parse cython command line args using argparse

Move custom argument parsing to a single location in main(),
which populates the appropriate global variables.

setup.py

@@ -42,14 +42,7 @@ def configure_extensions(exts, aliases=(), build_summary=None):
 
     This function modifies `sys.argv`.
     """
-    global config_file, config_file_present
-
-    #### Determine the name of the configuration file.
-    config_file_option = 'configfile'
-    parser = argparse.ArgumentParser(add_help=False)
-    parser.add_argument('--' + config_file_option)
-    cmdline_args, _ = parser.parse_known_args()
-    config_file = getattr(cmdline_args, config_file_option) or 'build.conf'
+    global config_file_present
 
     #### Read build configuration file.
     configs = configparser.ConfigParser()
@@ -156,13 +149,7 @@ def init_cython():
     """
     global cythonize, cython_help
 
-    cython_option = '--cython'
     required_cython_version = (0, 22)
-    try:
-        sys.argv.remove(cython_option)
-        cythonize = True
-    except ValueError:
-        cythonize = version_is_from_git
 
     if cythonize:
         try:
@@ -545,6 +532,20 @@ def main():
 
     aliases = [('mumps', 'kwant.linalg._mumps')]
 
+    # Parse custom command-line parameters
+
+    config_file_option = 'configfile'
+    cython_option = 'cython'
+    parser = argparse.ArgumentParser(add_help=False)
+    parser.add_argument('--' + config_file_option, default='build.conf')
+    parser.add_argument('--' + cython_option, action='store_true',
+                        default=version_is_from_git)
+    cmdline_args, _ = parser.parse_known_args()
+
+    global config_file, cythonize
+    config_file = getattr(cmdline_args, config_file_option)
+    cythonize = getattr(cmdline_args, cython_option)
+
     init_cython()
 
     global build_summary