Add standard pre-commit hooks (#146)

* Add a few more pre-commit hooks

* Apply pre-commit fixes

* Apply pre-commit fixes

* Add back CSS

* Remove csslint

* Pretty format JSON

* Add some more pre-commit hooks

* Remove a comment

* Remove flaky pre-commit hook

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

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

---------

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

Author: namurphy

.circleci/config.yml

@@ -5,7 +5,7 @@ jobs:
       - image: continuumio/miniconda3
     steps:
       - checkout
-      - run: 
+      - run:
           name: "Install nikola"
           command: pip install nikola
       - run:

.github/workflows/deploy.yml

@@ -16,4 +16,4 @@ jobs:
     - name: Build and Deploy Nikola
       uses: getnikola/nikola-action@v8
       with:
-        dry_run: false
+        dry_run: false

.gitignore

@@ -20,4 +20,4 @@ web/.doit.db.dir
 *.egg
 .venv
 venv
-ENV
+ENV

.pre-commit-config.yaml

@@ -4,10 +4,31 @@ ci:
 
 repos:
 
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-merge-conflict
+    exclude: .*\.rst
+  - id: check-case-conflict
+  - id: check-json
+  - id: pretty-format-json
+    args: [--autofix, --no-sort-keys]
+  - id: detect-private-key
+  - id: check-toml
+  - id: check-yaml
+  - id: mixed-line-ending
+
 - repo: https://github.com/codespell-project/codespell
   rev: v2.2.5
   hooks:
   - id: codespell
     args: [--write-changes]
     additional_dependencies:
     - tomli
+
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.26.3
+  hooks:
+  - id: check-github-workflows

CONTRIBUTING.md

@@ -2,12 +2,12 @@
 
 ## Prerequisites
 
-[PlasmaPy's website](https://www.plasmapy.org) is built using the 
-[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 
+[PlasmaPy's website](https://www.plasmapy.org) is built using the
+[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
 be done for your local Python installation using `pip`.
-   
+
 ```bash
 pip install nikola
 ```
@@ -23,20 +23,20 @@ pip install nikola
 The following steps will set up your local computer in order to submit a
 contribution of code or content to PlasmaPy's website.
 
-1. [Create a fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) of the [PlasmaPy/plasmapy.github.io repository](https://github.com/PlasmaPy/plasmapy.github.io) on GitHub. 
+1. [Create a fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) of the [PlasmaPy/plasmapy.github.io repository](https://github.com/PlasmaPy/plasmapy.github.io) on GitHub.
 
 2. [Clone your fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo#step-2-create-a-local-clone-of-your-fork) using [git](https://git-scm.com/), and enter the directory.
 
    ```bash
-   git clone https://github.com/username/plasmapy.github.io.git  
+   git clone https://github.com/username/plasmapy.github.io.git
    cd plasmapy.github.io
    ```
 
 where *username* is your GitHub username.
 
 3. [Add a remote](https://help.github.com/en/github/using-git/adding-a-remote)
    to connect to the upstream repository.
-   
+
    ```bash
    git remote add upstream https://github.com/PlasmaPy/plasmapy.github.io.git
    ```
@@ -47,21 +47,21 @@ Nikola's source files are located on the `src` git branch, and the built HTML fi
 
 ## Submitting a code contribution
 
-1. Fetch the most recent updates to the repository. 
+1. Fetch the most recent updates to the repository.
 
     ```bash
     git fetch --all
     ```
-   
-2. Create and check out a branch based off of the 
+
+2. Create and check out a branch based off of the
    [`src`](https://github.com/PlasmaPy/plasmapy.github.io/tree/src)
    branch of the upstream repository, and connect it to a new branch
    in your fork on GitHub.
 
    ```bash
    git checkout -b new-branch-name upstream/src
    git push --set-upstream origin new-branch-name
-   ```  
+   ```
 
 3. Make and commit changes in the `web/` directory.  Most of the pages
    are in `web/pages/` while blog posts are in `web/posts/`.
@@ -77,15 +77,15 @@ Nikola's source files are located on the `src` git branch, and the built HTML fi
 
    ```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) 
+
+6. [Create a pull request](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request)
    to the `src` branch on the main repository.
-   
-7. The website will be rebuilt automatically after the pull request is merged. 
+
+7. 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
 
-The quickest way to contact PlasmaPy developers is through the 
+The quickest way to contact PlasmaPy developers is through the
 [Matrix](https://riot.im/app/#/room/#plasmapy:openastronomy.org)/[Gitter](https://gitter.im/PlasmaPy/Lobby)
-channel.  
+channel.

conf.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 import time
 
 # !! This is the configuration of Nikola. !! #

data/affiliated_pkgs.json

@@ -14,7 +14,11 @@
       "long": "PlasmaPy is an open-source community developed Python 3 package for plasma physics.  PlasmaPy intends to be a collection of functionality commonly used and shared between plasma physicists and researchers globally."
     },
     "affiliated": false,
-    "keywords": ["plasma", "physics", "Python 3"],
+    "keywords": [
+      "plasma",
+      "physics",
+      "Python 3"
+    ],
     "dates": {
       "added": "2020 November 12",
       "last_updated": "2020 November 12"
@@ -37,7 +41,13 @@
       "long": "<code>tofu</code> is an open-source python library.  It aims at providing the user with a ready-set toolbox for modelling synthetic diagnostics and performing tomographic inversions on linear or toroidal (quasi-axisymmetric) fusion devices.  It is relevant for diagnostics integrating an emissivity on a set of Lines of Sight or Volumes of Sight corresponding to as many detectors or pixels, and for which the plasma can be considered transparent (i.e. not for radio-frequencies / microwaves)."
     },
     "affiliated": true,
-    "keywords": ["plasma", "physics", "Python 3", "fusion", "diagnostics"],
+    "keywords": [
+      "plasma",
+      "physics",
+      "Python 3",
+      "fusion",
+      "diagnostics"
+    ],
     "dates": {
       "added": "2020 November 17",
       "last_updated": "2020 November 17"
@@ -60,7 +70,15 @@
       "long": "OMFIT - One Modeling Framework for Integrated Tasks - is an integrated modeling  and experimental data analysis framework written in python.  The goal of OMFIT is to enhance existing scientific workflows and enable new integrated modeling capabilities."
     },
     "affiliated": false,
-    "keywords": ["plasma", "physics", "Python", "Python 3", "fusion", "simulation", "diagnostics"],
+    "keywords": [
+      "plasma",
+      "physics",
+      "Python",
+      "Python 3",
+      "fusion",
+      "simulation",
+      "diagnostics"
+    ],
     "dates": {
       "added": "2021 June 22",
       "last_updated": "2021 June 22"
@@ -83,7 +101,13 @@
       "long": "A Monte Carlo simulation of electron transport in low temperature plasmas."
     },
     "affiliated": false,
-    "keywords": ["plasma", "physics", "Python 3", "simulation", "low-temperature"],
+    "keywords": [
+      "plasma",
+      "physics",
+      "Python 3",
+      "simulation",
+      "low-temperature"
+    ],
     "dates": {
       "added": "2021 June 23",
       "last_updated": "2021 June 23"
@@ -106,7 +130,14 @@
       "long": "<code>ALOHA</code> is a coupling code for Lower Hybrid Current Drive antennas facing tokamak magnetized fusion plasma.  This coupling code is based on the linear coupling theory. It allows one to model the coupling of a 'grill'-like antenna to a cold plasma of the kind one can find in Tokamaks. It allows taking into account advanced antennas (such as multijunctions or passive-active multijunction antennas)."
     },
     "affiliated": false,
-    "keywords": ["Fortran", "MatLab", "plasma", "physics", "fusion", "simulation"],
+    "keywords": [
+      "Fortran",
+      "MatLab",
+      "plasma",
+      "physics",
+      "fusion",
+      "simulation"
+    ],
     "dates": {
       "added": "2021 July 16",
       "last_updated": "2021 July 16"

pages/affiliates/index.md

@@ -2,25 +2,25 @@ title: Plasma Packages
 hidetitle: True
 author: Erik T. Everson
 
-PlasmaPy's charter includes promoting open-source software for all of 
-the plasma community, and not just `plasmapy`.  We feel the entire community 
-benefits when there are multiple efforts trying to build functionality for all 
+PlasmaPy's charter includes promoting open-source software for all of
+the plasma community, and not just `plasmapy`.  We feel 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 
+page displays projects that have requested to be shown.  If you want your
 project include, and increase its visibility, then please submit a request.
 
 <div style="width: 100%">
     <a href=https://docs.google.com/forms/d/e/1FAIpQLSfz2djEihWkODbkr1ZC5splkX7ZKLAh_Kuy-aXOngTELIm3xQ/viewform?usp=sf_link
-            class="feature-card feature-link btn-plasmapy-bluegreen" 
+            class="feature-card feature-link btn-plasmapy-bluegreen"
             style="width: 200px">
         <div>Submit Request</div>
     </a>
 </div>
 <br>
 
-All projects/packages are considered **Community Packages** 
+All projects/packages are considered **Community Packages**
 <span style="vertical-align: 2px">{{% community_shield %}}</span>, but packages designed with
-`plasmapy` interoperability are marked as **Affiliated Packages** 
+`plasmapy` interoperability are marked as **Affiliated Packages**
 <span style="vertical-align: 2px">{{% affiliated_shield %}}</span>.
 
 ----

pages/contribute.md

@@ -6,7 +6,7 @@ slug: contribute
 There are numerous ways to contribute to PlasmaPy, including by
 providing code and documentation, suggesting and discussing ideas,
 submitting issues and bug reports, and engaging the broader plasma
-physics community.  
+physics community.
 
 **Imposter syndrome disclaimer**: We want your help. No, really.
 
@@ -30,8 +30,8 @@ the errors and assumptions that seasoned contributors have glossed over.
 
 *This disclaimer was originally written by
 [Adrienne Lowe](https://github.com/adriennefriend) for a
-[PyCon talk](https://www.youtube.com/watch?v=6Uj746j9Heo), and was adapted by 
-[yt](https://github.com/yt-project/yt) in their README file based on its use 
+[PyCon talk](https://www.youtube.com/watch?v=6Uj746j9Heo), and was adapted by
+[yt](https://github.com/yt-project/yt) in their README file based on its use
 in the README file for the [MetPy project](https://github.com/Unidata/MetPy).
 It was then adapted by PlasmaPy.*
 
@@ -50,10 +50,10 @@ early stages of PlasmaPy development:
   [submit issues](https://github.com/PlasmaPy/plasmapy/issues) and
   review [pull requests](https://github.com/PlasmaPy/plasmapy/pulls).
 
-* The PlasmaPy [Matrix](https://app.element.io/#/room/#plasmapy:openastronomy.org) or 
+* The PlasmaPy [Matrix](https://app.element.io/#/room/#plasmapy:openastronomy.org) or
   [Gitter](https://gitter.im/PlasmaPy/Lobby) joint channel
   is a great place to have informal conversations, coordinate efforts,
-  and share ideas.  
+  and share ideas.
 * We have biweekly telecons which are announced on the email list.
 
 ## Contributing code or documentation to PlasmaPy

pages/index.md

@@ -6,9 +6,9 @@ hidetitle: True
     <!-- Feature 1 -->
     <div class="feature-column">
         <a class="feature-link" href="meetings/office_hours">
-        <div class="feature-card" 
+        <div class="feature-card"
               style="background-image: linear-gradient(rgba(255, 255, 255, 0.5),
-                                       rgba(255, 255, 255, 0.5)), 
+                                       rgba(255, 255, 255, 0.5)),
                                        none;
               background-color: var(--plasmapy-light-red)">
             <div>
@@ -33,9 +33,9 @@ hidetitle: True
     <!-- Feature 3 -->
     <div class="feature-column">
         <a class="feature-link" href="https://hack.plasmapy.org">
-        <div class="feature-card" 
-              style="background-image: linear-gradient(rgba(255, 255, 255, 0.0), 
-                                       rgba(255, 255, 255, 0.0)), 
+        <div class="feature-card"
+              style="background-image: linear-gradient(rgba(255, 255, 255, 0.0),
+                                       rgba(255, 255, 255, 0.0)),
                                        none;
                      background-color: var(--plasmapy-darkblue)">
             <div>
@@ -53,7 +53,7 @@ hidetitle: True
 <div class="aspect-ratio-80pc">
     <iframe src="https://www.youtube-nocookie.com/embed/E8RwQF5wcXM"
             style="border: 1px solid black"
-            frameborder="0" 
+            frameborder="0"
             allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture"
             allowfullscreen>
     </iframe>
@@ -79,14 +79,14 @@ If you have a working installation of [conda](https://docs.conda.io/en/latest/),
 conda install -c conda-forge plasmapy
 ```
 
-[PlasmaPy's online documentation](https://docs.plasmapy.org/) contains more 
+[PlasmaPy's online documentation](https://docs.plasmapy.org/) contains more
 detailed [installation instructions](https://docs.plasmapy.org/en/latest/install.html).
-If you are unfamiliar with Python, please check out the 
+If you are unfamiliar with Python, please check out the
 [Python website](https://www.python.org/) for more information.
 
 ## Learn PlasmaPy
 
-[PlasmaPy's documentation](http://docs.plasmapy.org/en/latest) describes how to use PlasmaPy and provides several [examples](https://docs.plasmapy.org/en/latest/examples.html). 
+[PlasmaPy's documentation](http://docs.plasmapy.org/en/latest) describes how to use PlasmaPy and provides several [examples](https://docs.plasmapy.org/en/latest/examples.html).
 
 ## Get Help