Cythonize将.so文件安装到错误的位置

Question

我想问一个关于如何用Cython、setuptools扩展等配置setup.py的问题。我正在尝试用Cython.Distutils的build_ext来计算一个子模块。但是问题不是Cython.Distutils的扩展模块(如果它存在的话)，因为它没有加载。只有build_ext。所以我在列表中创建了一个setuptools.extension扩展，然后计算扩展对象的列表。列表中只有一个扩展，如下所示。

Extension("distance", ["kmerdb/distance.pyx"], include_dirs=[np.get_include()])

我尝试过不同的安装方法，从python setup.py install到pip install -e .，到生成轮毂文件和安装车轮。我找不到有用的东西..。

好吧，所以我对这个过程知之甚少，这可能就是我被挂断的原因，但我已经搜索了整个网站，没有运气。就这么办了。

我正在运行下面的shell脚本来在本地安装我的包，它运行得很好。问题是安装没有将.so和.py文件移动到我要导出的kmerdb模块中。有什么建议吗？谢谢

>python setup.py sdist bdist_wheel
>/bin/auditwheel repair --plat manylinux2014_x86_64 dist/kmerdb-*linux_x86_64.whl
>mv wheelhouse/* dist
>rm dist/*linux_x86_64.whl
>pip install dist/kmerdb-*-manylinux2014_x86_64.whl
>ls ~/.pyenv/versions/kdb/lib/python3.10/site-packages/kmerdb-0.6.5-py3.10-linux-x86_64.egg/
distance.cpython-310-x86_64-linux-gnu.so    distance.py    kmerdb    ...

同样，distance.cpython-310-x86_64-linux-gno.so文件没有移动到kmerdb模块中，这是我的Python，我正在尝试在本地安装这个包，并为.whl上传到PyPI进行配置。

Python 3.10.1 (main, Jan  1 2022, 21:28:19) [GCC 11.1.0] on linux
Cython==0.29.26

setup.py

    Extension("distance", ["kmerdb/distance.pyx"], include_dirs=[np.get_include()], define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")],),
    setup(
        name=NAME,
        version=VERSION,
        description=DESCRIPTION,
        long_description=long_description,
        long_description_content_type='text/markdown',
        author=AUTHOR,
        author_email=EMAIL,
        python_requires=REQUIRES_PYTHON,
        url=URL,
        download_url=CURRENT_RELEASE,
        keywords = ["k-mer", "kmer", "k-merdb", "kmerdb", "kdb"],
        classifiers=[
            "Development Status :: 1 - Planning",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3.8",
            "Programming Language :: Python :: 3.9",
            "Programming Language :: Python :: 3.10",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries :: Python Modules",
        ],
        packages=find_packages(exclude=["tests", "*.tests", "*.tests.*", "tests.*"]),
        package_dir={'kmerdb': 'kmerdb'},
        package_data={'kmerdb': ['CITATION']},
        # If your package is a single module, use this instead of 'packages':
        #py_modules=['kmerdb'],
        #scripts=['bin/kmerdb', 'bin/kmerdb_report.R'],
        entry_points={
            'console_scripts': ['kmerdb=kmerdb:cli'],
        },
        install_requires=REQUIRED,#['Cython==0.29.21', 'numpy==1.18.1'],
        extras_require=EXTRAS,
        include_package_data=True,
        license='GPLv3+',
        test_suite='test',
        #    tests_require=['mamba', 'expect'],
        ext_modules=cythonize(extensions),
        library_dirs=["."],
        zip_safe=False,
    )

Answer 1

我要自己回答这个问题。这个问题是由一个不恰当的扩展引起的。

    Extension("kmerdb.distance", ["kmerdb/distance.pyx"], include_dirs=[np.get_include()])

我所要做的就是包括完全指定的子模块层次结构的模块名。修好了！