Merging upstream version 2.11.0.

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

2 files changed, 143 insertions, 0 deletions

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,
+        )