CYTHON : Generating coverage for pyx file - code-coverage

Question

I am trying to generate code coverage report for a cython module, an d facing issues.
I have a simple c++ code : apple.h and apple.cpp files.
The cpp file is simple as :
using namespace std;
namespace mango {
apple::apple(int key) {
_key = key;
};
int apple::execute()
{
return _key*_key;
};
}
I have written a basic cython code over this in "cyApple.pyx" :
# cython: linetrace=True
from libcpp.list cimport list as clist
from libcpp.string cimport string
from libc.stdlib cimport malloc
cdef extern from "apple.h" namespace "mango" :
cdef cppclass apple:
apple(int)
int execute()
cdef class pyApple:
cdef apple* aa
def __init__(self, number):
self.aa = new apple(number)
def getSquare(self):
return self.aa.execute()
My setup.py file :
from distutils.core import setup, Extension
from Cython.Build import cythonize
compiler_directives = {}
define_macros = []
compiler_directives['profile'] = True
compiler_directives['linetrace'] = True
define_macros.append(('CYTHON_TRACE', '1'))
setup(ext_modules = cythonize(Extension(
"cyApple",
sources=["cyApple.pyx", "apple.cpp"],
define_macros=define_macros,
language="c++",
), compiler_directives=compiler_directives))
This generates a proper library cyApple.so.
I have also written a simple appletest.py file to run test cases :
import cyApple, unittest
class APPLETests(unittest.TestCase):
def test1(self):
temp = 5
apple1 = cyApple.pyApple(temp)
self.assertEqual(25, apple1.getSquare())
suite = unittest.TestLoader().loadTestsFromTestCase(APPLETests)
unittest.TextTestRunner(verbosity=3).run(suite)
The test works fine.
The problem is I need to get code coverage for my cyApple.pyx file
When i run "coverage report -m"
I get the error and coverage for only my test file not pyx file.
cyApple.pyx NotPython: Couldn't parse '/home/final/cyApple.pyx' as Python source: 'invalid syntax' at line 2
Name Stmts Miss Cover Missing
--------------------------------------------
appletest.py 8 1 88% 9
I tried to look online and get some help , so i added
.coveragerc file with contents as :
[run]
plugins = Cython.Coverage
On running "coverage run appletest.py" i get errors :
...
...
...
ImportError: No module named Coverage
I want to generate simple code coverage report for my pyx file. How i can do it in a simple way ?
I reinstalled Cython-0.28.3.
Now on running "coverage run appletest.py"
I am getting error :
test1 (__main__.APPLETests) ... Segmentation fault (core dumped)
This is my apple.h file :
#include<iostream>
namespace mango {
class apple {
public:
apple(int key);
int execute();
private:
int _key;
};
}

Answer 1

You must update Cython. The documentation states:
Since Cython 0.23, line tracing (see above) also enables support for
coverage reporting with the coverage.py tool.

Answer 2

I created a simple helper script that:
Runs all cython files in the directory
Creates a linetrace version of cython code, but cleans up after execution, so this won't interfere with production versions.
Produces cython annotated report with line coverage, takes care of .coveragerc creation and all technical stuff
Works well with pyximport, no need to build setup.py and rebuild cython modules
Caveats
It works only for linux (but it's doable to adapt it for another OS)
Built for anaconda python
Project:
https://github.com/alexveden/cython_coverage_script
Source code:
https://github.com/alexveden/cython_coverage_script/blob/master/cy_test/tests/run_cython_coverage_annotations.py
Hopefully this helps anyone, because I spent an enormous amount of time to figure out how to deal with coverage under Cython. It's appeared not a trivial task because, Cython coverage plugin has issues with mapping .pyx paths and pyximport doesn't support coverage directives.