implement health check for language:r

lorenzwalthert · lorenzwalthert · commit be5ca7579b0f · 2024-07-23T16:15:10.000+02:00
diff --git a/pre_commit/languages/r.py b/pre_commit/languages/r.py
@@ -6,6 +6,7 @@
 import shutil
 import tempfile
 import textwrap
+import typing
 from collections.abc import Generator
 from collections.abc import Sequence
 
@@ -20,7 +21,56 @@
 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, **kwargs: typing.Any) -> str:
+    with _r_code_in_tempfile(code) as f:
+        cmd_out = cmd_output_b(_rscript_exec(), '--vanilla', f, **kwargs)
+    return cmd_out[1].decode().rstrip('\n')
+
+
+def _read_installed_version(envdir: str) -> str:
+    return _execute_vanilla_r_code_as_script(
+        'cat(renv::settings$r.version())', cwd=envdir,
+    )
+
+
+def _read_executable_version(envdir: str) -> str:
+    return _execute_vanilla_r_code_as_script(
+        'cat(as.character(getRversion()))',
+        cwd=envdir,
+    )
+
+
+def _write_current_r_version(envdir: str) -> None:
+    _execute_vanilla_r_code_as_script(
+        'renv::settings$r.version(as.character(getRversion()))',
+        cwd=envdir,
+    )
+
+
+def health_check(prefix: Prefix, version: str) -> str | None:
+    # prefix: cloned hook repo  .../{precommit}
+    # env dir .../{precommit}/renv-default/
+    envdir = lang_base.environment_dir(prefix, ENVIRONMENT_DIR, version)
+
+    r_version_installation = _read_installed_version(envdir=envdir)
+    # TODO what if none set? -> record current?
+    # TODO how is this affecting old hooks environments
+    r_version_current_executable = _read_executable_version(envdir=envdir)
+    if r_version_installation in {'NULL', ''}:
+        return (
+            '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}, '
+            'but current R executable has version '
+            f'{r_version_current_executable}'
+        )
+
+    return None
 
 
 @contextlib.contextmanager
@@ -130,7 +180,6 @@ def install_environment(
           'setwd(old); ',
           'renv::load("', getwd(), '");}})'
         )
-        writeLines(activate_statement, 'activate.R')
         is_package <- tryCatch(
           {{
               path_desc <- file.path(prefix_dir, 'DESCRIPTION')
@@ -142,11 +191,13 @@ def install_environment(
         if (is_package) {{
             renv::install(prefix_dir)
         }}
+        writeLines(activate_statement, 'activate.R')
         """
 
     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)
     if additional_dependencies:
         r_code_inst_add = 'renv::install(commandArgs(trailingOnly = TRUE))'
         with in_env(prefix, version):
diff --git a/tests/languages/r_test.py b/tests/languages/r_test.py
@@ -2,10 +2,13 @@
 
 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
@@ -247,3 +250,71 @@ def test_r_inline(tmp_path):
         args=('hi', 'hello'),
     )
     assert ret == (0, b'hi, hello, from R!\n')
+
+
+@pytest.fixture
+def prefix(tmpdir):
+    with tmpdir.as_cwd():
+        prefix = tmpdir.ensure_dir()
+        # prefix: cloned hook repo  .../{precommit}
+        # env dir .../{precommit}/renv-default/
+        prefix = Prefix(str(prefix))
+        yield prefix
+
+
+@pytest.fixture()  # TODO module level might be desirable?
+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
+
+
+@pytest.fixture
+def older_r_version():
+    with mock.patch.object(
+        r, '_read_installed_version', lambda envdir: '1.0.0',
+    ):
+        yield
+
+
+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, older_r_version):
+    msg = 'Hooks were installed for R version'
+    prefix, _ = installed_environment
+    check_output = r.health_check(prefix, C.DEFAULT)
+    assert check_output is not None and check_output.startswith(msg)
+
+
+@pytest.fixture(params=('NULL', 'NA', "''"))
+def installed_env_without_r_version_info(request, installed_environment):
+    _, env_dir = installed_environment
+    r._execute_vanilla_r_code_as_script(
+        f'renv::settings$r.version({request.param})', cwd=env_dir,
+    )
+    yield
+
+
+def test_health_check_without_version(
+        prefix,
+        installed_env_without_r_version_info,
+):
+    # TODO not sure that test and functionality is requried since it will
+    # only run on new pre-commit and then, probably all envs are
+    # re-installed anyways?
+    # 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)
