Creating the website

Last updated on 22 Jan 2023

This website uses a Hugo site with the Wowchemy template ‘Research Group’. It is hosted on Github, served by Netlify and has a custom domain from Google domains.

Getting started

Previously, I’d used a ‘Feeling Responsive’ theme for Jekyll on Github, but this became cumbersome to keep up-to-date (too complicated).

After googling for ‘research group website’, I found one I liked and followed their instructions: How to Build Academic Website for Research Group in 2021

I didn’t follow all the instructions, but stuck to:

  1. Hugo static web generator
  2. Wowchemy research group template
  3. Github
  4. Netlify
  5. Google domain - mostly because this is where I’d previously purchased a domain name.

Some other examples for how-to are by Ashis Saha.

Implementation

Hugo, Wowchemy + Github

I followed the Hugo installation guide which required installing Homebrew on my Mac and then

brew install hugo

I also needed Go.

I then cloned the Wowchemy `Research group’ theme onto my computer. In that directory, I can run

hugo server

and my site shows up locally at localhost:1313 (entered into the location bar of a browser window). After making necessary changes, I use the Github desktop app to commit the changes, and then push to origin. At this point, they become visible on the Netlify version of the website.

Basic updates

All the basic customisation is given in Hugo Site Customization including:

  • Personalising the domain name: Get Your Own Domain Name. I had a google domain so I followed the instruction to link them on Netlify.
  • Adding a website icon. I had a previou favicon so I followed the instructions for this.
  • Change the font to ‘medium’ from the default ’large’. (The publications information became too hard to read otherwise.)
  • Shortening the website name in config/_default/params.yaml since it was too long for a mobile rendering of the website (website name was overlying the menu).
  • Left default colors minimal and fonts native
  • Updated the menu choices to my preferred option: “Research”, “Teaching”, “Publications”, “Group” - but with the url pointing to the UHH website, “Manual” - where there is a new starter guide that I patterned after E Wallace, and “News”. I’m still debating/figuring out how to add a “Data” menu patterned after “Publication” and possibly an “Events” menu which is forward-looking for upcoming events/talks (rather than “News” which is backwards).

Creating the publications list

I started by using the command-line tool (instruction here)to create the publications directories from a “*.bib” file. This required

pip3 install -U academic

Then importing my publications from the website main directory (GitHub/ifmeo) using

academic import --bibtex data/publications.bib

This is easiest if the publications.bib file already has the paper abstracts in it, as well as the doi number. Otherwise, these can be added later but re-running this may overwrite the directories and you’ll have to do all the manual edits again.

This creates a subdirectory for each bibtex entry, where the naming convention is based on the citekeys. Within each directory is an index.md file and a cite.bib file, where the citation can be downloaded, and the index.md contains a bunch of information about the publication.

Manual edits to the index.md file that I found necessary were:

  • Change my author name to match the folder/username specified in the content/authors/ directories
  • Add tags, where various tags I found relevant for my work were “AMOC”, “gliders”, “Southern Ocean”, “mesoscale”, “submesoscale”, “bottom pressure”, “methods”, “mixing”, “Labrador Sea”. I’m not quite sure whether the names are case sensitive or not, but I needed to create the directory content/tags/ with a subdirectory for each tag, like content/tags/gliders which contains an _index.md file where the title is changed to “Gliders”. This is the name that will appear in the Tag at the bottom of each publication, and it is case-sensitive/space-sensitive, etc.
  • In a few cases, I’ve added a featured.jpg to the directory for a publication
  • In some cases, adding the project name to the projects: [projectname] list if I had created a content/project/projectname/ entry.
  • In some cases (need to update all) I’ve added the url_pdf: to the header as well, for the URL where the publication is contained in an institutional archive (in case the reader doesn’t have a subscription to the journal in question).

More complex changes:

I’d like to change the publications_type that is refereneced by each content/publication/frajkawilliams-etal-2011 to also include a type for “Dataset” and “Grey literature”. At the moment, the list is

0 = Uncategorized
1 = Conference paper
2 = Journal article
3 = Preprint / Working Paper
4 = Report
5 = Book 
6 = Book section
7 = Thesis
8 = Patent

but I don’t need the Patent item, and possibly not the Uncategorized option. This appears editable in

Modifying Publication Types

To rename publication types, edit the associated pub_* values in your language pack. If your language pack hasn’t been updated recently, you can copy the latest options from the English language pack.

To do this, I followed the instructions here to download the English language pack into a new folder ifmeo/i18n/ as ifmeo/content/en.yaml. Within this, I scrolled down to id: pub_patent and changed the translation to Dataset.

So my list is now

0 = Uncategorized
1 = Conference paper
2 = Journal article
3 = Preprint / Working Paper
4 = Report
5 = Grey literature 
6 = Book section
7 = Thesis
8 = Dataset

Updating the website

Updating the website can be done in the Github repository, in which case new changes need to be fetched and pulled to update the repository on my computer. I don’t use the more robust option specified by Jed Yang’s instructions.

Adding a new publication

I do this from the command line as (instruction here)

hugo new content/publication/<my-publication>

Then edit the contents of the index.md file.

Adding a new dataset

Again, as for publications, I do this from the command line as (instruction here)

hugo new content/publication/data-YYYY-ID

where all datasets start with data then the year the data end (for moorings from 2017-2018, use 2018) is the YYYY and the ID is some other identifying information: either the cruise information, like MSM21 for a Merian cruise 21, or project rapid or mooring name like DS2.

Then edit the contents of the index.md file. Here, the publication type is 8 or [“8”], the category is [“data”] and if applicable, the project is [“dsow”] or [“rapid”] or [“terific”].

  • Within the index.md file, the date: YYYY-MM-DDTHH:MM:SS must be entered in this format. If only the year is known, then enter the year followed by 2018-01-01T12:00:00. (The date can be adjusted to order datasets sequentially.)
  • The publication is the data centre holding the data, e.g. “British Oceanographic Data Centre” with publication_short: "BODC" or publication: PANGAEA or publication: SEANOE.
  • The shortened abstract (summary:) should include the data type (e.g., moored CTD, hydrographic CTD) and date range of the data to nearest month and year.
  • Enter the url_dataset: if known.

For datasets downloaded from PANGAEA, the bibtex citation information can also be downloaded to the publication folder, and then renamed to cite.bib.

Later updates: Add a map with the data location. This can be a static map, screenshot from PANGAEA or similar.

Adding a new person

This is explained in the Hugo steps to customise a theme but I’ve modified it somewhat (not sure whether things will break later) to use lastname-firstname.

hugo new content/authors/Lastname-Firstname

Then, within the new folder, edit _index.md fixing the order of the name in title, adding the role (e.g. PhD student, Technician, Research Scientist) and update the user_groups to ‘Group’.