These books have been formatted to be print friendly (using CSS media queries). That means that you should be able to print them directly from your browser of choice (usually Ctrl-P on Windows and Linux, or Cmd-P on Mac).
We've taken some care to set up sensible page breaks in the printed versions, though you still may find a few odd artifacts here and there. For example, the latest version of Markdeep can let images/figures and their captions land on different pages. This issue has been reported, and there may be a fix in the works for this.
I've gone back and created PDFs for each book for versions v2.0.0, v3.0.0, v3.2.3. You can find these in the assets section of each release on the GitHub releases page. We will include PDFs for all books with all future releases.
If you wish to create your own PDF of any of these books (like for a version currently in development, or to test the results on your own changes), the easiest way is to use a save-to-PDF print driver. When viewing a book in your browser, issue your browser's print command, and look through the available destination printers. Hopefully you'll find a save-to-PDF printer already set up and available. If not, you should be able to search for and find such a print driver for your particular operating system.