Merging upstream version 2.11.0.

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

11 files changed, 188 insertions, 8 deletions

diff --git a/pre_commit/clientlib.py b/pre_commit/clientlib.py
index 8f35057..962c7fa 100644
--- a/pre_commit/clientlib.py
+++ b/pre_commit/clientlib.py
@@ -128,7 +128,8 @@ class WarnMutableRev(cfgv.ConditionalOptional):
                     f'(moving tag / branch).  Mutable references are never '
                     f'updated after first install and are not supported.  '
                     f'See https://pre-commit.com/#using-the-latest-version-for-a-repository '  # noqa: E501
-                    f'for more details.',
+                    f'for more details.  '
+                    f'Hint: `pre-commit autoupdate` often fixes this.',
                 )
 
 
diff --git a/pre_commit/commands/hook_impl.py b/pre_commit/commands/hook_impl.py
index 25c5fdf..a766ee9 100644
--- a/pre_commit/commands/hook_impl.py
+++ b/pre_commit/commands/hook_impl.py
@@ -76,6 +76,7 @@ def _ns(
         remote_url: Optional[str] = None,
         commit_msg_filename: Optional[str] = None,
         checkout_type: Optional[str] = None,
+        is_squash_merge: Optional[str] = None,
 ) -> argparse.Namespace:
     return argparse.Namespace(
         color=color,
@@ -88,6 +89,7 @@ def _ns(
         commit_msg_filename=commit_msg_filename,
         all_files=all_files,
         checkout_type=checkout_type,
+        is_squash_merge=is_squash_merge,
         files=(),
         hook=None,
         verbose=False,
@@ -158,6 +160,7 @@ _EXPECTED_ARG_LENGTH_BY_HOOK = {
     'post-commit': 0,
     'pre-commit': 0,
     'pre-merge-commit': 0,
+    'post-merge': 1,
     'pre-push': 2,
 }
 
@@ -199,6 +202,8 @@ def _run_ns(
             hook_type, color,
             from_ref=args[0], to_ref=args[1], checkout_type=args[2],
         )
+    elif hook_type == 'post-merge':
+        return _ns(hook_type, color, is_squash_merge=args[0])
     else:
         raise AssertionError(f'unexpected hook type: {hook_type}')
 
diff --git a/pre_commit/commands/run.py b/pre_commit/commands/run.py
index 891488d..05c3268 100644
--- a/pre_commit/commands/run.py
+++ b/pre_commit/commands/run.py
@@ -245,7 +245,7 @@ def _compute_cols(hooks: Sequence[Hook]) -> int:
 
 def _all_filenames(args: argparse.Namespace) -> Collection[str]:
     # these hooks do not operate on files
-    if args.hook_stage in {'post-checkout', 'post-commit'}:
+    if args.hook_stage in {'post-checkout', 'post-commit', 'post-merge'}:
         return ()
     elif args.hook_stage in {'prepare-commit-msg', 'commit-msg'}:
         return (args.commit_msg_filename,)
@@ -379,6 +379,9 @@ def run(
     if args.checkout_type:
         environ['PRE_COMMIT_CHECKOUT_TYPE'] = args.checkout_type
 
+    if args.is_squash_merge:
+        environ['PRE_COMMIT_IS_SQUASH_MERGE'] = args.is_squash_merge
+
     # Set pre_commit flag
     environ['PRE_COMMIT'] = '1'
 
diff --git a/pre_commit/constants.py b/pre_commit/constants.py
index 5150fdc..3dcbbac 100644
--- a/pre_commit/constants.py
+++ b/pre_commit/constants.py
@@ -18,7 +18,7 @@ VERSION = importlib_metadata.version('pre_commit')
 # `manual` is not invoked by any installed git hook.  See #719
 STAGES = (
     'commit', 'merge-commit', 'prepare-commit-msg', 'commit-msg',
-    'post-commit', 'manual', 'post-checkout', 'push',
+    'post-commit', 'manual', 'post-checkout', 'push', 'post-merge',
 )
 
 DEFAULT = 'default'
diff --git a/pre_commit/git.py b/pre_commit/git.py
index bec816c..4bf2823 100644
--- a/pre_commit/git.py
+++ b/pre_commit/git.py
@@ -52,10 +52,10 @@ def get_root() -> str:
     # "rev-parse --show-cdup" to get the appropriate path, but must perform
     # an extra check to see if we are in the .git directory.
     try:
-        root = os.path.realpath(
+        root = os.path.abspath(
             cmd_output('git', 'rev-parse', '--show-cdup')[1].strip(),
         )
-        git_dir = os.path.realpath(get_git_dir())
+        git_dir = os.path.abspath(get_git_dir())
     except CalledProcessError:
         raise FatalError(
             'git failed. Is it installed, and are you in a Git repository '
diff --git a/pre_commit/languages/all.py b/pre_commit/languages/all.py
index 9c2e59d..fde6000 100644
--- a/pre_commit/languages/all.py
+++ b/pre_commit/languages/all.py
@@ -16,6 +16,7 @@ from pre_commit.languages import node
 from pre_commit.languages import perl
 from pre_commit.languages import pygrep
 from pre_commit.languages import python
+from pre_commit.languages import r
 from pre_commit.languages import ruby
 from pre_commit.languages import rust
 from pre_commit.languages import script
@@ -52,6 +53,7 @@ languages = {
     'perl': Language(name='perl', ENVIRONMENT_DIR=perl.ENVIRONMENT_DIR, get_default_version=perl.get_default_version, healthy=perl.healthy, install_environment=perl.install_environment, run_hook=perl.run_hook),  # noqa: E501
     'pygrep': Language(name='pygrep', ENVIRONMENT_DIR=pygrep.ENVIRONMENT_DIR, get_default_version=pygrep.get_default_version, healthy=pygrep.healthy, install_environment=pygrep.install_environment, run_hook=pygrep.run_hook),  # noqa: E501
     'python': Language(name='python', ENVIRONMENT_DIR=python.ENVIRONMENT_DIR, get_default_version=python.get_default_version, healthy=python.healthy, install_environment=python.install_environment, run_hook=python.run_hook),  # noqa: E501
+    'r': Language(name='r', ENVIRONMENT_DIR=r.ENVIRONMENT_DIR, get_default_version=r.get_default_version, healthy=r.healthy, install_environment=r.install_environment, run_hook=r.run_hook),  # noqa: E501
     'ruby': Language(name='ruby', ENVIRONMENT_DIR=ruby.ENVIRONMENT_DIR, get_default_version=ruby.get_default_version, healthy=ruby.healthy, install_environment=ruby.install_environment, run_hook=ruby.run_hook),  # noqa: E501
     'rust': Language(name='rust', ENVIRONMENT_DIR=rust.ENVIRONMENT_DIR, get_default_version=rust.get_default_version, healthy=rust.healthy, install_environment=rust.install_environment, run_hook=rust.run_hook),  # noqa: E501
     'script': Language(name='script', ENVIRONMENT_DIR=script.ENVIRONMENT_DIR, get_default_version=script.get_default_version, healthy=script.healthy, install_environment=script.install_environment, run_hook=script.run_hook),  # noqa: E501
diff --git a/pre_commit/languages/r.py b/pre_commit/languages/r.py
new file mode 100644
index 0000000..1d42fea
--- /dev/null
+++ b/pre_commit/languages/r.py
@@ -0,0 +1,141 @@
+import contextlib
+import os
+import shlex
+import shutil
+from typing import Generator
+from typing import Sequence
+from typing import Tuple
+
+from pre_commit.envcontext import envcontext
+from pre_commit.envcontext import PatchesT
+from pre_commit.hook import Hook
+from pre_commit.languages import helpers
+from pre_commit.prefix import Prefix
+from pre_commit.util import clean_path_on_failure
+from pre_commit.util import cmd_output_b
+
+ENVIRONMENT_DIR = 'renv'
+get_default_version = helpers.basic_get_default_version
+healthy = helpers.basic_healthy
+
+
+def get_env_patch(venv: str) -> PatchesT:
+    return (
+        ('R_PROFILE_USER', os.path.join(venv, 'activate.R')),
+    )
+
+
+@contextlib.contextmanager
+def in_env(
+        prefix: Prefix,
+        language_version: str,
+) -> Generator[None, None, None]:
+    envdir = _get_env_dir(prefix, language_version)
+    with envcontext(get_env_patch(envdir)):
+        yield
+
+
+def _get_env_dir(prefix: Prefix, version: str) -> str:
+    return prefix.path(helpers.environment_dir(ENVIRONMENT_DIR, version))
+
+
+def _prefix_if_file_entry(
+    entry: Sequence[str],
+    prefix: Prefix,
+) -> Sequence[str]:
+    if entry[1] == '-e':
+        return entry[1:]
+    else:
+        return (prefix.path(entry[1]),)
+
+
+def _entry_validate(entry: Sequence[str]) -> None:
+    """
+    Allowed entries:
+    # Rscript -e expr
+    # Rscript path/to/file
+    """
+    if entry[0] != 'Rscript':
+        raise ValueError('entry must start with `Rscript`.')
+
+    if entry[1] == '-e':
+        if len(entry) > 3:
+            raise ValueError('You can supply at most one expression.')
+    elif len(entry) > 2:
+        raise ValueError(
+            'The only valid syntax is `Rscript -e {expr}`',
+            'or `Rscript path/to/hook/script`',
+        )
+
+
+def _cmd_from_hook(hook: Hook) -> Tuple[str, ...]:
+    opts = ('--no-save', '--no-restore', '--no-site-file', '--no-environ')
+    entry = shlex.split(hook.entry)
+    _entry_validate(entry)
+
+    return (
+        *entry[:1], *opts,
+        *_prefix_if_file_entry(entry, hook.prefix),
+        *hook.args,
+    )
+
+
+def install_environment(
+        prefix: Prefix,
+        version: str,
+        additional_dependencies: Sequence[str],
+) -> None:
+    env_dir = _get_env_dir(prefix, version)
+    with clean_path_on_failure(env_dir):
+        os.makedirs(env_dir, exist_ok=True)
+        path_desc_source = prefix.path('DESCRIPTION')
+        if os.path.exists(path_desc_source):
+            shutil.copy(path_desc_source, env_dir)
+        shutil.copy(prefix.path('renv.lock'), env_dir)
+        cmd_output_b(
+            'Rscript', '--vanilla', '-e',
+            """\
+            missing_pkgs <- setdiff(
+                "renv", unname(installed.packages()[, "Package"])
+            )
+            options(
+                repos = c(CRAN = "https://cran.rstudio.com"),
+                renv.consent = TRUE
+            )
+            install.packages(missing_pkgs)
+            renv::activate()
+            renv::restore()
+            activate_statement <- paste0(
+              'renv::activate("', file.path(getwd()), '"); '
+            )
+            writeLines(activate_statement, 'activate.R')
+            is_package <- tryCatch(
+                suppressWarnings(
+                    unname(read.dcf('DESCRIPTION')[,'Type'] == "Package")
+                ),
+                error = function(...) FALSE
+            )
+            if (is_package) {
+                renv::install(normalizePath('.'))
+            }
+            """,
+            cwd=env_dir,
+        )
+        if additional_dependencies:
+            cmd_output_b(
+                'Rscript', '-e',
+                'renv::install(commandArgs(trailingOnly = TRUE))',
+                *additional_dependencies,
+                cwd=env_dir,
+            )
+
+
+def run_hook(
+        hook: Hook,
+        file_args: Sequence[str],
+        color: bool,
+) -> Tuple[int, bytes]:
+    with in_env(hook.prefix, hook.language_version):
+        return helpers.run_xargs(
+            hook, _cmd_from_hook(hook), file_args, color=color,
+        )
diff --git a/pre_commit/main.py b/pre_commit/main.py
index ce850c4..c66cfb9 100644
--- a/pre_commit/main.py
+++ b/pre_commit/main.py
@@ -67,8 +67,8 @@ class AppendReplaceDefault(argparse.Action):
 def _add_hook_type_option(parser: argparse.ArgumentParser) -> None:
     parser.add_argument(
         '-t', '--hook-type', choices=(
-            'pre-commit', 'pre-merge-commit', 'pre-push',
-            'prepare-commit-msg', 'commit-msg', 'post-commit', 'post-checkout',
+            'pre-commit', 'pre-merge-commit', 'pre-push', 'prepare-commit-msg',
+            'commit-msg', 'post-commit', 'post-checkout', 'post-merge',
         ),
         action=AppendReplaceDefault,
         default=['pre-commit'],
@@ -136,6 +136,13 @@ def _add_run_options(parser: argparse.ArgumentParser) -> None:
             'file from the index, flag=0).'
         ),
     )
+    parser.add_argument(
+        '--is-squash-merge',
+        help=(
+            'During a post-merge hook, indicates whether the merge was a '
+            'squash merge'
+        ),
+    )
 
 
 def _adjust_args_and_chdir(args: argparse.Namespace) -> None:
diff --git a/pre_commit/resources/empty_template_go.mod b/pre_commit/resources/empty_template_go.mod
index e69de29..de3e241 100644
--- a/pre_commit/resources/empty_template_go.mod
+++ b/pre_commit/resources/empty_template_go.mod
@@ -0,0 +1 @@
+module pre-commit-dummy-empty-module
diff --git a/pre_commit/resources/empty_template_renv.lock b/pre_commit/resources/empty_template_renv.lock
new file mode 100644
index 0000000..d6e31f8
--- /dev/null
+++ b/pre_commit/resources/empty_template_renv.lock
@@ -0,0 +1,20 @@
+{
+  "R": {
+    "Version": "4.0.3",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cran.rstudio.com"
+      }
+    ]
+  },
+  "Packages": {
+    "renv": {
+      "Package": "renv",
+      "Version": "0.12.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "5c0cdb37f063c58cdab3c7e9fbb8bd2c"
+    }
+  }
+}
diff --git a/pre_commit/store.py b/pre_commit/store.py
index e5522ec..187c9d3 100644
--- a/pre_commit/store.py
+++ b/pre_commit/store.py
@@ -189,7 +189,7 @@ class Store:
     LOCAL_RESOURCES = (
         'Cargo.toml', 'main.go', 'go.mod', 'main.rs', '.npmignore',
         'package.json', 'pre_commit_dummy_package.gemspec', 'setup.py',
-        'environment.yml', 'Makefile.PL',
+        'environment.yml', 'Makefile.PL', 'renv.lock',
     )
 
     def make_local(self, deps: Sequence[str]) -> str: