Create the repository

Create a blank github repo for the site. For my user, that is https://github.com/jean/jean.github.io.

Clone the repo and prepare the required branches. For a user site, Nikola will deploy to the master branch, so you need another branch to keep the site source in. I picked site-src; the documentation suggests deploy. Whatever name you choose, this will be the branch that you will keep checked out and use for authoring.

git clone git@github.com:USER/YOURSITE.github.io.git
cd YOURSITE.github.io
git checkout -b site-src
git push origin site-src

Bootstrap the site

Create the Nikola site. In my case I prefer to install Nikola into a virtualenv local to the site. Nikola is dropping support for Python 2 soon, so use Python 3.

virtualenv -p `which python3` .
. bin/activate
pip install nikola
nikola init YOURSITE
echo "
    include/
    lib/
    pip-selfcheck.json
    share/
    YOURSITE/cache
    YOURSITE/output
    YOURSITE/__pycache__
    YOURSITE/themes
    YOURSITE/.doit.db
    " > .gitignore
git add YOURSITE
git commit -a -m "First commit"

The default Nikola config assumes a project site (which publishes to the gh-pages branch), so needs to be updated to use the user format. Edit YOURSITE/conf.py.

GITHUB_SOURCE_BRANCH = 'site-src' # Or whatever you picked.
GITHUB_DEPLOY_BRANCH = 'master'

Add content and publish

Now you're ready to start adding posts and pages. To do this, you need to be in the YOURSITE directory:

cd YOURSITE
nikola new_post
# Edit post
nikola github_deploy

Nikola will build the static site in the output directory (by default) and push it to the master branch at github. Note however that the source will not be automatically committed. You need to do this. To commit everything in one go:

git add .
git commit -a -m "New post"

In my case I also installed a theme (nikola install_theme material-theme), and activated disqus as comments provider. These require some more changes to conf.py.