First shot at Cythonizing a whole Python source tree...

transmogrify.py

import os
import sys
import subprocess

#   gcc $(python3-config --cflags) -fPIC -c $file
#   gcc -shared $(python3-config --ldflags) utils.o -o utils.so

def flags():
    proc = subprocess.Popen(['python3-config', '--cflags'], stdout=subprocess.PIPE)
    cflags = proc.stdout.read().decode('ascii')
    proc = subprocess.Popen(['python3-config', '--ldflags'], stdout=subprocess.PIPE)
    ldflags = proc.stdout.read().decode('ascii')
    return cflags, ldflags


def filenames():
    for root, _, filenames in os.walk(sys.argv[1]):
        for filename in filenames:
            if filename.endswith('.py') and not filename[0] == '_':
                yield root, filename

def process(root, filename):
    cflags, ldflags = flags()
    subprocess.check_call(['cython', os.path.join(root, filename)])
    subprocess.check_call(
        ['gcc'] + cflags.split() + ['-fPIC', '-c', filename.replace('.py', '.c')],
        cwd=root)
    subprocess.check_call(
        ['gcc', '-shared'] + ldflags.split() + [
            filename.replace('.py', '.o'),
            '-o',
            filename.replace('.py', '.so')],
        cwd=root)

if __name__ == '__main__':
    for root, filename in filenames():
        process(root, filename)
        print(root, filename)