    "B007",
    "F841",
]
lint.select = [
    "F",  # Pyflakes
    "I",  # isort
    # "D",  # pydocstyle (PEP 257)  FIXME enable after https://github.com/PEtab-dev/petab_select/pull/67
    "S",  # flake8-bandit
    "B",  # flake8-bugbear
    "C4",  # flake8-comprehensions
    "T20",  # flake8-print
    "W",  # pycodestyle Warnings
    "E",  # pycodestyle Errors
    "UP",  # pyupgrade
    # "ANN",  # flakes-annotations
]
[tool.ruff.lint.pydocstyle]
convention = "pep257"