LANfactory/pyproject.toml at main · lnccbrown/LANfactory · GitHub

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[build-system]
requires = ["setuptools", "wheel"]

[project.urls]
"Homepage" = "https://github.com/lnccbrown/LANFactory"
"Bug Tracker" = "https://github.com/lnccbrown/LANFactory/issues"

[project]
name = "lanfactory"
version = "0.6.1"
authors = [
    { name = "Alexander Fengler", email = "alexander_fengler@brown.edu" },
    { name = "Carlos Paniagua", email = "carlos_paniagua@brown.edu" },
    { name = "Hannah Hafner", email = "hhafner@smith.edu" },
]
description = "Package with convenience functions to train LANs"
readme = "README.md"
license = { file = "LICENSE" }
requires-python = ">3.10, <3.14"
classifiers = [
    "Development Status :: 1 - Planning",
    "Environment :: Console",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering",
]

dependencies = [
    "ssm-simulators>=0.12.2",
    "scipy>=1.15.2",
    "pandas>=2.2.3",
    "torch>=2.7.0",
    "flax>=0.10.6",
    "tqdm>=4.67.1",
    "frozendict>=2.4.6",
    "onnx>=1.17.0",
    "matplotlib>=3.10.1",
    "typer>=0.9.0",
]

keywords = [
    "LANs",
    "generative models",
    "cognitive science",
    "neuroscience",
    "sbi",
]

[project.optional-dependencies]
mlflow = ["mlflow>=3.6.0"]
hf = ["huggingface-hub>=0.20.0"]
all = ["mlflow>=3.6.0", "huggingface-hub>=0.20.0"]

[dependency-groups]
dev = [
    "coverage>=7.6.4",
    "ipykernel>=6.29.5",
    "ipython>=8.31.0",
    "ipywidgets>=8.1.2",
    "jupyterlab>=4.2.4",
    "mypy>=1.11.1",
    "nbconvert>=7.16.5",
    "pre-commit>=2.20.0",
    "ptpython>=3.0.29",
    "pytest-cov>=6.1.1",
    "pytest-rerunfailures>=15.1",
    "pytest-timer>=1.0.0",
    "pytest-xdist>=3.6.1",
    "pytest>=8.3.1",
    "ruff>=0.14.4",
    "types-PyYAML",
    "mlflow>=3.6.0",
]

[tool.setuptools.packages.find]
where = ["src"]
include = ["lanfactory", "lanfactory.*"]


[tool.pytest.ini_options]
log_cli = true
log_cli_level = "INFO" # set minimum log level for console output
testpaths = ["tests"]
addopts = [
    "--cov=src",
    "--cov-report=term-missing",
    "--cov-report=xml",
    "--cov-report=html",
    "--exitfirst",
    "--timer-top-n=25",
]

[tool.ruff]
line-length = 88
src = ["src/lanfactory", "tests"]
exclude = [
    "notebooks/*",
    "docs/*",
    "docs/basic_tutorial/basic_tutorial.ipynb",
]

# Coverage settings
[tool.coverage.run]
source = ["src"]
branch = true                      # Measure branch coverage
parallel = true                    # Support parallel test execution
omit = [
    "*/tests/*",
    "*/__init__.py",
    "*/conftest.py",
    "*/cli/jax_train.py",          # CLI entry points are tested via smoke tests
    "*/cli/torch_train.py",        # CLI entry points are tested via smoke tests
    "*/cli/upload_hf.py",          # CLI entry points are tested via smoke tests
    "*/cli/download_hf.py",        # CLI entry points are tested via smoke tests
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "if __name__ == .__main__.:",
    "raise AssertionError",
    "raise NotImplementedError",
    "if TYPE_CHECKING:",
    "@abstractmethod",
    "except.*Exception",
    "except.*ImportError",
    "logger.error",
]


[project.scripts]
jaxtrain = "lanfactory.cli.jax_train:app"
torchtrain = "lanfactory.cli.torch_train:app"
transform-onnx = "lanfactory.onnx.transform_onnx:app"
upload-hf = "lanfactory.cli.upload_hf:app"
download-hf = "lanfactory.cli.download_hf:app"

[tool.setuptools.package-data]
"lanfactory.cli" = ["config_network_training_lan.yaml"]