Revise docs

[stefsmeets]

This PR revised the docs and moves it to mkdocs.

Todo

• [x] api pages
• [x] Sort pages
• [x] Add notebooks
• [x] Notebook index page
• [x] Add networking page
• [x] Add merlin page
• [x] Switch rtd to mkdocs

Closes #55 Closes #43 Closes #73 Closes #59