pyproject.toml

[build-system]
requires = ["setuptools", "wheel", "flit_core >=3.2,<4"]
build-backend = "flit_core.buildapi"

[project]
name = "Cell_BLAST"
version = "0.5.1"
description = "Single-cell transcriptome querying tool"
readme = "README.md"
requires-python = ">=3.6"
license = { file = "LICENSE" }
authors = [
    { name = "Zhi-Jie Cao", email = "caozj@mail.cbi.pku.edu.cn" },
    { name = "Runwei Lu", email = "lurw2000@126.com" },
]
keywords = ["bioinformatics", "deep-learning", "single-cell"]
classifiers = [
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Natural Language :: English",
    "Operating System :: MacOS :: MacOS X",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.6",
    "Programming Language :: Python :: 3.7",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
    "numba>=0.39.0",           # minimal version supporting np.unique
    "scipy>=1.0.0",            # minimal version supporting scipy.stats.energy_distance
    "joblib>=0.12.0",          # minimal version supporting locky backend
    "scikit-learn>=0.17.0",    # normalization issue
    "tqdm>=4.12.0",            # deprecation warning in the sys module
    "pandas>=0.21.0",          # optional, anndata requirement
    "h5py>=2.7.0",             # optional, anndata requirement
    "igraph>=0.7.1",
    "pronto>=0.10.2,<=0.12.2", # minimal version supporting python 3.6
    "seaborn>=0.9.0",          # minimal version supporting sns.scatterplot
    "umap-learn>=0.2.1",       # scipy.sparse.csgraph issue
    "anndata>=0.6.14",         # minimal version supporting write_h5ad
    "loompy>=2.0.6",           # minimal version to pass tests
    "statsmodels>=0.8.0",      # python and numpy version compatibility
    "plotly>=5.8.2",
    "torch>=1.7.1",
    "tensorboard>=2.9.1",
    "scanpy>=1.9.0",           # optional, weighting strategy requirement
    "leidenalg>=0.8.10",       # optional, weighting strategy requirement
    "pynvml>=8.0.1",
]

[project.optional-dependencies]
doc = [
    "sphinx<7",
    "sphinx-autodoc-typehints",
    "sphinx-copybutton",
    "nbsphinx",
    "sphinx-rtd-theme",
    "ipython",
    "jinja2",
    "autodocsumm",
]

[project.urls]
Github = "https://github.com/gao-lab/Cell_BLAST"

[tool.flit.sdist]
exclude = [".*", "D*", "d*", "N*", "t*", "e*"]