setup.py

from setuptools import find_packages, setup

with open("README.md", "r") as fh:
    long_description = fh.read()

setup(
    name="scanpy-scripts",
    version="1.9.301",
    author="nh3",
    author_email="nh3@users.noreply.github.com",
    description="Scripts for using scanpy from the command line",
    long_description=long_description,
    long_description_content_type="text/markdown",
    url="https://github.com/ebi-gene-expression-group/scanpy-scripts",
    packages=find_packages(),
    scripts=[
        "scanpy-scripts-tests.bats",
    ],
    entry_points=dict(
        console_scripts=[
            "scanpy-cli=scanpy_scripts.cli:cli",
            "scanpy-read-10x=scanpy_scripts.cmds:READ_CMD",
            "scanpy-filter-cells=scanpy_scripts.cmds:FILTER_CMD",
            "scanpy-filter-genes=scanpy_scripts.cmds:FILTER_CMD",
            "scanpy-normalise-data=scanpy_scripts.cmds:NORM_CMD",
            "scanpy-find-variable-genes=scanpy_scripts.cmds:HVG_CMD",
            "scanpy-scale-data=scanpy_scripts.cmds:SCALE_CMD",
            "scanpy-regress=scanpy_scripts.cmds:REGRESS_CMD",
            "scanpy-run-pca=scanpy_scripts.cmds:PCA_CMD",
            "scanpy-neighbors=scanpy_scripts.cmds:NEIGHBOR_CMD",
            "scanpy-run-tsne=scanpy_scripts.cmds:TSNE_CMD",
            "scanpy-run-umap=scanpy_scripts.cmds:UMAP_CMD",
            "scanpy-find-cluster=scanpy_scripts.cli:cluster",
            "scanpy-find-markers=scanpy_scripts.cmds:DIFFEXP_CMD",
        ]
    ),
    install_requires=[
        # "packaging",
        # "anndata",
        # "scipy",
        # "matplotlib",
        # "pandas",
        # "h5py<3.0.0",
        "scanpy==1.9.3",
        "louvain",
        "igraph",
        "leidenalg",
        "loompy",
        "Click<8",
        # "umap-learn",
        "harmonypy>=0.0.5",
        "bbknn>=1.5.0,<1.6.0",
        "mnnpy>=0.1.9.5",
        "scipy<1.9.0",
        "scikit-learn<1.3.0",
        "scrublet",
        "fa2",
    ],
)