Add pre-commit hooks (#154)

* Update pre-commit hooks

* Apply pre-commit hooks

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Revert a change

* Add uptodate to codespell ignore list

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: namurphy

.circleci/config.yml

@@ -2,29 +2,29 @@ version: 2
 jobs:
   build-website:
     docker:
-      - image: continuumio/miniconda3
+    - image: continuumio/miniconda3
     steps:
-      - checkout
-      - run:
-          name: "Install nikola"
-          command: pip install nikola
-      - run:
-          name: "Build website with STRIP_INDEXES=False"
-          command: |
-            echo "STRIP_INDEXES=False" >> conf.py
-            nikola build
-      - store_artifacts:
-          path: output
-      - run:
-          name: "Built website is available at:"
-          command: DOCS_URL="${CIRCLE_BUILD_URL}/artifacts/${CIRCLE_NODE_INDEX}/output/index.html"; echo $DOCS_URL
+    - checkout
+    - run:
+        name: Install nikola
+        command: pip install nikola
+    - run:
+        name: Build website with STRIP_INDEXES=False
+        command: |
+          echo "STRIP_INDEXES=False" >> conf.py
+          nikola build
+    - store_artifacts:
+        path: output
+    - run:
+        name: 'Built website is available at:'
+        command: DOCS_URL="${CIRCLE_BUILD_URL}/artifacts/${CIRCLE_NODE_INDEX}/output/index.html"; echo $DOCS_URL
 
 workflows:
   version: 2
   test-documentation:
     jobs:
-      - build-website
+    - build-website
 
 notify:
   webhooks:
-    - url: https://giles.cadair.dev/circleci
+  - url: https://giles.cadair.dev/circleci

.github/workflows/deploy.yml

@@ -9,7 +9,7 @@ on:
 jobs:
   nikola_build:
     runs-on: ubuntu-latest
-    name: 'Deploy Nikola to GitHub Pages'
+    name: Deploy Nikola to GitHub Pages
     steps:
     - name: Check out
       uses: actions/checkout@v3

.pre-commit-config.yaml

@@ -32,3 +32,33 @@ repos:
   rev: 0.27.4
   hooks:
   - id: check-github-workflows
+
+- repo: https://github.com/sirosen/texthooks
+  rev: 0.6.4
+  hooks:
+  - id: fix-smartquotes
+  - id: fix-spaces
+  - id: fix-ligatures
+  - id: forbid-bidi-controls
+
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+  rev: v2.12.0
+  hooks:
+  - id: pretty-format-ini
+    args: [--autofix]
+  - id: pretty-format-yaml
+    args: [--autofix]
+    # For the labeler GitHub Action, labels with spaces in them must
+    # be put in quotes. However, the pretty-format-yaml hook will
+    # remove the quotes which will break that action, so we should not
+    # run this hook on `labeler.yml` (or certain other files).
+    exclude: .github/labeler.yml|.pre-commit-search-and-replace.yaml
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.2.1
+  hooks:
+  - id: ruff
+    name: ruff (see https://docs.astral.sh/ruff/rules)
+    args: [--fix]
+  - id: ruff-format
+    name: autoformat source code with ruff formatter

CODE_OF_CONDUCT.rst

@@ -40,7 +40,7 @@ Examples of unacceptable behavior include:
 - Trolling, insulting or derogatory comments, and personal or political
   attacks
 - Public or private harassment
-- Publishing others’ private information, such as a physical or email
+- Publishing others' private information, such as a physical or email
   address, without their explicit permission
 - Other conduct which could reasonably be considered inappropriate in a
   professional setting
@@ -140,7 +140,7 @@ This Code of Conduct is adapted from the `Contributor Covenant`_,
 version 2.1, available at
 https://www.contributor-covenant.org/version/2/1/code_of_conduct\ .
 
-Community Impact Guidelines were inspired by `Mozilla’s code of conduct
+Community Impact Guidelines were inspired by `Mozilla's code of conduct
 enforcement ladder <https://github.com/mozilla/inclusion>`__.
 
 For answers to common questions about this code of conduct, see the FAQ

conf.py

@@ -123,7 +123,7 @@
 # this pattern is also used for metadata:
 #     something.meta -> something.pl.meta
 
-TRANSLATIONS_PATTERN = '{path}.{lang}.{ext}'
+TRANSLATIONS_PATTERN = "{path}.{lang}.{ext}"
 
 # Links for the sidebar / navigation bar.  (translatable)
 # This is a dict.  The keys are languages, and values are tuples.
@@ -146,9 +146,9 @@
 #          may present issues if the menu is too large.
 #          (in Bootstrap, the navbar can grow too large and cover contents.)
 # WARNING: If you link to directories, make sure to follow
-#          ``STRIP_INDEXES``.  If it’s set to ``True``, end your links
+#          ``STRIP_INDEXES``.  If it's set to ``True``, end your links
 #          with a ``/``, otherwise end them with ``/index.html`` — or
-#          else they won’t be highlighted when active.
+#          else they won't be highlighted when active.
 
 NAVIGATION_LINKS = {
     DEFAULT_LANG: (
@@ -166,7 +166,10 @@
         (
             (
                 (CHAT, "Chat room"),
-                ("https://github.com/PlasmaPy/PlasmaPy/discussions", "GitHub Discussions"),
+                (
+                    "https://github.com/PlasmaPy/PlasmaPy/discussions",
+                    "GitHub Discussions",
+                ),
                 (MAILING_LIST, "Email list"),
                 (FEEDBACK_BOX, "Suggestion box"),
             ),
@@ -191,16 +194,14 @@
 # Alternative navigation links. Works the same way NAVIGATION_LINKS does,
 # although themes may not always support them. (translatable)
 # (Bootstrap 4: right-side of navbar, Bootblog 4: right side of title)
-NAVIGATION_ALT_LINKS = {
-    DEFAULT_LANG: ()
-}
+NAVIGATION_ALT_LINKS = {DEFAULT_LANG: ()}
 
 # Name of the theme to use.
 THEME = "bootstrap4"
 
 # Primary color of your theme. This will be used to customize your theme.
 # Must be a HEX value.
-THEME_COLOR = '#5670d4'
+THEME_COLOR = "#5670d4"
 
 # Theme configuration. Fully theme-dependent. (translatable)
 # Examples below are for bootblog4.
@@ -310,7 +311,7 @@
 #
 # 0 = using DATE_FORMAT and TIMEZONE
 # 1 = using JS_DATE_FORMAT and local user time (via moment.js)
-# 2 = using a string like “2 days ago”
+# 2 = using a string like "2 days ago"
 #
 # Your theme must support it, Bootstrap already does.
 # DATE_FANCINESS = 0
@@ -341,18 +342,18 @@
 # 'markdown' is Markdown
 # 'html' assumes the file is HTML and just copies it
 COMPILERS = {
-    "rest": ('.rst', '.txt'),
-    "markdown": ('.md', '.mdown', '.markdown'),
-    "textile": ('.textile',),
-    "txt2tags": ('.t2t',),
-    "bbcode": ('.bb',),
-    "wiki": ('.wiki',),
-    "ipynb": ('.ipynb',),
-    "html": ('.html', '.htm'),
+    "rest": (".rst", ".txt"),
+    "markdown": (".md", ".mdown", ".markdown"),
+    "textile": (".textile",),
+    "txt2tags": (".t2t",),
+    "bbcode": (".bb",),
+    "wiki": (".wiki",),
+    "ipynb": (".ipynb",),
+    "html": (".html", ".htm"),
     # PHP files are rendered the usual way (i.e. with the full templates).
     # The resulting files have .php extensions, making it possible to run
     # them without reconfiguring your server to recognize them.
-    "php": ('.php',),
+    "php": (".php",),
     # Pandoc detects the input from the source filename
     # but is disabled by default as it would conflict
     # with many of the others.
@@ -423,7 +424,7 @@
 
 # Set descriptions for tag pages to make them more interesting. The
 # default is no description. The value is used in the meta description
-# and displayed underneath the tag list or index page’s title.
+# and displayed underneath the tag list or index page's title.
 # TAG_DESCRIPTIONS = {
 #    DEFAULT_LANG: {
 #        "blogging": "Meta-blog posts about blogging.",
@@ -442,7 +443,7 @@
 # If you do not want to display a tag publicly, you can mark it as hidden.
 # The tag will not be displayed on the tag list page and posts.
 # Tag pages will still be generated.
-HIDDEN_TAGS = ['mathjax']
+HIDDEN_TAGS = ["mathjax"]
 
 # Only include tags on the tag list/overview page if there are at least
 # TAGLIST_MINIMUM_POSTS number of posts or more with every tag. Every tag
@@ -496,7 +497,7 @@
 
 # Set descriptions for category pages to make them more interesting. The
 # default is no description. The value is used in the meta description
-# and displayed underneath the category list or index page’s title.
+# and displayed underneath the category list or index page's title.
 # CATEGORY_DESCRIPTIONS = {
 #    DEFAULT_LANG: {
 #        "blogging": "Meta-blog posts about blogging.",
@@ -575,7 +576,7 @@
 
 # Set descriptions for author pages to make them more interesting. The
 # default is no description. The value is used in the meta description
-# and displayed underneath the author list or index page’s title.
+# and displayed underneath the author list or index page's title.
 # AUTHOR_PAGES_DESCRIPTIONS = {
 #    DEFAULT_LANG: {
 #        "Juanjo Conti": "Python coder and writer.",
@@ -587,18 +588,16 @@
 # If you do not want to display an author publicly, you can mark it as hidden.
 # The author will not be displayed on the author list page and posts.
 # Tag pages will still be generated.
-HIDDEN_AUTHORS = ['Guest']
+HIDDEN_AUTHORS = ["Guest"]
 
 # Final location for the main blog page and sibling paginated pages is
 # output / TRANSLATION[lang] / INDEX_PATH / index-*.html
 # (translatable)
 INDEX_PATH = "news/"
 
-# Optional HTML that displayed on “main” blog index.html files.
+# Optional HTML that displayed on "main" blog index.html files.
 # May be used for a greeting. (translatable)
-FRONT_INDEX_HEADER = {
-    DEFAULT_LANG: ''
-}
+FRONT_INDEX_HEADER = {DEFAULT_LANG: ""}
 
 # Create per-month archives instead of per-year
 # CREATE_MONTHLY_ARCHIVE = False
@@ -697,11 +696,11 @@
 # For more details, read the manual:
 # https://getnikola.com/handbook.html#deploying-to-github
 # You will need to configure the deployment branch on GitHub.
-GITHUB_SOURCE_BRANCH = 'src'
-GITHUB_DEPLOY_BRANCH = 'main'
+GITHUB_SOURCE_BRANCH = "src"
+GITHUB_DEPLOY_BRANCH = "main"
 
 # The name of the remote where you wish to push to, using github_deploy.
-GITHUB_REMOTE_NAME = 'origin'
+GITHUB_REMOTE_NAME = "origin"
 
 # Whether or not github_deploy should commit to the source branch automatically
 # before deploying.
@@ -734,7 +733,7 @@
 # argument.
 #
 # By default, only .php files uses filters to inject PHP into
-# Nikola’s templates. All other filters must be enabled through FILTERS.
+# Nikola's templates. All other filters must be enabled through FILTERS.
 #
 # Many filters are shipped with Nikola. A list is available in the manual:
 # <https://getnikola.com/handbook.html#post-processing-filters>
@@ -858,15 +857,15 @@
 #
 #   .. image:: /images/tesla.jpg
 #
-# See the Nikola Handbook for details (in the “Embedding Images” and
-# “Thumbnails” sections)
+# See the Nikola Handbook for details (in the "Embedding Images" and
+# "Thumbnails" sections)
 
 # Images will be scaled down according to IMAGE_THUMBNAIL_SIZE and MAX_IMAGE_SIZE
 # options, but will have to be referenced manually to be visible on the site
 # (the thumbnail has ``.thumbnail`` added before the file extension by default,
 # but a different naming template can be configured with IMAGE_THUMBNAIL_FORMAT).
 
-IMAGE_FOLDERS = {'images': 'images'}
+IMAGE_FOLDERS = {"images": "images"}
 # IMAGE_THUMBNAIL_SIZE = 400
 # IMAGE_THUMBNAIL_FORMAT = '{name}.thumbnail{ext}'
 
@@ -951,10 +950,10 @@
 # HTML fragments with the Read more... links.
 # The following tags exist and are replaced for you:
 # {link}                        A link to the full post page.
-# {read_more}                   The string “Read more” in the current language.
+# {read_more}                   The string "Read more" in the current language.
 # {reading_time}                An estimate of how long it will take to read the post.
 # {remaining_reading_time}      An estimate of how long it will take to read the post, sans the teaser.
-# {min_remaining_read}          The string “{remaining_reading_time} min remaining to read” in the current language.
+# {min_remaining_read}          The string "{remaining_reading_time} min remaining to read" in the current language.
 # {paragraph_count}             The amount of paragraphs in the post.
 # {remaining_paragraph_count}   The amount of paragraphs in the post, sans the teaser.
 # {post_title}                  The title of the post.
@@ -989,9 +988,9 @@
 # A small copyright notice for the page footer (in HTML).
 # (translatable)
 CONTENT_FOOTER = (
-    'Contents &copy; {date} {author}'
+    "Contents &copy; {date} {author}"
     '- <a href="{repo}">GitHub</a> '
-    '- {license} '
+    "- {license} "
     '- <a href="{facebook}">Facebook</a> '
     '- <a href="{twitter}">Twitter</a> '
     '- <a href="{youtube}">YouTube</a> '
@@ -1148,10 +1147,12 @@
 #       with the MarkdownExtension class and should not be added here.
 # Defaults are markdown.extensions.(fenced_code|codehilite|extra)
 # markdown.extensions.meta is required for Markdown metadata.
-MARKDOWN_EXTENSIONS = ['markdown.extensions.fenced_code',
-                       'markdown.extensions.codehilite',
-                       'markdown.extensions.extra',
-                       'markdown.extensions.meta']
+MARKDOWN_EXTENSIONS = [
+    "markdown.extensions.fenced_code",
+    "markdown.extensions.codehilite",
+    "markdown.extensions.extra",
+    "markdown.extensions.meta",
+]
 
 # Options to be passed to markdown extensions (See https://python-markdown.github.io/reference/)
 # Default is {} (no config at all)
@@ -1402,7 +1403,7 @@
 # (defaults to 1.)
 # DEMOTE_HEADERS = 1
 
-# If you don’t like slugified file names ([a-z0-9] and a literal dash),
+# If you don't like slugified file names ([a-z0-9] and a literal dash),
 # and would prefer to use all the characters your file system allows.
 # USE WITH CARE!  This is also not guaranteed to be perfect, and may
 # sometimes crash Nikola, your web server, or eat your cat.

dependabot.yml

@@ -1,7 +1,7 @@
 version: 2
 updates:
 
-  - package-ecosystem: "github-actions"
-    directory: "/"
-    schedule:
-      interval: "weekly"
+- package-ecosystem: github-actions
+  directory: /
+  schedule:
+    interval: weekly