1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
|
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_b
from pre_commit.util import win_exe
ENVIRONMENT_DIR = 'renv'
RSCRIPT_OPTS = ('--no-save', '--no-restore', '--no-site-file', '--no-environ')
get_default_version = lang_base.basic_get_default_version
health_check = lang_base.basic_health_check
@contextlib.contextmanager
def _r_code_in_tempfile(code: str) -> Generator[str, None, None]:
"""
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, None, 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], *RSCRIPT_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)
}}
"""
with _r_code_in_tempfile(r_code_inst_environment) as f:
cmd_output_b(_rscript_exec(), '--vanilla', f, cwd=env_dir)
if additional_dependencies:
r_code_inst_add = 'renv::install(commandArgs(trailingOnly = TRUE))'
with in_env(prefix, version):
with _r_code_in_tempfile(r_code_inst_add) as f:
cmd_output_b(
_rscript_exec(), *RSCRIPT_OPTS,
f,
*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,
)
|
