diff --git a/pre_commit/commands/autoupdate.py b/pre_commit/commands/autoupdate.py
index 872de173..714dfd97 100644
--- a/pre_commit/commands/autoupdate.py
+++ b/pre_commit/commands/autoupdate.py
@@ -1,8 +1,6 @@
 from __future__ import print_function
 from __future__ import unicode_literals
 
-import logging
-
 from aspy.yaml import ordered_dump
 from aspy.yaml import ordered_load
 
@@ -12,7 +10,6 @@ from pre_commit.clientlib.validate_config import CONFIG_JSON_SCHEMA
 from pre_commit.clientlib.validate_config import is_local_hooks
 from pre_commit.clientlib.validate_config import load_config
 from pre_commit.jsonschema_extensions import remove_defaults
-from pre_commit.logging_handler import LoggingHandler
 from pre_commit.ordereddict import OrderedDict
 from pre_commit.repository import Repository
 from pre_commit.util import CalledProcessError
@@ -20,9 +17,6 @@ from pre_commit.util import cmd_output
 from pre_commit.util import cwd
 
 
-logger = logging.getLogger('pre_commit')
-
-
 class RepositoryCannotBeUpdatedError(RuntimeError):
     pass
 
@@ -69,10 +63,6 @@ def _update_repository(repo_config, runner):
 
 def autoupdate(runner):
     """Auto-update the pre-commit config to the latest versions of repos."""
-    # Set up our logging handler
-    logger.addHandler(LoggingHandler(False))
-    logger.setLevel(logging.WARNING)
-
     retv = 0
     output_configs = []
     changed = False
diff --git a/pre_commit/commands/install_uninstall.py b/pre_commit/commands/install_uninstall.py
index 520c4f1e..1277ec35 100644
--- a/pre_commit/commands/install_uninstall.py
+++ b/pre_commit/commands/install_uninstall.py
@@ -2,21 +2,15 @@ from __future__ import print_function
 from __future__ import unicode_literals
 
 import io
-import logging
-import os
 import os.path
 import sys
 
 from pre_commit import output
-from pre_commit.logging_handler import LoggingHandler
 from pre_commit.util import make_executable
 from pre_commit.util import mkdirp
 from pre_commit.util import resource_filename
 
 
-logger = logging.getLogger('pre_commit')
-
-
 # This is used to identify the hook file we install
 PREVIOUS_IDENTIFYING_HASHES = (
     '4d9958c90bc262f47553e2c073f14cfe',
@@ -88,9 +82,6 @@ def install(runner, overwrite=False, hooks=False, hook_type='pre-commit'):
 
     # If they requested we install all of the hooks, do so.
     if hooks:
-        # Set up our logging handler
-        logger.addHandler(LoggingHandler(False))
-        logger.setLevel(logging.INFO)
         for repository in runner.repositories:
             repository.require_installed()
 
diff --git a/pre_commit/commands/run.py b/pre_commit/commands/run.py
index 43a76bb4..67d0b778 100644
--- a/pre_commit/commands/run.py
+++ b/pre_commit/commands/run.py
@@ -8,7 +8,6 @@ import sys
 from pre_commit import color
 from pre_commit import git
 from pre_commit import output
-from pre_commit.logging_handler import LoggingHandler
 from pre_commit.output import get_hook_message
 from pre_commit.staged_files_only import staged_files_only
 from pre_commit.util import cmd_output
@@ -178,9 +177,6 @@ def _has_unstaged_config(runner):
 
 def run(runner, args, environ=os.environ):
     no_stash = args.no_stash or args.all_files or bool(args.files)
-    # Set up our logging handler
-    logger.addHandler(LoggingHandler(args.color))
-    logger.setLevel(logging.INFO)
 
     # Check if we have unresolved merge conflict files and fail fast.
     if _has_unmerged_paths(runner):
diff --git a/pre_commit/git.py b/pre_commit/git.py
index 17b42905..96e7390d 100644
--- a/pre_commit/git.py
+++ b/pre_commit/git.py
@@ -2,7 +2,6 @@ from __future__ import unicode_literals
 
 import functools
 import logging
-import os
 import os.path
 import re
 
diff --git a/pre_commit/logging_handler.py b/pre_commit/logging_handler.py
index f8472e07..78c2827a 100644
--- a/pre_commit/logging_handler.py
+++ b/pre_commit/logging_handler.py
@@ -6,6 +6,8 @@ from pre_commit import color
 from pre_commit import output
 
 
+logger = logging.getLogger('pre_commit')
+
 LOG_LEVEL_COLORS = {
     'DEBUG': '',
     'INFO': '',
@@ -30,3 +32,8 @@ class LoggingHandler(logging.Handler):
                 record.getMessage(),
             )
         )
+
+
+def add_logging_handler(*args, **kwargs):
+    logger.addHandler(LoggingHandler(*args, **kwargs))
+    logger.setLevel(logging.INFO)
diff --git a/pre_commit/main.py b/pre_commit/main.py
index 1afbef0b..97281890 100644
--- a/pre_commit/main.py
+++ b/pre_commit/main.py
@@ -15,6 +15,7 @@ from pre_commit.commands.install_uninstall import install
 from pre_commit.commands.install_uninstall import uninstall
 from pre_commit.commands.run import run
 from pre_commit.error_handler import error_handler
+from pre_commit.logging_handler import add_logging_handler
 from pre_commit.runner import Runner
 
 
@@ -25,6 +26,14 @@ from pre_commit.runner import Runner
 os.environ.pop('__PYVENV_LAUNCHER__', None)
 
 
+def _add_color_option(parser):
+    parser.add_argument(
+        '--color', default='auto', type=color.use_color,
+        metavar='{' + ','.join(color.COLOR_CHOICES) + '}',
+        help='Whether to use color in output.  Defaults to `%(default)s`.',
+    )
+
+
 def main(argv=None):
     argv = argv if argv is not None else sys.argv[1:]
     argv = [five.to_text(arg) for arg in argv]
@@ -44,6 +53,7 @@ def main(argv=None):
     install_parser = subparsers.add_parser(
         'install', help='Install the pre-commit script.',
     )
+    _add_color_option(install_parser)
     install_parser.add_argument(
         '-f', '--overwrite', action='store_true',
         help='Overwrite existing hooks / remove migration mode.',
@@ -63,25 +73,26 @@ def main(argv=None):
     uninstall_parser = subparsers.add_parser(
         'uninstall', help='Uninstall the pre-commit script.',
     )
+    _add_color_option(uninstall_parser)
     uninstall_parser.add_argument(
         '-t', '--hook-type', choices=('pre-commit', 'pre-push'),
         default='pre-commit',
     )
 
-    subparsers.add_parser('clean', help='Clean out pre-commit files.')
+    clean_parser = subparsers.add_parser(
+        'clean', help='Clean out pre-commit files.',
+    )
+    _add_color_option(clean_parser)
 
-    subparsers.add_parser(
+    autoupdate_parser = subparsers.add_parser(
         'autoupdate',
         help="Auto-update pre-commit config to the latest repos' versions.",
     )
+    _add_color_option(autoupdate_parser)
 
     run_parser = subparsers.add_parser('run', help='Run hooks.')
+    _add_color_option(run_parser)
     run_parser.add_argument('hook', nargs='?', help='A single hook-id to run')
-    run_parser.add_argument(
-        '--color', default='auto', type=color.use_color,
-        metavar='{' + ','.join(color.COLOR_CHOICES) + '}',
-        help='Whether to use color in output.  Defaults to `%(default)s`.',
-    )
     run_parser.add_argument(
         '--no-stash', default=False, action='store_true',
         help='Use this option to prevent auto stashing of unstaged files.',
@@ -140,6 +151,7 @@ def main(argv=None):
             parser.parse_args(['--help'])
 
     with error_handler():
+        add_logging_handler(args.color)
         runner = Runner.create()
 
         if args.command == 'install':
diff --git a/pre_commit/prefixed_command_runner.py b/pre_commit/prefixed_command_runner.py
index fc4a3198..6ae85099 100644
--- a/pre_commit/prefixed_command_runner.py
+++ b/pre_commit/prefixed_command_runner.py
@@ -1,6 +1,5 @@
 from __future__ import unicode_literals
 
-import os
 import os.path
 import subprocess
 
diff --git a/pre_commit/runner.py b/pre_commit/runner.py
index 35ab3427..c055b126 100644
--- a/pre_commit/runner.py
+++ b/pre_commit/runner.py
@@ -1,6 +1,5 @@
 from __future__ import unicode_literals
 
-import os
 import os.path
 
 from cached_property import cached_property
diff --git a/pre_commit/store.py b/pre_commit/store.py
index 9b2320e6..8e7e9ddf 100644
--- a/pre_commit/store.py
+++ b/pre_commit/store.py
@@ -3,7 +3,6 @@ from __future__ import unicode_literals
 import contextlib
 import io
 import logging
-import os
 import os.path
 import sqlite3
 import tempfile
diff --git a/pre_commit/util.py b/pre_commit/util.py
index a1435ae4..18394c3f 100644
--- a/pre_commit/util.py
+++ b/pre_commit/util.py
@@ -3,7 +3,6 @@ from __future__ import unicode_literals
 import contextlib
 import errno
 import functools
-import os
 import os.path
 import shutil
 import stat
diff --git a/testing/util.py b/testing/util.py
index a234adf6..10e84462 100644
--- a/testing/util.py
+++ b/testing/util.py
@@ -1,6 +1,5 @@
 from __future__ import unicode_literals
 
-import os
 import os.path
 import shutil
 
diff --git a/tests/commands/install_uninstall_test.py b/tests/commands/install_uninstall_test.py
index 331d857f..2d80d49f 100644
--- a/tests/commands/install_uninstall_test.py
+++ b/tests/commands/install_uninstall_test.py
@@ -2,7 +2,6 @@ from __future__ import absolute_import
 from __future__ import unicode_literals
 
 import io
-import os
 import os.path
 import re
 import shutil
diff --git a/tests/commands/run_test.py b/tests/commands/run_test.py
index 0618faf0..d0948378 100644
--- a/tests/commands/run_test.py
+++ b/tests/commands/run_test.py
@@ -2,7 +2,6 @@
 from __future__ import unicode_literals
 
 import io
-import os
 import os.path
 import subprocess
 import sys
diff --git a/tests/conftest.py b/tests/conftest.py
index b8227230..ca629e7f 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -4,7 +4,6 @@ from __future__ import unicode_literals
 import functools
 import io
 import logging
-import os
 import os.path
 
 import mock
diff --git a/tests/repository_test.py b/tests/repository_test.py
index 8fe2206b..79400ae1 100644
--- a/tests/repository_test.py
+++ b/tests/repository_test.py
@@ -3,7 +3,6 @@ from __future__ import unicode_literals
 
 import io
 import logging
-import os
 import os.path
 import re
 import shutil
diff --git a/tests/runner_test.py b/tests/runner_test.py
index 782e8d53..29bbee3e 100644
--- a/tests/runner_test.py
+++ b/tests/runner_test.py
@@ -1,7 +1,6 @@
 from __future__ import absolute_import
 from __future__ import unicode_literals
 
-import os
 import os.path
 
 import pre_commit.constants as C
diff --git a/tests/store_test.py b/tests/store_test.py
index 21aceb64..950693cf 100644
--- a/tests/store_test.py
+++ b/tests/store_test.py
@@ -2,7 +2,6 @@ from __future__ import absolute_import
 from __future__ import unicode_literals
 
 import io
-import os
 import os.path
 import sqlite3
 
diff --git a/tests/util_test.py b/tests/util_test.py
index 7fa25bcd..e9c7500a 100644
--- a/tests/util_test.py
+++ b/tests/util_test.py
@@ -1,6 +1,5 @@
 from __future__ import unicode_literals
 
-import os
 import os.path
 import random