diff options
| -rw-r--r-- | .pre-commit-config.yaml | 12 | ||||
| -rw-r--r-- | CHANGELOG.md | 9 | ||||
| -rw-r--r-- | pre_commit/languages/r.py | 77 | ||||
| -rw-r--r-- | pre_commit/util.py | 4 | ||||
| -rw-r--r-- | setup.cfg | 2 | ||||
| -rw-r--r-- | tests/conftest.py | 25 | ||||
| -rw-r--r-- | tests/languages/r_test.py | 100 |
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]) @@ -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) |