Merging upstream version 2.7.1.

Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>

13 files changed, 111 insertions, 80 deletions

diff --git a/pre_commit/clientlib.py b/pre_commit/clientlib.py
index 56ec0dd..8dfa947 100644
--- a/pre_commit/clientlib.py
+++ b/pre_commit/clientlib.py
@@ -12,8 +12,10 @@ import cfgv
 from identify.identify import ALL_TAGS
 
 import pre_commit.constants as C
+from pre_commit.color import add_color_option
 from pre_commit.error_handler import FatalError
 from pre_commit.languages.all import all_languages
+from pre_commit.logging_handler import logging_handler
 from pre_commit.util import parse_version
 from pre_commit.util import yaml_load
 
@@ -43,6 +45,7 @@ def _make_argparser(filenames_help: str) -> argparse.ArgumentParser:
     parser = argparse.ArgumentParser()
     parser.add_argument('filenames', nargs='*', help=filenames_help)
     parser.add_argument('-V', '--version', action='version', version=C.VERSION)
+    add_color_option(parser)
     return parser
 
 
@@ -92,14 +95,16 @@ load_manifest = functools.partial(
 def validate_manifest_main(argv: Optional[Sequence[str]] = None) -> int:
     parser = _make_argparser('Manifest filenames.')
     args = parser.parse_args(argv)
-    ret = 0
-    for filename in args.filenames:
-        try:
-            load_manifest(filename)
-        except InvalidManifestError as e:
-            print(e)
-            ret = 1
-    return ret
+
+    with logging_handler(args.color):
+        ret = 0
+        for filename in args.filenames:
+            try:
+                load_manifest(filename)
+            except InvalidManifestError as e:
+                print(e)
+                ret = 1
+        return ret
 
 
 LOCAL = 'local'
@@ -290,7 +295,11 @@ class InvalidConfigError(FatalError):
 def ordered_load_normalize_legacy_config(contents: str) -> Dict[str, Any]:
     data = yaml_load(contents)
     if isinstance(data, list):
-        # TODO: Once happy, issue a deprecation warning and instructions
+        logger.warning(
+            'normalizing pre-commit configuration to a top-level map.  '
+            'support for top level list will be removed in a future version.  '
+            'run: `pre-commit migrate-config` to automatically fix this.',
+        )
         return {'repos': data}
     else:
         return data
@@ -307,11 +316,13 @@ load_config = functools.partial(
 def validate_config_main(argv: Optional[Sequence[str]] = None) -> int:
     parser = _make_argparser('Config filenames.')
     args = parser.parse_args(argv)
-    ret = 0
-    for filename in args.filenames:
-        try:
-            load_config(filename)
-        except InvalidConfigError as e:
-            print(e)
-            ret = 1
-    return ret
+
+    with logging_handler(args.color):
+        ret = 0
+        for filename in args.filenames:
+            try:
+                load_config(filename)
+            except InvalidConfigError as e:
+                print(e)
+                ret = 1
+        return ret
diff --git a/pre_commit/color.py b/pre_commit/color.py
index eb906b7..4ddfdf5 100644
--- a/pre_commit/color.py
+++ b/pre_commit/color.py
@@ -1,3 +1,4 @@
+import argparse
 import os
 import sys
 
@@ -95,3 +96,12 @@ def use_color(setting: str) -> bool:
             os.getenv('TERM') != 'dumb'
         )
     )
+
+
+def add_color_option(parser: argparse.ArgumentParser) -> None:
+    parser.add_argument(
+        '--color', default=os.environ.get('PRE_COMMIT_COLOR', 'auto'),
+        type=use_color,
+        metavar='{' + ','.join(COLOR_CHOICES) + '}',
+        help='Whether to use color in output.  Defaults to `%(default)s`.',
+    )
diff --git a/pre_commit/commands/init_templatedir.py b/pre_commit/commands/init_templatedir.py
index f676fb1..5f17d9c 100644
--- a/pre_commit/commands/init_templatedir.py
+++ b/pre_commit/commands/init_templatedir.py
@@ -15,10 +15,15 @@ def init_templatedir(
         store: Store,
         directory: str,
         hook_types: Sequence[str],
+        skip_on_missing_config: bool = True,
 ) -> int:
     install(
-        config_file, store, hook_types=hook_types,
-        overwrite=True, skip_on_missing_config=True, git_dir=directory,
+        config_file,
+        store,
+        hook_types=hook_types,
+        overwrite=True,
+        skip_on_missing_config=skip_on_missing_config,
+        git_dir=directory,
     )
     try:
         _, out, _ = cmd_output('git', 'config', 'init.templateDir')
diff --git a/pre_commit/commands/install_uninstall.py b/pre_commit/commands/install_uninstall.py
index c8b7633..85fa53c 100644
--- a/pre_commit/commands/install_uninstall.py
+++ b/pre_commit/commands/install_uninstall.py
@@ -165,7 +165,7 @@ def _uninstall_hook_script(hook_type: str) -> None:
     output.write_line(f'{hook_type} uninstalled')
 
     if os.path.exists(legacy_path):
-        os.rename(legacy_path, hook_path)
+        os.replace(legacy_path, hook_path)
         output.write_line(f'Restored previous hooks to {hook_path}')
 
 
diff --git a/pre_commit/commands/run.py b/pre_commit/commands/run.py
index 567b7cd..1f28c8c 100644
--- a/pre_commit/commands/run.py
+++ b/pre_commit/commands/run.py
@@ -134,9 +134,10 @@ def _run_single_hook(
         hook: Hook,
         skips: Set[str],
         cols: int,
+        diff_before: bytes,
         verbose: bool,
         use_color: bool,
-) -> bool:
+) -> Tuple[bool, bytes]:
     filenames = classifier.filenames_for_hook(hook)
 
     if hook.id in skips or hook.alias in skips:
@@ -151,6 +152,7 @@ def _run_single_hook(
         )
         duration = None
         retcode = 0
+        diff_after = diff_before
         files_modified = False
         out = b''
     elif not filenames and not hook.always_run:
@@ -166,21 +168,20 @@ def _run_single_hook(
         )
         duration = None
         retcode = 0
+        diff_after = diff_before
         files_modified = False
         out = b''
     else:
         # print hook and dots first in case the hook takes a while to run
         output.write(_start_msg(start=hook.name, end_len=6, cols=cols))
 
-        diff_cmd = ('git', 'diff', '--no-ext-diff')
-        diff_before = cmd_output_b(*diff_cmd, retcode=None)
         if not hook.pass_filenames:
             filenames = ()
         time_before = time.time()
         language = languages[hook.language]
         retcode, out = language.run_hook(hook, filenames, use_color)
         duration = round(time.time() - time_before, 2) or 0
-        diff_after = cmd_output_b(*diff_cmd, retcode=None)
+        diff_after = _get_diff()
 
         # if the hook makes changes, fail the commit
         files_modified = diff_before != diff_after
@@ -212,7 +213,7 @@ def _run_single_hook(
             output.write_line_b(out.strip(), logfile_name=hook.log_file)
             output.write_line()
 
-    return files_modified or bool(retcode)
+    return files_modified or bool(retcode), diff_after
 
 
 def _compute_cols(hooks: Sequence[Hook]) -> int:
@@ -248,6 +249,11 @@ def _all_filenames(args: argparse.Namespace) -> Collection[str]:
         return git.get_staged_files()
 
 
+def _get_diff() -> bytes:
+    _, out, _ = cmd_output_b('git', 'diff', '--no-ext-diff', retcode=None)
+    return out
+
+
 def _run_hooks(
         config: Dict[str, Any],
         hooks: Sequence[Hook],
@@ -261,14 +267,16 @@ def _run_hooks(
         _all_filenames(args), config['files'], config['exclude'],
     )
     retval = 0
+    prior_diff = _get_diff()
     for hook in hooks:
-        retval |= _run_single_hook(
-            classifier, hook, skips, cols,
+        current_retval, prior_diff = _run_single_hook(
+            classifier, hook, skips, cols, prior_diff,
             verbose=args.verbose, use_color=args.color,
         )
+        retval |= current_retval
         if retval and config['fail_fast']:
             break
-    if retval and args.show_diff_on_failure and git.has_diff():
+    if retval and args.show_diff_on_failure and prior_diff:
         if args.all_files:
             output.write_line(
                 'pre-commit hook(s) made changes.\n'
diff --git a/pre_commit/error_handler.py b/pre_commit/error_handler.py
index b2321ae..13d78cb 100644
--- a/pre_commit/error_handler.py
+++ b/pre_commit/error_handler.py
@@ -18,10 +18,17 @@ class FatalError(RuntimeError):
 def _log_and_exit(msg: str, exc: BaseException, formatted: str) -> None:
     error_msg = f'{msg}: {type(exc).__name__}: '.encode() + force_bytes(exc)
     output.write_line_b(error_msg)
-    log_path = os.path.join(Store().directory, 'pre-commit.log')
-    output.write_line(f'Check the log at {log_path}')
 
-    with open(log_path, 'wb') as log:
+    storedir = Store().directory
+    log_path = os.path.join(storedir, 'pre-commit.log')
+    with contextlib.ExitStack() as ctx:
+        if os.access(storedir, os.W_OK):
+            output.write_line(f'Check the log at {log_path}')
+            log = ctx.enter_context(open(log_path, 'wb'))
+        else:  # pragma: win32 no cover
+            output.write_line(f'Failed to write to log at {log_path}')
+            log = sys.stdout.buffer
+
         _log_line = functools.partial(output.write_line, stream=log)
         _log_line_b = functools.partial(output.write_line_b, stream=log)
 
diff --git a/pre_commit/file_lock.py b/pre_commit/file_lock.py
index ff0dc5e..5e7a058 100644
--- a/pre_commit/file_lock.py
+++ b/pre_commit/file_lock.py
@@ -21,13 +21,13 @@ if os.name == 'nt':  # pragma: no cover (windows)
     ) -> Generator[None, None, None]:
         try:
             # TODO: https://github.com/python/typeshed/pull/3607
-            msvcrt.locking(fileno, msvcrt.LK_NBLCK, _region)  # type: ignore
+            msvcrt.locking(fileno, msvcrt.LK_NBLCK, _region)
         except OSError:
             blocked_cb()
             while True:
                 try:
                     # TODO: https://github.com/python/typeshed/pull/3607
-                    msvcrt.locking(fileno, msvcrt.LK_LOCK, _region)  # type: ignore  # noqa: E501
+                    msvcrt.locking(fileno, msvcrt.LK_LOCK, _region)
                 except OSError as e:
                     # Locking violation. Returned when the _LK_LOCK or _LK_RLCK
                     # flag is specified and the file cannot be locked after 10
@@ -46,7 +46,7 @@ if os.name == 'nt':  # pragma: no cover (windows)
             # "Regions should be locked only briefly and should be unlocked
             # before closing a file or exiting the program."
             # TODO: https://github.com/python/typeshed/pull/3607
-            msvcrt.locking(fileno, msvcrt.LK_UNLCK, _region)  # type: ignore
+            msvcrt.locking(fileno, msvcrt.LK_UNLCK, _region)
 else:  # pragma: win32 no cover
     import fcntl
 
diff --git a/pre_commit/languages/docker.py b/pre_commit/languages/docker.py
index 4091492..9c13119 100644
--- a/pre_commit/languages/docker.py
+++ b/pre_commit/languages/docker.py
@@ -7,9 +7,7 @@ import pre_commit.constants as C
 from pre_commit.hook import Hook
 from pre_commit.languages import helpers
 from pre_commit.prefix import Prefix
-from pre_commit.util import CalledProcessError
 from pre_commit.util import clean_path_on_failure
-from pre_commit.util import cmd_output_b
 
 ENVIRONMENT_DIR = 'docker'
 PRE_COMMIT_LABEL = 'PRE_COMMIT'
@@ -26,21 +24,6 @@ def docker_tag(prefix: Prefix) -> str:  # pragma: win32 no cover
     return f'pre-commit-{md5sum}'
 
 
-def docker_is_running() -> bool:  # pragma: win32 no cover
-    try:
-        cmd_output_b('docker', 'ps')
-    except CalledProcessError:
-        return False
-    else:
-        return True
-
-
-def assert_docker_available() -> None:  # pragma: win32 no cover
-    assert docker_is_running(), (
-        'Docker is either not running or not configured in this environment'
-    )
-
-
 def build_docker_image(
         prefix: Prefix,
         *,
@@ -63,7 +46,6 @@ def install_environment(
 ) -> None:  # pragma: win32 no cover
     helpers.assert_version_default('docker', version)
     helpers.assert_no_additional_deps('docker', additional_dependencies)
-    assert_docker_available()
 
     directory = prefix.path(
         helpers.environment_dir(ENVIRONMENT_DIR, C.DEFAULT),
@@ -101,7 +83,6 @@ def run_hook(
         file_args: Sequence[str],
         color: bool,
 ) -> Tuple[int, bytes]:  # pragma: win32 no cover
-    assert_docker_available()
     # Rebuild the docker image in case it has gone missing, as many people do
     # automated cleanup of docker images.
     build_docker_image(hook.prefix, pull=False)
diff --git a/pre_commit/languages/docker_image.py b/pre_commit/languages/docker_image.py
index 0c51df6..311d127 100644
--- a/pre_commit/languages/docker_image.py
+++ b/pre_commit/languages/docker_image.py
@@ -3,7 +3,6 @@ from typing import Tuple
 
 from pre_commit.hook import Hook
 from pre_commit.languages import helpers
-from pre_commit.languages.docker import assert_docker_available
 from pre_commit.languages.docker import docker_cmd
 
 ENVIRONMENT_DIR = None
@@ -17,6 +16,5 @@ def run_hook(
         file_args: Sequence[str],
         color: bool,
 ) -> Tuple[int, bytes]:  # pragma: win32 no cover
-    assert_docker_available()
     cmd = docker_cmd() + hook.cmd
     return helpers.run_xargs(hook, cmd, file_args, color=color)
diff --git a/pre_commit/languages/python.py b/pre_commit/languages/python.py
index 6f7c900..7a68580 100644
--- a/pre_commit/languages/python.py
+++ b/pre_commit/languages/python.py
@@ -191,7 +191,8 @@ def healthy(prefix: Prefix, language_version: str) -> bool:
 
     return (
         'version_info' in cfg and
-        _version_info(py_exe) == cfg['version_info'] and (
+        # always use uncached lookup here in case we replaced an unhealthy env
+        _version_info.__wrapped__(py_exe) == cfg['version_info'] and (
             'base-executable' not in cfg or
             _version_info(cfg['base-executable']) == cfg['version_info']
         )
diff --git a/pre_commit/main.py b/pre_commit/main.py
index 874eb53..8647960 100644
--- a/pre_commit/main.py
+++ b/pre_commit/main.py
@@ -8,8 +8,8 @@ from typing import Sequence
 from typing import Union
 
 import pre_commit.constants as C
-from pre_commit import color
 from pre_commit import git
+from pre_commit.color import add_color_option
 from pre_commit.commands.autoupdate import autoupdate
 from pre_commit.commands.clean import clean
 from pre_commit.commands.gc import gc
@@ -41,15 +41,6 @@ os.environ.pop('__PYVENV_LAUNCHER__', None)
 COMMANDS_NO_GIT = {'clean', 'gc', 'init-templatedir', 'sample-config'}
 
 
-def _add_color_option(parser: argparse.ArgumentParser) -> None:
-    parser.add_argument(
-        '--color', default=os.environ.get('PRE_COMMIT_COLOR', 'auto'),
-        type=color.use_color,
-        metavar='{' + ','.join(color.COLOR_CHOICES) + '}',
-        help='Whether to use color in output.  Defaults to `%(default)s`.',
-    )
-
-
 def _add_config_option(parser: argparse.ArgumentParser) -> None:
     parser.add_argument(
         '-c', '--config', default=C.CONFIG_FILE,
@@ -195,7 +186,7 @@ def main(argv: Optional[Sequence[str]] = None) -> int:
         'autoupdate',
         help="Auto-update pre-commit config to the latest repos' versions.",
     )
-    _add_color_option(autoupdate_parser)
+    add_color_option(autoupdate_parser)
     _add_config_option(autoupdate_parser)
     autoupdate_parser.add_argument(
         '--bleeding-edge', action='store_true',
@@ -216,11 +207,11 @@ def main(argv: Optional[Sequence[str]] = None) -> int:
     clean_parser = subparsers.add_parser(
         'clean', help='Clean out pre-commit files.',
     )
-    _add_color_option(clean_parser)
+    add_color_option(clean_parser)
     _add_config_option(clean_parser)
 
     hook_impl_parser = subparsers.add_parser('hook-impl')
-    _add_color_option(hook_impl_parser)
+    add_color_option(hook_impl_parser)
     _add_config_option(hook_impl_parser)
     hook_impl_parser.add_argument('--hook-type')
     hook_impl_parser.add_argument('--hook-dir')
@@ -230,7 +221,7 @@ def main(argv: Optional[Sequence[str]] = None) -> int:
     hook_impl_parser.add_argument(dest='rest', nargs=argparse.REMAINDER)
 
     gc_parser = subparsers.add_parser('gc', help='Clean unused cached repos.')
-    _add_color_option(gc_parser)
+    add_color_option(gc_parser)
     _add_config_option(gc_parser)
 
     init_templatedir_parser = subparsers.add_parser(
@@ -240,17 +231,23 @@ def main(argv: Optional[Sequence[str]] = None) -> int:
             '`git config init.templateDir`.'
         ),
     )
-    _add_color_option(init_templatedir_parser)
+    add_color_option(init_templatedir_parser)
     _add_config_option(init_templatedir_parser)
     init_templatedir_parser.add_argument(
         'directory', help='The directory in which to write the hook script.',
     )
+    init_templatedir_parser.add_argument(
+        '--no-allow-missing-config',
+        action='store_false',
+        dest='allow_missing_config',
+        help='Assume cloned repos should have a `pre-commit` config.',
+    )
     _add_hook_type_option(init_templatedir_parser)
 
     install_parser = subparsers.add_parser(
         'install', help='Install the pre-commit script.',
     )
-    _add_color_option(install_parser)
+    add_color_option(install_parser)
     _add_config_option(install_parser)
     install_parser.add_argument(
         '-f', '--overwrite', action='store_true',
@@ -280,32 +277,32 @@ def main(argv: Optional[Sequence[str]] = None) -> int:
             'useful.'
         ),
     )
-    _add_color_option(install_hooks_parser)
+    add_color_option(install_hooks_parser)
     _add_config_option(install_hooks_parser)
 
     migrate_config_parser = subparsers.add_parser(
         'migrate-config',
         help='Migrate list configuration to new map configuration.',
     )
-    _add_color_option(migrate_config_parser)
+    add_color_option(migrate_config_parser)
     _add_config_option(migrate_config_parser)
 
     run_parser = subparsers.add_parser('run', help='Run hooks.')
-    _add_color_option(run_parser)
+    add_color_option(run_parser)
     _add_config_option(run_parser)
     _add_run_options(run_parser)
 
     sample_config_parser = subparsers.add_parser(
         'sample-config', help=f'Produce a sample {C.CONFIG_FILE} file',
     )
-    _add_color_option(sample_config_parser)
+    add_color_option(sample_config_parser)
     _add_config_option(sample_config_parser)
 
     try_repo_parser = subparsers.add_parser(
         'try-repo',
         help='Try the hooks in a repository, useful for developing new hooks.',
     )
-    _add_color_option(try_repo_parser)
+    add_color_option(try_repo_parser)
     _add_config_option(try_repo_parser)
     try_repo_parser.add_argument(
         'repo', help='Repository to source hooks from.',
@@ -322,7 +319,7 @@ def main(argv: Optional[Sequence[str]] = None) -> int:
     uninstall_parser = subparsers.add_parser(
         'uninstall', help='Uninstall the pre-commit script.',
     )
-    _add_color_option(uninstall_parser)
+    add_color_option(uninstall_parser)
     _add_config_option(uninstall_parser)
     _add_hook_type_option(uninstall_parser)
 
@@ -383,6 +380,7 @@ def main(argv: Optional[Sequence[str]] = None) -> int:
             return init_templatedir(
                 args.config, store, args.directory,
                 hook_types=args.hook_types,
+                skip_on_missing_config=args.allow_missing_config,
             )
         elif args.command == 'install-hooks':
             return install_hooks(args.config, store)
diff --git a/pre_commit/repository.py b/pre_commit/repository.py
index 77734ee..46e96c1 100644
--- a/pre_commit/repository.py
+++ b/pre_commit/repository.py
@@ -48,7 +48,7 @@ def _write_state(prefix: Prefix, venv: str, state: object) -> None:
     with open(staging, 'w') as state_file:
         state_file.write(json.dumps(state))
     # Move the file into place atomically to indicate we've installed
-    os.rename(staging, state_filename)
+    os.replace(staging, state_filename)
 
 
 def _hook_installed(hook: Hook) -> bool:
@@ -82,6 +82,12 @@ def _hook_install(hook: Hook) -> None:
     lang.install_environment(
         hook.prefix, hook.language_version, hook.additional_dependencies,
     )
+    if not lang.healthy(hook.prefix, hook.language_version):
+        raise AssertionError(
+            f'BUG: expected environment for {hook.language} to be healthy() '
+            f'immediately after install, please open an issue describing '
+            f'your environment',
+        )
     # Write our state to indicate we're installed
     _write_state(hook.prefix, venv, _state(hook.additional_dependencies))
 
diff --git a/pre_commit/store.py b/pre_commit/store.py
index 6d8c40a..e5522ec 100644
--- a/pre_commit/store.py
+++ b/pre_commit/store.py
@@ -43,6 +43,10 @@ class Store:
     def __init__(self, directory: Optional[str] = None) -> None:
         self.directory = directory or Store.get_default_directory()
         self.db_path = os.path.join(self.directory, 'db.db')
+        self.readonly = (
+            os.path.exists(self.directory) and
+            not os.access(self.directory, os.W_OK)
+        )
 
         if not os.path.exists(self.directory):
             os.makedirs(self.directory, exist_ok=True)
@@ -75,7 +79,7 @@ class Store:
                 self._create_config_table(db)
 
             # Atomic file move
-            os.rename(tmpfile, self.db_path)
+            os.replace(tmpfile, self.db_path)
 
     @contextlib.contextmanager
     def exclusive_lock(self) -> Generator[None, None, None]:
@@ -218,6 +222,8 @@ class Store:
         )
 
     def mark_config_used(self, path: str) -> None:
+        if self.readonly:  # pragma: win32 no cover
+            return
         path = os.path.realpath(path)
         # don't insert config files that do not exist
         if not os.path.exists(path):