pyproject.toml

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

[project]
name = "flexynesis"
version = "0.2.14"
license = {file = "LICENSE"}
authors = [
    {name = "Bora Uyar", email = "bora.uyar@mdc-berlin.de"},
    {name = "Taras Savchyn", email = "Taras.Savchyn@mdc-berlin.de"},
    {name = "Ricardo Wurmus", email = "Ricardo.Wurmus@mdc-berlin.de" },
    {name = "Ahmet Sarigun", email = "Ahmet.Sariguen@mdc-berlin.de"}
]
description = "A deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction."
readme = "README.md"
requires-python = ">=3.11,<3.12"
classifiers=[
    "Programming Language :: Python :: 3.11",
]
dependencies = [
    "matplotlib",
    "numpy",
    "pandas",
    "lightning",
    "pyyaml",
    "scikit-optimize",
    "scipy",
    "seaborn",
    "torch",
    "torchvision",
    "tqdm",
    "umap-learn",
    "rich",
    "captum",
    "ipywidgets",
    "torch_geometric",
    "ipykernel",
    "lifelines",
    "papermill",
    "scikit-survival",
    "python-louvain",
    "xgboost",
    "pot",
    "geomloss"
]

[project.scripts]
flexynesis = "flexynesis.__main__:main"

[project.urls]
homepage = "https://github.com/BIMSBbioinfo/flexynesis"

[project.optional-dependencies]
test = [
    "pytest"
]

[tool.setuptools.packages.find]
include = ["flexynesis", "flexynesis.*"]

[tool.pytest.ini_options]
norecursedirs = [
    ".git",
    ".github",
    "dist",
    "build",
    "docs",
]
addopts = [
    "--strict-markers",
    "--doctest-modules",
    "--color=yes",
    "--disable-pytest-warnings",
]
filterwarnings = "ignore::DeprecationWarning"