我编写了一个依赖于某些C扩展的Python模块.这些C扩展依赖于几个已编译的C库.我希望能够分发与所有依赖项捆绑在一起的这个模块.
我把一个最小的例子(it can be found on GitHub in its entirety)放在一起.
目录结构是：
$tree .
.
├── README.md
├── poc
│ ├── __init__.py
│ ├── cython_extensions
│ │ ├── __init__.py
│ │ ├── cvRoberts_dns.c
│ │ ├── cvRoberts_dns.h
│ │ ├── helloworld.c
│ │ ├── helloworld.pxd
│ │ ├── helloworld.pyx
│ │ ├── test.c
│ │ └── test.h
│ ├── do_stuff.c
│ └── do_stuff.pyx
└── setup.py
setup.py构建扩展,并链接必要的库(在本例中为libsundials_cvode,libsundials_nvectorserial)：
from setuptools import setup, find_packages
from setuptools.extension import Extension
from Cython.Build import cythonize
ext_module_dostuff = Extension(
'poc.do_stuff',
['poc/do_stuff.pyx'],
)
ext_module_helloworld = Extension(
'poc.cython_extensions.helloworld',
['poc/cython_extensions/helloworld.pyx', 'poc/cython_extensions/test.c', 'poc/cython_extensions/cvRoberts_dns.c'],
include_dirs = ['/usr/local/include'],
libraries = ['m', 'sundials_cvodes', 'sundials_nvecserial'],
library_dirs = ['/usr/local/lib'],
)
cython_ext_modules = [
ext_module_dostuff,
ext_module_helloworld
]
setup (
name = "poc",
ext_modules = cythonize(cython_ext_modules),
packages=['poc', 'poc.cython_extensions'],
)
这一切都很好,但它确实要求最终用户首先安装日((在实际情况下,还有其他几个非常挑剔的库来启动和运行).
理想情况下,我希望能够仅在开发机器上进行设置,创建包含相应共享库的分发,并运送某种类型的分发包.
鉴于迄今为止我发现的各种教程,示例和SO帖子.我被引导相信我走在正确的轨道上.但是,我还有一些最后的步骤,我只是没有动摇.
任何帮助表示赞赏:-).
解决方法:
您可能知道,使用编译组件分发Python模块的推荐方法是使用wheel format.似乎没有任何标准的跨平台方法将第三方本机库捆绑到方框中.但是,为此目的,有特定于平台的工具.
在Linux上,使用auditwheel.
auditwheel修改现有的Linux轮盘文件以添加未包含在基本“manylinux”标准中的任何第三方库.以下是如何在干净安装Ubuntu 17.10时将其与项目一起使用的演练：
首先,安装基本的Python开发工具,以及带有标头的第三方库：
root@ubuntu-17:~# apt-get install cython python-pip unzip
root@ubuntu-17:~# apt-get install libsundials-serial-dev
然后将项目构建到wheel文件中：
root@ubuntu-17:~# cd cython-example/
root@ubuntu-17:~/cython-example# python setup.py bdist_wheel
[...]
root@ubuntu-17:~/cython-example# cd dist/
root@ubuntu-17:~/cython-example/dist# ll
total 80
drwxr-xr-x 2 root root 4096 Nov 8 11:28 ./
drwxr-xr-x 7 root root 4096 Nov 8 11:28 ../
-rw-r--r-- 1 root root 70135 Nov 8 11:28 poc-0.0.0-cp27-cp27mu-linux_x86_64.whl
root@ubuntu-17:~/cython-example/dist# unzip -l poc-0.0.0-cp27-cp27mu-linux_x86_64.whl
Archive: poc-0.0.0-cp27-cp27mu-linux_x86_64.whl
Length Date Time Name
--------- ---------- ----- ----
62440 2017-11-08 11:28 poc/do_stuff.so
2 2017-11-08 11:28 poc/__init__.py
116648 2017-11-08 11:28 poc/cython_extensions/helloworld.so
2 2017-11-08 11:28 poc/cython_extensions/__init__.py
10 2017-11-08 11:28 poc-0.0.0.dist-info/DESCRIPTION.rst
211 2017-11-08 11:28 poc-0.0.0.dist-info/metadata.json
4 2017-11-08 11:28 poc-0.0.0.dist-info/top_level.txt
105 2017-11-08 11:28 poc-0.0.0.dist-info/WHEEL
167 2017-11-08 11:28 poc-0.0.0.dist-info/METADATA
793 2017-11-08 11:28 poc-0.0.0.dist-info/RECORD
--------- -------
180382 10 files
现在可以在本地安装wheel文件并进行测试：
root@ubuntu-17:~/cython-example/dist# pip install poc-0.0.0-cp27-cp27mu-linux_x86_64.whl
[...]
root@ubuntu-17:~/cython-example/dist# python -c "from poc.do_stuff import hello; hello()"
hello cython
0.841470984808
trying to load the sundials program
3-species kinetics problem
At t = 2.6391e-01 y = 9.899653e-01 3.470564e-05 1.000000e-02
rootsfound[] = 0 1
At t = 4.0000e-01 y = 9.851641e-01 3.386242e-05 1.480205e-02
[...]
现在我们安装auditwheel工具.它需要Python 3,但它能够处理Python 2或3的*.
root@ubuntu-17:~/cython-example/dist# apt-get install python3-pip
root@ubuntu-17:~/cython-example/dist# pip3 install auditwheel
auditwheel使用另一个名为patchelf的工具来完成它的工作.不幸的是,Ubuntu 17.10附带的patchelf版本缺少a bugfix而没有auditwheel will not work.所以我们必须从源代码构建它(脚本取自the manylinux Docker image)：
root@ubuntu-17:~# apt-get install autoconf
root@ubuntu-17:~# PATCHELF_VERSION=6bfcafbba8d89e44f9ac9582493b4f27d9d8c369
root@ubuntu-17:~# curl -sL -o patchelf.tar.gz https://github.com/NixOS/patchelf/archive/$PATCHELF_VERSION.tar.gz
root@ubuntu-17:~# tar -xzf patchelf.tar.gz
root@ubuntu-17:~# (cd patchelf-$PATCHELF_VERSION && ./bootstrap.sh && ./configure && make && make install)
现在我们可以检查车轮需要哪些第三方库：
root@ubuntu-17:~/cython-example/dist# auditwheel show poc-0.0.0-cp27-cp27mu-linux_x86_64.whl
poc-0.0.0-cp27-cp27mu-linux_x86_64.whl is consistent with the
following platform tag: "linux_x86_64".
The wheel references external versioned symbols in these system-
provided shared libraries: libc.so.6 with versions {'GLIBC_2.4',
'GLIBC_2.2.5', 'GLIBC_2.3.4'}
The following external shared libraries are required by the wheel:
{
"libblas.so.3": "/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1",
"libc.so.6": "/lib/x86_64-linux-gnu/libc-2.26.so",
"libgcc_s.so.1": "/lib/x86_64-linux-gnu/libgcc_s.so.1",
"libgfortran.so.4": "/usr/lib/x86_64-linux-gnu/libgfortran.so.4.0.0",
"liblapack.so.3": "/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1",
"libm.so.6": "/lib/x86_64-linux-gnu/libm-2.26.so",
"libpthread.so.0": "/lib/x86_64-linux-gnu/libpthread-2.26.so",
"libquadmath.so.0": "/usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0",
"libsundials_cvodes.so.2": "/usr/lib/libsundials_cvodes.so.2.0.0",
"libsundials_nvecserial.so.0": "/usr/lib/libsundials_nvecserial.so.0.0.2"
}
In order to achieve the tag platform tag "manylinux1_x86_64" the
following shared library dependencies will need to be eliminated:
libblas.so.3, libgfortran.so.4, liblapack.so.3, libquadmath.so.0,
libsundials_cvodes.so.2, libsundials_nvecserial.so.0
并创建一个捆绑它们的新*：
root@ubuntu-17:~/cython-example/dist# auditwheel repair poc-0.0.0-cp27-cp27mu-linux_x86_64.whl
Repairing poc-0.0.0-cp27-cp27mu-linux_x86_64.whl
Grafting: /usr/lib/libsundials_nvecserial.so.0.0.2 -> poc/.libs/libsundials_nvecserial-42b4120e.so.0.0.2
Grafting: /usr/lib/libsundials_cvodes.so.2.0.0 -> poc/.libs/libsundials_cvodes-50fde5ee.so.2.0.0
Grafting: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1 -> poc/.libs/liblapack-549933c4.so.3.7.1
Grafting: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 -> poc/.libs/libblas-52fa99c8.so.3.7.1
Grafting: /usr/lib/x86_64-linux-gnu/libgfortran.so.4.0.0 -> poc/.libs/libgfortran-2df4b07d.so.4.0.0
Grafting: /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0 -> poc/.libs/libquadmath-0d7c3070.so.0.0.0
Setting RPATH: poc/cython_extensions/helloworld.so to "$ORIGIN/../.libs"
Previous filename tags: linux_x86_64
New filename tags: manylinux1_x86_64
Previous WHEEL info tags: cp27-cp27mu-linux_x86_64
New WHEEL info tags: cp27-cp27mu-manylinux1_x86_64
Fixed-up wheel written to /root/cython-example/dist/wheelhouse/poc-0.0.0-cp27-cp27mu-manylinux1_x86_64.whl
root@ubuntu-17:~/cython-example/dist# unzip -l wheelhouse/poc-0.0.0-cp27-cp27mu-manylinux1_x86_64.whl
Archive: wheelhouse/poc-0.0.0-cp27-cp27mu-manylinux1_x86_64.whl
Length Date Time Name
--------- ---------- ----- ----
167 2017-11-08 11:28 poc-0.0.0.dist-info/METADATA
4 2017-11-08 11:28 poc-0.0.0.dist-info/top_level.txt
10 2017-11-08 11:28 poc-0.0.0.dist-info/DESCRIPTION.rst
211 2017-11-08 11:28 poc-0.0.0.dist-info/metadata.json
1400 2017-11-08 12:08 poc-0.0.0.dist-info/RECORD
110 2017-11-08 12:08 poc-0.0.0.dist-info/WHEEL
62440 2017-11-08 11:28 poc/do_stuff.so
2 2017-11-08 11:28 poc/__init__.py
131712 2017-11-08 12:08 poc/cython_extensions/helloworld.so
2 2017-11-08 11:28 poc/cython_extensions/__init__.py
230744 2017-11-08 12:08 poc/.libs/libsundials_cvodes-50fde5ee.so.2.0.0
7005072 2017-11-08 12:08 poc/.libs/liblapack-549933c4.so.3.7.1
264024 2017-11-08 12:08 poc/.libs/libquadmath-0d7c3070.so.0.0.0
2039960 2017-11-08 12:08 poc/.libs/libgfortran-2df4b07d.so.4.0.0
17736 2017-11-08 12:08 poc/.libs/libsundials_nvecserial-42b4120e.so.0.0.2
452432 2017-11-08 12:08 poc/.libs/libblas-52fa99c8.so.3.7.1
--------- -------
10206026 16 files
如果我们卸载第三方库,以前安装的轮将停止工作：
root@ubuntu-17:~/cython-example/dist# apt-get remove libsundials-serial-dev && apt-get autoremove
[...]
root@ubuntu-17:~/cython-example/dist# python -c "from poc.do_stuff import hello; hello()"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "poc/do_stuff.pyx", line 1, in init poc.do_stuff
ImportError: libsundials_cvodes.so.2: cannot open shared object file: No such file or directory
但是带有捆绑库的*可以正常工作：
root@ubuntu-17:~/cython-example/dist# pip uninstall poc
[...]
root@ubuntu-17:~/cython-example/dist# pip install wheelhouse/poc-0.0.0-cp27-cp27mu-manylinux1_x86_64.whl
[...]
root@ubuntu-17:~/cython-example/dist# python -c "from poc.do_stuff import hello; hello()"
hello cython
0.841470984808
trying to load the sundials program
3-species kinetics problem
At t = 2.6391e-01 y = 9.899653e-01 3.470564e-05 1.000000e-02
rootsfound[] = 0 1
At t = 4.0000e-01 y = 9.851641e-01 3.386242e-05 1.480205e-02
[...]
在OSX上,使用delocate.
OS00的delocate显然与auditwheel非常相似.不幸的是,我没有可用于提供演练的OSX机器.
组合示例：
一个使用这两种工具的项目是SciPy. This repository,尽管它的名字,包含所有平台的官方SciPy构建过程,而不仅仅是Mac.具体来说,将Linux build script(使用auditwheel)与OSX build script(使用delocate)进行比较.
要查看此过程的结果,您可能需要下载并解压缩一些SciPy wheels from PyPI.例如,scipy-1.0.0-cp27-cp27m-manylinux1_x86_64.whl包含以下内容：
38513408 2017-10-25 06:02 scipy/.libs/libopenblasp-r0-39a31c03.2.18.so
1023960 2017-10-25 06:02 scipy/.libs/libgfortran-ed201abd.so.3.0.0
虽然scipy-1.0.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl包含：
273072 2017-10-25 07:03 scipy/.dylibs/libgcc_s.1.dylib
1550456 2017-10-25 07:03 scipy/.dylibs/libgfortran.3.dylib
279932 2017-10-25 07:03 scipy/.dylibs/libquadmath.0.dylib