DX: replace nbqa-ruff with official Ruff formatter

.cspell.json

@@ -69,6 +69,7 @@
     "conda",
     "fromdict",
     "indentless",
+    "ipynb",
     "jsonschema",
     "linkcheck",
     "maxdepth",

.pre-commit-config.yaml

@@ -112,8 +112,7 @@ repos:
     rev: v0.1.4
     hooks:
       - id: ruff
-        args:
-          - --fix
+        args: [--fix]
 
   - repo: https://github.com/ComPWA/mirrors-taplo
     rev: v0.8.1

src/repoma/check_dev_files/__init__.py

@@ -70,7 +70,7 @@ def main(argv: Optional[Sequence[str]] = None) -> int:
         executor(pytest.main)
         executor(pyupgrade.main)
         if not args.no_ruff:
-            executor(ruff.main)
+            executor(ruff.main, has_notebooks)
         executor(setup_cfg.main, args.ignore_author)
     if args.pin_requirements != "no":
         executor(

src/repoma/check_dev_files/black.py

@@ -1,5 +1,6 @@
 """Update :file:`pyproject.toml` black configuration."""
 
+from ruamel.yaml import YAML
 from ruamel.yaml.comments import CommentedMap
 
 from repoma.errors import PrecommitError
@@ -97,8 +98,8 @@ def _update_precommit_repo(has_notebooks: bool) -> None:
     if has_notebooks:
         black_jupyter = CommentedMap(
             id="black-jupyter",
-            args=["--line-length=85"],
-            types_or=["jupyter"],
+            args=YAML(typ="rt").load("[--line-length=85]"),
+            types_or=YAML(typ="rt").load("[jupyter]"),
         )
         expected_hook["hooks"].append(black_jupyter)
     update_single_hook_precommit_repo(expected_hook)

src/repoma/check_dev_files/pyupgrade.py

@@ -1,6 +1,7 @@
 """Install `pyupgrade <https://github.com/asottile/pyupgrade>`_ as a hook."""
 
-from ruamel.yaml.comments import CommentedMap
+from ruamel.yaml import YAML
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 from repoma.utilities import natural_sorting
 from repoma.utilities.executor import Executor
@@ -24,7 +25,7 @@ def _update_precommit_repo() -> None:
         hooks=[
             CommentedMap(
                 id="pyupgrade",
-                args=[__get_pyupgrade_version_argument()],
+                args=__get_pyupgrade_version_argument(),
             )
         ],
     )
@@ -36,20 +37,21 @@ def _update_precommit_nbqa_hook() -> None:
         repo_url="https://github.com/nbQA-dev/nbQA",
         expected_hook=CommentedMap(
             id="nbqa-pyupgrade",
-            args=[__get_pyupgrade_version_argument()],
+            args=__get_pyupgrade_version_argument(),
         ),
     )
 
 
-def __get_pyupgrade_version_argument() -> str:
+def __get_pyupgrade_version_argument() -> CommentedSeq:
     """Get the --py3x-plus argument for pyupgrade.
 
     >>> __get_pyupgrade_version_argument()
-    '--py36-plus'
+    ['--py36-plus']
     """
     supported_python_versions = sorted(
         (v.replace(".", "") for v in get_supported_python_versions()),
         key=natural_sorting,
     )
     lowest_version = supported_python_versions[0]
-    return f"--py{lowest_version}-plus"
+    yaml = YAML(typ="rt")
+    return yaml.load(f"[--py{lowest_version}-plus]")

src/repoma/check_dev_files/ruff.py

@@ -5,6 +5,7 @@
 from textwrap import dedent
 from typing import List, Set
 
+from ruamel.yaml import YAML
 from ruamel.yaml.comments import CommentedMap
 from tomlkit.items import Array, Table
 
@@ -17,7 +18,6 @@
 from repoma.utilities.executor import Executor
 from repoma.utilities.precommit import (
     remove_precommit_hook,
-    update_precommit_hook,
     update_single_hook_precommit_repo,
 )
 from repoma.utilities.project_info import (
@@ -30,7 +30,6 @@
     get_sub_table,
     load_pyproject,
     to_toml_array,
-    update_nbqa_settings,
     write_pyproject,
 )
 from repoma.utilities.readme import add_badge, remove_badge
@@ -42,7 +41,7 @@
 )
 
 
-def main() -> None:
+def main(has_notebooks: bool) -> None:
     executor = Executor()
     executor(
         add_badge,
@@ -51,14 +50,13 @@ def main() -> None:
     executor(_check_setup_cfg)
     executor(_remove_flake8)
     executor(_remove_isort)
+    executor(_remove_nbqa)
     executor(_remove_pydocstyle)
     executor(_remove_pylint)
-    executor(_update_nbqa_settings)
-    executor(_update_ruff_settings)
-    executor(_update_ruff_per_file_ignores)
+    executor(_update_ruff_settings, has_notebooks)
+    executor(_update_ruff_per_file_ignores, has_notebooks)
     executor(_update_ruff_pydocstyle_settings)
-    executor(_update_precommit_hook)
-    executor(_update_precommit_nbqa_hook)
+    executor(_update_precommit_hook, has_notebooks)
     executor(_update_pyproject)
     executor(_update_vscode_settings)
     executor.finalize()
@@ -268,28 +266,29 @@ def __add_package(optional_dependencies: Table, key: str, package: str) -> None:
         )
 
 
-def _update_nbqa_settings() -> None:
+def _remove_nbqa() -> None:
+    executor = Executor()
+    executor(__remove_nbqa_settings)
+    executor(remove_precommit_hook, "nbqa-ruff")
+    executor.finalize()
+
+
+def __remove_nbqa_settings() -> None:
     # cspell:ignore addopts
-    ruff_rules = [
-        "--extend-ignore=B018",
-        "--extend-ignore=C90",
-        "--extend-ignore=D",
-        "--extend-ignore=N806",
-        "--extend-ignore=N816",
-        "--extend-ignore=PLR09",
-        "--extend-ignore=PLR2004",
-        "--extend-ignore=PLW0602",
-        "--extend-ignore=PLW0603",
-        "--line-length=85",
-    ]
     pyproject = load_pyproject()
-    nbqa_table = get_sub_table(pyproject, "tool.nbqa.addopts", create=True)
-    ruff_rules.extend(nbqa_table.get("ruff", []))
-    ruff_rules = sorted(set(ruff_rules))
-    update_nbqa_settings("ruff", to_toml_array(ruff_rules))
+    nbqa_addopts = get_sub_table(pyproject, "tool.nbqa.addopts", create=True)
+    if "ruff" in nbqa_addopts:
+        del nbqa_addopts["ruff"]
+    if not nbqa_addopts:
+        tool_table = get_sub_table(pyproject, "tool", create=True)
+        del tool_table["nbqa"]
+    write_pyproject(pyproject)
+    if nbqa_addopts:
+        msg = f"Removed Ruff configuration for nbQA from {CONFIG_PATH.pyproject}"
+        raise PrecommitError(msg)
 
 
-def _update_ruff_settings() -> None:
+def _update_ruff_settings(has_notebooks: bool) -> None:
     pyproject = load_pyproject()
     settings = get_sub_table(pyproject, "tool.ruff", create=True)
     extend_ignore = [
@@ -315,6 +314,10 @@ def _update_ruff_settings() -> None:
         "target-version": __get_target_version(),
         "task-tags": __get_task_tags(settings),
     }
+    if has_notebooks:
+        extend_include = ["*.ipynb"]
+        extend_include = sorted({*settings.get("extend-include", []), *extend_include})
+        minimal_settings["extend-include"] = to_toml_array(extend_include)
     src_directories = __get_src_directories()
     if src_directories:
         minimal_settings["src"] = src_directories
@@ -404,10 +407,23 @@ def __get_target_version() -> str:
     return lowest_version
 
 
-def _update_ruff_per_file_ignores() -> None:
+def _update_ruff_per_file_ignores(has_notebooks: bool) -> None:
     pyproject = load_pyproject()
     settings = get_sub_table(pyproject, "tool.ruff.per-file-ignores", create=True)
     minimal_settings = {}
+    if has_notebooks:
+        notebook_ignores = [
+            "B018",
+            "C90",
+            "D",
+            "N806",
+            "N816",
+            "PLR09",
+            "PLR2004",
+            "PLW0602",
+            "PLW0603",
+        ]
+        minimal_settings["*.ipynb"] = to_toml_array(notebook_ignores)
     docs_dir = "docs"
     if os.path.exists(docs_dir) and os.path.isdir(docs_dir):
         key = f"{docs_dir}/*"
@@ -455,26 +471,19 @@ def _update_ruff_pydocstyle_settings() -> None:
         raise PrecommitError(msg)
 
 
-def _update_precommit_hook() -> None:
+def _update_precommit_hook(has_notebooks: bool) -> None:
     if not CONFIG_PATH.precommit.exists():
         return
-    expected_hook = CommentedMap(
+    yaml = YAML(typ="rt")
+    ruff_hook = CommentedMap(id="ruff", args=yaml.load("[--fix]"))
+    if has_notebooks:
+        types = yaml.load("[python, pyi, jupyter]")
+        ruff_hook["types_or"] = types
+    expected_repo = CommentedMap(
         repo="https://github.com/astral-sh/ruff-pre-commit",
-        hooks=[CommentedMap(id="ruff", args=["--fix"])],
-    )
-    update_single_hook_precommit_repo(expected_hook)
-
-
-def _update_precommit_nbqa_hook() -> None:
-    if not CONFIG_PATH.precommit.exists():
-        return
-    update_precommit_hook(
-        repo_url="https://github.com/nbQA-dev/nbQA",
-        expected_hook=CommentedMap(
-            id="nbqa-ruff",
-            args=["--fix"],
-        ),
+        hooks=[ruff_hook],
     )
+    update_single_hook_precommit_repo(expected_repo)
 
 
 def _update_vscode_settings() -> None:

src/repoma/check_dev_files/toml.py

@@ -7,6 +7,7 @@
 from typing import List, Union
 
 import tomlkit
+from ruamel.yaml import YAML
 from ruamel.yaml.comments import CommentedMap
 
 from repoma.errors import PrecommitError
@@ -73,7 +74,7 @@ def _update_tomlsort_config() -> None:
 def _update_tomlsort_hook() -> None:
     expected_hook = CommentedMap(
         repo="https://github.com/pappasam/toml-sort",
-        hooks=[CommentedMap(id="toml-sort", args=["--in-place"])],
+        hooks=[CommentedMap(id="toml-sort", args=YAML(typ="rt").load("[--in-place]"))],
     )
     excludes = []
     if glob("labels/*.toml"):