Update pre-commit configuration and add mdformat hook (#210)

* pre-commit autoupdate

* Update ruff hooks

* Add hook for mdformat

* Apply mdformat changes

* Add mdformat-ruff plugin

* Use mdformat --number for numbered lists

Author: namurphy

.pre-commit-config.yaml

@@ -50,7 +50,7 @@ repos:
   - id: forbid-bidi-controls
 
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.15.0
+  rev: v2.16.0
   hooks:
   - id: pretty-format-ini
     args: [--autofix]
@@ -63,10 +63,19 @@ repos:
     exclude: .github/labeler.yml|.pre-commit-search-and-replace.yaml
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.14.10
+  rev: v0.14.11
   hooks:
-  - id: ruff
-    name: ruff (see https://docs.astral.sh/ruff/rules)
+  - id: ruff-check
+    name: ruff-check (see https://docs.astral.sh/ruff/rules)
     args: [--fix]
   - id: ruff-format
     name: autoformat source code with ruff formatter
+
+- repo: https://github.com/hukkin/mdformat
+  rev: 1.0.0
+  hooks:
+  - id: mdformat
+    args: [--number]
+    additional_dependencies:
+    - mdformat-gfm
+    - mdformat-ruff

CONTRIBUTING.md

@@ -3,9 +3,9 @@
 ## Prerequisites
 
 [PlasmaPy's website](https://www.plasmapy.org) is built using the
-[Nikola](https://getnikola.com/) static website generator.  In order to build
+[Nikola](https://getnikola.com/) static website generator. In order to build
 the website locally on your computer, you will need to [install
-Nikola](https://getnikola.com/getting-started.html#install).  This may
+Nikola](https://getnikola.com/getting-started.html#install). This may
 be done for your local Python installation using `pip`.
 
 ```bash
@@ -14,9 +14,9 @@ pip install nikola
 
 ## Resources
 
- - [git](https://git-scm.com/)
- - [Nikola documentation](https://getnikola.com/documentation.html)
- - [Markdown guide](https://www.markdownguide.org/)
+- [git](https://git-scm.com/)
+- [Nikola documentation](https://getnikola.com/documentation.html)
+- [Markdown guide](https://www.markdownguide.org/)
 
 ## Getting started
 
@@ -52,9 +52,9 @@ Nikola's source files are located on the `main` git branch, and the built HTML f
 
 1. Fetch the most recent updates to the repository.
 
-    ```bash
-    git fetch --all
-    ```
+   ```bash
+   git fetch --all
+   ```
 
 2. Create and check out a branch based off of the
    [`main`](https://github.com/PlasmaPy/plasmapy.github.io/tree/main)
@@ -66,7 +66,7 @@ Nikola's source files are located on the `main` git branch, and the built HTML f
    git push --set-upstream origin new-branch-name
    ```
 
-3. Make and commit changes in the `pages/` directory.  Most of the pages
+3. Make and commit changes in the `pages/` directory. Most of the pages
    are in `pages/` while blog posts are in `web/posts/`.
 
    ```bash
@@ -81,10 +81,12 @@ Nikola's source files are located on the `main` git branch, and the built HTML f
    ```bash
    nikola auto --browser
 
-6. [Create a pull request](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request)
+   ```
+
+5. [Create a pull request](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request)
    to the `main` branch.
 
-7. The website will be rebuilt automatically after the pull request is merged.
+6. The website will be rebuilt automatically after the pull request is merged.
    After five to ten minutes, check that the website is functioning nominally.
 
 ## Getting help

LICENSE.md

@@ -2,7 +2,7 @@
 
 Source code files and code snippets included in this project are
 licensed under a [BSD 3-clause license with a patent
-grant](#bsd-3-clause-license-with-patent-grant).  All other content in
+grant](#bsd-3-clause-license-with-patent-grant). All other content in
 this project, including content produced directly from unmodified
 source code and code snippets, is licensed under a [Creative Commons
 Attribution 4.0 International (CC BY 4.0)
@@ -16,14 +16,14 @@ Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
 met:
 
-* Redistributions of source code must retain the above copyright
+- Redistributions of source code must retain the above copyright
   notice, this list of conditions and the following disclaimer.
 
-* Redistributions in binary form must reproduce the above copyright
+- Redistributions in binary form must reproduce the above copyright
   notice, this list of conditions and the following disclaimer in the
   documentation and/or other materials provided with the distribution.
 
-* Neither the name of PlasmaPy nor the names of its contributors may
+- Neither the name of PlasmaPy nor the names of its contributors may
   be used to endorse or promote products derived from this software
   without specific prior written permission.
 

pages/about.md

@@ -4,13 +4,13 @@ hidetitle: False
 
 # About PlasmaPy
 
-[Astropy]: https://www.astropy.org
-[PlasmaPy core package]: https://docs.plasmapy.org
-
 The mission of the PlasmaPy Project is to foster the creation of a
 fully open source software ecosystem for plasma research and
-education.  The [PlasmaPy core package] intends to be for plasma
+education. The [PlasmaPy core package] intends to be for plasma
 science what [Astropy] is for astronomy — a collection of
 functionality commonly used and shared between plasma physicists and
 researchers globally, running within and leveraging the open source
 scientific Python ecosystem.
+
+[astropy]: https://www.astropy.org
+[plasmapy core package]: https://docs.plasmapy.org

pages/affiliates/index.md

@@ -5,8 +5,8 @@ author: Erik T. Everson
 PlasmaPy's charter includes promoting open source software for all of
 the plasma community, and not just PlasmaPy. The entire community
 benefits when there are multiple efforts trying to build functionality for all
-aspects of the plasma field.  As such, we want to promote any ongoing effort.  This
-page displays projects that have requested to be shown.  If you want your
+aspects of the plasma field. As such, we want to promote any ongoing effort. This
+page displays projects that have requested to be shown. If you want your
 project include, and increase its visibility, then please submit a request
 to <team@plasmapy.org>.
 
@@ -15,6 +15,6 @@ All projects/packages are considered **Community Packages**
 PlasmaPy interoperability are marked as **Affiliated Packages**
 <span style="vertical-align: 2px">{{% affiliated_shield %}}</span>.
 
-----
+______________________________________________________________________
 
 {{% build_affiliated_pkg_list %}}

pages/index.md

@@ -1,25 +1,8 @@
 title: The PlasmaPy Project
 hidetitle: True
 
-[conda]: https://docs.conda.io/en/latest
-[pip]: https://pip.pypa.io/en/stable
-[code contribution workflow]: https://docs.plasmapy.org/en/latest/contributing/workflow.html
-[coding guidelines]: https://docs.plasmapy.org/en/latest/contributing/coding_guide.html
-[community meeting]: https://www.plasmapy.org/meetings/weekly/
-[**contributor guide**]: https://docs.plasmapy.org/en/latest/contributing/index.html
-[feature requests]: https://github.com/PlasmaPy/PlasmaPy/issues/new?assignees=&labels=feature+request&projects=&template=feature_request.yml
-[gallery of example notebooks]: https://docs.plasmapy.org/en/stable/examples.html
-[getting ready to contribute]: https://docs.plasmapy.org/en/latest/contributing/getting_ready.html
-[GitHub Discussions]: https://github.com/PlasmaPy/PlasmaPy/discussions
-[installation instructions]: https://docs.plasmapy.org/en/latest/install.html
-[many ways to contribute]: https://docs.plasmapy.org/en/latest/contributing/many_ways.html
-[PlasmaPy's documentation]: https://docs.plasmapy.org/en/stable
-[Python]: https://www.python.org
-[submitting bug reports]: https://github.com/PlasmaPy/PlasmaPy/issues/new?assignees=&labels=Bug&projects=&template=bug_report.yml
-[writing documentation]: https://docs.plasmapy.org/en/latest/contributing/doc_guide.html
-[writing tests]: https://docs.plasmapy.org/en/latest/contributing/testing_guide.html
-
 <!-- YouTube Video-->
+
 <div class="aspect-ratio-80pc">
     <iframe src="https://www.youtube-nocookie.com/embed/E8RwQF5wcXM"
             style="border: 1px solid black"
@@ -53,7 +36,7 @@ conda install -c conda-forge plasmapy
 ```
 
 [PlasmaPy's documentation] contains more detailed [installation
-instructions]. If you are unfamiliar with Python, please check out the
+instructions][installation instructions]. If you are unfamiliar with Python, please check out the
 [Python] website.
 
 ## Learn PlasmaPy
@@ -71,7 +54,7 @@ a PlasmaPy [community meeting].
 There are [many ways to contribute] to an open source project, including
 making [feature requests], [submitting bug reports], and organizing
 events. PlasmaPy's [**contributor guide**] covers [getting ready to
-contribute], the [code contribution workflow], [coding guidelines],
+contribute][getting ready to contribute], the [code contribution workflow], [coding guidelines],
 [writing tests], and [writing documentation].
 
 ## Acknowledgments
@@ -80,3 +63,21 @@ Development of PlasmaPy has been supported by the U.S. National Science
 Foundation, the U.S. Department of Energy, the Smithsonian Institution,
 NASA, and Google Summer of Code, with many contributions from the
 broader plasma physics and open source communities.
+
+[**contributor guide**]: https://docs.plasmapy.org/en/latest/contributing/index.html
+[code contribution workflow]: https://docs.plasmapy.org/en/latest/contributing/workflow.html
+[coding guidelines]: https://docs.plasmapy.org/en/latest/contributing/coding_guide.html
+[community meeting]: https://www.plasmapy.org/meetings/weekly/
+[conda]: https://docs.conda.io/en/latest
+[feature requests]: https://github.com/PlasmaPy/PlasmaPy/issues/new?assignees=&labels=feature+request&projects=&template=feature_request.yml
+[gallery of example notebooks]: https://docs.plasmapy.org/en/stable/examples.html
+[getting ready to contribute]: https://docs.plasmapy.org/en/latest/contributing/getting_ready.html
+[github discussions]: https://github.com/PlasmaPy/PlasmaPy/discussions
+[installation instructions]: https://docs.plasmapy.org/en/latest/install.html
+[many ways to contribute]: https://docs.plasmapy.org/en/latest/contributing/many_ways.html
+[pip]: https://pip.pypa.io/en/stable
+[plasmapy's documentation]: https://docs.plasmapy.org/en/stable
+[python]: https://www.python.org
+[submitting bug reports]: https://github.com/PlasmaPy/PlasmaPy/issues/new?assignees=&labels=Bug&projects=&template=bug_report.yml
+[writing documentation]: https://docs.plasmapy.org/en/latest/contributing/doc_guide.html
+[writing tests]: https://docs.plasmapy.org/en/latest/contributing/testing_guide.html

pages/license.md

@@ -5,7 +5,7 @@ slug: license
 
 Source code files and code snippets included in this project are
 licensed under a [BSD 3-clause license with a patent
-grant](#bsd-3-clause-license-with-patent-grant).  All other content in
+grant](#bsd-3-clause-license-with-patent-grant). All other content in
 this project, including content produced directly from unmodified
 source code and code snippets, is licensed under a [Creative Commons
 Attribution 4.0 International (CC BY 4.0)
@@ -19,14 +19,14 @@ Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
 met:
 
-* Redistributions of source code must retain the above copyright
+- Redistributions of source code must retain the above copyright
   notice, this list of conditions and the following disclaimer.
 
-* Redistributions in binary form must reproduce the above copyright
+- Redistributions in binary form must reproduce the above copyright
   notice, this list of conditions and the following disclaimer in the
   documentation and/or other materials provided with the distribution.
 
-* Neither the name of PlasmaPy nor the names of its contributors may
+- Neither the name of PlasmaPy nor the names of its contributors may
   be used to endorse or promote products derived from this software
   without specific prior written permission.