Add mypy, ruff, and refurb.

.pre-commit-config.yaml

@@ -9,19 +9,14 @@ repos:
     -   id: debug-statements
     -   id: end-of-file-fixer
 -   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0  # Use the ref you want to point at
+    rev: v1.9.0
     hooks:
     -   id: python-check-blanket-noqa
     -   id: python-check-mock-methods
     -   id: python-no-eval
     -   id: python-no-log-warn
     -   id: python-use-type-annotations
     -   id: text-unicode-replacement-char
--   repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.1
-    hooks:
-    -   id: pyupgrade
-        args: [--py37-plus]
 -   repo: https://github.com/asottile/reorder_python_imports
     rev: v3.9.0
     hooks:
@@ -40,27 +35,15 @@ repos:
     rev: 22.12.0
     hooks:
     -   id: black
--   repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.215
     hooks:
-    -   id: flake8
-        types: [python]
-        additional_dependencies: [
-            flake8-alfred,
-            flake8-bugbear,
-            flake8-builtins,
-            flake8-comprehensions,
-            flake8-docstrings,
-            flake8-eradicate,
-            flake8-print,
-            flake8-pytest-style,
-            flake8-todo,
-            flake8-typing-imports,
-            flake8-unused-arguments,
-            pep8-naming,
-            pydocstyle,
-            Pygments,
-        ]
+      - id: ruff
+-   repo: https://github.com/dosisod/refurb
+    rev: v1.9.1
+    hooks:
+    -   id: refurb
+        args: [--ignore, FURB126]
 -   repo: https://github.com/econchick/interrogate
     rev: 1.5.0
     hooks:
@@ -79,6 +62,21 @@ repos:
   rev: v2.2.2
   hooks:
     -   id: codespell
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v0.991'
+    hooks:
+    -   id: mypy
+        args: [
+            --no-strict-optional,
+            --ignore-missing-imports,
+        ]
+        additional_dependencies: [
+            attrs>=21.3.0,
+            click,
+            types-PyYAML,
+            types-setuptools
+        ]
+        pass_filenames: false
 -   repo: https://github.com/mgedmin/check-manifest
     rev: "0.49"
     hooks:

CHANGES.md

@@ -8,6 +8,7 @@ releases are available on [PyPI](https://pypi.org/project/pytask-r) and
 ## 0.3.0 - 2023-xx-xx
 
 - {pull}`33` deprecates INI configurations and aligns the plugin with pytask v0.3.
+- {pull}`34` adds mypy, ruff and refurb.
 
 ## 0.2.0 - 2022-04-16
 

pyproject.toml

@@ -5,3 +5,58 @@ build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 write_to = "src/pytask_r/_version.py"
+
+
+[tool.mypy]
+files = ["src", "tests"]
+check_untyped_defs = true
+disallow_any_generics = true
+disallow_incomplete_defs = true
+disallow_untyped_defs = true
+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 = "py37"
+select = ["ALL"]
+fix = true
+extend-ignore = [
+    # 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
+]
+
+
+[tool.ruff.per-file-ignores]
+"tests/*" = ["D", "ANN"]
+
+
+[tool.ruff.pydocstyle]
+convention = "numpy"

src/pytask_r/__init__.py

@@ -1,3 +1,4 @@
+"""This module contains the main namespace of pytask-r."""
 from __future__ import annotations
 
 try:

src/pytask_r/collect.py

@@ -5,6 +5,7 @@
 import subprocess
 from pathlib import Path
 from types import FunctionType
+from typing import Any
 
 from pytask import depends_on
 from pytask import has_mark
@@ -13,6 +14,7 @@
 from pytask import parse_nodes
 from pytask import produces
 from pytask import remove_marks
+from pytask import Session
 from pytask import Task
 from pytask_r.serialization import SERIALIZERS
 from pytask_r.shared import r
@@ -26,7 +28,9 @@ def run_r_script(script: Path, options: list[str], serialized: Path) -> None:
 
 
 @hookimpl
-def pytask_collect_task(session, path, name, obj):
+def pytask_collect_task(
+    session: Session, path: Path, name: str, obj: Any
+) -> Task | None:
     """Perform some checks."""
     __tracebackhide__ = True
 
@@ -62,7 +66,7 @@ def pytask_collect_task(session, path, name, obj):
         task = Task(
             base_name=name,
             path=path,
-            function=_copy_func(run_r_script),
+            function=_copy_func(run_r_script),  # type: ignore[arg-type]
             depends_on=dependencies,
             produces=products,
             markers=markers,
@@ -85,28 +89,33 @@ def pytask_collect_task(session, path, name, obj):
         )
 
         return task
+    return None
 
 
-def _parse_r_mark(mark, default_options, default_serializer, default_suffix):
+def _parse_r_mark(
+    mark: Mark,
+    default_options: list[str] | None,
+    default_serializer: str,
+    default_suffix: str,
+) -> Mark:
     """Parse a Julia mark."""
     script, options, serializer, suffix = r(**mark.kwargs)
 
     parsed_kwargs = {}
-    for arg_name, value, default in [
+    for arg_name, value, default in (
         ("script", script, None),
         ("options", options, default_options),
         ("serializer", serializer, default_serializer),
-    ]:
-        parsed_kwargs[arg_name] = value if value else default
+    ):
+        parsed_kwargs[arg_name] = value or default
 
-    if (
-        isinstance(parsed_kwargs["serializer"], str)
+    proposed_suffix = (
+        SERIALIZERS[parsed_kwargs["serializer"]]["suffix"]
+        if isinstance(parsed_kwargs["serializer"], str)
         and parsed_kwargs["serializer"] in SERIALIZERS
-    ):
-        proposed_suffix = SERIALIZERS[parsed_kwargs["serializer"]]["suffix"]
-    else:
-        proposed_suffix = default_suffix
-    parsed_kwargs["suffix"] = suffix if suffix else proposed_suffix
+        else default_suffix
+    )
+    parsed_kwargs["suffix"] = suffix or proposed_suffix  # type: ignore[assignment]
 
     mark = Mark("r", (), parsed_kwargs)
     return mark

src/pytask_r/config.py

@@ -1,12 +1,14 @@
 """Configure pytask."""
 from __future__ import annotations
 
+from typing import Any
+
 from pytask import hookimpl
 from pytask_r.serialization import SERIALIZERS
 
 
 @hookimpl
-def pytask_parse_config(config):
+def pytask_parse_config(config: dict[str, Any]) -> None:
     """Register the r marker."""
     config["markers"]["r"] = "Tasks which are executed with Rscript."
     config["r_serializer"] = config.get("r_serializer", "json")
@@ -23,7 +25,6 @@ def _parse_value_or_whitespace_option(value: str | None) -> None | str | list[st
     """Parse option which can hold a single value or values separated by new lines."""
     if value is None:
         return None
-    elif isinstance(value, list):
+    if isinstance(value, list):
         return list(map(str, value))
-    else:
-        raise ValueError(f"'r_options' is {value} and not a list.")
+    raise ValueError(f"'r_options' is {value} and not a list.")

src/pytask_r/execute.py

@@ -15,7 +15,7 @@
 
 
 @hookimpl
-def pytask_execute_task_setup(task):
+def pytask_execute_task_setup(task: Task) -> None:
     """Perform some checks when a task marked with the r marker is executed."""
     marks = get_marks(task, "r")
     if marks:

src/pytask_r/parametrize.py

@@ -1,13 +1,14 @@
 """Parametrize tasks."""
 from __future__ import annotations
 
+from typing import Any
+
 import pytask
 from pytask import hookimpl
 
 
 @hookimpl
-def pytask_parametrize_kwarg_to_marker(obj, kwargs):
+def pytask_parametrize_kwarg_to_marker(obj: Any, kwargs: dict[Any, Any]) -> None:
     """Attach parametrized r arguments to the function with a marker."""
-    if callable(obj):
-        if "r" in kwargs:
-            pytask.mark.r(**kwargs.pop("r"))(obj)
+    if callable(obj) and "r" in kwargs:
+        pytask.mark.r(**kwargs.pop("r"))(obj)

src/pytask_r/plugin.py

@@ -1,6 +1,7 @@
 """Register hook specifications and implementations."""
 from __future__ import annotations
 
+from pluggy import PluginManager
 from pytask import hookimpl
 from pytask_r import collect
 from pytask_r import config
@@ -9,7 +10,7 @@
 
 
 @hookimpl
-def pytask_add_hooks(pm):
+def pytask_add_hooks(pm: PluginManager) -> None:
     """Register hook implementations."""
     pm.register(collect)
     pm.register(config)

src/pytask_r/serialization.py

@@ -50,14 +50,17 @@ def create_file_name(task: Task, suffix: str) -> str:
 
 
 def serialize_keyword_arguments(
-    serializer: str | Callable[dict[str, Any], str],
+    serializer: str | Callable[..., str],
     path_to_serialized: Path,
     kwargs: dict[str, Any],
 ) -> None:
+    """Serialize keyword arguments."""
     if callable(serializer):
         serializer_func = serializer
     elif isinstance(serializer, str) and serializer in SERIALIZERS:
-        serializer_func = SERIALIZERS[serializer]["serializer"]
+        serializer_func = SERIALIZERS[serializer][
+            "serializer"
+        ]  # type: ignore[assignment]
     else:
         raise ValueError(f"Serializer {serializer!r} is not known.")
 

src/pytask_r/shared.py

@@ -1,6 +1,8 @@
+"""This module contains shared functions."""
 from __future__ import annotations
 
 from pathlib import Path
+from typing import Any
 from typing import Callable
 from typing import Iterable
 from typing import Sequence
@@ -39,17 +41,9 @@ def r(
     return script, options, serializer, suffix
 
 
-def _to_list(scalar_or_iter):
+def _to_list(scalar_or_iter: Any) -> list[Any]:
     """Convert scalars and iterables to list.
 
-    Parameters
-    ----------
-    scalar_or_iter : str or list
-
-    Returns
-    -------
-    list
-
     Examples
     --------
     >>> _to_list("a")

tests/test_collect.py

@@ -9,9 +9,9 @@
 from pytask_r.serialization import SERIALIZERS
 
 
-@pytest.mark.unit
+@pytest.mark.unit()
 @pytest.mark.parametrize(
-    "args, kwargs, expectation, expected",
+    ("args", "kwargs", "expectation", "expected"),
     [
         (
             (),
@@ -43,9 +43,16 @@ def test_r(args, kwargs, expectation, expected):
         assert result == expected
 
 
-@pytest.mark.unit
+@pytest.mark.unit()
 @pytest.mark.parametrize(
-    "mark, default_options, default_serializer, default_suffix, expectation, expected",
+    (
+        "mark",
+        "default_options",
+        "default_serializer",
+        "default_suffix",
+        "expectation",
+        "expected",
+    ),
     [
         (
             Mark("r", (), {"script": "script.r"}),

tests/test_config.py

@@ -4,7 +4,7 @@
 from pytask import main
 
 
-@pytest.mark.end_to_end
+@pytest.mark.end_to_end()
 def test_marker_is_configured(tmp_path):
     session = main({"paths": tmp_path})