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README.md

The Drummond Lab main website

Our website, http://drummondlab.org, is a GitHub Pages site built with Jekyll and Bootstrap, originally pulled from Trevor Bedford's site and heavily modified.

Editing the site

Here's a step-by-step guide to making modifications to the site, focused initially on adding typical content. You'll need a working Unix-like environment and working knowledge of Git, Markdown, HTML, and Unix commands. You'll need a working Ruby installation, with gems for Jekyll, GitHub Pages, and their dependencies installed. For now, if you need help getting set up, ask someone who's already up and running.

Clone the repository

If you're a member of the Drummond Lab team, you have access to the website repository.

To clone the repository, making a local copy on your machine:

git clone git@github.com:drummondlab/drummondlab.github.io

Enter your local repository and check out the staging branch, where you'll make changes before promoting them to the master branch and publishing them:

cd drummondlab.github.io
git checkout staging

Overview of the structure

Let's assume you're familiar with HTML pages. A site is a collection of HTML pages. For our site (and many others), there are page types, like a paper page, or a lab member page, which are the same in design but different in content. In the web-accessible site, these are indeed different pages. However, as you might hope, they are generated from a single template file filled in with information from many paper- or member-specific data files. This generation is done every time the site changes; it's handled by GitHub Pages, the service we use.

The template files are weird-looking HTML files residing in the _includes/themes/lab folder.

How to add content

For most common actions---adding a lab member, paper, protocol, or news item---you'll be making a new Markdown file in the proper location, naming it properly, and filling in the required fields. In almost all cases, you can (and should!) copy an existing item, change the name, and change its content, rather than trying to write a Markdown document from scratch.

For example, suppose you want to add a news item, which will appear on the front page, announcing that you have created a yeast strain capable of secreting high-quality chardonnay. Go into the news/_posts folder. Copy one of the existing items into a new file named with today's date (it matters!) and a brief title:

cp 2017-12-15-allan-tenure.md 2020-01-31-wine-yeast.md

The date is used by the generator; it's inelegant and perhaps there's a way to do it differently, but that's how it is for now. Now edit the new file to make the content what you want. Just open it in your favorite editor and type away. By the time you're done, hopefully you have something like this:

---
layout: news
title: "New yeast strain makes chardonnay"
author: "X. Obsequious Trenchant"
author_handle: "xot"
image: /assets/images/news/default-news.png
category: news
tags: [breakthrough]
---
Today we are thrilled to announce a new strain of yeast that secretes beautifully oaked chardonnay. See more details in our [preprint](http://biorxiv.org/content/10.1101/0000000)!

Now add it to the repository:

git add 2020-01-31-wine-yeast.md

And, when you're happy with it, commit and push:

git commit -m "announcing new yeast strain"
git push

This new announcement won't yet be public. The next section shows you how to do that.

The same basic process is used to add protocols, team members, etc.

Updating the public site

All edits should be made on the staging branch. When you start work, make sure you're on the staging branch:

git checkout staging

Once your edits are done, preview the site. Generate the pages and start the private webserver:

rake preview

...and then open the local test site, http://127.0.0.1:4000. Look at anything you've changed and make sure it's good to go.

Then move the changes to the master branch:

git checkout master
git merge staging

and push to GitHub:

git push

Changes won't be immediate, so wait a minute or two while GitHub's servers regenerate the site and publish it. Check to make sure the public site http://drummondlab.org looks the way you intend.

Finally, check out staging again so that you don't accidentally start working on the master branch the next time you sit down:

git checkout staging

Changing look and feel

Fonts, colors, spacing, and similar stylings are separate from the template pages. Like most sites, we use Cascading Style Sheets (CSS),

To-dos

See Issues on the site.

License

MIT

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