Monocle2-python/pyproject.toml at main · Bio-Babel/Monocle2-python · GitHub

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

[project]
name = "monocle2-python"
version = "2.9.0"
description = "Python port of the R monocle2 package (tracks cole-trapnell-lab/monocle-release 2.9.0 @ 7df1050) — single-cell trajectory, differential expression, BEAM."
readme = "README.md"
requires-python = ">=3.10"
license = "Artistic-2.0"
license-files = ["LICENSE"]
authors = [
    { name = "Jeffery Liu", email = "jeffliu.lucky@gmail.com" },
]
keywords = [
    "monocle2",
    "monocle",
    "single-cell",
    "scRNA-seq",
    "trajectory",
    "pseudotime",
    "BEAM",
    "differential-expression",
    "DDRTree",
    "R-port",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Visualization",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Typing :: Typed",
]
dependencies = [
    "numpy>=1.24",
    "scipy>=1.10",
    "pandas>=2.0",
    "anndata>=0.10",
    "scikit-learn>=1.3",
    "statsmodels>=0.14",
    "patsy>=0.5",
    "python-igraph>=0.10",
    "ddrtree-python>=0.1.6",
    "ggplot2-python>=4.0.2.9000",
    "pheatmap-python>=1.0.13",
    "rgrid-python>=4.5.3",
    "gtable-python>=0.3.6",
    "scales-python>=1.4.0",
    "ggrepel-python>=0.9.8",
]

[project.optional-dependencies]
dev = ["pytest", "pytest-cov", "ruff", "build", "twine"]
docs = [
    "mkdocs",
    "mkdocstrings[python]",
    "mkdocs-material",
    "mkdocs-jupyter",
]

[project.urls]
Homepage            = "https://github.com/Bio-Babel/Monocle2-python"
Repository          = "https://github.com/Bio-Babel/Monocle2-python"
Issues              = "https://github.com/Bio-Babel/Monocle2-python/issues"
Documentation       = "https://github.com/Bio-Babel/Monocle2-python#readme"
"Upstream (R package)"    = "https://github.com/cole-trapnell-lab/monocle-release"
"Tutorial data (Zenodo)"  = "https://zenodo.org/records/19699224"

[tool.hatch.build.targets.wheel]
packages = ["monocle2py"]

[tool.hatch.build.targets.sdist]
exclude = [
    "tutorials/",
    "docs/",
    "tests/",
    "site/",
    "validation/",
    "mkdocs.yml",
    ".github/",
    "*.egg-info/",
    "build/",
    "dist/",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
markers = [
    "slow: marks tests as slow integration tests (deselect with '-m \"not slow\"')",
]