Repository: pre-commit/pre-commit (python)

Issue:
.pre-commit directory is not cleaned up
I noticed at one point that my ~/.pre-commit directory was 3G in size, which seems pretty large.

I asked around and @struys said:

> jtwang: we don't do garbage collection
> so when you get a new version of hooks, the old one stays there
> jtwang: you can also use `pre-commit clean` to remove the files
> rm'ing the directory directly isn't a great idea
> jtwang: mind filing a ticket on pre-commit - https://github.com/pre-commit/pre-commit
> we should add some form of GC based on the last time you used a hook repo


Pull request description:
pre-commit gc
Resolves #283

Patch:
diff --git a/pre_commit/commands/gc.py b/pre_commit/commands/gc.py
new file mode 100644
index 0000000..9722643
--- /dev/null
+++ b/pre_commit/commands/gc.py
@@ -0,0 +1,83 @@
+from __future__ import absolute_import
+from __future__ import unicode_literals
+
+import os.path
+
+import pre_commit.constants as C
+from pre_commit import output
+from pre_commit.clientlib import InvalidConfigError
+from pre_commit.clientlib import InvalidManifestError
+from pre_commit.clientlib import is_local_repo
+from pre_commit.clientlib import is_meta_repo
+from pre_commit.clientlib import load_config
+from pre_commit.clientlib import load_manifest
+
+
+def _mark_used_repos(store, all_repos, unused_repos, repo):
+    if is_meta_repo(repo):
+        return
+    elif is_local_repo(repo):
+        for hook in repo['hooks']:
+            deps = hook.get('additional_dependencies')
+            unused_repos.discard((
+                store.db_repo_name(repo['repo'], deps), C.LOCAL_REPO_VERSION,
+            ))
+    else:
+        key = (repo['repo'], repo['rev'])
+        path = all_repos.get(key)
+        # can't inspect manifest if it isn't cloned
+        if path is None:
+            return
+
+        try:
+            manifest = load_manifest(os.path.join(path, C.MANIFEST_FILE))
+        except InvalidManifestError:
+            return
+        else:
+            unused_repos.discard(key)
+            by_id = {hook['id']: hook for hook in manifest}
+
+        for hook in repo['hooks']:
+            if hook['id'] not in by_id:
+                continue
+
+            deps = hook.get(
+                'additional_dependencies',
+                by_id[hook['id']]['additional_dependencies'],
+            )
+            unused_repos.discard((
+                store.db_repo_name(repo['repo'], deps), repo['rev'],
+            ))
+
+
+def _gc_repos(store):
+    configs = store.select_all_configs()
+    repos = store.select_all_repos()
+
+    # delete config paths which do not exist
+    dead_configs = [p for p in configs if not os.path.exists(p)]
+    live_configs = [p for p in configs if os.path.exists(p)]
+
+    all_repos = {(repo, ref): path for repo, ref, path in repos}
+    unused_repos = set(all_repos)
+    for config_path in live_configs:
+        try:
+            config = load_config(config_path)
+        except InvalidConfigError:
+            dead_configs.append(config_path)
+            continue
+        else:
+            for repo in config['repos']:
+                _mark_used_repos(store, all_repos, unused_repos, repo)
+
+    store.delete_configs(dead_configs)
+    for db_repo_name, ref in unused_repos:
+        store.delete_repo(db_repo_name, ref, all_repos[(db_repo_name, ref)])
+    return len(unused_repos)
+
+
+def gc(store):
+    with store.exclusive_lock():
+        repos_removed = _gc_repos(store)
+    output.write_line('{} repo(s) removed.'.format(repos_removed))
+    return 0
diff --git a/pre_commit/error_handler.py b/pre_commit/error_handler.py
index 7206780..3b0a4c5 100644
--- a/pre_commit/error_handler.py
+++ b/pre_commit/error_handler.py
@@ -32,7 +32,6 @@ def _log_and_exit(msg, exc, formatted):
     ))
     output.write(error_msg)
     store = Store()
-    store.require_created()
     log_path = os.path.join(store.directory, 'pre-commit.log')
     output.write_line('Check the log at {}'.format(log_path))
     with open(log_path, 'wb') as log:
diff --git a/pre_commit/main.py b/pre_commit/main.py
index 6a9c120..be0fa7f 100644
--- a/pre_commit/main.py
+++ b/pre_commit/main.py
@@ -11,6 +11,7 @@ from pre_commit import five
 from pre_commit import git
 from pre_commit.commands.autoupdate import autoupdate
 from pre_commit.commands.clean import clean
+from pre_commit.commands.gc import gc
 from pre_commit.commands.install_uninstall import install
 from pre_commit.commands.install_uninstall import install_hooks
 from pre_commit.commands.install_uninstall import uninstall
@@ -176,6 +177,11 @@ def main(argv=None):
     )
     _add_color_option(clean_parser)
     _add_config_option(clean_parser)
+
+    gc_parser = subparsers.add_parser('gc', help='Clean unused cached repos.')
+    _add_color_option(gc_parser)
+    _add_config_option(gc_parser)
+
     autoupdate_parser = subparsers.add_parser(
         'autoupdate',
         help="Auto-update pre-commit config to the latest repos' versions.",
@@ -251,9 +257,11 @@ def main(argv=None):
     with error_handler(), logging_handler(args.color):
         _adjust_args_and_chdir(args)
 
-        store = Store()
         git.check_for_cygwin_mismatch()
 
+        store = Store()
+        store.mark_config_used(args.config)
+
         if args.command == 'install':
             return install(
                 args.config, store,
@@ -267,6 +275,8 @@ def main(argv=None):
             return uninstall(hook_type=args.hook_type)
         elif args.command == 'clean':
             return clean(store)
+        elif args.command == 'gc':
+            return gc(store)
         elif args.command == 'autoupdate':
             if args.tags_only:
                 logger.warning('--tags-only is the default')
diff --git a/pre_commit/store.py b/pre_commit/store.py
index 3200a56..8301eca 100644
--- a/pre_commit/store.py
+++ b/pre_commit/store.py
@@ -13,6 +13,7 @@ from pre_commit import git
 from pre_commit.util import clean_path_on_failure
 from pre_commit.util import cmd_output
 from pre_commit.util import resource_text
+from pre_commit.util import rmtree
 
 
 logger = logging.getLogger('pre_commit')
@@ -33,10 +34,43 @@ def _get_default_directory():
 
 class Store(object):
     get_default_directory = staticmethod(_get_default_directory)
-    __created = False
 
     def __init__(self, directory=None):
         self.directory = directory or Store.get_default_directory()
+        self.db_path = os.path.join(self.directory, 'db.db')
+
+        if not os.path.exists(self.directory):
+            os.makedirs(self.directory)
+            with io.open(os.path.join(self.directory, 'README'), 'w') as f:
+                f.write(
+                    'This directory is maintained by the pre-commit project.\n'
+                    'Learn more: https://github.com/pre-commit/pre-commit\n',
+                )
+
+        if os.path.exists(self.db_path):
+            return
+        with self.exclusive_lock():
+            # Another process may have already completed this work
+            if os.path.exists(self.db_path):  # pragma: no cover (race)
+                return
+            # To avoid a race where someone ^Cs between db creation and
+            # execution of the CREATE TABLE statement
+            fd, tmpfile = tempfile.mkstemp(dir=self.directory)
+            # We'll be managing this file ourselves
+            os.close(fd)
+            with self.connect(db_path=tmpfile) as db:
+                db.executescript(
+                    'CREATE TABLE repos ('
+                    '    repo TEXT NOT NULL,'
+                    '    ref TEXT NOT NULL,'
+                    '    path TEXT NOT NULL,'
+                    '    PRIMARY KEY (repo, ref)'
+                    ');',
+                )
+                self._create_config_table_if_not_exists(db)
+
+            # Atomic file move
+            os.rename(tmpfile, self.db_path)
 
     @contextlib.contextmanager
     def exclusive_lock(self):
@@ -46,62 +80,30 @@ class Store(object):
         with file_lock.lock(os.path.join(self.directory, '.lock'), blocked_cb):
             yield
 
-    def _write_readme(self):
-        with io.open(os.path.join(self.directory, 'README'), 'w') as readme:
-            readme.write(
-                'This directory is maintained by the pre-commit project.\n'
-                'Learn more: https://github.com/pre-commit/pre-commit\n',
-            )
-
-    def _write_sqlite_db(self):
-        # To avoid a race where someone ^Cs between db creation and execution
-        # of the CREATE TABLE statement
-        fd, tmpfile = tempfile.mkstemp(dir=self.directory)
-        # We'll be managing this file ourselves
-        os.close(fd)
+    @contextlib.contextmanager
+    def connect(self, db_path=None):
+        db_path = db_path or self.db_path
         # sqlite doesn't close its fd with its contextmanager >.<
         # contextlib.closing fixes this.
         # See: https://stackoverflow.com/a/28032829/812183
-        with contextlib.closing(sqlite3.connect(tmpfile)) as db:
-            db.executescript(
-                'CREATE TABLE repos ('
-                '    repo TEXT NOT NULL,'
-                '    ref TEXT NOT NULL,'
-                '    path TEXT NOT NULL,'
-                '    PRIMARY KEY (repo, ref)'
-                ');',
-            )
+        with contextlib.closing(sqlite3.connect(db_path)) as db:
+            # this creates a transaction
+            with db:
+                yield db
 
-        # Atomic file move
-        os.rename(tmpfile, self.db_path)
-
-    def _create(self):
-        if not os.path.exists(self.directory):
-            os.makedirs(self.directory)
-            self._write_readme()
-
-        if os.path.exists(self.db_path):
-            return
-        with self.exclusive_lock():
-            # Another process may have already completed this work
-            if os.path.exists(self.db_path):  # pragma: no cover (race)
-                return
-            self._write_sqlite_db()
-
-    def require_created(self):
-        """Require the pre-commit file store to be created."""
-        if not self.__created:
-            self._create()
-            self.__created = True
+    @classmethod
+    def db_repo_name(cls, repo, deps):
+        if deps:
+            return '{}:{}'.format(repo, ','.join(sorted(deps)))
+        else:
+            return repo
 
     def _new_repo(self, repo, ref, deps, make_strategy):
-        self.require_created()
-        if deps:
-            repo = '{}:{}'.format(repo, ','.join(sorted(deps)))
+        repo = self.db_repo_name(repo, deps)
 
         def _get_result():
             # Check if we already exist
-            with sqlite3.connect(self.db_path) as db:
+            with self.connect() as db:
                 result = db.execute(
                     'SELECT path FROM repos WHERE repo = ? AND ref = ?',
                     (repo, ref),
@@ -125,7 +127,7 @@ class Store(object):
                 make_strategy(directory)
 
             # Update our db with the created repo
-            with sqlite3.connect(self.db_path) as db:
+            with self.connect() as db:
                 db.execute(
                     'INSERT INTO repos (repo, ref, path) VALUES (?, ?, ?)',
                     [repo, ref, directory],
@@ -175,6 +177,43 @@ class Store(object):
             'local', C.LOCAL_REPO_VERSION, deps, make_local_strategy,
         )
 
-    @property
-    def db_path(self):
-        return os.path.join(self.directory, 'db.db')
+    def _create_config_table_if_not_exists(self, db):
+        db.executescript(
+            'CREATE TABLE IF NOT EXISTS configs ('
+            '   path TEXT NOT NULL,'
+            '   PRIMARY KEY (path)'
+            ');',
+        )
+
+    def mark_config_used(self, path):
+        path = os.path.realpath(path)
+        # don't insert config files that do not exist
+        if not os.path.exists(path):
+            return
+        with self.connect() as db:
+            # TODO: eventually remove this and only create in _create
+            self._create_config_table_if_not_exists(db)
+            db.execute('INSERT OR IGNORE INTO configs VALUES (?)', (path,))
+
+    def select_all_configs(self):
+        with self.connect() as db:
+            self._create_config_table_if_not_exists(db)
+            rows = db.execute('SELECT path FROM configs').fetchall()
+            return [path for path, in rows]
+
+    def delete_configs(self, configs):
+        with self.connect() as db:
+            rows = [(path,) for path in configs]
+            db.executemany('DELETE FROM configs WHERE path = ?', rows)
+
+    def select_all_repos(self):
+        with self.connect() as db:
+            return db.execute('SELECT repo, ref, path from repos').fetchall()
+
+    def delete_repo(self, db_repo_name, ref, path):
+        with self.connect() as db:
+            db.execute(
+                'DELETE FROM repos WHERE repo = ? and ref = ?',
+                (db_repo_name, ref),
+            )
+        rmtree(path)


Test patch:
diff --git a/testing/fixtures.py b/testing/fixtures.py
index b0606ee..70d0750 100644
--- a/testing/fixtures.py
+++ b/testing/fixtures.py
@@ -82,7 +82,7 @@ def modify_config(path='.', commit=True):
         git_commit(msg=modify_config.__name__, cwd=path)
 
 
-def config_with_local_hooks():
+def sample_local_config():
     return {
         'repo': 'local',
         'hooks': [{
@@ -94,6 +94,10 @@ def config_with_local_hooks():
     }
 
 
+def sample_meta_config():
+    return {'repo': 'meta', 'hooks': [{'id': 'check-useless-excludes'}]}
+
+
 def make_config_from_repo(repo_path, rev=None, hooks=None, check=True):
     manifest = load_manifest(os.path.join(repo_path, C.MANIFEST_FILE))
     config = {
diff --git a/tests/clientlib_test.py b/tests/clientlib_test.py
index c9908a2..dbae4aa 100644
--- a/tests/clientlib_test.py
+++ b/tests/clientlib_test.py
@@ -11,7 +11,7 @@ from pre_commit.clientlib import MANIFEST_SCHEMA
 from pre_commit.clientlib import MigrateShaToRev
 from pre_commit.clientlib import validate_config_main
 from pre_commit.clientlib import validate_manifest_main
-from testing.fixtures import config_with_local_hooks
+from testing.fixtures import sample_local_config
 from testing.util import get_resource_path
 
 
@@ -94,7 +94,7 @@ def test_config_valid(config_obj, expected):
 
 
 def test_local_hooks_with_rev_fails():
-    config_obj = {'repos': [config_with_local_hooks()]}
+    config_obj = {'repos': [sample_local_config()]}
     config_obj['repos'][0]['rev'] = 'foo'
     with pytest.raises(cfgv.ValidationError):
         cfgv.validate(config_obj, CONFIG_SCHEMA)
diff --git a/tests/commands/autoupdate_test.py b/tests/commands/autoupdate_test.py
index 0892617..8daf986 100644
--- a/tests/commands/autoupdate_test.py
+++ b/tests/commands/autoupdate_test.py
@@ -15,9 +15,9 @@ from pre_commit.commands.autoupdate import RepositoryCannotBeUpdatedError
 from pre_commit.util import cmd_output
 from testing.auto_namedtuple import auto_namedtuple
 from testing.fixtures import add_config_to_repo
-from testing.fixtures import config_with_local_hooks
 from testing.fixtures import make_config_from_repo
 from testing.fixtures import make_repo
+from testing.fixtures import sample_local_config
 from testing.fixtures import write_config
 from testing.util import get_resource_path
 from testing.util import git_commit
@@ -125,7 +125,7 @@ def test_autoupdate_out_of_date_repo_with_correct_repo_name(
     stale_config = make_config_from_repo(
         out_of_date_repo.path, rev=out_of_date_repo.original_rev, check=False,
     )
-    local_config = config_with_local_hooks()
+    local_config = sample_local_config()
     config = {'repos': [stale_config, local_config]}
     # Write out the config
     write_config('.', config)
@@ -139,7 +139,7 @@ def test_autoupdate_out_of_date_repo_with_correct_repo_name(
     assert ret == 0
     assert before != after
     assert out_of_date_repo.head_rev in after
-    assert local_config['repo'] in after
+    assert 'local' in after
 
 
 def test_autoupdate_out_of_date_repo_with_wrong_repo_name(
@@ -316,7 +316,7 @@ def test_autoupdate_hook_disappearing_repo(
 
 
 def test_autoupdate_local_hooks(in_git_dir, store):
-    config = config_with_local_hooks()
+    config = sample_local_config()
     add_config_to_repo('.', config)
     assert autoupdate(C.CONFIG_FILE, store, tags_only=False) == 0
     new_config_writen = load_config(C.CONFIG_FILE)
@@ -330,7 +330,7 @@ def test_autoupdate_local_hooks_with_out_of_date_repo(
     stale_config = make_config_from_repo(
         out_of_date_repo.path, rev=out_of_date_repo.original_rev, check=False,
     )
-    local_config = config_with_local_hooks()
+    local_config = sample_local_config()
     config = {'repos': [local_config, stale_config]}
     write_config('.', config)
     assert autoupdate(C.CONFIG_FILE, store, tags_only=False) == 0
diff --git a/tests/commands/clean_test.py b/tests/commands/clean_test.py
index 3bfa46a..dc33ebb 100644
--- a/tests/commands/clean_test.py
+++ b/tests/commands/clean_test.py
@@ -21,7 +21,6 @@ def fake_old_dir(tempdir_factory):
 
 
 def test_clean(store, fake_old_dir):
-    store.require_created()
     assert os.path.exists(fake_old_dir)
     assert os.path.exists(store.directory)
     clean(store)
@@ -30,6 +29,7 @@ def test_clean(store, fake_old_dir):
 
 
 def test_clean_idempotent(store):
+    clean(store)
     assert not os.path.exists(store.directory)
     clean(store)
     assert not os.path.exists(store.directory)
diff --git a/tests/commands/gc_test.py b/tests/commands/gc_test.py
new file mode 100644
index 0000000..2f958f6
--- /dev/null
+++ b/tests/commands/gc_test.py
@@ -0,0 +1,158 @@
+import os
+
+import pre_commit.constants as C
+from pre_commit import git
+from pre_commit.commands.autoupdate import autoupdate
+from pre_commit.commands.gc import gc
+from pre_commit.repository import all_hooks
+from testing.fixtures import make_config_from_repo
+from testing.fixtures import make_repo
+from testing.fixtures import modify_config
+from testing.fixtures import sample_local_config
+from testing.fixtures import sample_meta_config
+from testing.fixtures import write_config
+from testing.util import git_commit
+
+
+def _repo_count(store):
+    return len(store.select_all_repos())
+
+
+def _config_count(store):
+    return len(store.select_all_configs())
+
+
+def _remove_config_assert_cleared(store, cap_out):
+    os.remove(C.CONFIG_FILE)
+    assert not gc(store)
+    assert _config_count(store) == 0
+    assert _repo_count(store) == 0
+    assert cap_out.get().splitlines()[-1] == '1 repo(s) removed.'
+
+
+def test_gc(tempdir_factory, store, in_git_dir, cap_out):
+    path = make_repo(tempdir_factory, 'script_hooks_repo')
+    old_rev = git.head_rev(path)
+    git_commit(cwd=path)
+
+    write_config('.', make_config_from_repo(path, rev=old_rev))
+    store.mark_config_used(C.CONFIG_FILE)
+
+    # update will clone both the old and new repo, making the old one gc-able
+    assert not autoupdate(C.CONFIG_FILE, store, tags_only=False)
+
+    assert _config_count(store) == 1
+    assert _repo_count(store) == 2
+    assert not gc(store)
+    assert _config_count(store) == 1
+    assert _repo_count(store) == 1
+    assert cap_out.get().splitlines()[-1] == '1 repo(s) removed.'
+
+    _remove_config_assert_cleared(store, cap_out)
+
+
+def test_gc_repo_not_cloned(tempdir_factory, store, in_git_dir, cap_out):
+    path = make_repo(tempdir_factory, 'script_hooks_repo')
+    write_config('.', make_config_from_repo(path))
+    store.mark_config_used(C.CONFIG_FILE)
+
+    assert _config_count(store) == 1
+    assert _repo_count(store) == 0
+    assert not gc(store)
+    assert _config_count(store) == 1
+    assert _repo_count(store) == 0
+    assert cap_out.get().splitlines()[-1] == '0 repo(s) removed.'
+
+
+def test_gc_meta_repo_does_not_crash(store, in_git_dir, cap_out):
+    write_config('.', sample_meta_config())
+    store.mark_config_used(C.CONFIG_FILE)
+    assert not gc(store)
+    assert cap_out.get().splitlines()[-1] == '0 repo(s) removed.'
+
+
+def test_gc_local_repo_does_not_crash(store, in_git_dir, cap_out):
+    write_config('.', sample_local_config())
+    store.mark_config_used(C.CONFIG_FILE)
+    assert not gc(store)
+    assert cap_out.get().splitlines()[-1] == '0 repo(s) removed.'
+
+
+def test_gc_unused_local_repo_with_env(store, in_git_dir, cap_out):
+    config = {
+        'repo': 'local',
+        'hooks': [{
+            'id': 'flake8', 'name': 'flake8', 'entry': 'flake8',
+            # a `language: python` local hook will create an environment
+            'types': ['python'], 'language': 'python',
+        }],
+    }
+    write_config('.', config)
+    store.mark_config_used(C.CONFIG_FILE)
+
+    # this causes the repositories to be created
+    all_hooks({'repos': [config]}, store)
+
+    assert _config_count(store) == 1
+    assert _repo_count(store) == 1
+    assert not gc(store)
+    assert _config_count(store) == 1
+    assert _repo_count(store) == 1
+    assert cap_out.get().splitlines()[-1] == '0 repo(s) removed.'
+
+    _remove_config_assert_cleared(store, cap_out)
+
+
+def test_gc_config_with_missing_hook(
+        tempdir_factory, store, in_git_dir, cap_out,
+):
+    path = make_repo(tempdir_factory, 'script_hooks_repo')
+    write_config('.', make_config_from_repo(path))
+    store.mark_config_used(C.CONFIG_FILE)
+
+    with modify_config() as config:
+        # just to trigger a clone
+        all_hooks(config, store)
+        # add a hook which does not exist, make sure we don't crash
+        config['repos'][0]['hooks'].append({'id': 'does-not-exist'})
+
+    assert _config_count(store) == 1
+    assert _repo_count(store) == 1
+    assert not gc(store)
+    assert _config_count(store) == 1
+    assert _repo_count(store) == 1
+    assert cap_out.get().splitlines()[-1] == '0 repo(s) removed.'
+
+    _remove_config_assert_cleared(store, cap_out)
+
+
+def test_gc_deletes_invalid_configs(store, in_git_dir, cap_out):
+    config = {'i am': 'invalid'}
+    write_config('.', config)
+    store.mark_config_used(C.CONFIG_FILE)
+
+    assert _config_count(store) == 1
+    assert not gc(store)
+    assert _config_count(store) == 0
+    assert cap_out.get().splitlines()[-1] == '0 repo(s) removed.'
+
+
+def test_invalid_manifest_gcd(tempdir_factory, store, in_git_dir, cap_out):
+    # clean up repos from old pre-commit versions
+    path = make_repo(tempdir_factory, 'script_hooks_repo')
+    write_config('.', make_config_from_repo(path))
+    store.mark_config_used(C.CONFIG_FILE)
+
+    # trigger a clone
+    assert not autoupdate(C.CONFIG_FILE, store, tags_only=False)
+
+    # we'll "break" the manifest to simulate an old version clone
+    (_, _, path), = store.select_all_repos()
+    os.remove(os.path.join(path, C.MANIFEST_FILE))
+
+    assert _config_count(store) == 1
+    assert _repo_count(store) == 1
+    assert not gc(store)
+    assert _config_count(store) == 1
+    assert _repo_count(store) == 0
+    assert cap_out.get().splitlines()[-1] == '1 repo(s) removed.'
diff --git a/tests/commands/run_test.py b/tests/commands/run_test.py
index 84ab1b2..2426068 100644
--- a/tests/commands/run_test.py
+++ b/tests/commands/run_test.py
@@ -22,6 +22,7 @@ from testing.fixtures import add_config_to_repo
 from testing.fixtures import make_consuming_repo
 from testing.fixtures import modify_config
 from testing.fixtures import read_config
+from testing.fixtures import sample_meta_config
 from testing.util import cmd_output_mocked_pre_commit_home
 from testing.util import cwd
 from testing.util import git_commit
@@ -656,11 +657,7 @@ def test_pcre_deprecation_warning(cap_out, store, repo_with_passing_hook):
 
 
 def test_meta_hook_passes(cap_out, store, repo_with_passing_hook):
-    config = {
-        'repo': 'meta',
-        'hooks': [{'id': 'check-useless-excludes'}],
-    }
-    add_config_to_repo(repo_with_passing_hook, config)
+    add_config_to_repo(repo_with_passing_hook, sample_meta_config())
 
     _test_run(
         cap_out,
diff --git a/tests/main_test.py b/tests/main_test.py
index c5db3da..e5573b8 100644
--- a/tests/main_test.py
+++ b/tests/main_test.py
@@ -65,8 +65,8 @@ def test_adjust_args_try_repo_repo_relative(in_git_dir):
 
 
 FNS = (
-    'autoupdate', 'clean', 'install', 'install_hooks', 'migrate_config', 'run',
-    'sample_config', 'uninstall',
+    'autoupdate', 'clean', 'gc', 'install', 'install_hooks', 'migrate_config',
+    'run', 'sample_config', 'uninstall',
 )
 CMDS = tuple(fn.replace('_', '-') for fn in FNS)
 
diff --git a/tests/store_test.py b/tests/store_test.py
index 8ef10a9..238343f 100644
--- a/tests/store_test.py
+++ b/tests/store_test.py
@@ -12,7 +12,6 @@ import six
 from pre_commit import git
 from pre_commit.store import _get_default_directory
 from pre_commit.store import Store
-from pre_commit.util import rmtree
 from testing.fixtures import git_dir
 from testing.util import cwd
 from testing.util import git_commit
@@ -48,9 +47,7 @@ def test_uses_environment_variable_when_present():
         assert ret == '/tmp/pre_commit_home'
 
 
-def test_store_require_created(store):
-    assert not os.path.exists(store.directory)
-    store.require_created()
+def test_store_init(store):
     # Should create the store directory
     assert os.path.exists(store.directory)
     # Should create a README file indicating what the directory is about
@@ -63,30 +60,6 @@ def test_store_require_created(store):
             assert text_line in readme_contents
 
 
-def test_store_require_created_does_not_create_twice(store):
-    assert not os.path.exists(store.directory)
-    store.require_created()
-    # We intentionally delete the directory here so we can figure out if it
-    # calls it again.
-    rmtree(store.directory)
-    assert not os.path.exists(store.directory)
-    # Call require_created, this should not trigger a call to create
-    store.require_created()
-    assert not os.path.exists(store.directory)
-
-
-def test_does_not_recreate_if_directory_already_exists(store):
-    assert not os.path.exists(store.directory)
-    # We manually create the directory.
-    # Note: we're intentionally leaving out the README file.  This is so we can
-    # know that `Store` didn't call create
-    os.mkdir(store.directory)
-    open(store.db_path, 'a').close()
-    # Call require_created, this should not call create
-    store.require_created()
-    assert not os.path.exists(os.path.join(store.directory, 'README'))
-
-
 def test_clone(store, tempdir_factory, log_info_mock):
     path = git_dir(tempdir_factory)
     with cwd(path):
@@ -110,34 +83,25 @@ def test_clone(store, tempdir_factory, log_info_mock):
     assert git.head_rev(ret) == rev
 
     # Assert there's an entry in the sqlite db for this
-    with sqlite3.connect(store.db_path) as db:
-        path, = db.execute(
-            'SELECT path from repos WHERE repo = ? and ref = ?',
-            (path, rev),
-        ).fetchone()
-        assert path == ret
+    assert store.select_all_repos() == [(path, rev, ret)]
 
 
 def test_clone_cleans_up_on_checkout_failure(store):
-    try:
+    with pytest.raises(Exception) as excinfo:
         # This raises an exception because you can't clone something that
         # doesn't exist!
         store.clone('/i_dont_exist_lol', 'fake_rev')
-    except Exception as e:
-        assert '/i_dont_exist_lol' in six.text_type(e)
+    assert '/i_dont_exist_lol' in six.text_type(excinfo.value)
 
-    things_starting_with_repo = [
-        thing for thing in os.listdir(store.directory)
-        if thing.startswith('repo')
+    repo_dirs = [
+        d for d in os.listdir(store.directory) if d.startswith('repo')
     ]
-    assert things_starting_with_repo == []
+    assert repo_dirs == []
 
 
 def test_clone_when_repo_already_exists(store):
     # Create an entry in the sqlite db that makes it look like the repo has
     # been cloned.
-    store.require_created()
-
     with sqlite3.connect(store.db_path) as db:
         db.execute(
             'INSERT INTO repos (repo, ref, path) '
@@ -147,14 +111,24 @@ def test_clone_when_repo_already_exists(store):
     assert store.clone('fake_repo', 'fake_ref') == 'fake_path'
 
 
-def test_require_created_when_directory_exists_but_not_db(store):
+def test_create_when_directory_exists_but_not_db(store):
     # In versions <= 0.3.5, there was no sqlite db causing a need for
     # backward compatibility
-    os.makedirs(store.directory)
-    store.require_created()
+    os.remove(store.db_path)
+    store = Store(store.directory)
     assert os.path.exists(store.db_path)
 
 
+def test_create_when_store_already_exists(store):
+    # an assertion that this is idempotent and does not crash
+    Store(store.directory)
+
+
+def test_db_repo_name(store):
+    assert store.db_repo_name('repo', ()) == 'repo'
+    assert store.db_repo_name('repo', ('b', 'a', 'c')) == 'repo:a,b,c'
+
+
 def test_local_resources_reflects_reality():
     on_disk = {
         res[len('empty_template_'):]
@@ -162,3 +136,35 @@ def test_local_resources_reflects_reality():
         if res.startswith('empty_template_')
     }
     assert on_disk == set(Store.LOCAL_RESOURCES)
+
+
+def test_mark_config_as_used(store, tmpdir):
+    with tmpdir.as_cwd():
+        f = tmpdir.join('f').ensure()
+        store.mark_config_used('f')
+        assert store.select_all_configs() == [f.strpath]
+
+
+def test_mark_config_as_used_idempotent(store, tmpdir):
+    test_mark_config_as_used(store, tmpdir)
+    test_mark_config_as_used(store, tmpdir)
+
+
+def test_mark_config_as_used_does_not_exist(store):
+    store.mark_config_used('f')
+    assert store.select_all_configs() == []
+
+
+def _simulate_pre_1_14_0(store):
+    with store.connect() as db:
+        db.executescript('DROP TABLE configs')
+
+
+def test_select_all_configs_roll_forward(store):
+    _simulate_pre_1_14_0(store)
+    assert store.select_all_configs() == []
+
+
+def test_mark_config_as_used_roll_forward(store, tmpdir):
+    _simulate_pre_1_14_0(store)
+    test_mark_config_as_used(store, tmpdir)