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Adding upstream version 2.18.1.

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Signed-off-by: Daniel Baumann <daniel@debian.org>
This commit is contained in:
Daniel Baumann 2025-02-09 21:32:53 +01:00
parent 9c7f59905e
commit 75996f15a7
Signed by: daniel
GPG key ID: FBB4F0E80A80222F
116 changed files with 718 additions and 410 deletions
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38
pre_commit/languages/r.py
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@ -1,10 +1,11 @@
from __future__ import annotations
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
@ -58,7 +59,11 @@ def _prefix_if_non_local_file_entry(
def _rscript_exec() -> str:
return os.path.join(os.getenv('R_HOME', ''), 'Rscript')
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:
@ -80,7 +85,7 @@ def _entry_validate(entry: Sequence[str]) -> None:
)
def _cmd_from_hook(hook: Hook) -> Tuple[str, ...]:
def _cmd_from_hook(hook: Hook) -> tuple[str, ...]:
entry = shlex.split(hook.entry)
_entry_validate(entry)
@ -102,9 +107,7 @@ def install_environment(
shutil.copy(prefix.path('renv.lock'), env_dir)
shutil.copytree(prefix.path('renv'), os.path.join(env_dir, 'renv'))
cmd_output_b(
_rscript_exec(), '--vanilla', '-e',
f"""\
r_code_inst_environment = f"""\
prefix_dir <- {prefix.prefix_dir!r}
options(
repos = c(CRAN = "https://cran.rstudio.com"),
@ -131,24 +134,41 @@ def install_environment(
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',
'renv::install(commandArgs(trailingOnly = TRUE))',
_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]:
) -> tuple[int, bytes]:
with in_env(hook.prefix, hook.language_version):
return helpers.run_xargs(
hook, _cmd_from_hook(hook), file_args, color=color,