pre-commit/pre_commit/languages/r.py at v5-install · pre-commit/pre-commit · GitHub

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from __future__ import annotations

import contextlib

import os

import shlex

import shutil

import tempfile

import textwrap

from collections.abc import Generator

from collections.abc import Sequence

from pre_commit import lang_base

from pre_commit.envcontext import envcontext

from pre_commit.envcontext import PatchesT

from pre_commit.envcontext import UNSET

from pre_commit.prefix import Prefix

from pre_commit.util import cmd_output

from pre_commit.util import win_exe

ENVIRONMENT_DIR = 'renv'

get_default_version = lang_base.basic_get_default_version

_RENV_ACTIVATED_OPTS = (

'--no-save', '--no-restore', '--no-site-file', '--no-environ',

)

def _execute_r(

code: str, *,

prefix: Prefix, version: str, args: Sequence[str] = (), cwd: str,

cli_opts: Sequence[str],

) -> str:

with in_env(prefix, version), _r_code_in_tempfile(code) as f:

_, out, _ = cmd_output(

_rscript_exec(), *cli_opts, f, *args, cwd=cwd,

)

return out.rstrip('\n')

def _execute_r_in_renv(

code: str, *,

prefix: Prefix, version: str, args: Sequence[str] = (), cwd: str,

) -> str:

return _execute_r(

code=code, prefix=prefix, version=version, args=args, cwd=cwd,

cli_opts=_RENV_ACTIVATED_OPTS,

)

def _execute_vanilla_r(

code: str, *,

prefix: Prefix, version: str, args: Sequence[str] = (), cwd: str,

) -> str:

return _execute_r(

code=code, prefix=prefix, version=version, args=args, cwd=cwd,

cli_opts=('--vanilla',),

)

def _read_installed_version(envdir: str, prefix: Prefix, version: str) -> str:

return _execute_r_in_renv(

'cat(renv::settings$r.version())',

prefix=prefix, version=version,

cwd=envdir,

)

def _read_executable_version(envdir: str, prefix: Prefix, version: str) -> str:

return _execute_r_in_renv(

'cat(as.character(getRversion()))',

prefix=prefix, version=version,

cwd=envdir,

)

def _write_current_r_version(

envdir: str, prefix: Prefix, version: str,

) -> None:

_execute_r_in_renv(

'renv::settings$r.version(as.character(getRversion()))',

prefix=prefix, version=version,

cwd=envdir,

)

def health_check(prefix: Prefix, version: str) -> str | None:

envdir = lang_base.environment_dir(prefix, ENVIRONMENT_DIR, version)

r_version_installation = _read_installed_version(

envdir=envdir, prefix=prefix, version=version,

)

r_version_current_executable = _read_executable_version(

envdir=envdir, prefix=prefix, version=version,

)

if r_version_installation in {'NULL', ''}:

return (

f'Hooks were installed with an unknown R version. R version for '

f'hook repo now set to {r_version_current_executable}'

)

elif r_version_installation != r_version_current_executable:

return (

f'Hooks were installed for R version {r_version_installation}, '

f'but current R executable has version '

f'{r_version_current_executable}'

)

return None

@contextlib.contextmanager

def _r_code_in_tempfile(code: str) -> Generator[str]:

"""

To avoid quoting and escaping issues, avoid `Rscript [options] -e {expr}`

but use `Rscript [options] path/to/file_with_expr.R`

"""

with tempfile.TemporaryDirectory() as tmpdir:

fname = os.path.join(tmpdir, 'script.R')

with open(fname, 'w') as f:

f.write(_inline_r_setup(textwrap.dedent(code)))

yield fname

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, version: str) -> Generator[None]:

envdir = lang_base.environment_dir(prefix, ENVIRONMENT_DIR, version)

with envcontext(get_env_patch(envdir)):

yield

def _prefix_if_file_entry(

entry: list[str],

prefix: Prefix,

is_local: bool,

) -> Sequence[str]:

if entry[1] == '-e' or is_local:

return entry[1:]

else:

return (prefix.path(entry[1]),)

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', win_exe('Rscript'))

def _entry_validate(entry: list[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(

prefix: Prefix,

entry: str,

args: Sequence[str],

is_local: bool,

) -> tuple[str, ...]:

cmd = shlex.split(entry)

_entry_validate(cmd)

cmd_part = _prefix_if_file_entry(cmd, prefix, is_local=is_local)

return (cmd[0], *_RENV_ACTIVATED_OPTS, *cmd_part, *args)

def install_environment(

prefix: Prefix,

version: str,

additional_dependencies: Sequence[str],

) -> None:

lang_base.assert_version_default('r', version)

env_dir = lang_base.environment_dir(prefix, ENVIRONMENT_DIR, version)

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)

}}

"""

_execute_vanilla_r(

r_code_inst_environment,

prefix=prefix, version=version, cwd=env_dir,

)

_write_current_r_version(envdir=env_dir, prefix=prefix, version=version)

if additional_dependencies:

r_code_inst_add = 'renv::install(commandArgs(trailingOnly = TRUE))'

_execute_r_in_renv(

code=r_code_inst_add, prefix=prefix, version=version,

args=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 = [

textwrap.dedent("""\

options(

install.packages.compile.from.source = "never",

pkgType = "binary"

)

"""),

code,

]

return '\n'.join(with_option)

def run_hook(

prefix: Prefix,

entry: str,

args: Sequence[str],

file_args: Sequence[str],

is_local: bool,

require_serial: bool,

color: bool,

) -> tuple[int, bytes]:

cmd = _cmd_from_hook(prefix, entry, args, is_local=is_local)

return lang_base.run_xargs(

cmd,

file_args,

require_serial=require_serial,

color=color,

)

pre-commit/pre_commit/languages/r.py at v5-install · pre-commit/pre-commit · GitHub

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