One of the conveniences of Python is the package system which allows you to install your program and any dependencies smoothly. The package system works very well when the code is pure Python, but can run into trouble when code written in cython or c is part of the program.
I will illustrate some mis-steps I made while writing a install script for an example program that is a mixture of Python and Cython. I've put the code up on github and each step is a commit tag. You can follow along by setting up a virtual environment using virtualenvwrapper:
And then trying to install the appropriate tag, e.g:
I will illustrate some mis-steps I made while writing a install script for an example program that is a mixture of Python and Cython. I've put the code up on github and each step is a commit tag. You can follow along by setting up a virtual environment using virtualenvwrapper:
mkvirtualenv cy-test
And then trying to install the appropriate tag, e.g:
git clone git@github.com:kghose/cython-example.git cd cython-example git checkout ex2
ex1
The module installs without errors, but because of me not indicating the paths of the cython files properly (I omit the
kgcyex
directory in the path) the cython files do not compile. You will note this because there are no compilation messages during the install, though the failure is otherwise silentkghose$ kgcyex
Traceback (most recent call last):
File "/Users/kghose/.venvs/blog/bin/kgcyex", line 9, in <module>
load_entry_point('kgcyex==1.0.0', 'console_scripts', 'kgcyex')()
File "/Users/kghose/.venvs/blog/lib/python2.7/site-packages/pkg_resources.py", line 356, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/Users/kghose/.venvs/blog/lib/python2.7/site-packages/pkg_resources.py", line 2431, in load_entry_point
return ep.load()
File "/Users/kghose/.venvs/blog/lib/python2.7/site-packages/pkg_resources.py", line 2147, in load
['__name__'])
File "/Users/kghose/.venvs/blog/lib/python2.7/site-packages/kgcyex/main.py", line 2, in <module>
import kgcyex.cy1 as cy1
ImportError: No module named cy1
ex2
I correctly write out the full paths of the cython modules, and everything installs and runs fine.
kghose$ kgcyex
foo from kgcyex.mod1
foo from kgcyex.cy1
foo from kgcyex.lib.mod2
foo from kgcyex.lib.cy2
ex3
Suppose the other user does not have Cython? The cython documentation suggests that we distribute the generated c code with the source. There is some debate as to whether this is "proper" since the .c files are actually generated from the .pyx files and in principle we should only really be distributing files which can not be auto-generated from the "real" source. For now, we put pragmatism over principle. Note that the
setup.py
changes a bit
If you read the setup.py you will note that I have used a check to test if the user has Cython or not. This check then tells setup to either use the .pyx files or the .c files. This is standard stuff recommended by the Cython folks. Look carefully at the
setup.py
where I add the extensions.extensions = [Extension("cy1", ["kgcyex/cy1"+ext]), Extension("cy2", ["kgcyex/lib/cy2"+ext])]
Things compile properly because I've remembered to indicate the peoper path to the
.pyx
(or .c
) files. When we run setup.py
we can see the modules being compiled. But what the #$%@! when we go to run the code it again complains that it can find the compiled modules! In real life this error caused me to lose about an hour :(
My error was that though I had correctly indicated the path to the source (the second parameter for
Extension
) I had not given the proper dotted path for the modules themselves. If you look undersite-packages
of your installation you will note that there are two compiled modules cy1.so
andcy2.so
directly under site-packages
rather than in their proper places under kgcyex
andkgcyex/lib
. The correct form of this line is ...ex4
extensions = [Extension("kgcyex.cy1", ["kgcyex/cy1"+ext]), Extension("kgcyex.lib.cy2", ["kgcyex/lib/cy2"+ext])]
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