convert a new version of pumping notebook to markdown

This takes over Jay's changes from
!40
6 jobs for pumpingv2 in 7 minutes (queued for 1 second)
Status Job ID Name Coverage
  Execute
failed execute_ipynbs #97429

00:07:00

passed mirror to github #97430

00:00:37

 
  Build
skipped edx archive #97431
skipped ocw website #97433
skipped pelican website #97432
 
  Deploy
skipped upload test website #97434
 
Name Stage Failure
failed
execute_ipynbs Execute
kwant/operator.pyx in kwant.operator._LocalOperator.__init__()

ValueError: Number of orbitals not defined.
Declare the number of orbitals using the `norbs` keyword argument when constructing the site families (lattices).
ValueError: Number of orbitals not defined.
Declare the number of orbitals using the `norbs` keyword argument when constructing the site families (lattices).

Authenticating with credentials from /root/.docker/config.json
ERROR: Job failed: exit code 1