Fix interspersed positional arguments in cythonize.py (GH-2988)

Cython/Build/Cythonize.py

@@ -201,8 +201,17 @@ def create_args_parser():
 
 
 def parse_args_raw(parser, args):
-    options = parser.parse_args(args)
-    return (options, options.sources)
+    options, unknown = parser.parse_known_args(args)
+    sources = options.sources
+    # if positional arguments were interspersed
+    # some of them are in unknown
+    for option in unknown:
+        if option.startswith('-'):
+            parser.error("unknown option "+option)
+        else:
+            sources.append(option)
+    delattr(options, 'sources')
+    return (options, sources)
 
 
 def parse_args(args):

Cython/Build/Tests/TestCythonizeArgsParser.py

@@ -4,7 +4,12 @@ from Cython.Build.Cythonize import (
 )
 from unittest import TestCase
 
-import argparse
+import sys
+try:
+    from StringIO import StringIO
+except ImportError:
+    from io import StringIO  # doesn't accept 'str' in Py2
+
 
 class TestCythonizeArgsParser(TestCase):
 
@@ -392,6 +397,46 @@ class TestCythonizeArgsParser(TestCase):
         self.assertEqual(options.build_inplace, True)
         self.assertTrue(self.are_default(options, ['build_inplace']))
 
+    def test_interspersed_positional(self):
+        options, sources = self.parse_args([
+             'file1.pyx', '-a',
+             'file2.pyx'
+        ])
+        self.assertEqual(sources, ['file1.pyx', 'file2.pyx'])
+        self.assertEqual(options.annotate, 'default')
+        self.assertTrue(self.are_default(options, ['annotate']))
+
+    def test_interspersed_positional2(self):
+        options, sources = self.parse_args([
+             'file1.pyx', '-a',
+             'file2.pyx', '-a', 'file3.pyx'
+        ])
+        self.assertEqual(sources, ['file1.pyx', 'file2.pyx', 'file3.pyx'])
+        self.assertEqual(options.annotate, 'default')
+        self.assertTrue(self.are_default(options, ['annotate']))
+
+    def test_interspersed_positional3(self):
+        options, sources = self.parse_args([
+             '-f', 'f1', 'f2', '-a',
+             'f3', 'f4', '-a', 'f5'
+        ])
+        self.assertEqual(sources, ['f1', 'f2', 'f3', 'f4', 'f5'])
+        self.assertEqual(options.annotate, 'default')
+        self.assertEqual(options.force, True)
+        self.assertTrue(self.are_default(options, ['annotate', 'force']))
+
+    def test_wrong_option(self):
+        old_stderr = sys.stderr
+        stderr = sys.stderr = StringIO()
+        try:
+            self.assertRaises(SystemExit, self.parse_args,
+                              ['--unknown-option']
+                              )
+        finally:
+            sys.stderr = old_stderr
+        self.assertTrue(stderr.getvalue())
+
+
 class TestParseArgs(TestCase):
 
     def test_build_set_for_inplace(self):