Info specific to SCINet Website Development

These are the instructions for how to contribute to the SCINet USDA webpage if you have been contacted to contribute.

There are two ways to do this.

Using Github pull requests (preferred)
edit online in github
Sent your markdown file to Adam Rivers

The github command line

get a GitHub account if you don't have one
clone the repository to your computer: git clone https://github.com/USDA-ARS-GBRU/scinet-site.git
create a new brach for your work
Edit your assigned page, photos go in /assets/img/ and docs go in the location you were assigned
When you are done commit your changes:

git add .
git commit -m "here is a description of what I did what I did"
git push

Then go the main scinet repository and create a pull request

Edit online in Github

get a GitHub account if you don't have one
go to the scinet repository: https://github.com/USDA-ARS-GBRU/scinet-site and navigate to your file and click the pencil. this will "fork the archive for you". 3 edit it and say what you did in the comment box and click "propose file change"

Info on the Jekyll + U.S. Web Design System template

This is a Jekyll theme for the U.S. Web Design System.

Installation

Install the theme as a Ruby Gem by adding it to your Gemfile like so:
```
gem 'uswds-jekyll'
```
Fetch and update your bundled gems by running:
```
bundle
```
Set the theme in your site's Jekyll configuration, _config.yml:
```
theme: uswds-jekyll
```

You will need to restart your Jekyll server to see the effects.

Install as a new Jekyll site

Create a new Jekyll site:
```
jekyll new
```
Replace the default gem "minima", "~> 2.0" gem with the uswds-jekyll gem in your Gemfile:
```
gem 'uswds-jekyll', :git => 'https://github.com/18F/uswds-jekyll.git'
```
Set the theme in your site's Jekyll configuration, _config.yml:
```
theme: uswds-jekyll
```
Fetch and update your bundled gems by running:
```
bundle
```
Run Jekyll jekyll serve to build your site locally at http://localhost:4000/

Development

To develop this theme and/or test it locally:

Clone this repo
Run Jekyll (jekyll serve) in the local clone of this repo; or
Create a new Jekyll project, follow the installation instructions, then change your Gemfile to point at the local clone of this repo:
```
gem 'uswds-jekyll', :path => '../path/to/uswds-jekyll'
```

Publish to Rubygems

Update spec.version = "NUMBER HERE" in the uswds-jekyll.gemspec file to the version you want to publish
Run bundle install
Add a PR for the update and get it merged
Run bundle exec rake release
Add a GitHub release to the releases page with the same version number
You should see the latest version here https://rubygems.org/gems/uswds-jekyll

Versioning

To reference a specific version of this plugin:

Visit the releases page and decide which version you want to use.
Specify the version in your Gemfile.
```
gem 'uswds-jekyll', '1.4.1'
```

Configuration

Configuration of common elements (header, footer, navigation, etc.) happens in your project's data files. See this project's data directory for reference configurations of each component.

The default layout also provides a mechanism for automatically including stylesheets and scripts on a site-wide, layout-wide, and per-page basis. See asset load order for more information.

Site title

You can change your site's title with the title field in your _config.yml. If you want to provide an alternate title for use only in the site header, you can set the title field in _data/header.yml.

Site description

You can change your site's description with the description field in your _config.yml. If you want to override it for a particular page, you can set the description field in that page's frontmatter.

Navigation

This theme's navigation system is powerful and flexible. Named navigational lists live in your project's _data/navigation.yml, e.g.

By default all links are assumed to be internal to the site. You can add external: true to links that are external. You can also add class: class-name to add a class to a specific link.

# _data/navigation.yml
primary:
  - text: Documentation
    href: /docs/
  - text: Support
    href: /help/
  - text: External link
    href: https://18f.gsa.gov
    external: true

  # link objects with a 'links' field will be presented as
  # collapsible link lists. The 'links' field can either be a
  # reference to another link list in this file, or a literal list.
  - text: Section title
    links: <links>

This scheme allows you to define navigational elements that can be shared by different components, such as the header and footer. See the documentation for those components for more info.

Page title

Set each page's title in its frontmatter:

---
title: About us
---

Page subnavigation

If you're using the page layout, each page may declare its own side navigation and subnavigation in its front matter:

---
sidenav: documentation
subnav:
  - text: Section one
    href: '#section-one'
  - text: Section two
    href: '#section-two
---
## Section one

## Section two

As with the header and footer, the sidenav field may either reference a common navigation list from _data/navigation.yml (recommended) or be a literal list of links.

The subnav field should be used to link to sections within the current page, because links to other pages will cause the linking page's side navigation to collapse when visited.

sidenav is a key into _data/navigation.yml. See the navigation docs for more info.

A page's "current" or "active" state in the sidenav is determined by whether a link's href matches page.url or page.permalink for each page being rendered.

subnav is a list of links to display on this page under its own link in the side navigation.

Note that subnav link hrefs are not prefixed with site.baseurl because this breaks hash links prefixed with #.

Pro tip: Unless your Jekyll configuration specifies otherwise, the default Markdown formatter (Kramdown) will automatically generate predictable id attributes for your page headings and convert markdown like this:

## Section one

into:

<h2 id="section-one">Section one</h2>

If you're using Redcarpet, you will need to configure it to enable the with_toc_data extension in your _config.yml, like so:

markdown: redcarpet
redcarpet:
  extensions:
    - with_toc_data

Pro tip: If you're like us and prefer your navigation sticky, you can add sticky_sidenav: true on page, project, and team member layouts to have the sidenav follow as you scroll.

Hero

hero: # optional
  image: /path/to/image.jpg # optional
  callout:
    alt: Callout white text! # optional
    text: The rest of the callout
  button: # optional
    text: The button text
    href: /button-href/

Tagline intro

# optional, but must be used in conjunction with 'intro', below
tagline: A tagline for your page
# also optional, but must be used with 'tagline', above
intro: |
  Some introductory text content.

  This will be processed as **Markdown**.

Graphics list

# an optional list of graphics to display before or after the content
graphics:
  - image:
      # note the indentation here: graphics[n].image.src
      src: /path/to/image.ext
      alt: optional alt text
    title: Optional graphic title, rendered as an <h3>
    description: Graphic description text, processed as _Markdown_.

# optional
graphics_position: (before|after)

Color and font configuration

The default colors and fonts can be configured in the _data/theme.yml file.

Search

Search.gov is used for search and can be configured in _config.yml.

Before configuring your search you will need to create a search.gov account and set up your website with search.gov.

After setting up your site on search.gov you can then add your search_site_handle to the config.yml.

Analytics

Google Analytics

You can add Google Analytics to your site by uncommenting the google_analytics_ua line and replacing UA-????????-?? with your Google analytics UA code.

# Configuration for Google Analytics, add your UA code here:
# google_analytics_ua: UA-????????-??

Digital Analytics Program (DAP)

You can add DAP to your site by uncommenting the dap_agency line and, if need be, replacing GSA with the appropriate agency key. For more information visit https://www.digitalgov.gov/services/dap/

# Configuration for DAP, add your agency ID here:
# dap_agency: GSA

Last modified date

You can show the last date a page was last modified by uncommenting this line from the footer.yml data file. This will add the date right before the footer component and uses the last-modified.html include.

# Used to show the "Last updated" date and time;
# last_updated: true

Anchor JS

You can show an anchor link next to header tags by uncommenting this section from the _config.yml data file. This will add an anchor link after the header tag on the page and post layouts making ech header linkable. See https://github.com/bryanbraun/anchorjs for more information.

# anchor_js_targets: [h1, h2, h3, h4, h5, h6]

Assets

The stylesheet and script includes each incorporate the USWDS CSS and JS files if the corresponding styles and scripts lists aren't defined in your _config.yml. So unless you add one or both of those manually, your HTML will include the following:

<!-- in the <head> -->
<link rel="stylesheet" href="/assets/uswds/css/uswds.min.css" media="screen">
<!-- before </body> -->
<script src="/assets/uswds/js/uswds.min.js" async>

Read more about customizing stylesheets and scripts below.

Stylesheets

As a general rule, all stylesheets are inserted in a layouts' <head>, which qualifies them as "render-blocking". Site stylesheets can be specified in _config.yml or a layout or page's front matter YAML in the following form:

styles:
  - /path/to/sheet.css
  - href: /path/to/sheet.css
    media: (screen|print|all) # optional

Stylesheets specified as objects (in the latter item above) must have an href property. The media defaults to screen.

Scripts

As a general rule, all scripts are inserted before a layouts' </body>, which prevents them from blocking the rendering of your page's content. Scripts can be specified in _config.yml or a layout or page's front matter YAML in the following form:

scripts:
  - /path/to/script.js
  - src: /path/to/script.js
    async: true # optional

Scripts specified as objects (in the latter item above) must have a src property. Scripts with async: true will get an async attribute, which tells the browser not to let this script's loading block the execution of subsequent scripts. If the execution order of your scripts is not important, setting async: true may provide performance benefits to your users. (Conversely, if you don't know whether your scripts need to execute in a particular order, then you should not set async: true because it may prevent your scripts from running propertly.)

Asset load order

Both stylesheets and scripts can be configured

Assets configured at the site level (in your _config.yml) will be loaded in all pages that use the USWDS layouts.
Those configured at the layout level (in that layout's front matter) will be loaded on all pages that use that layout, after site assets.
Those configured at the page level (in the page's front matter) will be loaded last.

Customization

You have two options for customizing the CSS: Sass or CSS overrides. Individual sites can also selectively override individual includes and layouts.

Customizing with Sass

Create a Sass (or SCSS) entry point that sets variables and then imports the USWDS source files:

---
# assets/css/main.scss
---
// set your variables or @import them here.

// at the very least, you should set the USWDS font and image paths
// to the correct paths relative to assets/main.css, like so:
$font-path: '../uswds/fonts';
$image-path: '../uswds/img';

@import 'uswds/all';

All of the USWDS SCSS source files are placed in the _sass/uswds directory and are available as Sass imports via @import 'uswds/<path>';. See the Jekyll docs for more information about its Sass/SCSS support, and configuring its Sass renderer in your site's config.

Customizing with CSS overrides

Create a new CSS or Sass file that defines your customizations, e.g.

---
# assets/uswds-overrides.scss
---
.usa-header {
  // overrides here
}

Add the new stylesheet's path to your _config.yml after uswds.min.css:

styles:
  - /assets/uswds/css/uswds.min.css
  - /assets/uswds-overrides.css

Overriding includes and layouts

Any include or layout can be overridden by your site by placing a file with the same name into your site's _includes or _layouts directory. For instance:

To change how stylesheets are loaded or referenced, you can create your own _includes/styles.html, which will subsequently change how stylesheets are loaded in all layouts that inherit from the USWDS default layout.
You can change how the side navigation is rendered (but not which data it receives) in the page layout by creating your own _includes/sidenav.html.
You can change how and whether the side navigation is displayed at all in the page layout by overriding _layouts/page.html.

Components

For some USWDS components, there are two different files that control how data is passed to the template:

components/{component}.html is the low-level template that assumes a similarly named global template variable. For instance, the header component operates on the header template variable.
{component}.html is the "concrete" implementation of the component that sets the appropriate global variable then includes the low-level template.

This separation allows you to override either of the component includes in your own Jekyll site without having to re-implement either the high- or low-level logic. For instance, if you want your header data to come directly from the Jekyll configuration file (_config.yml) rather than _data/header.yml, you can override _includes/header.html to look like this:

{% assign header = site.data.header %}
{% include components/header--basic.html %}

Header

The header.html include sets the header template variable to site.data.header, the value of which is set in your Jekyll project's _data/header.yml file. Then it includes components/header.html to render the header's markup.

See this repo's header.yml for more info.

Footer

The footer.html include sets the header template variable to site.data.footer, the value of which is set in your Jekyll project's _data/footer.yml file. Then it includes components/footer.html to render the footer's markup.

See this repo's footer.yml for more info.

Layouts

This theme provides the following layouts, which you can use by setting the layout front matter on each page, like so:

---
layout: name
---

Supported (optional) front matter for page layouts.

page navigation
hero
tagline intro
graphics list

`layout: default`

This is the bare-bones USWDS layout, which does all of the basic page scaffolding then drops the page content into the <main> element. All of the other layouts "inherit" this one and provide other features in the content block.

The default layout provides a layout front matter hook to add attributes to the <main> element. You can see how this works in the page layout.

`layout: home`

This layout implements the home page template, which accommodates the following front matter:

Check out the YAML front matter in the home demo page for an example of how to structure it.

`layout: page`

This layout implements the document page template.

See the page demo page for an example of how this works, and see _data/navigation.yml for how to structure named navigation data for your site.

`layout: post`

This layout is identical to the layout page and is included to allow for easier site creation using Jekyll new.

`layout: project`

This layout is used to show details for an individual project and uses the following front matter.

layout: project
title: Title of project
permalink: /projects/link-to-project/
description: Project description.
large_image: /path/to/image.ext
small_image: /path/to/image.ext
image_alt: The image alt text

To show a listing of projects on a page add {% include project-list.html %} to the page

`layout: team-member`

This layout is used to show details for an individual team member and uses the following front matter.

layout: team-member
permalink: /team/link-to-team-member/
name: Team member name
image: /path/to/image.ext
job_title: Team member job title
phone: 123-456-7890
email: [email protected]

To show a listing of team members on a page add {% include team-list.html %} to the page

Name		Name	Last commit message	Last commit date
Latest commit History 1,705 Commits
_data		_data
_includes		_includes
_layouts		_layouts
_posts		_posts
_sass		_sass
_team		_team
_tutorials		_tutorials
_workshops		_workshops
assets		assets
pages		pages
script		script
.gitignore		.gitignore
.travis.yml		.travis.yml
CONTRIBUTING.md		CONTRIBUTING.md
Gemfile		Gemfile
Gemfile.lock		Gemfile.lock
LICENSE.md		LICENSE.md
README.md		README.md
Rakefile		Rakefile
_config.yml		_config.yml
package-lock.json		package-lock.json
package.json		package.json
processapps.py		processapps.py
uswds-jekyll.gemspec		uswds-jekyll.gemspec

License

ISUgenomics/scinet-site

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