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authorDaniel Baumann <daniel.baumann@progress-linux.org>2021-03-08 17:48:51 +0000
committerDaniel Baumann <daniel.baumann@progress-linux.org>2021-03-08 17:49:10 +0000
commit84c011ae6133fb007046d8eb66c01d0de80b3500 (patch)
tree60b2be37885c99f0bf69434223b01cc5a2b92203 /pre_commit/languages
parentReleasing debian version 2.10.1-1. (diff)
downloadpre-commit-84c011ae6133fb007046d8eb66c01d0de80b3500.tar.xz
pre-commit-84c011ae6133fb007046d8eb66c01d0de80b3500.zip
Merging upstream version 2.11.0.
Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>
Diffstat (limited to 'pre_commit/languages')
-rw-r--r--pre_commit/languages/all.py2
-rw-r--r--pre_commit/languages/r.py141
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,
+ )