pyproject.toml

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

[project]
name = "perturbench"
description = "PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis"
readme = "README.md"
requires-python = ">=3.10"
license = {text = "..."}
classifiers = [
    "Programming Language :: Python :: 3",
]
dependencies = [
    'numpy',
    'pyyaml',
    'pandas',
    'anndata',
    'scanpy',
    'scipy==1.12.0',
    'tqdm',
    'lightning',
    "torch<=2.5.1",
    "torchvision",
    "tensorboard",
    "hydra-core",
    "hydra_colorlog",
    'mlflow-skinny',
    'matplotlib',
    'seaborn',
    'scikit-learn',
    'scikit-misc',
    'adjusttext',
    'pytest',
    'rich',
    'psycopg2-binary',
    'optuna',
    'ray',
    'python-dotenv',
    'geomloss',
]
dynamic = ["version"]

[project.optional-dependencies]
dev = [
    "ruff",
]
test = [
    "pytest",
    "pytest-cov",
]
cli = [
    "click",
    "rich",
]

[project.scripts]
train = "perturbench.modelcore.train:main"
predict = "perturbench.modelcore.predict:main"
download = "perturbench.data.accessors.download_all_datasets:main"

[tool.setuptools.packages.find]
where = ["src"]  # list of folders that contain the packages (["."] by default)
include = ["perturbench*"]  # package names should match these glob patterns (["*"] by default)
exclude = ["tests", "docs", "examples"]  # exclude packages matching these glob patterns (empty by default)
# namespaces = false  # to disable scanning PEP 420 namespaces (true by default)

[tool.setuptools.dynamic]
version = {attr = "perturbench.modelcore.VERSION"}

[tool.pytest.ini_options]
addopts = ["--import-mode=importlib"]


[tool.ruff.lint.per-file-ignores]
# Ignore `E402` (import violations) in all `__init__.py` files, and in `path/to/file.py`.
"__init__.py" = ["F401"]
"*.ipynb" = ["E402", "F401"]
# "path/to/file.py" = ["E402"]