Zathura-Pywal is a set of helper scripts that dynamically theme zathura based on colors set by pywal.
To install, simply move into the clone directory and run sudo ./install.sh
zth filename
Instead of running zathura, you can now run zth, or whatever you want to alias it to. Every time it is run, it will execute the genzathurarc script, which will populate your configuration file based on your current colorscheme.
By default, this script overwrites your current config. If you had anything special in that config, add it to the script so it is always in you config.