[nc-time-axis] QA refresh linter hooks (#293)

* Updated pre-commit-config.yaml with:
  - trailing-whitespace hook
  - CI chore
  - global file list

* Added blacken-docs hook.
  - Required manually disabling on @savefig lines in docs/examples.rst
  - Update files list to include doc/*.rst in filespre-commit-config.yaml

* small update to tpyes in codespell hook

* Added Ruff linter to replace black, flake8 and isort.
Includes Ruff autofixes:
 - 11 × D212 (multi-line-summary-first-line)
 - 1 × RET506 (superfluous-else-raise)
 - 1 × RET505 (superfluous-else-return)
 - 1 × I001 (unsorted-imports)
Added `PLR5501` to exclude list to preserve readability of TODO
block in convert method

* Ignores for Ruff linter

* Autofixes

* Added mypy linter and exceptions

* Added numpydoc and exceptions

* Reorder hooks alphabetically

* Added sort-all hook

* Added validate-pyproject hook

* Added sp-repo-review hook and excludes.
  - Applied some fixes to [tool.pytest.ini_options]

* Added references to SciTools linters Wiki

* Fixed repo-review "PP304" [Sets the log level in pytest]

* Fixed sp-repo-review: "GH212" [Require GHA update grouping]

* Removed wheel from build (Fixes sp-repo-review "PP003")

* Alphabetised pyproject.toml sections (manually)

* Try to fix brocken docs build

* Fixed docs build (had to make `.. blacken-docs:off` apply to whole code block

* Better comment on ruff select list

* Added annotations to ruff ignore list

.flake8

@@ -23,7 +23,7 @@ ignore =
     W503,
     # W504: line break after binary operator
     W504
-exclude = 
+exclude =
     .eggs
     build
     docs/conf.py

.github/ISSUE_TEMPLATE/bug-report.md

@@ -13,14 +13,14 @@ assignees: ''
 ## How to Reproduce
 Steps to reproduce the behaviour:
 
-1. 
-2. 
-3. 
+1.
+2.
+3.
 
 ## Expected Behaviour
 <!-- A clear and concise description of what you expected to happen -->
 
-## Environment 
+## Environment
  - OS & Version: [e.g., Ubuntu 20.04 LTS]
  - nc-time-axis Version: [e.g., From the command line run `python -c "import nc_time_axis; print(nc_time_axis.__version__)"`]
 

.github/dependabot.yml

@@ -13,6 +13,10 @@ updates:
       day: "thursday"
       time: "01:00"
       timezone: "Europe/London"
+    groups:
+      dependencies:
+        patterns:
+          - "*"
     labels:
       - "New: Pull Request"
       - "Bot"

.pre-commit-config.yaml

@@ -1,7 +1,26 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+# See https://pre-commit.ci/#configuration
+# See https://github.com/scientific-python/cookie#sp-repo-review
+# See https://github.com/SciTools/.github/wiki/Linting for common linter rules
+
+ci:
+    autofix_prs: false
+    autoupdate_commit_msg: "chore: update pre-commit hooks"
+
+# Alphabetised, for lack of a better order.
+files: |
+    (?x)(
+        docs\/.+\.(py|rst)|
+        pyproject\.toml|
+        setup\.py|
+        src\/.+\.py
+    )
+minimum_pre_commit_version: 1.21.0
 
 repos:
+
+# Hook for pre-commit's built-in checks:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: 'v5.0.0'
     hooks:
@@ -19,37 +38,69 @@ repos:
     -   id: check-toml
         # Check YAML file syntax.
     -   id: check-yaml
-        # Makes sure files end in a newline and only a newline
+        # Makes sure files end in a newline and only a newline.
+        # Duplicates Ruff W292 but also works on non-Python files.
     -   id: end-of-file-fixer
         # Replaces or checks mixed line ending
     -   id: mixed-line-ending
         # Don't commit to main branch.
     -   id: no-commit-to-branch
+        # Trims trailing whitespace.
+        # Duplicates Ruff W291 but also works on non-Python files.
+    -   id: trailing-whitespace
 
--   repo: https://github.com/psf/black
-    rev: '24.10.0'
+# Hooks for all other repos.
+# Keep these alphabetised by hook (aka 'id') order.
+
+-   repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.19.1
     hooks:
-    -   id: black
+    -   id: blacken-docs
+        types: [file, rst]
+
+-   repo: https://github.com/codespell-project/codespell
+    rev: 'v2.3.0'
+    hooks:
+    -   id: codespell
+        types_or: [asciidoc, python, markdown, rst]
+        additional_dependencies: [tomli]
+
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.13.0'
+    hooks:
+    -   id: mypy
+        exclude: 'noxfile\.py|docs/conf\.py'
+
+-   repo: https://github.com/numpy/numpydoc
+    rev: v1.8.0
+    hooks:
+      - id: numpydoc-validation
         types: [file, python]
-        args: [--config=./pyproject.toml, .]
 
--   repo: https://github.com/PyCQA/flake8
-    rev: '7.1.1'
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.7.4"
     hooks:
-    -   id: flake8
+    -   id: ruff
+        types: [file, python]
+        args: [--fix, --show-fixes]
+    -   id: ruff-format
         types: [file, python]
-        args: [--config=./.flake8]
 
--   repo: https://github.com/pycqa/isort
-    rev: '5.13.2'
+-   repo: https://github.com/aio-libs/sort-all
+    rev: v1.3.0
     hooks:
-    -   id: isort
+    -   id: sort-all
         types: [file, python]
-        args: ["--profile", "black", "--filter-files"]
 
--   repo: https://github.com/codespell-project/codespell
-    rev: 'v2.3.0'
+-   repo: https://github.com/scientific-python/cookie
+    rev: 2024.08.19
     hooks:
-    -   id: codespell
-        types_or: [python, markdown, rst]
-        additional_dependencies: [tomli]
+    - id: sp-repo-review
+      additional_dependencies: ["repo-review[cli]"]
+      args: ["--show=errskip"]
+
+-   repo: https://github.com/abravalheri/validate-pyproject
+    # More exhaustive than Ruff RUF200.
+    rev: "v0.23"
+    hooks:
+    - id: validate-pyproject

CONTRIBUTING.md

@@ -13,6 +13,6 @@ We would love to hear from you!
   - [View/discuss existing pull requests](https://github.com/SciTools/nc-time-axis/pulls)
   - [Raise a new pull request](https://github.com/SciTools/nc-time-axis/compare)
 
-Note that all authors on pull requests will automatically be asked to sign the 
+Note that all authors on pull requests will automatically be asked to sign the
 [SciTools Contributor Licence Agreement](https://cla-assistant.io/SciTools/)
-(CLA), if they have not already done so. 
+(CLA), if they have not already done so.

LICENSE

@@ -1,5 +1,5 @@
 BSD 3-Clause License
-Copyright (c) 2016, Met Office. 
+Copyright (c) 2016, Met Office.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

docs/examples.rst

@@ -13,6 +13,11 @@ Basic Usage
 `matplotlib`_.  To register its converters, simply ``import nc_time_axis``.  Then you
 will be able to make plots with :py:class:`cftime.datetime` axes.
 
+..
+    comment: @savefig causes blacken-docs to fail
+
+.. blacken-docs:off
+
 .. ipython:: python
     :okwarning:
 
@@ -30,6 +35,8 @@ will be able to make plots with :py:class:`cftime.datetime` axes.
     @savefig basic.png
     fig.show()
 
+.. blacken-docs:on
+
 Setting the Axes Ticks and Tick Format
 --------------------------------------
 
@@ -43,14 +50,22 @@ documentation
 for acceptable format codes) and the calendar type of the axis (see
 the :py:class:`cftime.datetime` documentation for valid calendar strings).
 
+..
+    @savefig causes blacken-docs to fail
+
+.. blacken-docs:off
+
 .. ipython:: python
     :okwarning:
 
     fig, ax = plt.subplots(1, 1)
-    ax.plot(times, y);
-    ax.set_xticks([cftime.datetime(2000, 1, day, calendar="noleap") for day in range(2, 19, 4)]);
+    ax.plot(times, y)
+    ax.set_xticks(
+        [cftime.datetime(2000, 1, day, calendar="noleap") for day in range(2, 19, 4)]
+    )
     formatter = nc_time_axis.CFTimeFormatter("%m-%d %H:%M", "noleap")
     ax.xaxis.set_major_formatter(formatter)
-
     @savefig set_ticks.png
     fig.show()
+
+.. blacken-docs:on

docs/index.rst

@@ -8,7 +8,7 @@ nc-time-axis
 ============
 
 ``nc-time-axis`` is a package that enables making plots in `matplotlib`_ with axes made
-up of :py:class:`cftime.datetime` dates with any calendar type.  
+up of :py:class:`cftime.datetime` dates with any calendar type.
 
 .. toctree::
    :caption: Getting started

docs/release-notes.rst

@@ -94,7 +94,7 @@ v1.4.0 (October 23rd, 2021)
 ---------------------------
 
 Deprecations
-~~~~~~~~~~~~ 
+~~~~~~~~~~~~
 
 * The :py:class:`CalendarDateTime` class has been deprecated and will be removed
   in ``nc-time-axis`` version 1.5.0. Please switch to plotting instances or
@@ -122,10 +122,10 @@ Bug Fixes
   :py:meth:`matplotlib.axes.Axes.fill_between` to work properly with `cftime`_
   values (:issue:`47`, :issue:`74`, :pull:`78`).
   By `Pascal Bourgault`_.
-* Fixed a bug that resulted in the resolution of tick labels being inconsistent 
+* Fixed a bug that resulted in the resolution of tick labels being inconsistent
   with the resolution of tick values (:issue:`48`, :pull:`79`).
   By `Spencer Clark`_.
-* Fixed a bug that prevented users from being able to explicitly set the ticks 
+* Fixed a bug that prevented users from being able to explicitly set the ticks
   along axes using :py:meth:`matplotlib.axes.Axes.set_xticks` or
   :py:meth:`matplotlib.axes.Axes.set_yticks` (:issue:`41`, :pull:`84`).
   By `Spencer Clark`_.