Update ruff-pre-commit config

.pre-commit-config.yaml

@@ -17,14 +17,37 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
+# - repo: https://github.com/PyCQA/docformatter
+#   rev: master
+#   hooks:
+#     - id: docformatter
+#       additional_dependencies: [tomli]
+#       args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+#       # --config, ./pyproject.toml
+
+# - repo: https://github.com/psf/black
+#   rev: 24.8.0
+#   hooks:
+#   - id: black
+#     language_version: python3
+
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.15.6
+  rev: v0.16.2
   hooks:
-    - id: ruff
-      args: [--fix, --exit-non-zero-on-fix]
+    # Run the linter.
+    - id: ruff-check
+      args: [--fix, --exit-zero]
+    # Run the formatter.
     - id: ruff-format
 
+## If like to embrace black styles even in the docs:
+# - repo: https://github.com/asottile/blacken-docs
+#   rev: v1.13.0
+#   hooks:
+#   - id: blacken-docs
+#     additional_dependencies: [black]
+
 ## Check for misspells in documentation files:
 # - repo: https://github.com/codespell-project/codespell
 #   rev: v2.2.5

pyproject.toml

@@ -11,15 +11,17 @@ version_scheme = "no-guess-dev"
 [tool.ruff]
 line-length = 120
 src = ["src"]
-exclude = ["tests"]
-lint.extend-ignore = ["F821"]
+exclude = ["tests", "docs"]
+
+[tool.ruff.lint]
+extend-ignore = ["F821"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
 
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
+
 [tool.ruff.format]
 docstring-code-format = true
 docstring-code-line-length = 20
-
-[tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["E402", "F401"]

setup.py

@@ -12,7 +12,7 @@
 if __name__ == "__main__":
     try:
         setup(use_scm_version={"version_scheme": "no-guess-dev"})
-    except:  # noqa
+    except:
         print(
             "\n\nAn error occurred while building the project, "
             "please ensure you have the most updated version of setuptools, "

src/biocsetup/create_repository.py

@@ -1,6 +1,5 @@
 import shutil
 from pathlib import Path
-from typing import Optional
 
 from pyscaffold import api, file_system, shell
 from pyscaffoldext.markdown.extension import Markdown
@@ -12,7 +11,7 @@
 
 def create_repository(
     project_path: str,
-    description: Optional[str] = "Add a short description here!",
+    description: str | None = "Add a short description here!",
     license: str = "MIT",
     rst: bool = False,
 ) -> None:
@@ -154,18 +153,20 @@ def create_repository(
 [tool.ruff]
 line-length = 120
 src = ["src"]
-exclude = ["tests"]
-lint.extend-ignore = ["F821"]
+exclude = ["tests", "docs"]
+
+[tool.ruff.lint]
+extend-ignore = ["F821"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
 
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
+
 [tool.ruff.format]
 docstring-code-format = true
 docstring-code-line-length = 20
-
-[tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["E402", "F401"]
 """
 
     with open(pyprj_path, "w") as f:

src/biocsetup/templates/precommit/pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -17,14 +17,37 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
+# - repo: https://github.com/PyCQA/docformatter
+#   rev: master
+#   hooks:
+#     - id: docformatter
+#       additional_dependencies: [tomli]
+#       args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+#       # --config, ./pyproject.toml
+
+# - repo: https://github.com/psf/black
+#   rev: 24.8.0
+#   hooks:
+#   - id: black
+#     language_version: python3
+
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.8.2
+  rev: v0.16.2
   hooks:
-    - id: ruff
-      args: [--fix, --exit-non-zero-on-fix]
+    # Run the linter.
+    - id: ruff-check
+      args: [--fix, --exit-zero]
+    # Run the formatter.
     - id: ruff-format
 
+## If like to embrace black styles even in the docs:
+# - repo: https://github.com/asottile/blacken-docs
+#   rev: v1.13.0
+#   hooks:
+#   - id: blacken-docs
+#     additional_dependencies: [black]
+
 ## Check for misspells in documentation files:
 # - repo: https://github.com/codespell-project/codespell
 #   rev: v2.2.5