Two problems I didn't see before that are now fixed.

First, I never got around to testing my changes to @kilian's patch for #23 and
just found that I had mistyped a variable.

Also, on more complex code that what I had tested on previously, my patch to
pep8 was insufficient. This should work without error now.

flake8/pep8.py

@@ -482,6 +482,9 @@ def continuation_line_indentation(logical_line, tokens, indent_level, verbose):
         print(">>> " + tokens[0][4].rstrip())
 
     for token_type, text, start, end, line in tokens:
+        if line.strip().lower().endswith('# nopep8'):
+            continue
+
         newline = row < start[0] - first_row
         if newline:
             row = start[0] - first_row
@@ -1205,8 +1208,7 @@ class Checker(object):
         self.line_number += 1
         if self.line_number > len(self.lines):
             return ''
-        line = self.lines[self.line_number - 1]
-        return '' if line.lower().strip().endswith('# nopep8') else line
+        return self.lines[self.line_number - 1]
 
     def readline_check_physical(self):
         """

flake8/run.py

@@ -52,7 +52,7 @@ def _get_python_files(paths):
                         yield fullpath
 
         else:
-            if not skip_file(path) or pep8style.excluded(fullpath):
+            if not skip_file(path) or pep8style.excluded(path):
                 yield path