Fix.

Author: tobiasraabe

.pre-commit-config.yaml

@@ -17,33 +17,19 @@ repos:
     -   id: python-no-log-warn
     -   id: python-use-type-annotations
     -   id: text-unicode-replacement-char
--   repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.12.0
-    hooks:
-    -   id: reorder-python-imports
-        args: [--py37-plus, --add-import, 'from __future__ import annotations']
 -   repo: https://github.com/asottile/setup-cfg-fmt
     rev: v2.5.0
     hooks:
     -   id: setup-cfg-fmt
--   repo: https://github.com/psf/black
-    rev: 24.4.0
-    hooks:
-    -   id: black
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.3.7
     hooks:
       - id: ruff
+      - id: ruff-format
 -   repo: https://github.com/dosisod/refurb
     rev: v2.0.0
     hooks:
     -   id: refurb
-        args: [--ignore, FURB126]
--   repo: https://github.com/econchick/interrogate
-    rev: 1.7.0
-    hooks:
-    -   id: interrogate
-        args: [-v, --fail-under=40, src, tests]
 -   repo: https://github.com/executablebooks/mdformat
     rev: 0.7.17
     hooks:
@@ -74,7 +60,7 @@ repos:
     hooks:
     -   id: check-manifest
         args: [--no-build-isolation]
-        additional_dependencies: [setuptools-scm, toml]
+        additional_dependencies: [setuptools-scm, wheel, toml]
 -   repo: meta
     hooks:
     -   id: check-hooks-apply

pyproject.toml

@@ -2,11 +2,9 @@
 requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
 build-backend = "setuptools.build_meta"
 
-
 [tool.setuptools_scm]
 write_to = "src/pytask_r/_version.py"
 
-
 [tool.mypy]
 files = ["src", "tests"]
 check_untyped_defs = true
@@ -17,56 +15,41 @@ no_implicit_optional = true
 warn_redundant_casts = true
 warn_unused_ignores = true
 
-
 [[tool.mypy.overrides]]
 module = "tests.*"
 disallow_untyped_defs = false
 ignore_errors = true
 
-
 [tool.ruff]
 target-version = "py38"
-select = ["ALL"]
 fix = true
+unsafe-fixes = true
+
+[tool.ruff.lint]
 extend-ignore = [
-    "TCH",
-    "TRY",
-    # Numpy docstyle
-    "D107",
-    "D203",
-    "D212",
-    "D213",
-    "D402",
-    "D413",
-    "D415",
-    "D416",
-    "D417",
-    # Others.
-    "D404",  # Do not start module docstring with "This".
-    "RET504",  # unnecessary variable assignment before return.
     "S101",  # raise errors for asserts.
     "B905",  # strict parameter for zip that was implemented in py310.
-    "I",  # ignore isort
     "ANN101",  # type annotating self
     "ANN102",  # type annotating cls
     "FBT",  # flake8-boolean-trap
     "EM",  # flake8-errmsg
     "ANN401",  # flake8-annotate typing.Any
     "PD",  # pandas-vet
-    "COM812",  # trailing comma missing, but black takes care of that
+    "COM812",  # Comply with ruff-format
+    "ISC001",  # Comply with ruff-format
 ]
+select = ["ALL"]
 
-
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "tests/*" = ["D", "ANN"]
 
-
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
+[tool.ruff.lint.isort]
+force-single-line = true
 
 [tool.pytest.ini_options]
-# Do not add src since it messes with the loading of pytask-parallel as a plugin.
 testpaths = ["tests"]
 markers = [
     "wip: Tests that are work-in-progress.",

src/pytask_r/__init__.py

@@ -1,4 +1,4 @@
-"""This module contains the main namespace of pytask-r."""
+"""Contains the main namespace of pytask-r."""
 
 from __future__ import annotations
 

src/pytask_r/collect.py

@@ -7,27 +7,31 @@
 from pathlib import Path
 from typing import Any
 
-from pytask import has_mark
-from pytask import hookimpl
-from pytask import is_task_function
 from pytask import Mark
 from pytask import NodeInfo
-from pytask import parse_dependencies_from_task_function
-from pytask import parse_products_from_task_function
 from pytask import PathNode
 from pytask import PTask
 from pytask import PythonNode
-from pytask import remove_marks
 from pytask import Session
 from pytask import Task
 from pytask import TaskWithoutPath
-from pytask_r.serialization import create_path_to_serialized
+from pytask import has_mark
+from pytask import hookimpl
+from pytask import is_task_function
+from pytask import parse_dependencies_from_task_function
+from pytask import parse_products_from_task_function
+from pytask import remove_marks
+
 from pytask_r.serialization import SERIALIZERS
+from pytask_r.serialization import create_path_to_serialized
 from pytask_r.shared import r
 
 
 def run_r_script(
-    _script: Path, _options: list[str], _serialized: Path, **kwargs: Any  # noqa: ARG001
+    _script: Path,
+    _options: list[str],
+    _serialized: Path,
+    **kwargs: Any,  # noqa: ARG001
 ) -> None:
     """Run an R script."""
     cmd = ["Rscript", _script.as_posix(), *_options, str(_serialized)]
@@ -50,10 +54,11 @@ def pytask_collect_task(
         # Parse @pytask.mark.r decorator.
         obj, marks = remove_marks(obj, "r")
         if len(marks) > 1:
-            raise ValueError(
+            msg = (
                 f"Task {name!r} has multiple @pytask.mark.r marks, but only one is "
                 "allowed."
             )
+            raise ValueError(msg)
 
         mark = _parse_r_mark(
             mark=marks[0],
@@ -89,10 +94,11 @@ def pytask_collect_task(
         )
 
         if not (isinstance(script_node, PathNode) and script_node.path.suffix == ".r"):
-            raise ValueError(
+            msg = (
                 "The 'script' keyword of the @pytask.mark.r decorator must point "
                 f"to Julia file with the .r suffix, but it is {script_node}."
             )
+            raise ValueError(msg)
 
         options_node = session.hook.pytask_collect_node(
             session=session,
@@ -182,5 +188,4 @@ def _parse_r_mark(
     )
     parsed_kwargs["suffix"] = suffix or proposed_suffix  # type: ignore[assignment]
 
-    mark = Mark("r", (), parsed_kwargs)
-    return mark
+    return Mark("r", (), parsed_kwargs)

src/pytask_r/config.py

@@ -5,6 +5,7 @@
 from typing import Any
 
 from pytask import hookimpl
+
 from pytask_r.serialization import SERIALIZERS
 
 
@@ -14,10 +15,11 @@ def pytask_parse_config(config: dict[str, Any]) -> None:
     config["markers"]["r"] = "Tasks which are executed with Rscript."
     config["r_serializer"] = config.get("r_serializer", "json")
     if config["r_serializer"] not in SERIALIZERS:
-        raise ValueError(
+        msg = (
             f"'r_serializer' is {config['r_serializer']} and not one of "
             f"{list(SERIALIZERS)}."
         )
+        raise ValueError(msg)
     config["r_suffix"] = config.get("r_suffix", "")
     config["r_options"] = _parse_value_or_whitespace_option(config.get("r_options"))
 
@@ -28,4 +30,5 @@ def _parse_value_or_whitespace_option(value: Any) -> list[str] | None:
         return None
     if isinstance(value, list):
         return list(map(str, value))
-    raise ValueError(f"'r_options' is {value} and not a list.")
+    msg = f"'r_options' is {value} and not a list."
+    raise ValueError(msg)

src/pytask_r/execute.py

@@ -5,12 +5,13 @@
 import shutil
 from typing import Any
 
-from pytask import get_marks
-from pytask import hookimpl
 from pytask import PPathNode
 from pytask import PTask
 from pytask import PythonNode
+from pytask import get_marks
+from pytask import hookimpl
 from pytask.tree_util import tree_map
+
 from pytask_r.serialization import serialize_keyword_arguments
 from pytask_r.shared import r
 
@@ -21,9 +22,10 @@ def pytask_execute_task_setup(task: PTask) -> None:
     marks = get_marks(task, "r")
     if marks:
         if shutil.which("Rscript") is None:
-            raise RuntimeError(
+            msg = (
                 "Rscript is needed to run R scripts, but it is not found on your PATH."
             )
+            raise RuntimeError(msg)
 
         assert len(marks) == 1
 
@@ -32,9 +34,9 @@ def pytask_execute_task_setup(task: PTask) -> None:
         assert suffix
 
         serialized_node: PythonNode = task.depends_on["_serialized"]  # type: ignore[assignment]
-        serialized_node.value.parent.mkdir(parents=True, exist_ok=True)
+        serialized_node.value.parent.mkdir(parents=True, exist_ok=True)  # type: ignore[union-attr]
         kwargs = collect_keyword_arguments(task)
-        serialize_keyword_arguments(serializer, serialized_node.value, kwargs)
+        serialize_keyword_arguments(serializer, serialized_node.value, kwargs)  # type: ignore[arg-type]
 
 
 def collect_keyword_arguments(task: PTask) -> dict[str, Any]:

src/pytask_r/plugin.py

@@ -2,12 +2,17 @@
 
 from __future__ import annotations
 
-from pluggy import PluginManager
+from typing import TYPE_CHECKING
+
 from pytask import hookimpl
+
 from pytask_r import collect
 from pytask_r import config
 from pytask_r import execute
 
+if TYPE_CHECKING:
+    from pluggy import PluginManager
+
 
 @hookimpl
 def pytask_add_hooks(pm: PluginManager) -> None:

src/pytask_r/serialization.py

@@ -1,4 +1,4 @@
-"""This module contains the code to serialize keyword arguments to the task."""
+"""Contains the code to serialize keyword arguments to the task."""
 
 from __future__ import annotations
 
@@ -10,7 +10,6 @@
 from pytask import PTask
 from pytask import PTaskWithPath
 
-
 _HIDDEN_FOLDER = ".pytask/pytask-r"
 
 
@@ -30,8 +29,7 @@ def create_path_to_serialized(task: PTask, suffix: str) -> Path:
     """Create path to serialized."""
     parent = task.path.parent if isinstance(task, PTaskWithPath) else Path.cwd()
     file_name = create_file_name(task, suffix)
-    path = parent.joinpath(_HIDDEN_FOLDER, file_name).with_suffix(suffix)
-    return path
+    return parent.joinpath(_HIDDEN_FOLDER, file_name).with_suffix(suffix)
 
 
 def create_file_name(task: PTask, suffix: str) -> str:
@@ -60,11 +58,10 @@ def serialize_keyword_arguments(
     if callable(serializer):
         serializer_func = serializer
     elif isinstance(serializer, str) and serializer in SERIALIZERS:
-        serializer_func = SERIALIZERS[serializer][
-            "serializer"
-        ]  # type: ignore[assignment]
+        serializer_func = SERIALIZERS[serializer]["serializer"]  # type: ignore[assignment]
     else:
-        raise ValueError(f"Serializer {serializer!r} is not known.")
+        msg = f"Serializer {serializer!r} is not known."
+        raise ValueError(msg)
 
     serialized = serializer_func(kwargs)
     path_to_serialized.write_text(serialized)

src/pytask_r/shared.py

@@ -1,13 +1,16 @@
-"""This module contains shared functions."""
+"""Contains shared functions."""
 
 from __future__ import annotations
 
-from pathlib import Path
+from typing import TYPE_CHECKING
 from typing import Any
 from typing import Callable
 from typing import Iterable
 from typing import Sequence
 
+if TYPE_CHECKING:
+    from pathlib import Path
+
 
 def r(
     *,

tests/conftest.py

@@ -8,7 +8,6 @@
 import pytest
 from click.testing import CliRunner
 
-
 needs_rscript = pytest.mark.skipif(
     shutil.which("Rscript") is None, reason="R with Rscript needs to be installed."
 )
@@ -37,7 +36,7 @@ class SysPathsSnapshot:
     """A snapshot for sys.path."""
 
     def __init__(self) -> None:
-        self.__saved = list(sys.path), list(sys.meta_path)
+        self.__saved = sys.path.copy(), sys.meta_path.copy()
 
     def restore(self) -> None:
         sys.path[:], sys.meta_path[:] = self.__saved
@@ -48,7 +47,7 @@ class SysModulesSnapshot:
 
     def __init__(self, preserve: Callable[[str], bool] | None = None) -> None:
         self.__preserve = preserve
-        self.__saved = dict(sys.modules)
+        self.__saved = sys.modules.copy()
 
     def restore(self) -> None:
         if self.__preserve: