to use nikola you need to install it with some other packages as well pip instal nikola markdown ws4py watchdog

then to enable markdown, you need to change the conf.py variable POSTS and PAGES

POSTS = (
    ("posts/*.md", "posts", "post.tmpl"),
    ("posts/*.rst", "posts", "post.tmpl"),
    ("posts/*.txt", "posts", "post.tmpl"),
    ("posts/*.html", "posts", "post.tmpl"),
)
PAGES = (
    ("pages/*.md", "pages", "story.tmpl"),
    ("pages/*.rst", "pages", "story.tmpl"),
    ("pages/*.txt", "pages", "story.tmpl"),
    ("pages/*.html", "pages", "story.tmpl"),
)

you may also need to change the github settings for easy github deploy

Then new post can be added using markdown format by nikola new_post -f markdown