add --ignore-submodules to apply_issue.py

checkout.py

 # coding=utf8
 # Copyright (c) 2012 The Chromium Authors. All rights reserved.
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 """Manages a project checkout.
 
 Includes support for svn, git-svn and git.
 """
 
 import ConfigParser
@@ skipping 598 matching lines @@
             ['checkout', '--force', '--quiet', self.master_branch])
       self._sync_remote_branch()
 
       if self.working_branch in branches:
         self._call_git(['branch', '-D', self.working_branch])
     return self._get_head_commit_hash()
 
   def _sync_remote_branch(self):
     """Syncs the remote branch."""
     # We do a 'git pull origin master:refs/remotes/origin/master' instead of
-    # 'git pull origin master' because from the manpage for git-pull: 
+    # 'git pull origin master' because from the manpage for git-pull:
     #   A parameter <ref> without a colon is equivalent to <ref>: when
     #   pulling/fetching, so it merges <ref> into the current branch without
     #   storing the remote branch anywhere locally.
     remote_tracked_path = 'refs/remotes/%s/%s' % (
         self.remote, self.remote_branch)
     self._check_call_git(
         ['pull', self.remote,
          '%s:%s' % (self.remote_branch, remote_tracked_path),
          '--quiet'])
 
   def _get_head_commit_hash(self):
     """Gets the current revision (in unicode) from the local branch."""
     return unicode(self._check_output_git(['rev-parse', 'HEAD']).strip())
 
-  def apply_patch(self, patches, post_processors=None, verbose=False, 
+  def apply_patch(self, patches, post_processors=None, verbose=False,
                   name=None, email=None):
     """Applies a patch on 'working_branch' and switches to it.
 
     Also commits the changes on the local branch.
 
     Ignores svn properties and raise an exception on unexpected ones.
     """
     post_processors = post_processors or self.post_processors or []
     # It this throws, the checkout is corrupted. Maybe worth deleting it and
     # trying again?
@@ skipping 71 matching lines @@
       cmd = ['-c', 'user.email=%s' % email, '-c', 'user.name=%s' % name] + cmd
     if verbose:
       cmd.append('--verbose')
     self._check_call_git(cmd)
     if self.base_ref:
       base_ref = self.base_ref
     else:
       base_ref = '%s/%s' % (self.remote,
                             self.remote_branch or self.master_branch)
     found_files = self._check_output_git(
-        ['diff', base_ref,
+        ['diff', base_ref, '--ignore-submodules',
          '--name-only']).splitlines(False)
     assert sorted(patches.filenames) == sorted(found_files), (
         sorted(patches.filenames), sorted(found_files))
 
   def commit(self, commit_message, user):
     """Commits, updates the commit message and pushes."""
     assert self.commit_user
     assert isinstance(commit_message, unicode)
     current_branch = self._check_output_git(
         ['rev-parse', '--abbrev-ref', 'HEAD']).strip()
     assert current_branch == self.working_branch
- 
+
     commit_cmd = ['commit', '--amend', '-m', commit_message]
     if user and user != self.commit_user:
       # We do not have the first or last name of the user, grab the username
       # from the email and call it the original author's name.
       # TODO(rmistry): Do not need the below if user is already in
       #                "Name <email>" format.
       name = user.split('@')[0]
       commit_cmd.extend(['--author', '%s <%s>' % (name, user)])
     self._check_call_git(commit_cmd)
 
@@ skipping 88 matching lines @@
   def revisions(self, rev1, rev2):
     return self.checkout.revisions(rev1, rev2)
 
   @property
   def project_name(self):
     return self.checkout.project_name
 
   @property
   def project_path(self):
     return self.checkout.project_path