It should be possible to build a PDF from source. The setup guide is here: https://github.com/DS-100/textbook/blob/master/SETUP.md

I tried the following in a python 3.7 virtual environment, but it didn't quite work:

  sudo apt-get update
  sudo apt-get install -y --no-install-recommends npm calibre jekyll ca-certificates
  git clone https://github.com/DS-100/textbook
  cd textbook
  pip install -r requirements.txt
  pip install datascience # due to version conflict
  pip install --upgrade folium # due to version conflict
  pip install beautifulsoup4
  pip install lxml py-mathjax # not sure if these are needed
  sudo npm install -g gitbook-cli
  sudo gitbook fetch
  sudo gitbook install
  make build

I'd assume because you have the --no-install-recommends flag on your apt-get call. Maybe something you're doing requires the recommended (but not dependent) packages. I haven't done it yet, but that's my assumption at first glance, so take it with a grain of salt.

Sorry, I misled you a bit there. I didn't actually use that flag when I did it, as I already had the packages installed.