Installation Issue - Githubissues

Hi There,

Thanks for the package, I'm excited to try the modeling on my data. That said, I encountered some issues when trying to install scVIC in a Python 3.9/3.10 environment due to the wrong depiction of the README file in the setup.py (depicted as .rst while it is actually .md) and major dependency conflicts that can be listed as:

torch<=2.0 might conflict with the specific version of numpy and scikit-learn.
scikit-learn<=0.22.2 is quite outdated, which might not be compatible with other packages or Python 3.7.
importlib-metadata<=4.8.1 is often used internally by Python and might cause issues if the version conflicts with other tools.

After resolving these, I updated the setup.py file to work with Python 3.9 and 3.10. Below is the updated setup.py:


#!/usr/bin/env python
# -*- coding: utf-8 -*-

from setuptools import setup, find_packages

with open('README.md') as readme_file:
    readme = readme_file.read()

requirements = [
    "anndata==0.10.8",
    "array-api-compat==1.8",
    "cloudpickle==3.0.0",
    "contourpy==1.2.1",
    "cycler==0.12.1",
    "exceptiongroup==1.2.2",
    "filelock==3.15.4",
    "fonttools==4.53.1",
    "fsspec==2024.6.1",
    "future==1.0.0",
    "get-annotations==0.1.2",
    "h5py==3.11.0",
    "hyperopt==0.2.7",
    "importlib-resources==6.4.3",
    "jinja2==3.1.4",
    "joblib==1.4.2",
    "kiwisolver==1.4.5",
    "legacy-api-wrap==1.4",
    "llvmlite==0.43.0",
    "loompy==3.0.7",
    "markupsafe==2.1.5",
    "matplotlib==3.9.2",
    "mpmath==1.3.0",
    "natsort==8.4.0",
    "networkx==3.2.1",
    "numba==0.60.0",
    "numpy==1.26.4",
    "numpy-groupies==0.11.2",
    "pandas==2.2.2",
    "patsy==0.5.6",
    "pillow==10.4.0",
    "py4j==0.10.9.7",
    "pynndescent==0.5.13",
    "pyparsing==3.1.2",
    "python-dateutil==2.9.0.post0",
    "pytz==2024.1",
    "scanpy==1.10.2",
    "scikit-learn==1.5.1",
    "scikit-misc==0.3.1",
    "scipy==1.13.1",
    "seaborn==0.13.2",
    "session-info==1.0.0",
    "six==1.16.0",
    "statsmodels==0.14.2",
    "stdlib-list==0.10.0",
    "sympy==1.13.2",
    "threadpoolctl==3.5.0",
    "torch==2.4.0",
    "tqdm==4.66.5",
    "typing-extensions==4.12.2",
    "tzdata==2024.1",
    "umap-learn==0.5.6",
    "xlrd==2.0.1"
]

setup_requirements = ['pytest-runner', ]
test_requirements = ['pytest', ]

setup(
    author='Jiankang Xiong',
    author_email='hibearme@163.com',
    classifiers=[
        'Development Status :: 4 - Beta',
        'Intended Audience :: Science/Research',
        'License :: OSI Approved :: MIT License',
        'Programming Language :: Python :: 3.9',
        'Programming Language :: Python :: 3.10',
        'Operating System :: MacOS :: MacOS X',
        'Operating System :: Microsoft :: Windows',
        'Operating System :: POSIX :: Linux',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
    ],
    description="scVIC: Deep generative modeling "
                "of heterogeneity for scRNA-seq data",
    install_requires=requirements,
    license="MIT license",
    long_description=readme,
    include_package_data=True,
    keywords='scvic',
    name='scvic',
    packages=find_packages(),
    setup_requires=setup_requirements,
    test_suite='tests',
    tests_require=test_requirements,
    url='https://github.com/HibearME/scVIC',
    version='1.0',
    zip_safe=False,
)

HiBearME / scVIC

Installation Issue #1