How to use atexit in Cython? - cython

Question

I am trying to make the following code in cython to compile
from cython_gsl cimport *
import atexit
cdef gsl_rng_type * rng_T = gsl_rng_default
cdef gsl_rng * rng_r
gsl_rng_env_setup()
rng_r = gsl_rng_alloc(rng_T)
#atexit.register
def free_gsl_rng():
gsl_rng_free(rng_r)
But I always get the error
Assignment to non-lvalue 'atexit'
Corresponding .pxd file
from cython_gsl cimport *
cdef gsl_rng * rng_r
I am actually compiling this with SageMath 8.7 by
sage setup.py build_ext --inplace
Here is my setup.py
from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize
import cython_gsl
extensions = [
Extension("gsl_rand", ["gsl_rand.pyx"],
libraries=cython_gsl.get_libraries(),
library_dirs=[cython_gsl.get_library_dir()],
include_dirs=[cython_gsl.get_cython_include_dir()]
),
]
setup(
name='Simulation of k-cut on conditional Galton-Watson trees',
cmdclass={'build_ext': build_ext},
include_dirs = [cython_gsl.get_include()],
ext_modules=cythonize(extensions),
)
Full error log here
sage setup.py build_ext --inplace
Compiling gsl_rand.pyx because it changed.
[1/1] Cythonizing gsl_rand.pyx
/home/xing/Downloads/software/sage/8.7/local/lib/python2.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/xing/Dropbox/Research/2017/k-cut/GW/sage/moments/cython-v5/gsl_rand.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
warning: /home/xing/Downloads/software/sage/8.7/local/lib/python2.7/site-packages/cython_gsl/gsl_integration.pxd:65:9: 'GSL_EMAXITER' redeclared
warning: /home/xing/Downloads/software/sage/8.7/local/lib/python2.7/site-packages/cython_gsl/gsl_integration.pxd:67:9: 'GSL_EROUND' redeclared
warning: /home/xing/Downloads/software/sage/8.7/local/lib/python2.7/site-packages/cython_gsl/gsl_integration.pxd:69:9: 'GSL_ESING' redeclared
warning: /home/xing/Downloads/software/sage/8.7/local/lib/python2.7/site-packages/cython_gsl/gsl_integration.pxd:71:9: 'GSL_EDIVERGE' redeclared
warning: gsl_rand.pyx:14:0: Overriding cdef method with def method.
Error compiling Cython file:
------------------------------------------------------------
...
# cython: profile=False
from cython_gsl cimport *
import atexit
^
------------------------------------------------------------
gsl_rand.pyx:5:7: Assignment to non-lvalue 'atexit'
Error compiling Cython file:
------------------------------------------------------------
...
cdef gsl_rng * rng_r
gsl_rng_env_setup()
rng_r = gsl_rng_alloc(rng_T)
#atexit.register
^
------------------------------------------------------------
gsl_rand.pyx:13:0: Object of type 'int (void (*)(void) nogil) nogil' has no attribute 'register'
Traceback (most recent call last):
File "setup.py", line 29, in <module>
ext_modules=cythonize(extensions),
File "/home/xing/Downloads/software/sage/8.7/local/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 1097, in cythonize
cythonize_one(*args)
File "/home/xing/Downloads/software/sage/8.7/local/lib/python2.7/site-packages/Cython/Build/Dependencies.py", line 1220, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: gsl_rand.pyx

Answer 1

atexit is getting cimported with from cython_gsl cimport *. This appears to happen with the line from libc.stdlib cimport *. This name therefore conflicts with the Python atexit module. I think this is a good example of why from something [c]import * is not recommended, both in your code and in cython_gsl's code. It gets slightly more confusing because Cython has two types of names (for Python and C) so you get odd error messages.
The best solution is to either do cimport cython_gsl or to cimport the specific symbols you need: from cython_gsl cimport gsl_rng, etc. Remember to change both the pyx and pxd file.
The worse workround is to rename the atexit module when you import it: import atexit as ae.