SmithLab Website

About

Our website is based on the open source templates designed and shared by the labs of D. Allan Drummond, Trevor Bedford and Stephan Sanders. We downloaded source codes from their repository and modified our contents based on shared templates. We greatly thank them for allowing reuse of their codebase.

The website is deployed using GitHub Pages and the source code is available on GitHub. Please feel free to reuse this code (making sure to cite the Bedford lab, Drummond lab and Sanders Lab as the original sources of the lab website template).

Maintenance

The workflow is to update and build the website locally, then push the changes to the Github repository.

1. Install jekyll locally

The website is built by jekyll, so we need to install jekyll locally.

(one-time installation) First Install Homebrew package in the terminal/command if it's not available yet.

(one-time installation) Then install ruby through terminal/command. Install customizd ruby in addition to the default ruby.

brew install chruby ruby-install

ruby-install ruby

echo 'source /usr/local/opt/chruby/share/chruby/auto.sh' >>~/.bash_profile

(may need to repeat every time) Switch from default ruby to the customized ruby.

source /usr/local/opt/chruby/share/chruby/chruby.sh 

chruby ruby-3.1.2 

source /usr/local/opt/chruby/share/chruby/auto.sh

(one-time installation) Install jekyll.

gem install bundler jekyll

2. Clone the site repo to local machine

# move to the local directory
cd <path to the local directory>  

# clone the remote repo to the local directory
gh repo clone <repo name>

# move to the cloned repo
cd <repo name> 

3. Build the website locally

# move to the local repo directory

# start website locally
bundle exec jekyll serve --livereload

# add if error "Load error: cannot load such file – webrick"
bundle add webrick

# open website in local browser
# Server address: http://127.0.0.1:4000/

# make changes (see details in the following section Make changes)

# build website after finishing updates
jekyll build

# exit the updating mode
# press control^+C

4. Push the changes to the Github

# check the file status: tracked/untracked
git status 

# stage the files ready to be committed
git add . 

# commit the changes locally with message
git commit -m “<description of the change>”  

# push the changes to the remote repo
git push

Make changes

1. Add new members

• Add a square sized photo to images/teampic/<firstnamelastname>.png. (can crop the photo online)
• Add markdown file to team/<firstnamelastname>.md, change the content accordinly.
• Add a new item in _data/team_members.yml, change the content accordingly.

2. Add new publications

• Add a journal photo in images/pubpic/<journalyear>.png
• Add a new item in _data/publist.yml, change the content accordingly.

3. Add media news

• Add a new item in _data/news.yml, change the content accordingly.

4. Add code

• Add a new item in _pages/code.md, change the content accordingly.

5. Change home page

• Make change in _pages/home.md.