Internal notes for maintaining this site.

How to create a new instance of this site

  1. Create a new project repository on GitHub and give it any name. For instance, the project described here was named manuals. This initial setup will be the project’s master branch. After this is done, clone the new repostitory to your local computer. If you are new to GitHub here are some basic instructions for creating and managing GitHub repositories

  2. Download or clone the Jekyll Documentation Theme from Tom Johnson. Then copy the directory’s content to your new project repository (here manuals directory). Subsequently, commit and push its entire content to the master branch on GitHub.

  3. Add a gh-pages branch to your newly created GitHub project repository. By adding a gh-pages branch to a GitHub project, one can host from this branch a web site (here Jekyll site) for a GitHub project repository. The master branch of this project contains the source code of the site and its gh-pages branch the pre-built web site components. Instruction for setting up a gh-pages branch for an existing project are available here.

Edit a page

Built and test site locally

Run following command within the root directory of the project’s git repository (here ~/Dropbox/Websites/manuals) and then preview the site at the URL printed to the terminal. Note, all paths are given here relative to this directory.

jekyll serve --config configs/mydoc/config_designers.yml

Edit site in master branch

Edits should be made in the project’s master branch and then committed from there to the corresponding branch on GitHub.

git checkout master
vim ./mydoc/ # Make changes to *.md pages in ./mydoc/
git commit -am "some edits"; git push -u origin master

Sync changes to gh-pages branch

Currently, the changes to ../doc_outputs/mydoc/designers need to be synced into the gh-pages branch of the project repository. The following accomplishes this with rsync. The last two lines add, commit and push all changes to the gh-pages branch. After this the changes should show up in the life version of the web site. Note, prior to the syncing, one usually wants to shut down the locally running Jekyell server with Ctrl-c in its terminal window.

git checkout gh-pages
rsync -avh --stats --progress ~/Dropbox/Websites/doc_outputs/mydoc/designers/ ~/Dropbox/Websites/manuals/
git add -A :/
git commit -am "some edits"; git push -u origin gh-pages
git checkout master

Bash script for automation

To automate the above workflow, run the following bash script from the root directory of the repository’s master branch.


Adding a new page

Create page

The easiest is usually to copy an existing page in \mydoc and then make the necessary changes to its Jekyll front matter section and content.

Next, the new page needs to be registered properly in the sidebar and URL configuration files.

vim _data/mydoc/mydoc_sidebar.yml
vim _data/mydoc/mydoc_urls.yml

After this the new page should be viewable in the local preview of your browser. This requires a running session of jekyll serve ... in the root directory of the repository as shown above.

Commit to GitHub

Similar as above add, commit and push changes to the master and gh-pages branches of the local and remote repositories or just run

git checkout master
git commit -am "some edits"; git push -u origin master
git checkout gh-pages
rsync -avh --stats --progress ~/Dropbox/Websites/doc_outputs/mydoc/designers/ ~/Dropbox/Websites/manuals/
git add -A :/
git commit -am "some edits"; git push -u origin gh-pages
git checkout master

Set theme color

Pick you favorite color here, then apply changes at the proper lines in ./css/theme-blue.css. This task can be greatly simplified by using vimdiff:

vimdiff css/theme-blue.css css/theme-blue_orig.css

R markdown integration

(1) Write R markdown vignette (*.Rmd file) in ./vignettes directory (e.g. ./vignettes/Rbasics).

(2) Render vignette to .md and .html files with rmarkdown::render().

(3) Append .md file (here to corresponding .md file in ./mydoc directory.

(4) Remove front matter genereted by R markdown, but leave the one required for Jekyll

(5) Replace chode chunk tags to the ones required by Jekyll Doc Theme

(6) Move images into proper directory and adjust their path in the .md file

Run steps (2)-(6) with one command using the render() function and the md2jekyll.R script:

echo "rmarkdown::render('Rbasics.Rmd', clean=FALSE)" | R --slave; R CMD Stangle Rbasics.Rmd; Rscript ../md2jekyll.R 3

Usage of custom domain

  • Register a domain name with a provider such as GoogleDomains or GoDaddy.
  • Next, configure the domain settings on your provider’s website to point to GitHub pages. Sample instructions for GoogleDomains and GitHub pages are given on Curtis Larson’s Blog. Note, if you run a web site under the gh-pages branch of a GitHub project repository then you will still just use under the CNAME entry (see table below) without appending the name of the project repository. Also adding a dot at the end of this entry is important. The table below is an example how the settings would look like under the DNS tab on GoogleDomains. The two IP addresses in the first two lines of the table should be the same for all sites hosted on GitHub.

    Name Type TTL Data
    @ A 1h

    www CNAME 1h
  • Subsequently, add the domain name (e.g. associated with this entry to the CNAME file in the gh-pages branch of your GitHub project repository.
  • Very important, if you experience any rendering problems on GitHub, check whether the _config.yml file of your Jekyll site contains a line starting with baseurl: "...". If so remove this line or the page will not render properly on GitHub.

Favicon icon

A favicon is an icon displayed in the web site tabs of a browser or next to the site name in a bookmark list. The source image can be generted with most graphics programs (e.g. in SVG format in Inkscape). To generate the final favicon, the image needs to be exported in bitmap format (e.g. PNG format) to a file. Subsequently, this file is converted to the final favicon.ico file using one of the many favicon generation tools such as FavIcon Generator. The favicon.ico file is then placed into the images directory of the Jekyll Doc Theme.

Useful utilities

Site-wide configurations

Edit this file accordingly.


Change sidebar behavior

The fixed sidebar is a nice feature of this theme. However, if there are too many section entries then it may be desirable to switch contitionally to a floating behavior depending on the size of the viewport available on a system. This can be achieved by changing the height value in ‘js/customscripts.js’ to a larger value (e.g. 800 to 1200):

if (h > 800) {
    $( "#mysidebar" ).attr("class", "nav affix");

Check differences in directories

One can also double-check by downloading the changes from GitHub and then run diff

diff -r ~/Dropbox/Websites/doc_outputs/mydoc/designers/ ~/Dropbox/Websites/manuals/