Merge pull request #1799 from lorenzwalthert/renv

Support for R / renv as a language

azure-pipelines.yml

@@ -26,6 +26,10 @@ jobs:
         Write-Host "##vso[task.prependpath]C:\Strawberry\perl\site\bin"
         Write-Host "##vso[task.prependpath]C:\Strawberry\c\bin"
       displayName: Add strawberry perl to PATH
+    - task: PowerShell@2
+      inputs:
+        filePath: "testing/get-r.ps1"
+      displayName: install R
 - template: job--python-tox.yml@asottile
   parameters:
     toxenvs: [py37]
@@ -42,6 +46,8 @@ jobs:
         testing/get-swift.sh
         echo '##vso[task.prependpath]/tmp/swift/usr/bin'
       displayName: install swift
+    - bash: testing/get-r.sh
+      displayName: install R
 - template: job--python-tox.yml@asottile
   parameters:
     toxenvs: [pypy3, py36, py37, py38, py39]
@@ -56,3 +62,5 @@ jobs:
         testing/get-swift.sh
         echo '##vso[task.prependpath]/tmp/swift/usr/bin'
       displayName: install swift
+    - bash: testing/get-r.sh
+      displayName: install R

pre_commit/languages/all.py

@@ -16,6 +16,7 @@
 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 @@ class Language(NamedTuple):
     '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

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,
+        )

pre_commit/resources/empty_template_renv.lock

@@ -0,0 +1,20 @@
+{
+  "R": {
+    "Version": "4.0.3",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cran.rstudio.com"
+      }
+    ]
+  },
+  "Packages": {
+    "renv": {
+      "Package": "renv",
+      "Version": "0.12.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "5c0cdb37f063c58cdab3c7e9fbb8bd2c"
+    }
+  }
+}

pre_commit/store.py

@@ -189,7 +189,7 @@ def _git_cmd(*args: str) -> None:
     LOCAL_RESOURCES = (
         'Cargo.toml', 'main.go', 'go.mod', 'main.rs', '.npmignore',
         'package.json', 'pre_commit_dummy_package.gemspec', 'setup.py',
-        'environment.yml', 'Makefile.PL',
+        'environment.yml', 'Makefile.PL', 'renv.lock',
     )
 
     def make_local(self, deps: Sequence[str]) -> str:

testing/gen-languages-all

@@ -2,9 +2,9 @@
 import sys
 
 LANGUAGES = [
-    'conda', 'coursier', 'docker', 'dotnet', 'docker_image', 'fail', 'golang',
-    'node', 'perl', 'pygrep', 'python', 'ruby', 'rust', 'script', 'swift',
-    'system',
+    'conda', 'coursier', 'docker', 'docker_image', 'dotnet', 'fail', 'golang',
+    'node', 'perl', 'pygrep', 'python', 'r', 'ruby', 'rust', 'script',
+    'swift', 'system',
 ]
 FIELDS = [
     'ENVIRONMENT_DIR', 'get_default_version', 'healthy', 'install_environment',

testing/get-r.ps1

@@ -0,0 +1,6 @@
+$dir = $Env:Temp
+$urlR = "https://cran.r-project.org/bin/windows/base/old/4.0.4/R-4.0.4-win.exe"
+$outputR = "$dir\R-win.exe"
+$wcR = New-Object System.Net.WebClient
+$wcR.DownloadFile($urlR, $outputR)
+Start-Process -FilePath $outputR -ArgumentList "/S /v/qn"

testing/get-r.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+sudo apt install r-base
+# create empty folder for user library.
+# necessary for non-root users who have
+# never installed an R package before.
+# Alternatively, we require the renv
+# package to be installed already, then we can
+# omit that.
+Rscript -e 'dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)'

testing/resources/r_hooks_repo/.pre-commit-hooks.yaml

@@ -0,0 +1,48 @@
+# parsing file
+-   id: parse-file-no-opts-no-args
+    name: Say hi
+    entry: Rscript parse-file-no-opts-no-args.R
+    language: r
+    types: [r]
+-   id: parse-file-no-opts-args
+    name: Say hi
+    entry: Rscript parse-file-no-opts-args.R
+    args: [--no-cache]
+    language: r
+    types: [r]
+## parsing expr
+-   id: parse-expr-no-opts-no-args-1
+    name: Say hi
+    entry: Rscript -e '1+1'
+    language: r
+    types: [r]
+-   id: parse-expr-args-in-entry-2
+    name: Say hi
+    entry: Rscript -e '1+1' -e '3' --no-cache3
+    language: r
+    types: [r]
+# real world
+-   id: hello-world
+    name: Say hi
+    entry: Rscript hello-world.R
+    args: [blibla]
+    language: r
+    types: [r]
+-   id: hello-world-inline
+    name: Say hi
+    entry: |
+      Rscript -e
+      'stopifnot(
+        packageVersion("rprojroot") == "1.0",
+        packageVersion("gli.clu") == "0.0.0.9000"
+      )
+      cat(commandArgs(trailingOnly = TRUE), "from R!\n", sep = ", ")
+      '
+    args: ['Hi-there']
+    language: r
+    types: [r]
+-   id: additional-deps
+    name: Check additional deps
+    entry: Rscript additional-deps.R
+    language: r
+    types: [r]

testing/resources/r_hooks_repo/DESCRIPTION

@@ -0,0 +1,19 @@
+Package: gli.clu
+Title: What the Package Does (One Line, Title Case)
+Type: Package
+Version: 0.0.0.9000
+Authors@R:
+    person(given = "First",
+           family = "Last",
+           role = c("aut", "cre"),
+           email = "first.last@example.com",
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: `use_mit_license()`, `use_gpl3_license()` or friends to
+    pick a license
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1
+Imports:
+    rprojroot

testing/resources/r_hooks_repo/additional-deps.R

@@ -0,0 +1,2 @@
+suppressPackageStartupMessages(library("cachem"))
+cat("OK\n")

testing/resources/r_hooks_repo/hello-world.R

@@ -0,0 +1,5 @@
+stopifnot(
+    packageVersion('rprojroot') == '1.0',
+    packageVersion('gli.clu') == '0.0.0.9000'
+)
+cat("Hello, World, from R!\n")

testing/resources/r_hooks_repo/renv.lock

@@ -0,0 +1,27 @@
+{
+  "R": {
+    "Version": "4.0.3",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cloud.r-project.org"
+      }
+    ]
+  },
+  "Packages": {
+    "renv": {
+      "Package": "renv",
+      "Version": "0.12.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "5c0cdb37f063c58cdab3c7e9fbb8bd2c"
+    },
+    "rprojroot": {
+      "Package": "rprojroot",
+      "Version": "1.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "86704667fe0860e4fec35afdfec137f3"
+    }
+  }
+}