pyproject.toml

[project]
name = "bento-tools"
description = "A toolkit for subcellular analysis of spatial transcriptomics data"
authors = [{ name = "ckmah", email = "clarence.k.mah@gmail.com" }]
dynamic = ["version"]
dependencies = [
    "adjusttext>=1.1.1",
    "astropy>=6.0.1",
    "decoupler>=1.7.0",
    "emoji>=2.11.0",
    "kneed>=0.8.5",
    "matplotlib-scalebar>=0.8.1",
    "minisom>=2.3.2",
    "pandas>=2.2.2",
    "rasterio>=1.3.9",
    "rtree>=1.2.0",
    "scipy~=1.10.0",
    "seaborn>=0.13.2",
    "shapely~=2.0.1",
    "sparse>=0.15.1",
    "spatialdata>=0.2.2",
    "tensorly>=0.8.1",
    "tqdm>=4.66.2",
    "upsetplot>=0.9.0",
    "xgboost>=2.0.3",
    "statsmodels>=0.14.1",
    "scikit-learn<1.6.0",
    "ipywidgets>=8.1.5",
    "tomli>=2.2.1",
]
license = "BSD-2-Clause"
readme = "README.md"
requires-python = ">= 3.10"


[project.optional-dependencies]
docs = [
    "sphinx>=7.2.6",
    "sphinx-design>=0.5.0",
    "sphinxawesome-theme>=5.1.1",
    "myst-nb>=1.0.0",
    "sphinx-autodoc-typehints>=2.0.1",
    "sphinx-autobuild<=2024.2.4",
]
extras = ["torch>=2.2.2", "spatialdata-plot>=0.2.4"]
all = ["bento-tools[docs]", "bento-tools[extras]"]

[build-system]
requires = ["hatchling==1.26.3"]
build-backend = "hatchling.build"

[tool.rye]
managed = true
version.source = "pyproject"
dev-dependencies = [
    "pytest>=8.2.2",
    "pytest-cov>=5.0.0",
    "pytest-watcher>=0.4.2",
    "pytest-mock>=3.14.0",
]

[tool.hatch.build]
include = [
    "bento/datasets/datasets.csv",
    "bento/models/**/*",
    "bento/tools/gene_sets/*",
]

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.build.targets.sdist]
include = ["bento"]

[tool.hatch.build.targets.wheel]
packages = ["bento"]

[tool.hatch.version]
path = "bento/__init__.py"