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from __future__ import annotations
import contextlib
import os
import shlex
import shutil
from typing import Generator
from typing import Sequence
from pre_commit.envcontext import envcontext
from pre_commit.envcontext import PatchesT
from pre_commit.envcontext import UNSET
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'
RSCRIPT_OPTS = ('--no-save', '--no-restore', '--no-site-file', '--no-environ')
get_default_version = helpers.basic_get_default_version
health_check = helpers.basic_health_check
def get_env_patch(venv: str) -> PatchesT:
return (
('R_PROFILE_USER', os.path.join(venv, 'activate.R')),
('RENV_PROJECT', UNSET),
)
@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_non_local_file_entry(
entry: Sequence[str],
prefix: Prefix,
src: str,
) -> Sequence[str]:
if entry[1] == '-e':
return entry[1:]
else:
if src == 'local':
path = entry[1]
else:
path = prefix.path(entry[1])
return (path,)
def _rscript_exec() -> str:
r_home = os.environ.get('R_HOME')
if r_home is None:
return 'Rscript'
else:
return os.path.join(r_home, 'bin', 'Rscript')
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, ...]:
entry = shlex.split(hook.entry)
_entry_validate(entry)
return (
*entry[:1], *RSCRIPT_OPTS,
*_prefix_if_non_local_file_entry(entry, hook.prefix, hook.src),
*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)
shutil.copy(prefix.path('renv.lock'), env_dir)
shutil.copytree(prefix.path('renv'), os.path.join(env_dir, 'renv'))
r_code_inst_environment = f"""\
prefix_dir <- {prefix.prefix_dir!r}
options(
repos = c(CRAN = "https://cran.rstudio.com"),
renv.consent = TRUE
)
source("renv/activate.R")
renv::restore()
activate_statement <- paste0(
'suppressWarnings({{',
'old <- setwd("', getwd(), '"); ',
'source("renv/activate.R"); ',
'setwd(old); ',
'renv::load("', getwd(), '");}})'
)
writeLines(activate_statement, 'activate.R')
is_package <- tryCatch(
{{
path_desc <- file.path(prefix_dir, 'DESCRIPTION')
suppressWarnings(desc <- read.dcf(path_desc))
"Package" %in% colnames(desc)
}},
error = function(...) FALSE
)
if (is_package) {{
renv::install(prefix_dir)
}}
"""
cmd_output_b(
_rscript_exec(), '--vanilla', '-e',
_inline_r_setup(r_code_inst_environment),
cwd=env_dir,
)
if additional_dependencies:
r_code_inst_add = 'renv::install(commandArgs(trailingOnly = TRUE))'
with in_env(prefix, version):
cmd_output_b(
_rscript_exec(), *RSCRIPT_OPTS, '-e',
_inline_r_setup(r_code_inst_add),
*additional_dependencies,
cwd=env_dir,
)
def _inline_r_setup(code: str) -> str:
"""
Some behaviour of R cannot be configured via env variables, but can
only be configured via R options once R has started. These are set here.
"""
with_option = f"""\
options(install.packages.compile.from.source = "never")
{code}
"""
return with_option
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,
)
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