Fix for #157 (with upstream changes)

Conflicts:
	tests/commands/run_test.py

pre_commit/commands/run.py

@@ -129,6 +129,18 @@ def _has_unmerged_paths(runner):
     return bool(stdout.strip())
 
 
+def _has_unstaged_config(runner):
+    retcode, stdout, stderr = runner.cmd_runner.run(
+        [
+            'git', 'diff', '--exit-code', runner.config_file_path
+        ],
+        retcode=None,
+        encoding=None,
+    )
+    # be explicit, other git errors don't mean it has an unstaged config.
+    return retcode == 1
+
+
 def run(runner, args, write=sys_stdout_write_wrapper, environ=os.environ):
     # Set up our logging handler
     logger.addHandler(LoggingHandler(args.color, write=write))
@@ -141,6 +153,16 @@ def run(runner, args, write=sys_stdout_write_wrapper, environ=os.environ):
     if bool(args.source) != bool(args.origin):
         logger.error('Specify both --origin and --source.')
         return 1
+    if _has_unstaged_config(runner) and not args.no_stash:
+        if args.allow_unstaged_config:
+            logger.warn('You have an unstaged config file and have '
+                        'specified the --allow-unstaged-config option.\n'
+                        'Note that your config will be stashed before the '
+                        'config is parsed unless --no-stash is specified.')
+        else:
+            logger.error('You have an unstaged config file and have not '
+                         'specified the --allow-unstaged-config option.\n')
+            return 1
 
     # Don't stash if specified or files are specified
     if args.no_stash or args.all_files or args.files:

pre_commit/main.py

@@ -94,6 +94,11 @@ def main(argv=None):
         '--source', '-s',
         help='The remote branch"s commit_id when using `git push`',
     )
+    run_parser.add_argument(
+        '--allow-unstaged-config', default=False, action='store_true',
+        help='Allow an unstaged config to be present.  Note that this will'
+        'be stashed before parsing unless --no-stash is specified'
+    )
     run_mutex_group = run_parser.add_mutually_exclusive_group(required=False)
     run_mutex_group.add_argument(
         '--all-files', '-a', action='store_true', default=False,

tests/commands/run_test.py

@@ -55,6 +55,7 @@ def _get_opts(
         no_stash=False,
         origin='',
         source='',
+        allow_unstaged_config=False,
 ):
     # These are mutually exclusive
     assert not (all_files and files)
@@ -67,6 +68,7 @@ def _get_opts(
         no_stash=no_stash,
         origin=origin,
         source=source,
+        allow_unstaged_config=allow_unstaged_config,
     )
 
 
@@ -397,3 +399,60 @@ def test_local_hook_fails(
         expected_ret=1,
         stage=False
     )
+
+
+def test_allow_unstaged_config_option(repo_with_passing_hook,
+                                      mock_out_store_directory):
+
+    with cwd(repo_with_passing_hook):
+        with io.open(
+            '.pre-commit-config.yaml', 'a+',
+        ) as config_file:
+            # writing a newline should be relatively harmless to get a change
+            config_file.write('\n')
+
+    args = _get_opts(allow_unstaged_config=True)
+    ret, printed = _do_run(repo_with_passing_hook, args)
+    common_msg = 'You have an unstaged config file'
+    warning_msg = 'have specified the --allow-unstaged-config option.'
+
+    assert common_msg in printed
+    assert warning_msg in printed
+    assert ret == 0
+
+
+def test_no_allow_unstaged_config_option(repo_with_passing_hook,
+                                         mock_out_store_directory):
+
+    with cwd(repo_with_passing_hook):
+        with io.open(
+            '.pre-commit-config.yaml', 'a+',
+        ) as config_file:
+            # writing a newline should be relatively harmless to get a change
+            config_file.write('\n')
+
+    args = _get_opts(allow_unstaged_config=False)
+    ret, printed = _do_run(repo_with_passing_hook, args)
+    common_msg = 'You have an unstaged config file'
+    error_msg = 'have not specified the --allow-unstaged-config option.\n'
+
+    assert common_msg in printed
+    assert error_msg in printed
+    assert ret == 1
+
+
+def test_no_stash_suppresses_allow_unstaged_config_option(
+        repo_with_passing_hook, mock_out_store_directory):
+
+    with cwd(repo_with_passing_hook):
+        with io.open(
+            '.pre-commit-config.yaml', 'a+',
+        ) as config_file:
+            # writing a newline should be relatively harmless to get a change
+            config_file.write('\n')
+
+    args = _get_opts(allow_unstaged_config=False, no_stash=True)
+    ret, printed = _do_run(repo_with_passing_hook, args)
+    common_msg = 'You have an unstaged config file'
+
+    assert common_msg not in printed