Apply linting & formatting globally

.github/FUNDING.yml

@@ -9,4 +9,4 @@ community_bridge: # Replace with a single Community Bridge project-name e.g., cl
 liberapay: # Replace with a single Liberapay username
 issuehunt: # Replace with a single IssueHunt username
 otechie: # Replace with a single Otechie username
-custom: ['https://giving.ucsb.edu/Funds/Give?id=353']
+custom: ["https://giving.ucsb.edu/Funds/Give?id=353"]

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,17 +1,17 @@
 ---
 name: Bug report
 about: Create a report to help us improve
-title: ''
+title: ""
 labels: bug
-assignees: ''
-
+assignees: ""
 ---
 
 **Describe the bug**
 A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
+
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
@@ -24,15 +24,17 @@ A clear and concise description of what you expected to happen.
 If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
+
+- OS: [e.g. iOS]
+- Browser [e.g. chrome, safari]
+- Version [e.g. 22]
 
 **Smartphone (please complete the following information):**
- - Device: [e.g. iPhone6]
- - OS: [e.g. iOS8.1]
- - Browser [e.g. stock browser, safari]
- - Version [e.g. 22]
+
+- Device: [e.g. iPhone6]
+- OS: [e.g. iOS8.1]
+- Browser [e.g. stock browser, safari]
+- Version [e.g. 22]
 
 **Additional context**
 Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,10 +1,9 @@
 ---
 name: Feature request
 about: Suggest an idea for MetacatUI
-title: ''
+title: ""
 labels: enhancement
-assignees: ''
-
+assignees: ""
 ---
 
 **Describe the feature you'd like**

.github/workflows/test.js.yml

@@ -6,14 +6,13 @@ name: Tests
 on:
   push:
     branches-ignore:
-    - 'ignore-*'
+      - "ignore-*"
   pull_request:
     branches-ignore:
-    - 'ignore-*'
+      - "ignore-*"
 
 jobs:
   test:
-
     runs-on: ubuntu-latest
 
     strategy:
@@ -22,15 +21,15 @@ jobs:
         # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Use Node.js ${{ matrix.node-version }}
-      uses: actions/setup-node@v3
-      with:
-        node-version: ${{ matrix.node-version }}
-        cache: 'npm'
-    - name: install dependencies
-      run: npm ci
-    - name: Run tests
-      run: npm test
-    - name: Dry run jsdoc
-      run: npm run jsdoc-dry-run
+      - uses: actions/checkout@v3
+      - name: Use Node.js ${{ matrix.node-version }}
+        uses: actions/setup-node@v3
+        with:
+          node-version: ${{ matrix.node-version }}
+          cache: "npm"
+      - name: install dependencies
+        run: npm ci
+      - name: Run tests
+        run: npm test
+      - name: Dry run jsdoc
+        run: npm run jsdoc-dry-run

.prettierrc

@@ -1,7 +1,5 @@
 {
-  "plugins": [
-    "@shopify/prettier-plugin-liquid"
-  ],
+  "plugins": ["@shopify/prettier-plugin-liquid"],
   "overrides": [
     {
       "files": "docs/_includes/*.html",
@@ -16,4 +14,4 @@
       }
     }
   ]
-}
+}

CONTRIBUTING.md

@@ -17,7 +17,7 @@
 ## Types of contributions
 
 We welcome all types of contributions, including bug fixes, feature enhancements,
-bug reports, documentation, graphics, and many others.  You might consider contributing by:
+bug reports, documentation, graphics, and many others. You might consider contributing by:
 
 - Report a bug or request a new feature in our [issue tracker](https://github.com/NCEAS/metacatui/issues)
 - Fix a bug and contribute the code with a Pull Request
@@ -28,8 +28,8 @@ bug reports, documentation, graphics, and many others.  You might consider contr
 - ...
 
 MetacatUI is an open source project, and we welcome full
-participation in the project.  Contributions are reviewed and suggestions are
-made to increase the value of MetacatUI to the community.  We strive to
+participation in the project. Contributions are reviewed and suggestions are
+made to increase the value of MetacatUI to the community. We strive to
 incorporate code, documentation, and other useful contributions quickly and
 efficiently while maintaining a high-quality repository software product.
 
@@ -38,6 +38,7 @@ If you have any questions about contributing, please feel free to ask on the
 on the [DataONE Slack team](https://slack.dataone.org/).
 
 ## Pull Requests
+
 We use the pull-request model for contributions. See [GitHub's help on pull-requests](https://help.github.com/articles/about-pull-requests/).
 
 In short:
@@ -53,7 +54,7 @@ In short:
 
 ## Development Workflow
 
-Development is managed through the git repository at https://github.com/NCEAS/metacatui.  The repository is organized into several branches, each with a specific purpose.  
+Development is managed through the git repository at https://github.com/NCEAS/metacatui. The repository is organized into several branches, each with a specific purpose.
 
 **main**. Releases are merged from the `develop` branch to the `main` branch, and the resulting commit is tagged with the release tag (e.g., `2.4.0`). The tip of the `main` branch always reflects the most recent release of the software. The version number in all configuration files and the README on the `main` branch follows [semantic versioning](https://semver.org/) and should always be set to the current release version, for example, `2.8.5`.
 
@@ -65,22 +66,23 @@ Feature branches are named as `feature-` + `#{issue}` + `-{short-description}-`.
 
 All `feature-*` branches should be frequently merged with changes from `develop` to
 ensure that the feature branch stays up to date with other features that have
-been tested and are awaiting release.  Thus, each `feature-*` branch represents an opportunity
+been tested and are awaiting release. Thus, each `feature-*` branch represents an opportunity
 for integration testing of the set of features intended to work together for a
 particular release.
 
 **dev-X.X**. Development branches named after their minor version number can be used when a patch release
 needs to be created that is behind the main **develop** branch.
 
-**bugfix**. A final branch type are `bugfix` branches, which work the same as feature branches, but fix bugs rather than adding new functionality. Bugfix branches are named similarly, following the pattern: `bugfix-` + `{issue}` +  `-{short-description}`, with `{issue}` being the GitHub issue number related to that bug. e.g. `bugfix-83-fix-name-display`.
+**bugfix**. A final branch type are `bugfix` branches, which work the same as feature branches, but fix bugs rather than adding new functionality. Bugfix branches are named similarly, following the pattern: `bugfix-` + `{issue}` + `-{short-description}`, with `{issue}` being the GitHub issue number related to that bug. e.g. `bugfix-83-fix-name-display`.
 
 ### Development flow overview
+
 ```mermaid
-%%{init: {  'theme': 'base', 
+%%{init: {  'theme': 'base',
             'gitGraph': {
                 'rotateCommitLabel': false,
                 'showCommitLabel': false
-            },            
+            },
             'themeVariables': {
               'commitLabelColor': '#ffffffff',
               'commitLabelBackground': '#000000'
@@ -110,8 +112,8 @@ gitGraph
 ## Release process
 
 1. Our release process starts with integration testing in a `develop` branch. Once all
-changes that are desired in a release are merged into the `develop` branch, we run
-the full set of tests on a clean checkout of the `develop` branch.
+   changes that are desired in a release are merged into the `develop` branch, we run
+   the full set of tests on a clean checkout of the `develop` branch.
 2. After testing, the `develop` branch is merged to main.
 3. Then the `main` branch can be tagged with the new version number (e.g. `2.11.2`).
 4. Releases can be downloaded from the [Github releases page for the MetacatUI repository](https://github.com/NCEAS/metacatui/releases).
@@ -121,9 +123,9 @@ the full set of tests on a clean checkout of the `develop` branch.
 **Unit and integration tests**. MetacatUI has a full suite of unit tests and
 integration tests in the `tests` subdirectory.
 Any new code developed should include a robust set of unit tests for each public
-method, as well as integration tests from new feature sets.  Tests should fully
+method, as well as integration tests from new feature sets. Tests should fully
 exercise the feature to ensure that it responds correctly to both good data inputs
-and various classes of corrupt or bad data.  All tests should pass before submitting a PR
+and various classes of corrupt or bad data. All tests should pass before submitting a PR
 or merging to `develop`.
 
 Tests are automatically run via GitHub Actions. Check the root `README.md` file
@@ -136,7 +138,7 @@ Read more documentation about how tests are run and viewed in [/test/README.md](
 ## Code style
 
 Code should be written to professional standards to enable clean, well-documented,
-readable, and maintainable software.  While there has been significant variability
+readable, and maintainable software. While there has been significant variability
 in the coding styles applied historically, new contributions should strive for
 clean code formatting.
 
@@ -145,19 +147,23 @@ clean code formatting.
 All JavaScript code should be fully documented with [JSDoc](https://jsdoc.app/) comments.
 
 For Models and Views:
+
 - Gives a brief overview of what the class / file does and give a few short example of how you might use the class / file.
 - Create a screenshot of the View and use the `@screenshot` tag to include it in the built docs.
 - Use the `@classcategory` tag to organize the class file in the built docs navigational menu
 
 For Model and View methods:
+
 - Say what each class method does and how to use it (use `@param` and `@returns`)
 - Use `@example` tags to give examples of parameters and return values
 - Use `@fires` to indicate Backbone Events that are fired by a method
 
 For Model and View attributes:
+
 - Describe the purpose of the attribute, its `@default` value, and one or more `@example`s
 
 For everything:
+
 - Use the `@since` tag to indicate the version the class/method/attribute was added
 - Use `@deprecated` for deprecated APIs and features
 - Use `@link` to link to other JSDoc pages when mentioning other classes, attributes, and methods (e.g. `{@link Model#method}`)
@@ -257,7 +263,7 @@ California (hereafter, the "Regents").
    your Contributions to the Regents, or that your employer has
    executed a separate Corporate CLA with the Regents.
 5. You represent that each of Your Contributions is Your original
-   creation (see section 7 for submissions on behalf of others).  You
+   creation (see section 7 for submissions on behalf of others). You
    represent that Your Contribution submissions include complete
    details of any third-party license or other restriction (including,
    but not limited to, related patents and trademarks) of which you

README.md

@@ -1,6 +1,6 @@
 ## MetacatUI: A client-side web interface for DataONE data repositories
 
-- **Author**: Matthew B. Jones, Chris Jones, Lauren Walker, Robyn Thiessen-Bock, Ben Leinfelder, Peter Slaughter, Bryce Mecum, Rushiraj Nenuji, Hesham Elbashandy, Val Hendrix 
+- **Author**: Matthew B. Jones, Chris Jones, Lauren Walker, Robyn Thiessen-Bock, Ben Leinfelder, Peter Slaughter, Bryce Mecum, Rushiraj Nenuji, Hesham Elbashandy, Val Hendrix
 - **DOI**: [doi:10.18739/A2KD1QN1N](https://doi.org/10.18739/A2KD1QN1N)
 - **License**: [Apache 2](http://opensource.org/licenses/Apache-2.0)
 - [Package source code on Github](https://github.com/NCEAS/metacatui)
@@ -9,9 +9,9 @@
 
 ![Tests Status](https://github.com/NCEAS/metacatui/actions/workflows/test.js.yml/badge.svg)
 
-MetacatUI is a client-side web interface for querying Metacat servers and other servers that implement the DataONE REST API.  Currently, it is used as the basis for the [KNB Data Repository](http://knb.ecoinformatics.org), the [NSF Arctic Data Center](https://arcticdata.io/catalog/), the [DataONE federation](https://search.dataone.org), and other repositories.
+MetacatUI is a client-side web interface for querying Metacat servers and other servers that implement the DataONE REST API. Currently, it is used as the basis for the [KNB Data Repository](http://knb.ecoinformatics.org), the [NSF Arctic Data Center](https://arcticdata.io/catalog/), the [DataONE federation](https://search.dataone.org), and other repositories.
 
-MetacatUI is an open source, community project.  We [welcome contributions](https://github.com/NCEAS/metacatui/blob/main/CONTRIBUTING.md) in many forms, including code, graphics, documentation, bug reports, testing, etc.  Use the [discussion list](https://github.com/NCEAS/metacatui/issues) to discuss these contributions with us.
+MetacatUI is an open source, community project. We [welcome contributions](https://github.com/NCEAS/metacatui/blob/main/CONTRIBUTING.md) in many forms, including code, graphics, documentation, bug reports, testing, etc. Use the [discussion list](https://github.com/NCEAS/metacatui/issues) to discuss these contributions with us.
 
 ## Citation
 
@@ -27,15 +27,16 @@ The main search view
 The dataset landing page
 ![Arctic Data Center Metadata View](https://raw.githubusercontent.com/NCEAS/metacatui/main/docs/screenshots/metacatui-arctic-1200w.png)
 
------------------
+---
 
 ## Documentation
 
 Documentation can be found on the [MetacatUI website](https://nceas.github.io/metacatui).
 
------------------
+---
 
 ## License
+
 ```
 Copyright [2013] [Regents of the University of California]
 
@@ -53,13 +54,14 @@ limitations under the License.
 ```
 
 ## Acknowledgements
+
 Work on this package was supported by:
 
 - NSF-ABI grant #1262458 to C. Gries, M. B. Jones, and S. Collins.
 - NSF-DATANET grant #1430508 to W. Michener, M. B. Jones, D. Vieglais, S. Allard and P. Cruse
 - NSF DIBBS grant #1443062 to T. Habermann and M. B. Jones
 - NSF-PLR grant #1546024 to M. B. Jones, S. Baker-Yeboah, J. Dozier, M. Schildhauer, and A. Budden
-- NSF-PLR grant #2042102 to M. B. Jones,  A. Budden, M. Schildhauer, and  J. Dozier
+- NSF-PLR grant #2042102 to M. B. Jones, A. Budden, M. Schildhauer, and J. Dozier
 
 Additional support was provided for working group collaboration by the National Center for Ecological Analysis and Synthesis, a Center funded by the University of California, Santa Barbara, and the State of California.
 

docs/README.md

@@ -1,11 +1,13 @@
 # MetacatUI Documentation
+
 This folder of the MetacatUI repository contains the documentation for MetacatUI. This documentation includes:
+
 - Basic information about MetacatUI
 - Installation instructions
 - Developer documentation for the MetacatUI application
 
-
 ## Building Developer documentation
+
 MetacatUI uses [JSDoc](https://github.com/jsdoc/jsdoc) comments to provide inline documentation of classes, methods, and variables. A JSDoc documentation generator will collect all those comments and generate HTML webpages for easier reading and navigation.
 
 The MetacatUI git repository already contains these generated HTML pages in the `docs/docs` directory. However, if you have made changes to the MetacatUI code and documentation and want to update the HTML doc pages, you will need to run the JSDoc generator.
@@ -79,8 +81,10 @@ For example, to install and use Ruby 3.1.x with `rbenv`:
 After setting up the correct Ruby version, try running `bundle install` and then `bundle exec jekyll serve` again.
 
 ## Adding to this site
+
 Feel free to add pages to the MetacatUI docs website by adding markdown files to this `docs` directory. Use subdirectories
 as much as possible to keep things organized. Use relative links with `.html` suffixes instead of `.md` so that the links work on the Github Pages site.
 
 ## Anything missing?
+
 We maintain a list of questions about MetacatUI that are reviewed and worked into this documentation. If you have a question that was not answered by these docs, or want to make a suggestion for these docs, please add to the list by commenting on [the FAQ Github issue](https://github.com/NCEAS/metacatui/issues/1389)

docs/_includes/header.html

@@ -1,6 +1,9 @@
 <header>
   <nav>
-    <a class="logo" href="{{ site.url }}">{% include icons/cat.svg %} {% include icons/metacatui.svg %}</a>
+    <a class="logo" href="{{ site.url }}">
+      {%- include icons/cat.svg %}
+      {% include icons/metacatui.svg -%}
+    </a>
     <a href="https://demo.nceas.ucsb.edu">Live Demo</a>
     <a href="https://github.com/NCEAS/metacatui">Github</a>
     {% include download.html %}

docs/_includes/homepage.html

@@ -4,5 +4,5 @@ <h1>MetacatUI is a web interface for scientific data repositories.</h1>
     <a href="https://demo.nceas.ucsb.edu/">Try a live demo</a> |
     <a href="{{ site.url }}/screenshots/index.html">Screenshots</a>
   </p>
-  <img src="{{site.url}}/screenshots/screenshot-search.png" />
+  <img src="{{site.url}}/screenshots/screenshot-search.png">
 </section>

docs/_layouts/default.html

@@ -4,7 +4,7 @@
     <meta charset="utf-8">
     <title>{{ page.title }}</title>
 
-    <link rel="shortcut icon" href="{{ site.url }}/assets/images/favicons/favicon.ico"/>
+    <link rel="shortcut icon" href="{{ site.url }}/assets/images/favicons/favicon.ico">
     <link rel="apple-touch-icon" sizes="180x180" href="{{ site.url }}/assets/images/favicons/apple-icon-180x180.png">
     <link rel="icon" type="image/png" sizes="32x32" href="{{ site.url }}/assets/images/favicons/favicon-32x32.png">
     <link rel="icon" type="image/png" sizes="16x16" href="{{ site.url }}/assets/images/favicons/favicon-16x16.png">

docs/_layouts/guide.html

@@ -1,14 +1,10 @@
 ---
 layout: default
 ---
-
 <a href="{{ site.baseurl }}/guides">← See all guides</a>
 
-
 <h1>{{ page.title }}</h1>
 
 <section class="guide">
-
-{{ content }}
-
+  {{ content }}
 </section>