pyproject.toml

[tool.poetry]
name = "stories-jax"
packages = [
    { include="stories", from="." },
]
version = "0.1.0"
description = "Learn spatially informed Waddington-like potentials for single-cell gene expression"
authors = ["Geert-Jan Huizing <gjhuizing@gmail.com>", "Gabriel Peyré", "Laura Cantini"]
readme = "README.md"

[tool.poetry.dependencies]
python = "^3.10"
anndata = "^0.10.7"
jaxlib = "^0.4.25"
jax = "^0.4.25"
optax = "^0.2.2"
flax = "^0.8.2"
jaxopt = "^0.8.3"
numpy = "^1.26.4"
tqdm = "^4.66.2"
ott-jax = "^0.4.5"
orbax-checkpoint = "^0.5.20"
scikit-learn = "^1.5.1"
seaborn = "^0.13.2"
cellrank = "^2.0.4"

myst-parser = { version = "^3.0.1", optional = true }
sphinxawesome-theme = { version = "^5.2.0", optional = true }
sphinx-design = { version = "^0.6.0", optional = true }
nbsphinx = { version = "^0.9.4", optional = true }

[tool.poetry.extras]
docs = ["myst-parser", "sphinxawesome-theme", "sphinx-design", "nbsphinx"]

[tool.coverage.report]
exclude_also = [
    "raise AssertionError",
    "raise NotImplementedError",
    "@(abc\\.)?abstractmethod",
]

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"