autoemulate/pyproject.toml at main · alan-turing-institute/autoemulate · GitHub

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[project]
name = "autoemulate"
version = "2.0.0"
description = "A python package for semi-automated emulation"
license = "MIT"
authors = [{ name = "AutoEmulate contributors (see our GitHub page)" }]
readme = "README.md"
requires-python = ">=3.10,<3.13"
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering",
]
dependencies = [
    "matplotlib>=3.7.2",
    "seaborn>=0.12.2",
    "scikit-learn>=1.3.0,<1.6.0",
    "pandas>=2.1",
    "torch>=2.1.0",
    "scipy>=1.11.3",
    "numpy>=1.24",
    "joblib>=1.3.2",
    "tqdm>=4.66.2",
    "lightgbm>=4.3.0",
    "ipywidgets>=8.1.2",
    "gpytorch>=1.12",
    "salib>=1.5.1",
    "torcheval>=0.0.7",
    "anytree>=2.12.1",
    "torchmetrics>=1.7.1",
    "pyro-ppl>=1.9.1",
    "torchrbf>=0.0.1",
    "arviz>=0.21.0",
    "getdist>=1.7.2",
    "einops>=0.8.1",
    "harmonic>=1.3.0",
]

[project.urls]
Homepage = "https://alan-turing-institute.github.io/autoemulate/"
Documentation = "https://alan-turing-institute.github.io/autoemulate/"
Repository = "https://github.com/alan-turing-institute/autoemulate"
"Bug Tracker" = "https://github.com/alan-turing-institute/autoemulate/issues"

[project.optional-dependencies]
docs = [
    "furo>=2023.9.10",
    "sphinx-copybutton>=0.5.2",
    "sphinx-autodoc-typehints>=1.24.0",
]
dev = [
    "ipykernel>=6.25.0",
    "pytest>=7.4.0",
    "sphinx>=7.2.6",
    "myst-parser>=2.0.0",
    "furo>=2023.9.10",
    "sphinx-copybutton>=0.5.2",
    "sphinx-autodoc-typehints>=1.24.0",
    "black>=23.10.1",
    "pre-commit>=3.5.0",
    "jupyter-book>=1.0.0,<2.0.0",
    "pytest-cov>=4.1.0",
    "coverage>=7.6.4",
    "plotnine>=0.13.6",
    "pyright==1.1.405",
    "ruff==0.12.11",
]
spatiotemporal = ["the-well>=1.1.0", "neuraloperator>=1.0.2"]

[tool.setuptools]
zip-safe = false
include-package-data = true

[tool.setuptools.packages.find]
include = ["autoemulate*"]

[tool.setuptools.package-data]
autoemulate = ["datasets/**/*"]

[tool.setuptools.exclude-package-data]
autoemulate = ["**/__pycache__", "**/*.pyc"]

[tool.uv]
# uvloop does not support Windows (no wheels, setup.py raises RuntimeError).
# It's pulled in via harmonic -> flax -> orbax-checkpoint -> uvloop.
# orbax-checkpoint falls back to the default asyncio loop when uvloop is absent,
# so skipping it on Windows is safe. On Linux/macOS it is still installed normally.
override-dependencies = ["uvloop>=0.0.0; sys_platform != 'win32'"]

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"


[tool.coverage.run]
relative_files = true
source = [".", "/tmp"]

[tool.pytest.ini_options]
addopts = "--ignore=v0"

[tool.pyright]
venvPath = "."
venv = ".venv"
include = ["autoemulate/*", "tests/*", "benchmarks/*"]

[tool.ruff]
src = ["autoemulate/"]
line-length = 88
include = ["autoemulate/**/*.py", "tests/**/*.py", "benchmarks/**/*.py"]
target-version = "py310"

[tool.ruff.format]
docstring-code-format = true

[tool.ruff.lint]
select = [
    "D",   # docstring conventions
    "E",
    "F",
    "W",   # flake8
    "B",   # flake8-bugbear
    "I",   # isort
    "ARG", # flake8-unused-arguments
    "C4",  # flake8-comprehensions
    "EM",  # flake8-errmsg
    "ICN", # flake8-import-conventions
    "ISC", # flake8-implicit-str-concat
    "G",   # flake8-logging-format
    "PGH", # pygrep-hooks
    "PIE", # flake8-pie
    "PL",  # pylint
    "PT",  # flake8-pytest-style
    "RET", # flake8-return
    "RUF", # Ruff-specific
    "SIM", # flake8-simplify
    "UP",  # pyupgrade
    "YTT", # flake8-2020
    "EXE", # flake8-executable
]

ignore = [
    "PLR2004", # Magic value used in comparison
    "EM102",   # Exception must not use an f-string literal, assign to variable first
    "ISC001",  # Conflicts with formatter
    # "D417",    # Missing trailing new line in docstring
    "D100",    # Missing docstring in public module
    "D104",    # Missing docstring in public package
    "PLR0913", # too many arguments
]

unfixable = [
    "F401", # Would remove unused imports
    "F841", # Would remove unused variables
]
flake8-unused-arguments.ignore-variadic-names = true # allow unused *args/**kwargs

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.ruff.lint.per-file-ignores]
"tests/*.py" = ["D"]