Due to extreme trouble with disqus (compare previous posts), I switched my discussion and commenting system to isso.
My server runs at this point Ubuntu 16.04 and therefore you can either use the available isso package (just do apt install isso) or install a newer package from an external source as described here.
Both sources have similar issues: they do install well, but most of the networking and startup related options in the respective configuration options are wrong or described at wrong locations. As the native ubuntu package didn't work for me, I describe here the way how I installed the package from the external source. They ask you to install the key with apt-key add, however as curl falls in a trap downloading the file, and therefore I suggest downloading the file manually with your browser and then install it locally like this:
cat /tmp/downloaded.key | apt-key add -v
You can follow the rest on that page.
Now make sure to have gunicorn installed (apt install gunicorn) and create a file /etc/isso.conf - use this here as a base and configure as described here. Just remember that the local server will always run on localhost, port 8000 independent of what you configure here or in /etc/default/isso.
Make sure that both isso and Nikola either run normal http or both ssl only and let your isso run on a virtual server with a name like comment.yourserver.tdl. In my case isso runs on https over ssl on comment.ulno.net and my webpage (as you know) on ulno.net. However, as described in a previous post, I redirect now also normal http requests to https. To make this work correctly, you might have to create a valid certificate (you can get a free one and a decent description how on http://letsencrypt.org).
In Nikola specify COMMENT_SYSTEM = "isso" and COMMENT_SYSTEM_ID = "https://comment.ulno.net/" (Adjust ulno.net to your sever!) and recompile your blog.
Start isso with systemctl restart isso, eventually restart your web-server (nginx, apache, or lighttpd) and enjoy comments without spying from a system that you can eventually even debug if some things do not work.