Menu
I'm developing a Python package, EcoPy, that is mostly written in pure Python. The main folder is called ecopy. There's a subfolder called regression that has a Cython file that's already been built. The main setup.py file includes the code:
ext_modules = cythonize([
Extension(
'ecopy.regression.isoFunc', ['ecopy/regression/isoFunc.pyx'], **opts),
])
When I run
sudo pip install ecopy -e . --upgrade --force-reinstall
the module builds fine. It even re-compiles the isoFunc.c file if I've deleted it. The problem is that Cython doesn't then convert the .c file to the .so file, which I need in order to import the function. If I try loading the module without it, I get
ImportError: No module named isoFunc
If I manually setup file using the command line
python setup.py build_ext --inplace
Cython DOES generate the .so file. How do I get it to generate the .so file using pip? I've tried to figure out how statsmodels did it by reading their code, but honestly, its a mystery to me.
It's almost as if the pip command misses the build_ext argument.
850
Run the cythonize command-line utility. This is a good approach for compiling a single Cython source file directly to an extension. A source file can be built “in place” (so that the extension module is created next to the source file, ready to be imported) with cythonize -i filename. pyx .
Because Cython code compiles to C, it can interact with those libraries directly, and take Python's bottlenecks out of the loop. But NumPy, in particular, works well with Cython. Cython has native support for specific constructions in NumPy and provides fast access to NumPy arrays.
Fortunately, Cython tools can be conveniently accessed through the Jupyter notebook for a more streamlined and integrated experience. You can launch a notebook session by typing jupyter notebook in the command line and you can load the Cython magic by typing %load_ext cython in a cell.
I can answer this question, because I just learned that I'm an idiot.
sudo pip install ecopy -e . --upgrade --force-reinstall
was using an older version from the PyPI that didn't have the new setup.py with the Cython code. When I did it correctly
sudo pip install -e . --upgrade --force-reinstall
and used the latest version on my hard drive, it worked fine.
Little victories.
130
I came here because I wasn't sure if pip installing my package is sufficient to automatically compile the Cython sources. It looks like it does but by default the pip output doesn't seem to log that. I noticed that pip install -e . -v makes it very clear if / what exactly is done regarding the compile and link steps:
Running setup.py develop for mypackage
[...]
running build_ext
cythoning mypackage/my_cython_module.pyx to mypackage/my_cython_module.c
building 'mypackage.my_cython_module' extension
x86_64-linux-gnu-gcc [...] -c mypackage/my_cython_module.c -o build/temp.linux-x86_64-2.7/mypackage/my_cython_module.o
x86_64-linux-gnu-gcc [...] build/temp.linux-x86_64-2.7/mypackage/my_cython_module.o -o build/lib.linux-x86_64-2.7/mypackage/my_cython_module.so
copying build/lib.linux-x86_64-2.7/mypackage/my_cython_module.so -> mypackage
[...]
If you love us? You can donate to us via Paypal or buy me a coffee so we can maintain and grow! Thank you!
Donate Us With
