I have a Python project for which I wrap some C/C++ code (using the excellent PyBind library). I have a set of C and Python unit tests and I've configured Gitlab's CI to run them at each push. The C tests use a minimalist unit test framework called minunit and I use Python's unittest suite.
Before running the C tests, all the C code is compiled and then tested. I'd like to also compile the C/C++ wrapper for Python before running the Python tests, but have a hard time to do it.
Is there a standard/good way to get Gitlab-CI to build a Python extension using setuptools before running unit-tests?
To compile the C/C++ wrapper locally, I use setuptools with a setup.py file including a build_ext command.
I locally compile everything with python setup.py build_ext --inplace (the last arg --inplace will just copy the compiled file to the current directory).
As far as I know, this is quite standard.
What I tried to do on Gitlab is to have a Python script (code below) that will run a few commands using os.system command (which appears to be bad practice...).
The first command is to run a script building and running all C tests. This works but I'm happy to take recommendations (should I configure Gitlab CI to run C tests separately?).
Now, the problem comes when I try to build the C/C++ wrapper, with os.system("cd python/ \npython setup.py build_ext --inplace"). This generates the error
File "setup.py", line 1, in <module>
from setuptools import setup, Extension
ImportError: No module named setuptools
So I tried to modify my gitlab's CI configuration file to install python-dev. My .gitlab-ci.yml looks like
test:
script:
- apt-get install -y python-dev
- python run_tests.py
But, not being sudo on the gitlab's server, I get the following error E: Could not open lock file /var/lib/dpkg/lock - open (13: Permission denied).
Anyone knows a way around that, or a better way to tackle this problem?
Any help would be more than welcome!
import unittest
import os
from shutil import copyfile
import glob
class AllTests(unittest.TestCase):
def test_all(self):
# this automatically loads all tests in current dir
testsuite = unittest.TestLoader().discover('tests/Python_tests')
# run tests
result = unittest.TextTestRunner(verbosity=2).run(testsuite)
# send/print results
self.assertEqual(result.failures, [], 'Failure')
if __name__ == "__main__":
# run C tests
print(' ------------------------------------------------------ C TESTS')
os.system("cd tests/C_tests/ \nbash run_all.sh")
# now python tests
print(' ------------------------------------------------- PYTHON TESTS')
# first build and copy shared library compiled from C++ in the python test directory
# build lib
os.system("cd python/ \npython setup.py build_ext --inplace")
# copy lib it to right place
dest_dir = 'tests/Python_tests/'
for file in glob.glob(r'python/*.so'):
print('Copying file to test dir : ', file)
copyfile(file, dest_dir+file.replace('python/', ''))
# run Python tests
unittest.main(verbosity=0)
My suggestion would be moving the entire test running logic into the setup script.
test commandFirst of all, setuptools ships a test command, so you can run the tests via python setup.py test. Even better, the test calls build_ext command under the hood and places the built extensions so that they accessible in the tests, so no need for you to invoke python setup.py build_ext explicitly:
$ python setup.py test
running test
running egg_info
creating so.egg-info
writing so.egg-info/PKG-INFO
writing dependency_links to so.egg-info/dependency_links.txt
writing top-level names to so.egg-info/top_level.txt
writing manifest file 'so.egg-info/SOURCES.txt'
reading manifest file 'so.egg-info/SOURCES.txt'
writing manifest file 'so.egg-info/SOURCES.txt'
running build_ext
building 'wrap_fib' extension
creating build
creating build/temp.linux-aarch64-3.6
aarch64-unknown-linux-gnu-gcc -pthread -fPIC -I/data/gentoo64/usr/include/python3.6m -c wrap_fib.c -o build/temp.linux-aarch64-3.6/wrap_fib.o
aarch64-unknown-linux-gnu-gcc -pthread -fPIC -I/data/gentoo64/usr/include/python3.6m -c cfib.c -o build/temp.linux-aarch64-3.6/cfib.o
creating build/lib.linux-aarch64-3.6
aarch64-unknown-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -L. build/temp.linux-aarch64-3.6/wrap_fib.o build/temp.linux-aarch64-3.6/cfib.o -L/data/gentoo64/usr/lib64 -lpython3.6m -o build/lib.linux-aarch64-3.6/wrap_fib.cpython-36m-aarch64-linux-gnu.so
copying build/lib.linux-aarch64-3.6/wrap_fib.cpython-36m-aarch64-linux-gnu.so ->
test_fib_0 (test_fib.FibonacciTests) ... ok
test_fib_1 (test_fib.FibonacciTests) ... ok
test_fib_10 (test_fib.FibonacciTests) ... ok
----------------------------------------------------------------------
Ran 3 tests in 0.002s
OK
(I used the code from the Cython Book examples repository to play with, but the output should be pretty similar to what PyBind produces).
Another feature that may come handy are the extra keywords setuptools adds: test_suite, tests_require, test_loader (docs). Here's an example of embedding a custom test suite as you do in run_tests.py:
# setup.py
import unittest
from Cython.Build import cythonize
from setuptools import setup, Extension
exts = cythonize([Extension("wrap_fib", sources=["cfib.c", "wrap_fib.pyx"])])
def pysuite():
return unittest.TestLoader().discover('tests/python_tests')
if __name__ == '__main__':
setup(
name='so',
version='0.1',
ext_modules=exts,
test_suite='setup.pysuite'
)
test commandThe last requirement is running C tests. We can embed them by overriding the test command and invoking some custom code from there. The advantage of that is that distutils offers a command API with many useful functions, like copying files or executing external commands:
# setup.py
import os
import unittest
from Cython.Build import cythonize
from setuptools import setup, Extension
from setuptools.command.test import test as test_orig
exts = cythonize([Extension("wrap_fib", sources=["cfib.c", "wrap_fib.pyx"])])
class test(test_orig):
def run(self):
# run python tests
super().run()
# run c tests
self.announce('Running C tests ...')
pwd = os.getcwd()
os.chdir('tests/C_tests')
self.spawn(['bash', 'run_all.sh'])
os.chdir(pwd)
def pysuite():
return unittest.TestLoader().discover('tests/python_tests')
if __name__ == '__main__':
setup(
name='so',
version='0.1',
ext_modules=exts,
test_suite='setup.pysuite',
cmdclass={'test': test}
)
I extended the original test command, running some extra stuff after the python unit tests finish (notice calling of an external command via self.spawn). All that is left is replacing the default test command with the custom one via passing cmdclass in the setup function.
Now you have everything collected in the setup script and python setup.py test will do all the dirty job.
But, not being sudo on the gitlab's server, I get the following error
I don't have any experience with Gitlab CI, but I can't imagine there is no possibility to install packages on the build server. Maybe this question will be helpful: How to use sudo in build script for gitlab ci?
If there really is no other option, you can bootstrap a local copy of setuptools with ez_setup.py. Note, however, that although this method still works, it was deprecated recently.
Also, if you happen to use a recent version of Python (3.4 and newer), then you should have pip bundled with Python distribution, so it should be possible to install setuptools without root permissions with
$ python -m pip install --user setuptools