Merging upstream version 3.8.0.

Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>

7 files changed, 180 insertions, 49 deletions

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6caee40..1a9a8fe 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -14,7 +14,7 @@ repos:
     hooks:
     -   id: setup-cfg-fmt
 -   repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.12.0
+    rev: v3.13.0
     hooks:
     -   id: reorder-python-imports
         exclude: ^(pre_commit/resources/|testing/resources/python3_hooks_repo/)
@@ -24,21 +24,21 @@ repos:
     hooks:
     -   id: add-trailing-comma
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+    rev: v3.16.0
     hooks:
     -   id: pyupgrade
         args: [--py39-plus]
 -   repo: https://github.com/hhatto/autopep8
-    rev: v2.1.0
+    rev: v2.3.1
     hooks:
     -   id: autopep8
 -   repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
+    rev: 7.1.0
     hooks:
     -   id: flake8
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.11.0
     hooks:
     -   id: mypy
-        additional_dependencies: [types-all]
+        additional_dependencies: [types-pyyaml]
         exclude: ^testing/resources/
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 81d5b33..49094bb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,12 @@
+3.8.0 - 2024-07-28
+==================
+
+### Features
+- Implement health checks for `language: r` so environments are recreated if
+  the system version of R changes.
+    - #3206 issue by @lorenzwalthert.
+    - #3265 PR by @lorenzwalthert.
+
 3.7.1 - 2024-05-10
 ==================
 
diff --git a/pre_commit/languages/r.py b/pre_commit/languages/r.py
index 93b62bd..5d18bf1 100644
--- a/pre_commit/languages/r.py
+++ b/pre_commit/languages/r.py
@@ -14,13 +14,74 @@ 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 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
+
+
+def _execute_vanilla_r_code_as_script(
+        code: str, *,
+        prefix: Prefix, version: str, args: Sequence[str] = (), cwd: str,
+) -> str:
+    with in_env(prefix, version), _r_code_in_tempfile(code) as f:
+        _, out, _ = cmd_output(
+            _rscript_exec(), *RSCRIPT_OPTS, f, *args, cwd=cwd,
+        )
+    return out.rstrip('\n')
+
+
+def _read_installed_version(envdir: str, prefix: Prefix, version: str) -> str:
+    return _execute_vanilla_r_code_as_script(
+        'cat(renv::settings$r.version())',
+        prefix=prefix, version=version,
+        cwd=envdir,
+    )
+
+
+def _read_executable_version(envdir: str, prefix: Prefix, version: str) -> str:
+    return _execute_vanilla_r_code_as_script(
+        'cat(as.character(getRversion()))',
+        prefix=prefix, version=version,
+        cwd=envdir,
+    )
+
+
+def _write_current_r_version(
+        envdir: str, prefix: Prefix, version: str,
+) -> None:
+    _execute_vanilla_r_code_as_script(
+        'renv::settings$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
@@ -147,16 +208,14 @@ def install_environment(
     with _r_code_in_tempfile(r_code_inst_environment) as f:
         cmd_output_b(_rscript_exec(), '--vanilla', f, 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))'
-        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,
-                )
+        _execute_vanilla_r_code_as_script(
+            code=r_code_inst_add, prefix=prefix, version=version,
+            args=additional_dependencies,
+            cwd=env_dir,
+        )
 
 
 def _inline_r_setup(code: str) -> str:
diff --git a/pre_commit/util.py b/pre_commit/util.py
index b75c84a..12aa3c0 100644
--- a/pre_commit/util.py
+++ b/pre_commit/util.py
@@ -205,7 +205,7 @@ else:  # pragma: no cover
 def _handle_readonly(
         func: Callable[[str], object],
         path: str,
-        exc: Exception,
+        exc: BaseException,
 ) -> None:
     if (
             func in (os.rmdir, os.remove, os.unlink) and
@@ -223,7 +223,7 @@ if sys.version_info < (3, 12):  # pragma: <3.12 cover
     def _handle_readonly_old(
         func: Callable[[str], object],
         path: str,
-        excinfo: tuple[type[Exception], Exception, TracebackType],
+        excinfo: tuple[type[BaseException], BaseException, TracebackType],
     ) -> None:
         return _handle_readonly(func, path, excinfo[1])
 
diff --git a/setup.cfg b/setup.cfg
index 83c09ac..52b7681 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = pre_commit
-version = 3.7.1
+version = 3.8.0
 description = A framework for managing and maintaining multi-language pre-commit hooks.
 long_description = file: README.md
 long_description_content_type = text/markdown
diff --git a/tests/conftest.py b/tests/conftest.py
index 3076171..bd4af9a 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -209,36 +209,25 @@ def log_info_mock():
         yield mck
 
 
-class FakeStream:
-    def __init__(self):
-        self.data = io.BytesIO()
-
-    def write(self, s):
-        self.data.write(s)
-
-    def flush(self):
-        pass
-
-
 class Fixture:
-    def __init__(self, stream):
+    def __init__(self, stream: io.BytesIO) -> None:
         self._stream = stream
 
-    def get_bytes(self):
+    def get_bytes(self) -> bytes:
         """Get the output as-if no encoding occurred"""
-        data = self._stream.data.getvalue()
-        self._stream.data.seek(0)
-        self._stream.data.truncate()
+        data = self._stream.getvalue()
+        self._stream.seek(0)
+        self._stream.truncate()
         return data.replace(b'\r\n', b'\n')
 
-    def get(self):
+    def get(self) -> str:
         """Get the output assuming it was written as UTF-8 bytes"""
         return self.get_bytes().decode()
 
 
 @pytest.fixture
 def cap_out():
-    stream = FakeStream()
+    stream = io.BytesIO()
     write = functools.partial(output.write, stream=stream)
     write_line_b = functools.partial(output.write_line_b, stream=stream)
     with mock.patch.multiple(output, write=write, write_line_b=write_line_b):
diff --git a/tests/languages/r_test.py b/tests/languages/r_test.py
index 02c559c..10919e4 100644
--- a/tests/languages/r_test.py
+++ b/tests/languages/r_test.py
@@ -1,14 +1,17 @@
 from __future__ import annotations
 
 import os.path
-import shutil
+from unittest import mock
 
 import pytest
 
+import pre_commit.constants as C
 from pre_commit import envcontext
+from pre_commit import lang_base
 from pre_commit.languages import r
 from pre_commit.prefix import Prefix
 from pre_commit.store import _make_local_repo
+from pre_commit.util import resource_text
 from pre_commit.util import win_exe
 from testing.language_helpers import run_language
 
@@ -127,7 +130,8 @@ def test_path_rscript_exec_no_r_home_set():
         assert r._rscript_exec() == 'Rscript'
 
 
-def test_r_hook(tmp_path):
+@pytest.fixture
+def renv_lock_file(tmp_path):
     renv_lock = '''\
 {
   "R": {
@@ -157,6 +161,12 @@ def test_r_hook(tmp_path):
   }
 }
 '''
+    tmp_path.joinpath('renv.lock').write_text(renv_lock)
+    yield
+
+
+@pytest.fixture
+def description_file(tmp_path):
     description = '''\
 Package: gli.clu
 Title: What the Package Does (One Line, Title Case)
@@ -178,27 +188,39 @@ RoxygenNote: 7.1.1
 Imports:
     rprojroot
 '''
-    hello_world_r = '''\
+    tmp_path.joinpath('DESCRIPTION').write_text(description)
+    yield
+
+
+@pytest.fixture
+def hello_world_file(tmp_path):
+    hello_world = '''\
 stopifnot(
     packageVersion('rprojroot') == '1.0',
     packageVersion('gli.clu') == '0.0.0.9000'
 )
 cat("Hello, World, from R!\n")
 '''
+    tmp_path.joinpath('hello-world.R').write_text(hello_world)
+    yield
 
-    tmp_path.joinpath('renv.lock').write_text(renv_lock)
-    tmp_path.joinpath('DESCRIPTION').write_text(description)
-    tmp_path.joinpath('hello-world.R').write_text(hello_world_r)
+
+@pytest.fixture
+def renv_folder(tmp_path):
     renv_dir = tmp_path.joinpath('renv')
     renv_dir.mkdir()
-    shutil.copy(
-        os.path.join(
-            os.path.dirname(__file__),
-            '../../pre_commit/resources/empty_template_activate.R',
-        ),
-        renv_dir.joinpath('activate.R'),
-    )
+    activate_r = resource_text('empty_template_activate.R')
+    renv_dir.joinpath('activate.R').write_text(activate_r)
+    yield
+
 
+def test_r_hook(
+        tmp_path,
+        renv_lock_file,
+        description_file,
+        hello_world_file,
+        renv_folder,
+):
     expected = (0, b'Hello, World, from R!\n')
     assert run_language(tmp_path, r, 'Rscript hello-world.R') == expected
 
@@ -221,3 +243,55 @@ Rscript -e '
         args=('hi', 'hello'),
     )
     assert ret == (0, b'hi, hello, from R!\n')
+
+
+@pytest.fixture
+def prefix(tmpdir):
+    yield Prefix(str(tmpdir))
+
+
+@pytest.fixture
+def installed_environment(
+        renv_lock_file,
+        hello_world_file,
+        renv_folder,
+        prefix,
+):
+    env_dir = lang_base.environment_dir(
+        prefix, r.ENVIRONMENT_DIR, r.get_default_version(),
+    )
+    r.install_environment(prefix, C.DEFAULT, ())
+    yield prefix, env_dir
+
+
+def test_health_check_healthy(installed_environment):
+    # should be healthy right after creation
+    prefix, _ = installed_environment
+    assert r.health_check(prefix, C.DEFAULT) is None
+
+
+def test_health_check_after_downgrade(installed_environment):
+    prefix, _ = installed_environment
+
+    # pretend the saved installed version is old
+    with mock.patch.object(r, '_read_installed_version', return_value='1.0.0'):
+        output = r.health_check(prefix, C.DEFAULT)
+
+    assert output is not None
+    assert output.startswith('Hooks were installed for R version')
+
+
+@pytest.mark.parametrize('version', ('NULL', 'NA', "''"))
+def test_health_check_without_version(prefix, installed_environment, version):
+    prefix, env_dir = installed_environment
+
+    # simulate old pre-commit install by unsetting the installed version
+    r._execute_vanilla_r_code_as_script(
+        f'renv::settings$r.version({version})',
+        prefix=prefix, version=C.DEFAULT, cwd=env_dir,
+    )
+
+    # no R version specified fails as unhealty
+    msg = 'Hooks were installed with an unknown R version'
+    check_output = r.health_check(prefix, C.DEFAULT)
+    assert check_output is not None and check_output.startswith(msg)