Doc/jupyter sphinx

Merged Joseph Weston requested to merge doc/jupyter-sphinx into master

Supercedes !294 (merged) and closes #87 (closed).

Currently requires master version of

Importantly, here we're also revisiting the contents of the tutorial because some parts are obsolete and don't make sense to maintain.

So far we removed:

  • The site coloring in the graphene example is gone (kwant plotter now colors sites by default)
  • The eigenvalue computation in graphene is gone, because it's better handled in the closed systems


  • rely on a stable source of the jupyter execute machinery
  • rewrite and reorganize the tutorial code.

We now lose the possibility of arbitrarily skipping or including lines of code, therefore we should write shorter functions. On the other hand, we can hide complete cells of code, including those that generate output. Therefore we can for instance factor out helper functions for making plots nice and hide those.

Edited by Joseph Weston

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