Setting up this personal website from the template at academic pages involves several steps:

1. Set up localhost using ruby so that the website can be served for development.
2. Setting up the markdown generator .ipynb files to fill in Publications (from ORCID) and Talks (from a .csv file). Also manually add the corresponding PDF files for the Publications and Poster Talks.

Testing with Localhost

The academic pages template provides instructions to run the site on localhost. On MacOS, by default the command gem install bundler fails because the user doesn’t have permissions to override the system Ruby install. To overcome this issue, follow these steps:

1. Run which ruby. If it returns /usr/bin/ruby that means the system ruby install is being used, which is causing the failure.

2. Add the following to the profile ~/.zshrc:

   eval "$(/opt/homebrew/bin/brew shellenv)"
   export PATH="/opt/homebrew/opt/ruby/bin:$PATH"
   export PATH="`gem env gemdir`/bin:$PATH"
   

3. Reload the shell with source ~/.zshrc and verify that the ruby version has changed by running which ruby, which should now return /opt/homebrew/opt/ruby/bin/ruby.

4. Now, running gem install bundler should succeed.

5. According to the academic pages documentation, to serve the site on localhost:4000, run jekyll serve -l -H localhost. I find that bundle exec needs to be preprended, making the final command: bundle exec jekyll serve -l -H localhost

Updating the Live Site

To make your changes visible on the live web page, just use Git to commit and push your changes to GitHub.

Setting up Each Page

Publications

1. To make OrcidToBib.ipynb properly generate the output.bib file, the “citation” field of the work must be filled in on orcid.org using the Bibtex format. If not, it won’t be properly added to the output.bib file. The Bibtex formatted citation can be found by right clicking the item in Zotero with the Better Bibtex plugin installed, and clicking “copy bibtex to clipboard”.

2. Use the PubsFromBib.ipynb to convert the .bib file to the .md files that will be rendered on the website. Note that by default you will get an error about a missing pkg_resources package. Run pip install setuptools to fix this.

In the publist dictionary definition, comment out the “proceeding” key. Change the value of ["journal"]["file"] to output.bib.

Also, by default this .ipynb file does not work because it does not create a “category” field, which is required for the publication to be listed. Valid “category” fields appear to be manuscripts for a “Journal Articles” title, conferences for a “Conference Presentations” title.

I also added the paperurl field. Unfortunately right now I have to manually add the PDF files. Maybe could be automated from Zotero in the future.

Talks

1. Create a new talks.csv file and populate it with all of the talks given. For the url slug, I just used the abbreviation of the venue.
2. Run all of the cells in talks.ipynb.

CV

1. I added my CV PDF file to files/cv.pdf. I added a download link to _pages/cv.md.