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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
build-backend = "setuptools.build_meta"
[project]
name = "icomo"
authors = [
{ name = "Jonas Dehning", email = "jonas.dehning@ds.mpg.de" },
]
description = "This toolbox aims to simplify the construction of compartmental models and the inference of their parameters"
readme = "README.md"
classifiers = [
"License :: OSI Approved :: MIT License",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
dynamic = ["version"]
requires-python = '>=3.8.1'
dependencies = [
"numpy",
"matplotlib",
"tqdm",
"pymc == 5.*",
"pytensor",
"numpyro",
"graphviz",
"diffrax",
"optax",
"jaxopt",
]
[project.optional-dependencies]
dev = [
"pytest >= 7.3.2",
"pre-commit >= 3.3.2",
"ruff >= 0.0.272",
"ipykernel >= 6.0.0",
"Sphinx >= 6.2.1",
"sphinx-book-theme",
"importlib-metadata >= 6.5.1",
"myst-parser >= 0.19.2",
"nbsphinx >= 0.9.2",
"pandoc >= 2.3",
]
[project.urls]
Homepage = "https://github.com/Priesemann-Group/icomo"
"Bug Tracker" = "https://github.com/Priesemann-Group/icomo/issues"
Discussions = "https://github.com/Priesemann-Group/icomo/discussions"
Changelog = "https://github.com/Priesemann-Group/icomo/releases"
[tool.pytest.ini_options]
testpaths = [
"tests",
]
[tool.ruff.lint]
ignore = [
"E721", # ignore type comparisons
"E731", # ignore lambdas rewrites
"E741", # ignore ambiguous variable names, because of the example of the S,I,R model
]
select = [
"E", # pycodestyle
"F", # Pyflakes
"UP", # pyupgrade
"B", # flake8-bugbear
"I", # isort
"D", # pydocstyle
]
[tool.ruff.lint.per-file-ignores]
# Ignore `F401` (unused imports) in all `__init__.py` files.
"__init__.py" = ["F401"]
# Ignore pydocstyle rules everywhere except for the `icomo` directory.
"!icomo/**.py" = ["D"]
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.setuptools]
packages = ["icomo"]
[tool.setuptools_scm]
write_to = "icomo/_version.py"